Index: /issm/oecreview/Archive/11991-12009/Date.tex =================================================================== --- /issm/oecreview/Archive/11991-12009/Date.tex (revision 12325) +++ /issm/oecreview/Archive/11991-12009/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/11991-12009/ISSM-11991-11992.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-11991-11992.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-11991-11992.diff (revision 12325) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11991) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11992) +@@ -4,15 +4,14 @@ + rm -rf install + + #Select or create a new simlink +-#ln -s /usr/local/pkgs/matlab-7.6/ install ++ln -s /usr/local/pkgs/matlab-7.6/ install + #ln -s /usr/local/matlab704/ install + #ln -s /usr/local/matlab711/ install + #ln -s /usr/local/matlab712/ install +-#ln -s /usr/local/pkgs/matlab-7.6/ install + + # Macintosh (OSX) simlink + #ln -s /Applications/MATLAB_R2008a/ install + #ln -s /Applications/MATLAB_R2009a.app/ install + #ln -s /Applications/MATLAB_R2010a.app/ install + #ln -s /Applications/MATLAB_R2012a.app/ install +-ln -s /Applications/MATLAB*.app/ install ++#ln -s /Applications/MATLAB*.app/ install Index: /issm/oecreview/Archive/11991-12009/ISSM-11992-11993.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-11992-11993.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-11992-11993.diff (revision 12325) @@ -0,0 +1,7 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/README +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/README (revision 11992) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/README (revision 11993) +@@ -1,2 +0,0 @@ +-Go pick up the correct configure.make file in the config directory (according to your platform), +-copy it to the top triangle directory, and run install.sh Index: /issm/oecreview/Archive/11991-12009/ISSM-11993-11994.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-11993-11994.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-11993-11994.diff (revision 12325) @@ -0,0 +1,693 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11993) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11994) +@@ -190,11 +190,11 @@ + ;; + *darwin*) + dnl mex -v gives all the flags for compilation of mex files +- dnl if matlab version is 7.10 or more, we must use mexmaci64 (64 bits) ++ dnl if matlab version is 7.9 or more, we must use mexmaci64 (64 bits) + MEXLINK="-O -Wl,-flat_namespace -undefined suppress -arch i386 -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci/mexFunction.map" + MEXLIB=" -L$MATLAB_ROOT/bin/maci/ -lmx -lmex -lmat -lstdc++ -largeArrayDims" + if test $MATLAB_MAJOR -ge 7; then +- if test $MATLAB_MINOR -ge 10; then ++ if test $MATLAB_MINOR -ge 9; then + MEXLINK="-O -Wl,-flat_namespace -undefined suppress -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci64/mexFunction.map" + MEXLIB=" -L$MATLAB_ROOT/bin/maci64/ -lmx -lmex -lmat -lstdc++" + fi +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp (revision 11993) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp (revision 11994) +@@ -10,12 +10,101 @@ + #include "../../EnumDefinitions/EnumDefinitions.h" + + void PositiveDegreeDayx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters){ +- +- Element* element = NULL; + +- for(int i=0;iSize();i++){ +- element=(Element*)elements->GetObjectByOffset(i); +- element->PositiveDegreeDay(); +- } ++// void PositiveDegreeDayx(hd,vTempsea,vPrec,agd,Tsurf,ni){ ++// note "v" prefix means 12 monthly means, ie time dimension ++// INPUT parameters: ni: working size of arrays ++// INPUT: surface elevation (m): hd(NA) ++// monthly mean surface sealevel temperature (degrees C): vTempsea(NA ++// ,NTIME) ++// monthly mean precip rate (m/yr water equivalent): vPrec(NA,NTIME) ++// OUTPUT: mass-balance (m/yr ice): agd(NA) ++// mean annual surface temperature (degrees C): Tsurf(NA) + ++ int i, it, jj, itm; ++ double DT = 0.02, sigfac, snormfac; ++ double signorm = 5.5; // signorm : sigma of the temperature distribution for a normal day ++ double siglim; // sigma limit for the integration which is equal to 2.5 sigmanorm ++ double signormc; // sigma of the temperature distribution for cloudy day ++ double siglimc=0, siglim0, siglim0c; ++ double tstep, tsint, tint, tstepc; ++ int NPDMAX = 1504, NPDCMAX = 1454; ++ //double pdds[NPDMAX]={0}; ++ //double pds[NPDCMAX]={0}; ++ double pddt, pd ; // pd : snow/precip fraction, precipitation falling as snow ++ double PDup, PDCUT = 2.0; // PDcut: rain/snow cutoff temperature (C) ++ double tstar; // monthly mean surface temp ++ ++ double* pdds=NULL; ++ double* pds=NULL; ++ Element* element = NULL; ++ ++ pdds=(double*)xmalloc(NPDMAX*sizeof(double)+1); ++ pds=(double*)xmalloc(NPDCMAX*sizeof(double)+1); ++ ++ ++ // PDD constant ++ siglim = 2.5*signorm; ++ ++ // initialize PDD (creation of a lookup table) ++ tstep = 0.1; ++ tsint = tstep*0.5; ++ sigfac = -1.0/(2.0*pow(signorm,2)); ++ snormfac = 1.0/(signorm*sqrt(2.0*acos(-1.0))); ++ siglim = 2.5*signorm; ++ itm = (int)(2*siglim/DT + 1.5); ++ ++ if (itm >= NPDMAX){ ++ printf("increase NPDMAX in massBalance.cpp\n"); ++ exit (1); ++ } ++ for (it = 0; it < itm; it++){ ++ // tstar = REAL(it)*DT-siglim; ++ tstar = it*DT-siglim; ++ tint = tsint; ++ pddt = 0; ++ for ( jj = 0; jj < 600; jj++){ ++ if (tint > (tstar+siglim)){break;} ++ pddt = pddt + tint*exp(sigfac*(pow((tint-tstar),2)))*tstep; ++ tint = tint+tstep; ++ } ++ pdds[it] = pddt*snormfac; ++ } ++ pdds[itm+1] = siglim + DT; ++ ++ //*********compute PD(T) : snow/precip fraction. precipitation falling as snow ++ tstepc = 0.1; ++ tsint = PDCUT-tstepc*0.5; ++ signormc = signorm - 0.5; ++ sigfac = -1.0/(2.0*pow(signormc,2)); ++ snormfac = 1.0/(signormc*sqrt(2.0*acos(-1.0))); ++ siglimc = 2.5*signormc ; ++ itm = (int)((PDCUT+2.*siglimc)/DT + 1.5); ++ if (itm >= NPDCMAX){ ++ printf("'increase NPDCMAX in p35com'\n"); ++ exit (1); ++ } ++ for (it = 0; it < itm; it++ ){ ++ tstar = it*DT-siglimc; ++ // tstar = REAL(it)*DT-siglimc; ++ tint = tsint; // start against upper bound ++ pd = 0; ++ for (jj = 0; jj < 600; jj++){ ++ if (tint<(tstar-siglimc)) {break;} ++ pd = pd + exp(sigfac*(pow((tint-tstar),2)))*tstepc; ++ tint = tint-tstepc; ++ } ++ pds[it] = pd*snormfac; // gaussian integral lookup table for snow fraction ++ } ++ pds[itm+1] = 0; ++ // *******END initialize PDD ++ ++ for(i=0;iSize();i++){ ++ element=(Element*)elements->GetObjectByOffset(i); ++ element->PositiveDegreeDay(pdds,pds,signorm); ++ } ++ /*free ressouces: */ ++ xfree((void**)&pdds); ++ xfree((void**)&pds); ++ + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h (revision 11993) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h (revision 11994) +@@ -70,7 +70,7 @@ + virtual double TimeAdapt()=0; + virtual void MigrateGroundingLine(double* old_floating_ice,double* sheet_ungrounding)=0; + virtual void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding)=0; +- virtual void PositiveDegreeDay(void)=0; ++ virtual void PositiveDegreeDay(double* pdds,double* pds,double signorm)=0; + virtual int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf)=0; + virtual void ResetCoordinateSystem()=0; + virtual void SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius)=0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11993) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11994) +@@ -2234,9 +2234,226 @@ + } + /*}}}*/ + /*FUNCTION Tria::PositiveDegreeDay{{{1*/ +-void Tria::PositiveDegreeDay(){ ++void Tria::PositiveDegreeDay(double* pdds,double* pds,double signorm){ + +- _error_("Not implemented yet"); ++ int i,iqj,imonth; ++ double agd[NUMVERTICES]; // surface and basal ++ double saccu[NUMVERTICES] = {0}; // yearly surface accumulation ++ double smelt[NUMVERTICES] = {0}; // yearly melt ++ double precrunoff[NUMVERTICES]; // yearly runoff ++ double prect; // total precipitation during 1 year taking into account des. ef. ++ double water; //water=rain + snowmelt ++ double runoff; //meltwater only, does not include rain ++ double sconv; //rhow_rain/rhoi / 12 months ++ ++ double rho_water,rho_ice,density; ++ double lapser=6.5/1000, sealev=0; // lapse rate. degrees per meter. ++ double desfac = 0.5; //desert elevation factor ++ double s0p[NUMVERTICES]={0}; //should be set to elevation from precip source ++ double s0t[NUMVERTICES]={0}; //should be set to elevation from temperature source ++ double st; // elevation between altitude of the temp record and current altitude ++ double sp; // elevation between altitude of the prec record and current altitude ++ ++ ++ // PDD and PD constants and variables ++ double siglim; // sigma limit for the integration which is equal to 2.5 sigmanorm ++ double siglimc=0, siglim0, siglim0c; ++ double PDup, pddsig, PDCUT = 2.0; // PDcut: rain/snow cutoff temperature (C) ++ double DT = 0.02; ++ double pddt, pd; // pd: snow/precip fraction, precipitation falling as snow ++ ++ double q, qmpt; // q is desert/elev. fact, hnpfac is huybrect fact, and pd is normal dist. ++ double qm[NUMVERTICES] = {0}; // snow part of the precipitation ++ double qmt[NUMVERTICES] = {0}; // precipitation without desertification effect adjustment ++ double qmp[NUMVERTICES] = {0}; // desertification taken into account ++ double pdd[NUMVERTICES] = {0}; ++ double frzndd[NUMVERTICES] = {0}; ++ ++ double tstar; // monthly mean surface temp ++ double Tsum[NUMVERTICES]= {0}; // average summer (JJA) temperature ++ double Tsurf[NUMVERTICES] = {0}; // average annual temperature ++ ++ double h[NUMVERTICES],s[NUMVERTICES],ttmp[NUMVERTICES],prectmp[NUMVERTICES]; // ,b[NUMVERTICES] ++ double t[NUMVERTICES][12],prec[NUMVERTICES][12]; ++ double deltm=1/12; ++ int ismon[12]={12,1,2,3,4,5,6,7,8,9,10,11}; ++ ++ double snwm; // snow that could have been melted in a year. ++ double snwmf; // ablation factor for snow per positive degree day. ++ double smf; // ablation factor for ice per pdd (Braithwaite 1995 from tarasov 2002). ++ ++ double dfrz=1.5, CovrLm=2009./3.35e+5, dCovrLm=dfrz*CovrLm; //m*J kg^-1 C^-1 /(J kg^-1)=m/C yr ++ double supice,supcap,diffndd; ++ double fsupT=0.5, fsupndd=0.5; // Tsurf mode factors for supice ++ double pddtj[NUMVERTICES], hmx2; ++ ++ /*Recover info at the vertices: */ ++ GetInputListOnVertices(&h[0],ThicknessEnum); ++ GetInputListOnVertices(&s[0],SurfaceEnum); ++ GetInputListOnVertices(&ttmp[0],ThermalSpctemperatureEnum); ++ GetInputListOnVertices(&prectmp[0],SurfaceforcingsPrecipitationEnum); ++ ++ for(i=0;iGetRhoIce(); ++ rho_water=matpar->GetRhoWater(); ++ density=rho_ice/rho_water; ++ ++ sconv=(rho_water/rho_ice)/12.; //rhow_rain/rhoi / 12 months ++ ++ /*PDD constant*/ ++ siglim = 2.5*signorm; ++ siglim0 = siglim/DT + 0.5; ++ siglim0c = siglimc/DT + 0.5; ++ PDup = siglimc+PDCUT; ++ ++ // seasonal loop ++ for (iqj = 0; iqj < 12; iqj++){ ++ imonth = ismon[iqj]; ++ for (i = 0; i < NUMVERTICES; i++){ ++ st=(s[i]-s0t[i])/1000; ++ tstar = t[i][imonth] - lapser *max(st,sealev); ++ Tsurf[i] = tstar*deltm+Tsurf[i]; ++ ++ /*********compute PD ****************/ ++ if (tstar < PDup){ ++ pd = 1; ++ if (tstar >= -siglimc){ pd = pds[int(tstar/DT + siglim0c)];}} ++ else { ++ pd = 0;} ++ ++ /******exp des/elev precip reduction*******/ ++ sp=(s[i]-s0p[i])/1000; // deselev effect is wrt chng in topo ++ if (sp>0.0){q = exp(-desfac*sp);} ++ else {q = 1.0;} ++ ++ qmt[i]= qmt[i] + prec[i][imonth]*sconv; //*sconv to convert in m of ice equivalent ++ qmpt= q*prec[i][imonth]*sconv; ++ qmp[i]= qmp[i] + qmpt; ++ qm[i]= qm[i] + qmpt*pd; ++ ++ /*********compute PDD************/ ++ // ndd(month)=-(tstar-pdd(month)) since ndd+pdd gives expectation of ++ // gaussian=T_m, so ndd=-(Tsurf-pdd) ++ if (iqj>6 && iqj<10){ Tsum[i]=Tsum[i]+tstar;} ++ if (tstar >= siglim) {pdd[i] = pdd[i] + tstar*deltm;} ++ else if (tstar> -siglim){ ++ pddsig=pdds[int(tstar/DT + siglim0)]; ++ pdd[i] = pdd[i] + pddsig*deltm; ++ frzndd[i] = frzndd[i] - (tstar-pddsig)*deltm;} ++ else{frzndd[i] = frzndd[i] - tstar*deltm; } ++ } ++ } // end of seasonal loop ++ ++ //****************************************************************** ++ for(i=0;i2m) ++ // problem with water seepage into ice: should be sealed after ++ // refreezing ++ // so everything needs to be predicated on 1 year scale, except for ++ // thermal ++ // conductivity through ice ++ // also, need to account that melt season has low accum, so what's ++ // going to ++ // hold the meltwater around for refreezing? And melt-time will have ++ // low seasonal frzndd ++ ++ // Superimposed ice : Pfeffer et al. 1991, Tarasov 2002 ++ ++ supice= min(hmx2*CovrLm*frzndd[i]+2.2*(saccu[i]-snwm), water); // superimposed ice ++ supcap=min(2.2*(saccu[i]-snwm),water); ++ runoff=snwm - supice; //meltwater only, does not include rain ++ } ++ else { //all snow melted ++ supice= min(hmx2*CovrLm*frzndd[i], prect ); ++ runoff= saccu[i] + smf*(pddt-saccu[i]/snwmf) - supice; ++ supcap=0; ++ } ++ // pdd melting doesn't cool Tsurf, so ndd refreeze shouldn't warm it ++ // except pdd melt heat source is atmosphere, while refreeze is ++ // ground/ice stored interim ++ // assume pdd=ndd, then melt should equal refreeze and Tsurf should=0 ++ // assume ndd=2*pdd, then all supice is refrozen, but Tsurf should be ++ // <0 ++ // assume ndd>pdd, little melt => little supice ++ // bottom line: compare for Tsurf<0 : supice and no supice case, ++ // expect Tsurf difference ++ // except some of cooling flux comes from atmosphere// ++ // 1 dm supice should not raise Tsurf by 1/dCovrLm = 16.675C ++ // does supice make sense when H< 0.1m? then d=thermoactive ice layer //// ++ // < 0.1 ++ ++ // make more sense to just use residual pdd-ndd except that pdd ++ // residual not clear yet ++ // frzndd should not be used up by refreezing in snow, so stick in ++ // supcap. ++ diffndd=0; ++ if (frzndd[i]>0) { ++ diffndd=fsupndd*min((supice-supcap)/dCovrLm ,frzndd[i]); ++ frzndd[i]=frzndd[i]-diffndd; ++ } ++ if(runoff<0){ ++ saccu[i]= saccu[i] -runoff; ++ smelt[i] = 0; ++ precrunoff[i]=prect-saccu[i]; ++ //here assume pdd residual is 0, => ++ Tsurf[i]= max(Tsurf[i],-frzndd[i]); ++ } ++ else { ++ smelt[i] = runoff; ++ precrunoff[i]=prect-max(0.,supice)-saccu[i];} ++ //here really need pdd balance, try 0.5 fudge factor? ++ //at least runoff>0 => it's fairly warm, so Tsurf is !<<0, ++ //yet from site plots, can be ice free with Tsurf=-5.5C ++ if(Tsurf[i]<0) { ++ Tsurf[i]= min(Tsurf[i]+fsupT*diffndd , 0.);} ++ ++ agd[i] = -smelt[i]+saccu[i]; ++ pddtj[i]=pddt; ++ ++ /*Update inputs*/ ++ this->inputs->AddInput(new TriaP1Input(SurfaceforcingsMassBalanceEnum,&agd[0])); ////////verifier le nom ++ // this->inputs->AddInput(new TriaVertexInput(ThermalSpcTemperatureEnum,&Tsurf[0])); ++ this->inputs->AddInput(new TriaP1Input(ThermalSpctemperatureEnum,&Tsurf[0])); ++ ++ } //end of the for loop over the vertices + } + /*}}}*/ + /*FUNCTION Tria::ProcessResultsUnits{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 11993) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 11994) +@@ -107,7 +107,7 @@ + void MigrateGroundingLine(double* oldfloating,double* sheet_ungrounding); + int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); + void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding); +- void PositiveDegreeDay(void); ++ void PositiveDegreeDay(double* pdds,double* pds,double signorm); + void RequestedOutput(int output_enum,int step,double time); + void ListResultsInfo(int** results_enums,int** results_size,double** results_times,int** results_steps,int* num_results); + void PatchFill(int* pcount, Patch* patch); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 11993) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 11994) +@@ -2409,9 +2409,227 @@ + } + /*}}}*/ + /*FUNCTION Penta::PositiveDegreeDay{{{1*/ +-void Penta::PositiveDegreeDay(){ ++void Penta::PositiveDegreeDay(double* pdds,double* pds,double signorm){ + +- _error_("Not implemented yet"); ++ ++ int i,iqj,imonth; ++ double agd[NUMVERTICES]; // surface and basal ++ double saccu[NUMVERTICES] = {0}; // yearly surface accumulation ++ double smelt[NUMVERTICES] = {0}; // yearly melt ++ double precrunoff[NUMVERTICES]; // yearly runoff ++ double prect; // total precipitation during 1 year taking into account des. ef. ++ double water; //water=rain + snowmelt ++ double runoff; //meltwater only, does not include rain ++ double sconv; //rhow_rain/rhoi / 12 months ++ ++ double rho_water,rho_ice,density; ++ double lapser=6.5/1000, sealev=0; // lapse rate. degrees per meter. ++ double desfac = 0.5; //desert elevation factor ++ double s0p[NUMVERTICES]={0}; //should be set to elevation from precip source ++ double s0t[NUMVERTICES]={0}; //should be set to elevation from temperature source ++ double st; // elevation between altitude of the temp record and current altitude ++ double sp; // elevation between altitude of the prec record and current altitude ++ ++ ++ // PDD and PD constants and variables ++ double siglim; // sigma limit for the integration which is equal to 2.5 sigmanorm ++ double siglimc=0, siglim0, siglim0c; ++ double PDup, pddsig, PDCUT = 2.0; // PDcut: rain/snow cutoff temperature (C) ++ double DT = 0.02; ++ double pddt, pd; // pd: snow/precip fraction, precipitation falling as snow ++ ++ double q, qmpt; // q is desert/elev. fact, hnpfac is huybrect fact, and pd is normal dist. ++ double qm[NUMVERTICES] = {0}; // snow part of the precipitation ++ double qmt[NUMVERTICES] = {0}; // precipitation without desertification effect adjustment ++ double qmp[NUMVERTICES] = {0}; // desertification taken into account ++ double pdd[NUMVERTICES] = {0}; ++ double frzndd[NUMVERTICES] = {0}; ++ ++ double tstar; // monthly mean surface temp ++ double Tsum[NUMVERTICES]= {0}; // average summer (JJA) temperature ++ double Tsurf[NUMVERTICES] = {0}; // average annual temperature ++ ++ double h[NUMVERTICES],s[NUMVERTICES],ttmp[NUMVERTICES],prectmp[NUMVERTICES]; // ,b[NUMVERTICES] ++ double t[NUMVERTICES][12],prec[NUMVERTICES][12]; ++ double deltm=1/12; ++ int ismon[12]={12,1,2,3,4,5,6,7,8,9,10,11}; ++ ++ double snwm; // snow that could have been melted in a year. ++ double snwmf; // ablation factor for snow per positive degree day. ++ double smf; // ablation factor for ice per pdd (Braithwaite 1995 from tarasov 2002). ++ ++ double dfrz=1.5, CovrLm=2009./3.35e+5, dCovrLm=dfrz*CovrLm; //m*J kg^-1 C^-1 /(J kg^-1)=m/C yr ++ double supice,supcap,diffndd; ++ double fsupT=0.5, fsupndd=0.5; // Tsurf mode factors for supice ++ double pddtj[NUMVERTICES], hmx2; ++ ++ /*Recover info at the vertices: */ ++ GetInputListOnVertices(&h[0],ThicknessEnum); ++ GetInputListOnVertices(&s[0],SurfaceEnum); ++ GetInputListOnVertices(&ttmp[0],ThermalSpctemperatureEnum); ++ GetInputListOnVertices(&prectmp[0],SurfaceforcingsPrecipitationEnum); ++ ++ for(i=0;iGetRhoIce(); ++ rho_water=matpar->GetRhoWater(); ++ density=rho_ice/rho_water; ++ ++ sconv=(rho_water/rho_ice)/12.; //rhow_rain/rhoi / 12 months ++ ++ /*PDD constant*/ ++ siglim = 2.5*signorm; ++ siglim0 = siglim/DT + 0.5; ++ siglim0c = siglimc/DT + 0.5; ++ PDup = siglimc+PDCUT; ++ ++ // seasonal loop ++ for (iqj = 0; iqj < 12; iqj++){ ++ imonth = ismon[iqj]; ++ for (i = 0; i < NUMVERTICES; i++){ ++ st=(s[i]-s0t[i])/1000; ++ tstar = t[i][imonth] - lapser *max(st,sealev); ++ Tsurf[i] = tstar*deltm+Tsurf[i]; ++ ++ /*********compute PD ****************/ ++ if (tstar < PDup){ ++ pd = 1; ++ if (tstar >= -siglimc){ pd = pds[int(tstar/DT + siglim0c)];}} ++ else { ++ pd = 0;} ++ ++ /******exp des/elev precip reduction*******/ ++ sp=(s[i]-s0p[i])/1000; // deselev effect is wrt chng in topo ++ if (sp>0.0){q = exp(-desfac*sp);} ++ else {q = 1.0;} ++ ++ qmt[i]= qmt[i] + prec[i][imonth]*sconv; //*sconv to convert in m of ice equivalent ++ qmpt= q*prec[i][imonth]*sconv; ++ qmp[i]= qmp[i] + qmpt; ++ qm[i]= qm[i] + qmpt*pd; ++ ++ /*********compute PDD************/ ++ // ndd(month)=-(tstar-pdd(month)) since ndd+pdd gives expectation of ++ // gaussian=T_m, so ndd=-(Tsurf-pdd) ++ if (iqj>6 && iqj<10){ Tsum[i]=Tsum[i]+tstar;} ++ if (tstar >= siglim) {pdd[i] = pdd[i] + tstar*deltm;} ++ else if (tstar> -siglim){ ++ pddsig=pdds[int(tstar/DT + siglim0)]; ++ pdd[i] = pdd[i] + pddsig*deltm; ++ frzndd[i] = frzndd[i] - (tstar-pddsig)*deltm;} ++ else{frzndd[i] = frzndd[i] - tstar*deltm; } ++ } ++ } // end of seasonal loop ++ ++ //****************************************************************** ++ for(i=0;i2m) ++ // problem with water seepage into ice: should be sealed after ++ // refreezing ++ // so everything needs to be predicated on 1 year scale, except for ++ // thermal ++ // conductivity through ice ++ // also, need to account that melt season has low accum, so what's ++ // going to ++ // hold the meltwater around for refreezing? And melt-time will have ++ // low seasonal frzndd ++ ++ // Superimposed ice : Pfeffer et al. 1991, Tarasov 2002 ++ ++ supice= min(hmx2*CovrLm*frzndd[i]+2.2*(saccu[i]-snwm), water); // superimposed ice ++ supcap=min(2.2*(saccu[i]-snwm),water); ++ runoff=snwm - supice; //meltwater only, does not include rain ++ } ++ else { //all snow melted ++ supice= min(hmx2*CovrLm*frzndd[i], prect ); ++ runoff= saccu[i] + smf*(pddt-saccu[i]/snwmf) - supice; ++ supcap=0; ++ } ++ // pdd melting doesn't cool Tsurf, so ndd refreeze shouldn't warm it ++ // except pdd melt heat source is atmosphere, while refreeze is ++ // ground/ice stored interim ++ // assume pdd=ndd, then melt should equal refreeze and Tsurf should=0 ++ // assume ndd=2*pdd, then all supice is refrozen, but Tsurf should be ++ // <0 ++ // assume ndd>pdd, little melt => little supice ++ // bottom line: compare for Tsurf<0 : supice and no supice case, ++ // expect Tsurf difference ++ // except some of cooling flux comes from atmosphere// ++ // 1 dm supice should not raise Tsurf by 1/dCovrLm = 16.675C ++ // does supice make sense when H< 0.1m? then d=thermoactive ice layer //// ++ // < 0.1 ++ ++ // make more sense to just use residual pdd-ndd except that pdd ++ // residual not clear yet ++ // frzndd should not be used up by refreezing in snow, so stick in ++ // supcap. ++ diffndd=0; ++ if (frzndd[i]>0) { ++ diffndd=fsupndd*min((supice-supcap)/dCovrLm ,frzndd[i]); ++ frzndd[i]=frzndd[i]-diffndd; ++ } ++ if(runoff<0){ ++ saccu[i]= saccu[i] -runoff; ++ smelt[i] = 0; ++ precrunoff[i]=prect-saccu[i]; ++ //here assume pdd residual is 0, => ++ Tsurf[i]= max(Tsurf[i],-frzndd[i]); ++ } ++ else { ++ smelt[i] = runoff; ++ precrunoff[i]=prect-max(0.,supice)-saccu[i];} ++ //here really need pdd balance, try 0.5 fudge factor? ++ //at least runoff>0 => it's fairly warm, so Tsurf is !<<0, ++ //yet from site plots, can be ice free with Tsurf=-5.5C ++ if(Tsurf[i]<0) { ++ Tsurf[i]= min(Tsurf[i]+fsupT*diffndd , 0.);} ++ ++ agd[i] = -smelt[i]+saccu[i]; ++ pddtj[i]=pddt; ++ ++ /*Update inputs*/ ++ this->inputs->AddInput(new PentaP1Input(SurfaceforcingsMassBalanceEnum,&agd[0])); ////////verifier le nom ++ // this->inputs->AddInput(new TriaVertexInput(ThermalSpcTemperatureEnum,&Tsurf[0])); ++ this->inputs->AddInput(new PentaP1Input(ThermalSpctemperatureEnum,&Tsurf[0])); ++ ++ } //end of the for loop over the vertices + } + /*}}}*/ + /*FUNCTION Penta::PotentialSheetUngrounding{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 11993) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 11994) +@@ -111,7 +111,7 @@ + void ListResultsInfo(int** results_enums,int** results_size,double** results_times,int** results_steps,int* num_results); + void PatchFill(int* pcount, Patch* patch); + void PatchSize(int* pnumrows, int* pnumvertices,int* pnumnodes); +- void PositiveDegreeDay(void); ++ void PositiveDegreeDay(double* pdds,double* pds,double signorm); + void ProcessResultsUnits(void); + void ResetCoordinateSystem(void); + double SurfaceArea(void); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.m (revision 11993) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.m (revision 11994) +@@ -129,7 +129,7 @@ + fielddisplay(obj,'spcvx','x-axis velocity constraint (NaN means no constraint)'); + fielddisplay(obj,'spcvy','y-axis velocity constraint (NaN means no constraint)'); + fielddisplay(obj,'spcvz','z-axis velocity constraint (NaN means no constraint)'); +- fielddisplay(obj,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice'); ++ fielddisplay(obj,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice)'); + + disp(sprintf('\n %s','Rift options:')); + fielddisplay(obj,'rift_penalty_threshold','threshold for instability of mechanical constraints'); + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl +___________________________________________________________________ +Modified: svn:mergeinfo + Merged /issm/trunk:r11525-11526,11528-11993 +Modified: svn:ignore + - autom4te.cache +aclocal.m4 +bin +config.log +config.h +config.h.in +config.status +configure +doxygen +ISSM.paf +ISSM.ppf +ISSM.ppf_cache +libtool +list +Makefile +Makefile.in +stamp-h1 +svn-commit* +nightlylog + + + autom4te.cache +aclocal.m4 +bin +config.log +config.h +config.h.in +config.status +configure +ISSM.paf +ISSM.ppf +ISSM.ppf_cache +libtool +Makefile +Makefile.in +stamp-h1 +svn-commit* + + Index: /issm/oecreview/Archive/11991-12009/ISSM-11995-11996.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-11995-11996.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-11995-11996.diff (revision 12325) @@ -0,0 +1,6 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl +___________________________________________________________________ +Modified: svn:mergeinfo + Merged /issm/trunk:r11995 + Index: /issm/oecreview/Archive/11991-12009/ISSM-11996-11997.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-11996-11997.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-11996-11997.diff (revision 12325) @@ -0,0 +1,408 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 11996) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 11997) +@@ -2,41 +2,19 @@ + EXEEXT=$(WRAPPEREXT) + #Bin programs {{{1 + +-if NOSERIAL +-bin_PROGRAMS = +-else ++if MODULES + if MATLAB +-bin_PROGRAMS = AverageFilter\ +- AddExternalResult\ ++bin_PROGRAMS = AverageFilter\ + BamgMesher\ + BamgConvertMesh\ + BamgTriangulate\ + Chaco\ +- ComputeBasalStress\ +- ConfigureObjects \ +- ControlOptimization\ +- ControlInputGetGradient\ +- ControlInputScaleGradient\ +- ControlInputSetGradient\ + ContourToMesh \ + ContourToNodes \ +- CostFunction \ +- CreateNodalConstraints\ +- CreateJacobianMatrix\ +- Echo\ + ElementConnectivity\ + EnumToString\ + StringToEnum\ +- InputControlUpdate \ +- InputConvergence\ +- GetSolutionFromInputs\ +- GetVectorFromInputs\ +- Gradj\ +- GroundinglineMigration\ + HoleFiller \ +- InputDuplicate\ +- InputScale\ +- InputToResult\ + InternalFront\ + InterpFromGridToMesh \ + InterpFromMeshToMesh2d \ +@@ -50,93 +28,50 @@ + Ll2xy \ + Exp2Kml \ + Kml2Exp \ +- Mergesolutionfromftog\ + MeshPartition\ + MeshProfileIntersection\ +- ModelProcessor \ +- NodeConnectivity\ +- NodesDof\ +- Orth\ +- OutputResults\ +- ParsePetscOptions\ +- ConstraintsState\ + PointCloudFindNeighbors\ + PropagateFlagsFromConnectivity\ +- ProcessParams\ +- Reduceload\ +- Reducevectorgtos\ +- Reducevectorgtof\ +- Response\ +- ResetCoordinateSystem\ + Scotch\ +- Solver\ +- SparseToVector\ +- SpcNodes\ + Shp2Kml\ +- UpdateConstraints\ +- SurfaceArea\ +- SystemMatrices\ +- TimeAdapt\ + TriaSearch\ + TriMesh\ + TriMeshRifts\ + TriMeshNoDensity\ + TriMeshProcessRifts\ +- TriMeshRefine\ +- InputUpdateFromConstant\ +- InputUpdateFromSolution\ +- InputUpdateFromVector\ +- UpdateVertexPositions\ +- UpdateDynamicConstraints\ +- VerticesDof ++ TriMeshRefine + endif + if PYTHON + bin_PROGRAMS = TriMesh + endif + endif + #}}} +-#Dakota programs {{{1 +-if NOSERIAL +-bin_PROGRAMS += +-else +-if DAKOTA +-if MATLAB +-bin_PROGRAMS += DakotaResponses\ +- Dakota\ +- InputUpdateFromDakota +-endif +-endif +-endif +-#}}} + #Flags and libraries {{{1 +-LDADD = ../c/libISSM.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) ++LDADD = ../c/libISSMCore.a ../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) + +-#Initialize +-AM_CXXFLAGS = -D_SERIAL_ ++#Triangle library ++AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER + + if MATLAB +-AM_LDFLAGS = $(MEXLINK) ++AM_LDFLAGS = $(MEXLINK) + AM_CXXFLAGS += -DMATLAB -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread +-LDADD += $(MEXLIB) ++LDADD += $(MEXLIB) ../c/libISSMMatlab.a + + endif + + if PYTHON + AM_LDFLAGS = $(PYTHONLINK) +-AM_CXXFLAGS+= -DNPY_NO_DEPRECATED_API +-LDADD += $(BOOSTLIB) $(PYTHONLIB) ++AM_CXXFLAGS += -DNPY_NO_DEPRECATED_API ++LDADD += $(BOOSTLIB) $(PYTHONLIB) ../c/libISSMPython.a + endif + + +-#Triangle library +-AM_CXXFLAGS += -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER +- + #Optimization flags: + AM_CXXFLAGS += $(CXXOPTFLAGS) + #}}} + #Bin sources {{{1 +-AddExternalResult_SOURCES = AddExternalResult/AddExternalResult.cpp\ +- AddExternalResult/AddExternalResult.h ++AverageFilter_SOURCES = AverageFilter/AverageFilter.cpp\ ++ AverageFilter/AverageFilter.h + + BamgMesher_SOURCES = BamgMesher/BamgMesher.cpp\ + BamgMesher/BamgMesher.h +@@ -150,48 +85,12 @@ + Chaco_SOURCES = Chaco/Chaco.cpp\ + Chaco/Chaco.h + +-ComputeBasalStress_SOURCES = ComputeBasalStress/ComputeBasalStress.cpp\ +- ComputeBasalStress/ComputeBasalStress.h +- +-ConfigureObjects_SOURCES = ConfigureObjects/ConfigureObjects.cpp\ +- ConfigureObjects/ConfigureObjects.h +- + ContourToMesh_SOURCES = ContourToMesh/ContourToMesh.cpp\ + ContourToMesh/ContourToMesh.h + + ContourToNodes_SOURCES = ContourToNodes/ContourToNodes.cpp\ + ContourToNodes/ContourToNodes.h + +-ControlOptimization_SOURCES = ControlOptimization/ControlOptimization.cpp\ +- ControlOptimization/ControlOptimization.h +- +-ControlInputGetGradient_SOURCES = ControlInputGetGradient/ControlInputGetGradient.cpp\ +- ControlInputGetGradient/ControlInputGetGradient.h +- +-ControlInputScaleGradient_SOURCES = ControlInputScaleGradient/ControlInputScaleGradient.cpp\ +- ControlInputScaleGradient/ControlInputScaleGradient.h +- +-ControlInputSetGradient_SOURCES = ControlInputSetGradient/ControlInputSetGradient.cpp\ +- ControlInputSetGradient/ControlInputSetGradient.h +- +-InputControlUpdate_SOURCES = InputControlUpdate/InputControlUpdate.cpp\ +- InputControlUpdate/InputControlUpdate.h +- +-InputConvergence_SOURCES = InputConvergence/InputConvergence.cpp\ +- InputConvergence/InputConvergence.h +- +-CostFunction_SOURCES = CostFunction/CostFunction.cpp \ +- CostFunction/CostFunction.h +- +-CreateNodalConstraints_SOURCES = CreateNodalConstraints/CreateNodalConstraints.cpp \ +- CreateNodalConstraints/CreateNodalConstraints.h +- +-NodesDof_SOURCES = NodesDof/NodesDof.cpp\ +- NodesDof/NodesDof.h +- +-Echo_SOURCES = Echo/Echo.cpp\ +- Echo/Echo.h +- + ElementConnectivity_SOURCES = ElementConnectivity/ElementConnectivity.cpp\ + ElementConnectivity/ElementConnectivity.h + +@@ -201,30 +100,9 @@ + StringToEnum_SOURCES = StringToEnum/StringToEnum.cpp\ + StringToEnum/StringToEnum.h + +-GetSolutionFromInputs_SOURCES = GetSolutionFromInputs/GetSolutionFromInputs.cpp\ +- GetSolutionFromInputs/GetSolutionFromInputs.h +- +-GetVectorFromInputs_SOURCES = GetVectorFromInputs/GetVectorFromInputs.cpp\ +- GetVectorFromInputs/GetVectorFromInputs.h +- +-Gradj_SOURCES = Gradj/Gradj.cpp\ +- Gradj/Gradj.h +- +-GroundinglineMigration_SOURCES = GroundinglineMigration/GroundinglineMigration.cpp\ +- GroundinglineMigration/GroundinglineMigration.h +- + HoleFiller_SOURCES = HoleFiller/HoleFiller.cpp\ + HoleFiller/HoleFiller.h + +-InputDuplicate_SOURCES = InputDuplicate/InputDuplicate.cpp\ +- InputDuplicate/InputDuplicate.h +- +-InputScale_SOURCES = InputScale/InputScale.cpp\ +- InputScale/InputScale.h +- +-InputToResult_SOURCES = InputToResult/InputToResult.cpp\ +- InputToResult/InputToResult.h +- + InternalFront_SOURCES = InternalFront/InternalFront.cpp\ + InternalFront/InternalFront.h + +@@ -264,88 +142,24 @@ + Kml2Exp_SOURCES = Kml2Exp/Kml2Exp.cpp\ + Kml2Exp/Kml2Exp.h + +-AverageFilter_SOURCES = AverageFilter/AverageFilter.cpp\ +- AverageFilter/AverageFilter.h +- +-Mergesolutionfromftog_SOURCES = Mergesolutionfromftog/Mergesolutionfromftog.cpp\ +- Mergesolutionfromftog/Mergesolutionfromftog.h +- + MeshPartition_SOURCES = MeshPartition/MeshPartition.cpp\ + MeshPartition/MeshPartition.h + + MeshProfileIntersection_SOURCES = MeshProfileIntersection/MeshProfileIntersection.cpp\ + MeshProfileIntersection/MeshProfileIntersection.h + +-ModelProcessor_SOURCES = ModelProcessor/ModelProcessor.cpp \ +- ModelProcessor/ModelProcessor.h +- +-NodeConnectivity_SOURCES = NodeConnectivity/NodeConnectivity.cpp\ +- NodeConnectivity/NodeConnectivity.h +- +-Orth_SOURCES = Orth/Orth.cpp\ +- Orth/Orth.h +- +-OutputResults_SOURCES = OutputResults/OutputResults.cpp\ +- OutputResults/OutputResults.h +- +-ConstraintsState_SOURCES = ConstraintsState/ConstraintsState.cpp\ +- ConstraintsState/ConstraintsState.h +- + PointCloudFindNeighbors_SOURCES = PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\ + PointCloudFindNeighbors/PointCloudFindNeighbors.h + +-ProcessParams_SOURCES = ProcessParams/ProcessParams.cpp\ +- ProcessParams/ProcessParams.h +- + PropagateFlagsFromConnectivity_SOURCES = PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\ + PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h + +-Reduceload_SOURCES = Reduceload/Reduceload.cpp\ +- Reduceload/Reduceload.h +- +-Reducevectorgtos_SOURCES = Reducevectorgtos/Reducevectorgtos.cpp\ +- Reducevectorgtos/Reducevectorgtos.h +- +-Reducevectorgtof_SOURCES = Reducevectorgtof/Reducevectorgtof.cpp\ +- Reducevectorgtof/Reducevectorgtof.h +- +-Response_SOURCES = Response/Response.cpp\ +- Response/Response.h +- +-ResetCoordinateSystem_SOURCES = ResetCoordinateSystem/ResetCoordinateSystem.cpp\ +- ResetCoordinateSystem/ResetCoordinateSystem.h +- + Scotch_SOURCES = Scotch/Scotch.cpp\ + Scotch/Scotch.h + +-Solver_SOURCES = Solver/Solver.cpp\ +- Solver/Solver.h +- +-SparseToVector_SOURCES = SparseToVector/SparseToVector.cpp\ +- SparseToVector/SparseToVector.h +- +-SpcNodes_SOURCES = SpcNodes/SpcNodes.cpp\ +- SpcNodes/SpcNodes.h +- + Shp2Kml_SOURCES = Shp2Kml/Shp2Kml.cpp\ + Shp2Kml/Shp2Kml.h + +-UpdateConstraints_SOURCES = UpdateConstraints/UpdateConstraints.cpp\ +- UpdateConstraints/UpdateConstraints.h +- +-SystemMatrices_SOURCES = SystemMatrices/SystemMatrices.cpp\ +- SystemMatrices/SystemMatrices.h +- +- +-CreateJacobianMatrix_SOURCES = CreateJacobianMatrix/CreateJacobianMatrix.cpp\ +- CreateJacobianMatrix/CreateJacobianMatrix.h +- +-SurfaceArea_SOURCES = SurfaceArea/SurfaceArea.cpp\ +- SurfaceArea/SurfaceArea.h +- +-TimeAdapt_SOURCES = TimeAdapt/TimeAdapt.cpp\ +- TimeAdapt/TimeAdapt.h +- + TriaSearch_SOURCES = TriaSearch/TriaSearch.cpp\ + TriaSearch/TriaSearch.h + +@@ -364,33 +178,4 @@ + TriMeshRefine_SOURCES = TriMeshRefine/TriMeshRefine.cpp\ + TriMeshRefine/TriMeshRefine.h + +-InputUpdateFromConstant_SOURCES = InputUpdateFromConstant/InputUpdateFromConstant.cpp\ +- InputUpdateFromConstant/InputUpdateFromConstant.h +- +-InputUpdateFromSolution_SOURCES = InputUpdateFromSolution/InputUpdateFromSolution.cpp\ +- InputUpdateFromSolution/InputUpdateFromSolution.h +- +-InputUpdateFromVector_SOURCES = InputUpdateFromVector/InputUpdateFromVector.cpp\ +- InputUpdateFromVector/InputUpdateFromVector.h +- +-UpdateVertexPositions_SOURCES = UpdateVertexPositions/UpdateVertexPositions.cpp\ +- UpdateVertexPositions/UpdateVertexPositions.h +- +-UpdateDynamicConstraints_SOURCES = UpdateDynamicConstraints/UpdateDynamicConstraints.cpp\ +- UpdateDynamicConstraints/UpdateDynamicConstraints.h +- +-ParsePetscOptions_SOURCES = ParsePetscOptions/ParsePetscOptions.cpp\ +- ParsePetscOptions/ParsePetscOptions.h +- +-VerticesDof_SOURCES = VerticesDof/VerticesDof.cpp\ +- VerticesDof/VerticesDof.h +- + #}}} +-#Dakota sources {{{1 +-DakotaResponses_SOURCES = DakotaResponses/DakotaResponses.cpp\ +- DakotaResponses/DakotaResponses.h +-Dakota_SOURCES = Dakota/Dakota.cpp\ +- Dakota/Dakota.h +-InputUpdateFromDakota_SOURCES = InputUpdateFromDakota/InputUpdateFromDakota.cpp\ +- InputUpdateFromDakota/InputUpdateFromDakota.h +-#}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h (revision 11996) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h (revision 11997) +@@ -17,6 +17,7 @@ + #define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol + #endif + ++/*Header files: */ + #include "../../c/include/globals.h" + #include "../../c/toolkits/toolkits.h" + #include "../../c/include/include.h" +@@ -31,21 +32,19 @@ + #define DOMAINOUTLINE (mxArray *)prhs[0] + #define AREA (mxArray *)prhs[1] + #define ORDER (mxArray *)prhs[2] +- + /* serial output macros: */ + #define INDEX (mxArray**)&plhs[0] + #define X (mxArray**)&plhs[1] + #define Y (mxArray**)&plhs[2] + #define SEGMENTS (mxArray**)&plhs[3] + #define SEGMENTMARKERLIST (mxArray**)&plhs[4] +- + #endif ++ + #ifdef _HAVE_PYTHON_ + /* serial input macros: */ + #define DOMAINOUTLINE PyTuple_GetItem(args,0) + #define AREA PyTuple_GetItem(args,1) + #define ORDER PyTuple_GetItem(args,2) +- + /* serial output macros: */ + #define INDEX output,0 + #define X output,1 +@@ -54,9 +53,6 @@ + #define SEGMENTMARKERLIST output,4 + #endif + +-/* local prototypes: */ +-void TriMeshUsage(void); +- + #undef __FUNCT__ + #define __FUNCT__ "TriMesh" + +@@ -66,4 +62,7 @@ + #undef NRHS + #define NRHS 3 + ++/* local prototypes: */ ++void TriMeshUsage(void); ++ + #endif /* _TRIMESH_H */ Index: /issm/oecreview/Archive/11991-12009/ISSM-11999-12000.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-11999-12000.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-11999-12000.diff (revision 12325) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/Makefile.am (revision 11999) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/Makefile.am (revision 12000) +@@ -12,9 +12,6 @@ + ./model/solvers/*.m \ + ./planet/*.m \ + ./qmu/*.m \ +- ./shared/*.m \ +- ./solutions/*.m \ +- ./solvers/*.m \ + ./utils/*.m \ + ./utils/Analysis/*.m \ + ./utils/Array/*.m \ Index: /issm/oecreview/Archive/11991-12009/ISSM-12002-12003.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-12002-12003.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-12002-12003.diff (revision 12325) @@ -0,0 +1,19 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/io.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/io.h (revision 12002) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/io.h (revision 12003) +@@ -14,14 +14,6 @@ + + #include "./Disk/diskio.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "./Matlab/matlabio.h" +-#endif +- +-#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) +-#include "./Python/pythonio.h" +-#endif +- + /*printf: */ + int PrintfFunction(const char* format,...); + Index: /issm/oecreview/Archive/11991-12009/ISSM-12005-12006.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-12005-12006.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-12005-12006.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 12005) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 12006) +@@ -27,7 +27,6 @@ + #include "./mpi/mpiincludes.h" + #include "./metis/metisincludes.h" + #include "./triangle/triangleincludes.h" +-#include "./double/double.h" + #include "./toolkitsenums.h" + #include "./issm/issmtoolkit.h" + Index: /issm/oecreview/Archive/11991-12009/ISSM-12006-12007.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-12006-12007.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-12006-12007.diff (revision 12325) @@ -0,0 +1,107 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12006) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12007) +@@ -12,34 +12,18 @@ + AC_DEFINE([_ISSM_DEBUG_],[1],[Macro to enable debugging in ISSM]) + fi + dnl }}} +- dnl Serial build {{{ +- AC_ARG_WITH([serial], +- AS_HELP_STRING([--with-serial = value],[serial compilation. ]), +- [SERIAL_VALUE=$withval],[SERIAL_VALUE="yes"]) +- AC_MSG_CHECKING(for serial compilation) +- AM_CONDITIONAL([NOSERIAL], [test $SERIAL_VALUE = no]) +- AM_CONDITIONAL([SERIAL], [test $SERIAL_VALUE = yes]) +- AC_MSG_RESULT($SERIAL_VALUE) ++ dnl Modules build {{{ ++ AC_ARG_WITH([modules], ++ AS_HELP_STRING([--with-modules = value],[modules compilation. ]), ++ [MODULES_VALUE=$withval],[MODULES_VALUE="yes"]) ++ AC_MSG_CHECKING(for modules compilation) ++ AM_CONDITIONAL([NOMODULES], [test $MODULES_VALUE = no]) ++ AM_CONDITIONAL([MODULES], [test $MODULES_VALUE = yes]) ++ AC_MSG_RESULT($MODULES_VALUE) + dnl }}} +- dnl Parallel build {{{ +- AC_ARG_WITH([parallel], +- AS_HELP_STRING([--with-parallel = value], [parallel compilation. ]), +- [PARALLEL_VALUE=$withval],[PARALLEL_VALUE="yes"]) +- AC_MSG_CHECKING(for parallel compilation) +- AM_CONDITIONAL([NOPARALLEL], [test $PARALLEL_VALUE = no]) +- AM_CONDITIONAL([PARALLEL], [test $PARALLEL_VALUE = yes]) +- AC_MSG_RESULT($PARALLEL_VALUE) +- ISSMEXT=".exe" ++ dnl Extensions{{{ + AC_SUBST([ISSMEXT]) + dnl }}} +- dnl Serial or Parallel check {{{ +- dnl Check that at least serial or parallel builds have been requested! +- if test "$SERIAL_VALUE" != "yes" ; then +- if test "$PARALLEL_VALUE" != "yes"; then +- AC_MSG_ERROR([cannot request --with-serial=no and --with-parallel=no at the same time!]) +- fi +- fi +- dnl }}} + + dnl ISSM's externalpackages + dnl vendor{{{ +@@ -688,29 +672,6 @@ + fi + AC_MSG_RESULT($HAVE_TAO) + dnl }}} +- dnl mpiuni{{{ +- dnl when running in serial mode, MPI must be ignored, and set to internal petsc mpiuni: +- if test "$PARALLEL_VALUE" = "no" ; then +- HAVE_MPI=yes +- MPIINCL=-I"$PETSC_ROOT/include/mpiuni" +- +- case "${host_os}" in +- *cygwin*) +- dnl MPILIB="-link -LIBPATH:\"$PETSC_ROOT/$PETSC_ARCH/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libmpiuni.lib" +- ;; +- *linux*) +- MPILIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lmpiuni" +- ;; +- *darwin*) +- MPILIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lmpiuni" +- ;; +- esac +- +- AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src]) +- AC_SUBST([MPIINCL]) +- AC_SUBST([MPILIB]) +- fi +- dnl }}} + dnl slepc{{{ + AC_ARG_WITH([slepc-dir], + AS_HELP_STRING([--with-slepc-dir = DIR],[slepc root directory]), +@@ -1228,25 +1189,18 @@ + dnl checks{{{ + AC_MSG_CHECKING(consistency between all libraries) + +- dnl check that if petsc is requested in parallel, mpi should be specified ++ dnl check that if petsc is requested , mpi should be specified + if test "$HAVE_PETSC" = "yes" ; then + if test "$HAVE_MPI" = "NO"; then + AC_MSG_ERROR([petsc requires mpi!]); + fi + fi + +- dnl check that we have either python or matlab support if we only compile serially +- if test "$PARALLEL_VALUE" = "no" && test "$HAVE_MATLAB" = "no" && test "$HAVE_PYTHON" = "no"; then ++ dnl check that we have either python or matlab support if we compile the modules ++ if test "$MODULES_VALUE" = "yes" && test "$HAVE_MATLAB" = "no" && test "$HAVE_PYTHON" = "no"; then + AC_MSG_ERROR([need at least python or matlab support to compile only in serial mode!]); + fi + +- dnl check that we don't have with-matlab and with-python at the same time +- if test "$HAVE_PYTHON" = "yes" ; then +- if test "$HAVE_MATLAB" = "yes"; then +- AC_MSG_ERROR([cannot create matlab and python wrappers simultaneously! Please choose one or the other.]); +- fi +- fi +- + AC_MSG_RESULT(done) + dnl }}} + Index: /issm/oecreview/Archive/11991-12009/ISSM-12008-12009.diff =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-12008-12009.diff (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-12008-12009.diff (revision 12325) @@ -0,0 +1,16 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 12008) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 12009) +@@ -19,11 +19,6 @@ + #include "./petsc/petscincludes.h" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "./matlab/matlabincludes.h" +-#endif +- +- + #include "./mpi/mpiincludes.h" + #include "./metis/metisincludes.h" + #include "./triangle/triangleincludes.h" Index: /issm/oecreview/Archive/11991-12009/ISSM-DocReview-11991-12009.tex =================================================================== --- /issm/oecreview/Archive/11991-12009/ISSM-DocReview-11991-12009.tex (revision 12325) +++ /issm/oecreview/Archive/11991-12009/ISSM-DocReview-11991-12009.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11991-12009/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11991-12009/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/11991-12009/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +11991-12009 Index: /issm/oecreview/Archive/11991-12009/Makefile =================================================================== --- /issm/oecreview/Archive/11991-12009/Makefile (revision 12325) +++ /issm/oecreview/Archive/11991-12009/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11991-12009 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11991-12009/log.tex =================================================================== --- /issm/oecreview/Archive/11991-12009/log.tex (revision 12325) +++ /issm/oecreview/Archive/11991-12009/log.tex (revision 12325) @@ -0,0 +1,31 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11991-11992.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/matlab/install.sh \\ Export determination: 6. \\Rationale: reverted back to previous revision \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11992-11993.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/matlab/install.sh \\ Export determination: 6. \\Rationale: reverted back to previous revision +D /issm/trunk-jpl/externalpackages/triangle/README not needed anymore \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11993-11994.diff: \\ Function name: \\D /issm/trunk-jpl/externalpackages/triangle/README \\ Export determination: 6. \\Rationale: not needed anymore +M /issm/trunk-jpl M /issm/trunk-jpl/m4/issm\_options.m4 M /issm/trunk-jpl/src/c/modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp M /issm/trunk-jpl/src/c/objects/Elements/Element.h M /issm/trunk-jpl/src/c/objects/Elements/Penta.cpp M /issm/trunk-jpl/src/c/objects/Elements/Penta.h M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Elements/Tria.h M /issm/trunk-jpl/src/m/classes/diagnostic.m merged trunk and trunk-jpl \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11994-11995.diff: \\ Function name: \\M /issm/trunk-jpl M /issm/trunk-jpl/m4/issm\_options.m4 M /issm/trunk-jpl/src/c/modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp M /issm/trunk-jpl/src/c/objects/Elements/Element.h M /issm/trunk-jpl/src/c/objects/Elements/Penta.cpp M /issm/trunk-jpl/src/c/objects/Elements/Penta.h M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Elements/Tria.h M /issm/trunk-jpl/src/m/classes/diagnostic.m \\ Export determination: 6. \\Rationale: merged trunk and trunk-jpl \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11995-11996.diff: \\ Function name: \\M /issm/trunk-jpl \\ Export determination: 6. \\Rationale: Block revision 11995 from being merged into trunk-jpl \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11996-11997.diff: \\ Function name: \\M /issm/trunk-jpl \\ Export determination: 6. \\Rationale: Block revision 11995 from being merged into trunk-jpl +D /issm/trunk-jpl/src/mex/AddExternalResult D /issm/trunk-jpl/src/mex/ComputeBasalStress D /issm/trunk-jpl/src/mex/ConfigureObjects D /issm/trunk-jpl/src/mex/ConstraintsState D /issm/trunk-jpl/src/mex/ControlInputGetGradient D /issm/trunk-jpl/src/mex/ControlInputScaleGradient D /issm/trunk-jpl/src/mex/ControlInputSetGradient D /issm/trunk-jpl/src/mex/ControlOptimization D /issm/trunk-jpl/src/mex/CostFunction D /issm/trunk-jpl/src/mex/CreateJacobianMatrix D /issm/trunk-jpl/src/mex/CreateNodalConstraints D /issm/trunk-jpl/src/mex/Dakota D /issm/trunk-jpl/src/mex/DakotaResponses D /issm/trunk-jpl/src/mex/Echo D /issm/trunk-jpl/src/mex/GetSolutionFromInputs D /issm/trunk-jpl/src/mex/GetVectorFromInputs D /issm/trunk-jpl/src/mex/Gradj D /issm/trunk-jpl/src/mex/GroundinglineMigration D /issm/trunk-jpl/src/mex/InputControlUpdate D /issm/trunk-jpl/src/mex/InputConvergence D /issm/trunk-jpl/src/mex/InputDuplicate D /issm/trunk-jpl/src/mex/InputScale D /issm/trunk-jpl/src/mex/InputToResult D /issm/trunk-jpl/src/mex/InputUpdateFromConstant D /issm/trunk-jpl/src/mex/InputUpdateFromDakota D /issm/trunk-jpl/src/mex/InputUpdateFromSolution D /issm/trunk-jpl/src/mex/InputUpdateFromVector M /issm/trunk-jpl/src/mex/Makefile.am D /issm/trunk-jpl/src/mex/Mergesolutionfromftog D /issm/trunk-jpl/src/mex/ModelProcessor D /issm/trunk-jpl/src/mex/NodeConnectivity D /issm/trunk-jpl/src/mex/NodesDof D /issm/trunk-jpl/src/mex/Orth D /issm/trunk-jpl/src/mex/OutputResults D /issm/trunk-jpl/src/mex/OutputRifts D /issm/trunk-jpl/src/mex/ParameterOutput D /issm/trunk-jpl/src/mex/ParsePetscOptions D /issm/trunk-jpl/src/mex/ProcessParams D /issm/trunk-jpl/src/mex/Reduceload D /issm/trunk-jpl/src/mex/Reducevectorgtof D /issm/trunk-jpl/src/mex/Reducevectorgtos D /issm/trunk-jpl/src/mex/ResetCoordinateSystem D /issm/trunk-jpl/src/mex/Response D /issm/trunk-jpl/src/mex/Solver D /issm/trunk-jpl/src/mex/SparseToVector D /issm/trunk-jpl/src/mex/SpcNodes D /issm/trunk-jpl/src/mex/SurfaceArea D /issm/trunk-jpl/src/mex/SystemMatrices D /issm/trunk-jpl/src/mex/TimeAdapt M /issm/trunk-jpl/src/mex/TriMesh/TriMesh.h D /issm/trunk-jpl/src/mex/UpdateConstraints D /issm/trunk-jpl/src/mex/UpdateDynamicConstraints D /issm/trunk-jpl/src/mex/UpdateVertexPositions D /issm/trunk-jpl/src/mex/VerticesDof Starting to get rid of serial modules \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11997-11998.diff: \\ Function name: \\D /issm/trunk-jpl/src/mex/AddExternalResult D /issm/trunk-jpl/src/mex/ComputeBasalStress D /issm/trunk-jpl/src/mex/ConfigureObjects D /issm/trunk-jpl/src/mex/ConstraintsState D /issm/trunk-jpl/src/mex/ControlInputGetGradient D /issm/trunk-jpl/src/mex/ControlInputScaleGradient D /issm/trunk-jpl/src/mex/ControlInputSetGradient D /issm/trunk-jpl/src/mex/ControlOptimization D /issm/trunk-jpl/src/mex/CostFunction D /issm/trunk-jpl/src/mex/CreateJacobianMatrix D /issm/trunk-jpl/src/mex/CreateNodalConstraints D /issm/trunk-jpl/src/mex/Dakota D /issm/trunk-jpl/src/mex/DakotaResponses D /issm/trunk-jpl/src/mex/Echo D /issm/trunk-jpl/src/mex/GetSolutionFromInputs D /issm/trunk-jpl/src/mex/GetVectorFromInputs D /issm/trunk-jpl/src/mex/Gradj D /issm/trunk-jpl/src/mex/GroundinglineMigration D /issm/trunk-jpl/src/mex/InputControlUpdate D /issm/trunk-jpl/src/mex/InputConvergence D /issm/trunk-jpl/src/mex/InputDuplicate D /issm/trunk-jpl/src/mex/InputScale D /issm/trunk-jpl/src/mex/InputToResult D /issm/trunk-jpl/src/mex/InputUpdateFromConstant D /issm/trunk-jpl/src/mex/InputUpdateFromDakota D /issm/trunk-jpl/src/mex/InputUpdateFromSolution D /issm/trunk-jpl/src/mex/InputUpdateFromVector M /issm/trunk-jpl/src/mex/Makefile.am D /issm/trunk-jpl/src/mex/Mergesolutionfromftog D /issm/trunk-jpl/src/mex/ModelProcessor D /issm/trunk-jpl/src/mex/NodeConnectivity D /issm/trunk-jpl/src/mex/NodesDof D /issm/trunk-jpl/src/mex/Orth D /issm/trunk-jpl/src/mex/OutputResults D /issm/trunk-jpl/src/mex/OutputRifts D /issm/trunk-jpl/src/mex/ParameterOutput D /issm/trunk-jpl/src/mex/ParsePetscOptions D /issm/trunk-jpl/src/mex/ProcessParams D /issm/trunk-jpl/src/mex/Reduceload D /issm/trunk-jpl/src/mex/Reducevectorgtof D /issm/trunk-jpl/src/mex/Reducevectorgtos D /issm/trunk-jpl/src/mex/ResetCoordinateSystem D /issm/trunk-jpl/src/mex/Response D /issm/trunk-jpl/src/mex/Solver D /issm/trunk-jpl/src/mex/SparseToVector D /issm/trunk-jpl/src/mex/SpcNodes D /issm/trunk-jpl/src/mex/SurfaceArea D /issm/trunk-jpl/src/mex/SystemMatrices D /issm/trunk-jpl/src/mex/TimeAdapt M /issm/trunk-jpl/src/mex/TriMesh/TriMesh.h D /issm/trunk-jpl/src/mex/UpdateConstraints D /issm/trunk-jpl/src/mex/UpdateDynamicConstraints D /issm/trunk-jpl/src/mex/UpdateVertexPositions D /issm/trunk-jpl/src/mex/VerticesDof \\ Export determination: 6. \\Rationale: Starting to get rid of serial modules +D /issm/trunk-jpl/src/m/solutions Getting rid of serial capability \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11998-11999.diff: \\ Function name: \\D /issm/trunk-jpl/src/m/solutions \\ Export determination: 6. \\Rationale: Getting rid of serial capability +D /issm/trunk-jpl/src/m/shared D /issm/trunk-jpl/src/m/solvers Getting rid of serial capability \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11999-12000.diff: \\ Function name: \\D /issm/trunk-jpl/src/m/shared D /issm/trunk-jpl/src/m/solvers \\ Export determination: 6. \\Rationale: Getting rid of serial capability +M /issm/trunk-jpl/src/m/Makefile.am Getting rid of serial capability \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12000-12001.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/Makefile.am \\ Export determination: 6. \\Rationale: Getting rid of serial capability +D /issm/trunk-jpl/src/c/io/Matlab Moved to src/matlab \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12001-12002.diff: \\ Function name: \\D /issm/trunk-jpl/src/c/io/Matlab \\ Export determination: 6. \\Rationale: Moved to src/matlab +D /issm/trunk-jpl/src/c/io/Python Moved to src/python/io \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-12002-12003.diff: \\ Function name: \\D /issm/trunk-jpl/src/c/io/Python \\ Export determination: 6. \\Rationale: Moved to src/python/io +M /issm/trunk-jpl/src/c/io/io.h Moved to src/python/io \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-12003-12004.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/io/io.h \\ Export determination: 6. \\Rationale: Moved to src/python/io \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-12004-12005.diff: \\ Function name: \\D /issm/trunk-jpl/src/c/toolkits/double \\ Export determination: 6. \\Rationale: Gone to src/matlab/io \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-12005-12006.diff: \\ Function name: \\D /issm/trunk-jpl/src/c/toolkits/double \\ Export determination: 6. \\Rationale: Gone to src/matlab/io +M /issm/trunk-jpl/src/c/toolkits/toolkits.h Gone to src/matlab/io \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-12006-12007.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/toolkits/toolkits.h \\ Export determination: 6. \\Rationale: Gone to src/matlab/io +M /issm/trunk-jpl/m4/issm\_options.m4 New architecture where serial and parallel are replaced by module or not module \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-12007-12008.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: New architecture where serial and parallel are replaced by module or not module +D /issm/trunk-jpl/src/c/toolkits/matlab Moved to src/matlab/io \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-12008-12009.diff: \\ Function name: \\D /issm/trunk-jpl/src/c/toolkits/matlab \\ Export determination: 6. \\Rationale: Moved to src/matlab/io +M /issm/trunk-jpl/src/c/toolkits/toolkits.h Moved to src/matlab/io \\\\ Index: /issm/oecreview/Archive/11991-12009/r1.tex =================================================================== --- /issm/oecreview/Archive/11991-12009/r1.tex (revision 12325) +++ /issm/oecreview/Archive/11991-12009/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +11991 Index: /issm/oecreview/Archive/11991-12009/r2.tex =================================================================== --- /issm/oecreview/Archive/11991-12009/r2.tex (revision 12325) +++ /issm/oecreview/Archive/11991-12009/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12009 Index: /issm/oecreview/Archive/12010-12040/Date.tex =================================================================== --- /issm/oecreview/Archive/12010-12040/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12010-12040/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12010-12040/ISSM-12010-12011.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12010-12011.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12010-12011.diff (revision 12325) @@ -0,0 +1,5861 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12011) +@@ -1,6 +1,8 @@ + from model import * +-from TriMesh import * ++from TriMesh.Python import * + +-md=model() ++#md=model() ++#md=triangle(md,'../Exp/Square.exp',150000); ++ + [a,b,c,d,e]=TriMesh('../Exp/Square.exp',15000.0**2.0,True) + print(a,b,c,d,e) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh (revision 12011) +@@ -25,6 +25,8 @@ + --with-python=python3.2 \ + --with-python-root="$ISSM_TIER/externalpackages/python/install" + ++exit ++ + #Compile boost + ./bjam install + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/Container/Options.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/Container/Options.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/Container/Options.cpp (revision 12011) +@@ -0,0 +1,55 @@ ++/* ++ * \file Options.c ++ * \brief: implementation of the Options class methods that depend on Matlab ++ */ ++ ++/*Headers: {{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++ ++#include "./DataSet.h" ++#include "../shared/shared.h" ++#include "../io/io.h" ++#include "../include/include.h" ++#include "../shared/shared.h" ++#include "../EnumDefinitions/EnumDefinitions.h" ++#if _SERIAL_ ++#include "../io/io.h" ++#endif ++/*}}}*/ ++ ++/*Object constructors and destructor*/ ++/*FUNCTION Options::Options(int istart, int nrhs, const mxArray* prhs[]){{{1*/ ++Options::Options(int istart, int nrhs, void* module_references){ ++ ++ const mxArray** prhs = NULL; ++ int i; ++ char *name = NULL; ++ Option *option = NULL; ++ ++ /*Recover matlab references: */ ++ prhs=(const mxArray**)module_references; ++ ++ /*loop over each name and value*/ ++ for (i=istart; iAddOption(option); ++ option=NULL; ++ } ++ ++ /*echo the dataset */ ++ //if (this->Size()) for(i=0;iSize();i++) ((Option*)this->GetObjectByOffset(i))->Echo(); ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12011) +@@ -0,0 +1,50 @@ ++/* \file macros.h ++ * \brief: global macros used in the whole code ++ */ ++ ++/*Header {{{1*/ ++#ifndef _MATLAB_MACROS_H_ ++#define _MATLAB_MACROS_H_ ++ ++#include "./typedefs.h" ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++/*}}}*/ ++ ++/* MODULEBOOT/MODULEEND {{{1*/ ++ ++/*The following macros hide the error exception handling in a matlab module. Just put ++ * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions ++ * will be trapped. Really nifty!*/ ++ ++//Module Boot //{{{ ++#define MODULEBOOT(); ModuleBoot(); \ ++ try{ ++ ++#define MODULEEND(); ModuleEnd(); }\ ++ catch(ErrorException &exception){\ ++ exception.Report(); \ ++ mexErrMsgTxt(""); \ ++ }\ ++ catch (exception& e) {\ ++ _printf_(true,"Standard exception: %s\n",e.what());\ ++ mexErrMsgTxt(" ");\ ++ } ++//}}} ++/* WRAPPER {{{1*/ ++#ifdef _HAVE_MATLAB_ ++#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) ++#endif ++ ++/*}}}*/ ++/* CHECKARGUMENTS {{{1*/ ++#ifdef _HAVE_MATLAB_ ++#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer) ++#endif ++/*}}}*/ ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp (revision 12011) +@@ -0,0 +1,9 @@ ++SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ ++ ++ SeqMat* output=NULL; ++ ++ output=new SeqMat(); ++ MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref); ++ return output; ++ ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp (revision 12011) +@@ -0,0 +1,194 @@ ++/*\file OptionParse.c ++ *\brief: functions to parse the mex options. ++ */ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../../shared/shared.h" ++#include "../../io/io.h" ++#include "../../include/include.h" ++#include "./matlabio.h" ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++#include ++ ++/*FUNCTION OptionDoubleParse {{{1*/ ++OptionDouble* OptionDoubleParse( char* name, const mxArray* prhs[]){ ++ ++ OptionDouble *odouble = NULL; ++ ++ /*check and parse the name */ ++ odouble=new OptionDouble; ++ odouble->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); ++ memcpy(odouble->name,name,(strlen(name)+1)*sizeof(char)); ++ ++ /*check and parse the value */ ++ if (!mxIsClass(prhs[0],"double")){ ++ _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",odouble->name,"double",odouble->name,mxGetClassName(prhs[0])); ++ } ++ ++ FetchData(&odouble->values,&odouble->numel,&odouble->ndims,&odouble->size,prhs[0]); ++ ++ return(odouble); ++}/*}}}*/ ++/*FUNCTION OptionLogicalParse {{{1*/ ++OptionLogical* OptionLogicalParse( char* name, const mxArray* prhs[]){ ++ ++ OptionLogical *ological = NULL; ++ ++ /*check and parse the name */ ++ ological=new OptionLogical; ++ ological->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); ++ memcpy(ological->name,name,(strlen(name)+1)*sizeof(char)); ++ ++ /*check and parse the value */ ++ if (!mxIsClass(prhs[0],"logical")){ ++ _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ological->name,"logical",ological->name,mxGetClassName(prhs[0])); ++ } ++ ++ FetchData(&ological->values,&ological->numel,&ological->ndims,&ological->size,prhs[0]); ++ ++ return(ological); ++}/*}}}*/ ++/*FUNCTION OptionCharParse {{{1*/ ++OptionChar* OptionCharParse( char* name, const mxArray* prhs[]){ ++ ++ OptionChar *ochar = NULL; ++ ++ /*check and parse the name */ ++ ochar=new OptionChar; ++ ochar->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); ++ memcpy(ochar->name,name,(strlen(name)+1)*sizeof(char)); ++ ++ /*check and parse the value */ ++ if (!mxIsClass(prhs[0],"char")){ ++ _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ochar->name,"char",ochar->name,mxGetClassName(prhs[0])); ++ } ++ ++ FetchData(&ochar->values,&ochar->numel,&ochar->ndims,&ochar->size,prhs[0]); ++ ++ return(ochar); ++}/*}}}*/ ++/*FUNCTION OptionStructParse {{{1*/ ++OptionStruct* OptionStructParse( char* name, const mxArray* prhs[]){ ++ ++ int i; ++ char namei[161]; ++ OptionStruct *ostruct = NULL; ++ Option *option = NULL; ++ const mwSize *ipt = NULL; ++ const mxArray *structi; ++ mwIndex sindex; ++ ++ /*check and parse the name */ ++ ostruct=new OptionStruct; ++ ostruct->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); ++ memcpy(ostruct->name,name,(strlen(name)+1)*sizeof(char)); ++ ++ /*check and parse the value */ ++ if (!mxIsClass(prhs[0],"struct")){ ++ _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ostruct->name,"struct",ostruct->name,mxGetClassName(prhs[0])); ++ } ++ ++ ostruct->numel=mxGetNumberOfElements(prhs[0]); ++ ostruct->ndims=mxGetNumberOfDimensions(prhs[0]); ++ ipt =mxGetDimensions(prhs[0]); ++ ostruct->size =(int *) xmalloc(ostruct->ndims*sizeof(int)); ++ for (i=0; indims; i++) ostruct->size[i]=(int)ipt[i]; ++ if (ostruct->numel) ostruct->values=(Options**) xmalloc(ostruct->numel*sizeof(Options *)); ++ ++ /*loop through and process each element of the struct array */ ++ for (sindex=0; sindexnumel; sindex++) { ++ ostruct->values[sindex]=new Options; ++ ++ /*loop through and process each field for the element */ ++ for (i=0; ivalues[sindex]->AddObject((Object*)option); ++ option=NULL; ++ } ++ } ++ ++ return(ostruct); ++}/*}}}*/ ++/*FUNCTION OptionCellParse {{{1*/ ++OptionCell* OptionCellParse( char* name, const mxArray* prhs[]){ ++ ++ int i; ++ int *dims; ++ char namei[161]; ++ char cstr[81]; ++ OptionCell *ocell = NULL; ++ Option *option = NULL; ++ const mwSize *ipt = NULL; ++ const mxArray *celli; ++ mwIndex cindex; ++ ++ /*check and parse the name */ ++ ocell=new OptionCell; ++ ocell->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); ++ memcpy(ocell->name,name,(strlen(name)+1)*sizeof(char)); ++ ++ /*check and parse the value */ ++ if (!mxIsClass(prhs[0],"cell")){ ++ _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ocell->name,"cell",ocell->name,mxGetClassName(prhs[0])); ++ } ++ ++ ocell->numel=mxGetNumberOfElements(prhs[0]); ++ ocell->ndims=mxGetNumberOfDimensions(prhs[0]); ++ ipt =mxGetDimensions(prhs[0]); ++ ocell->size =(int *) xmalloc(ocell->ndims*sizeof(int)); ++ for (i=0; indims; i++) ocell->size[i]=(int)ipt[i]; ++ ocell->values=new Options; ++ ++ /*loop through and process each element of the cell array */ ++ dims=(int *) xmalloc(ocell->ndims*sizeof(int)); ++ for (cindex=0; cindexnumel; cindex++) { ++ ColumnWiseDimsFromIndex(dims,(int)cindex,ocell->size,ocell->ndims); ++ StringFromDims(cstr,dims,ocell->ndims); ++ #ifdef _INTEL_WIN_ ++ _snprintf(namei,161,"%s%s",name,cstr); ++ #else ++ snprintf(namei,161,"%s%s",name,cstr); ++ #endif ++ celli=mxGetCell(prhs[0],cindex); ++ ++ option=(Option*)OptionParse(namei,&celli); ++ ocell->values->AddObject((Object*)option); ++ option=NULL; ++ } ++ xfree((void**)&dims); ++ ++ return(ocell); ++}/*}}}*/ ++/*FUNCTION OptionParse{{{1*/ ++Option* OptionParse(char* name, const mxArray* prhs[]){ ++ ++ Option *option = NULL; ++ mxArray *lhs[1]; ++ ++ /*parse the value according to the matlab data type */ ++ if (mxIsClass(prhs[0],"double")) option=(Option*)OptionDoubleParse(name,prhs); ++ else if(mxIsClass(prhs[0],"logical")) option=(Option*)OptionLogicalParse(name,prhs); ++ else if(mxIsClass(prhs[0],"char")) option=(Option*)OptionCharParse(name,prhs); ++ else if(mxIsClass(prhs[0],"struct")) option=(Option*)OptionStructParse(name,prhs); ++ else if(mxIsClass(prhs[0],"cell")) option=(Option*)OptionCellParse(name,prhs); ++ else { ++ _printf_(true," Converting value of option \"%s\" from unrecognized class \"%s\" to class \"%s\".\n",name,mxGetClassName(prhs[0]),"struct"); ++ if (!mexCallMATLAB(1,lhs,1,(mxArray**)prhs,"struct")) { ++ option=(Option*)OptionStructParse(name,(const mxArray**)lhs); ++ mxDestroyArray(lhs[0]); ++ } ++ else _error_("Second argument value of option \"%s\" is of unrecognized class \"%s\".",name,mxGetClassName(prhs[0])); ++ } ++ ++ return(option); ++}/*}}}*/ ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 12011) +@@ -0,0 +1,35 @@ ++/*!\file CheckNumMatlabArguments.cpp: ++ * \brief: check number of arguments and report an usage error message. ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++ ++#include "../../shared/Exceptions/exceptions.h" ++#include "../../include/include.h" ++#include "mex.h" ++ ++int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* __FUNCT__, void (*function)( void )){ ++ ++ /*checks on arguments on the matlab side: */ ++ if (nrhs==0 && nlhs==0) { ++ /*unless NLHS=0 and NRHS=0, we are just asking for documentation: */ ++ if (NRHS==0 && NLHS==0)return 1; ++ /* special case: */ ++ function(); ++ _error_("usage: see above"); ++ } ++ else if (nlhs!=NLHS || nrhs!=NRHS ) { ++ function(); ++ _error_("usage error."); ++ } ++ return 1; ++} ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12011) +@@ -0,0 +1,744 @@ ++/*\file FetchData.cpp: ++ * \brief: general I/O interface to fetch data in matlab ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++#include ++/*FUNCTION FetchData(DataSet** pdataset,const mxArray* dataref){{{1*/ ++void FetchData(DataSet** pdataset,const mxArray* dataref){ ++ ++ /*output*/ ++ DataSet* outdataset=NULL; ++ char* outdataset_buffer=NULL; ++ int outdataset_size; ++ ++ /*First, check that our reference is a double, otherwise, error out: */ ++ if (mxIsClass(dataref,"double")){ ++ ++ /*We need to copy the data pointed by dataref, so that our dataset is not actually a pointer!:*/ ++ if (!mxIsEmpty(dataref)){ ++ outdataset_buffer=(char*)mxGetPr(dataref); ++ outdataset_size=mxGetM(dataref)*mxGetN(dataref); ++ if(outdataset_size)outdataset=DataSetDemarshall(outdataset_buffer); ++ } ++ } ++ else{ ++ if (mxIsEmpty(dataref)){ ++ /*Nothing to pick up. Just initialize pointer to NULL, and warn the server we are not uploading anything: */ ++ outdataset_size=0; ++ outdataset=NULL; ++ } ++ else{ ++ /*This is an error: we don't have the correct input!: */ ++ _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); ++ } ++ } ++ ++ /*Assign output pointers:*/ ++ *pdataset=outdataset; ++} ++/*}}}*/ ++/*FUNCTION FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/ ++void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){ ++ ++ double* outmatrix=NULL; ++ int outmatrix_rows,outmatrix_cols; ++ ++ if(mxIsEmpty(dataref) ){ ++ /*Nothing to pick up. Just initialize matrix pointer to NULL: */ ++ outmatrix_rows=0; ++ outmatrix_cols=0; ++ outmatrix=NULL; ++ } ++ else if(mxIsClass(dataref,"double") || mxIsClass(dataref,"single")){ ++ /*Check dataref is not pointing to NaN: */ ++ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ ++ outmatrix_rows=0; ++ outmatrix_cols=0; ++ outmatrix=NULL; ++ } ++ else{ ++ /*Convert matlab matrix to double* matrix: */ ++ MatlabMatrixToDoubleMatrix(&outmatrix,&outmatrix_rows,&outmatrix_cols,dataref); ++ } ++ } ++ else{ ++ /*This is an error: we don't have the correct input!: */ ++ _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); ++ } ++ ++ /*Assign output pointers:*/ ++ *pmatrix=outmatrix; ++ if (pM)*pM=outmatrix_rows; ++ if (pN)*pN=outmatrix_cols; ++ ++} ++/*}}}*/ ++/*FUNCTION FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{1*/ ++void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){ ++ ++ double* outmatrix=NULL; ++ int outmatrix_numel,outmatrix_ndims; ++ int* outmatrix_size=NULL; ++ ++ if(mxIsEmpty(dataref) ){ ++ /*Nothing to pick up. Just initialize matrix pointer to NULL: */ ++ outmatrix_numel=0; ++ outmatrix_ndims=0; ++ outmatrix_size =NULL; ++ outmatrix=NULL; ++ } ++ else if (mxIsClass(dataref,"double") ){ ++ ++ /*Check dataref is not pointing to NaN: */ ++ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1) ){ ++ outmatrix_numel=0; ++ outmatrix_ndims=0; ++ outmatrix_size =NULL; ++ outmatrix=NULL; ++ } ++ else{ ++ ++ /*Convert matlab n-dim array to double* matrix: */ ++ MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref); ++ } ++ } ++ else{ ++ /*This is an error: we don't have the correct input!: */ ++ _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); ++ } ++ ++ /*Assign output pointers:*/ ++ *pmatrix=outmatrix; ++ if (pnumel)*pnumel=outmatrix_numel; ++ if (pndims)*pndims=outmatrix_ndims; ++ if (psize )*psize =outmatrix_size; ++ else xfree((void**)&outmatrix_size); ++ ++} ++/*}}}*/ ++/*FUNCTION FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/ ++void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){ ++ ++ int i,outmatrix_rows,outmatrix_cols; ++ double *doublematrix=NULL; ++ int *outmatrix=NULL; ++ ++ if(mxIsEmpty(dataref) ){ ++ /*Nothing to pick up. Just initialize matrix pointer to NULL: */ ++ outmatrix_rows=0; ++ outmatrix_cols=0; ++ outmatrix=NULL; ++ } ++ else if (mxIsClass(dataref,"double") ){ ++ ++ /*Check dataref is not pointing to NaN: */ ++ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ ++ outmatrix_rows=0; ++ outmatrix_cols=0; ++ outmatrix=NULL; ++ } ++ else{ ++ ++ /*Convert matlab matrix to double* matrix: */ ++ MatlabMatrixToDoubleMatrix(&doublematrix,&outmatrix_rows,&outmatrix_cols,dataref); ++ ++ /*Convert double matrix into integer matrix: */ ++ outmatrix=(int*)xmalloc(outmatrix_rows*outmatrix_cols*sizeof(int)); ++ for(i=0;iAddObject(param); ++ ++ } ++ else{ ++ if (N==1){ ++ ++ /*vector: */ ++ param= new DoubleVecParam(enum_type,mxGetPr(pfield),M); ++ parameters->AddObject(param); ++ ++ } ++ else{ ++ /*matrix: first, transpose, then plug into Param */ ++ matrix=mxGetPr(pfield); ++ tmatrix=(double*)xmalloc(M*N*sizeof(double)); ++ for (i=0;iAddObject(param); ++ ++ /*Free ressources:*/ ++ xfree((void**)&tmatrix); ++ } ++ } ++ ++ } ++ else if (mxIsClass(pfield,"logical")){ ++ ++ M=mxGetM(pfield); ++ N=mxGetN(pfield); ++ ++ if (M==0 | N==0){ ++ _error_("array in parameters structure field %s is of size 0",name); ++ } ++ if (M==1 && N==1){ ++ /*we have a simple bool: */ ++ param= new BoolParam(enum_type,*mxGetLogicals(pfield)); ++ parameters->AddObject(param); ++ ++ } ++ else{ ++ _error_("Matrices of Booleans not supported yet in parameters"); ++ } ++ } ++ else if (mxIsClass(pfield,"char")){ ++ /* we have a string parameter:*/ ++ ++ int stringlen; ++ char* string=NULL; ++ ++ stringlen = mxGetM(pfield)*mxGetN(pfield)+1; ++ string = (char*)xmalloc(sizeof(mxChar)*stringlen); ++ mxGetString(pfield,string,stringlen); ++ ++ param= new StringParam(enum_type,string); ++ parameters->AddObject(param); ++ ++ xfree((void**)&string); ++ } ++ else if (mxIsClass(pfield,"cell")){ ++ ++ /*This can be a string array, or a matrix array. Check the first ++ *element type to decide: */ ++ pfield2=mxGetCell(pfield,0); ++ if (mxIsClass(pfield2,"char")){ ++ ++ /*string array: */ ++ M=mxGetM(pfield); ++ stringarray=(char**)xmalloc(M*sizeof(char*)); ++ ++ for(i=0;iAddObject(param); ++ ++ /*Free ressources:*/ ++ for(i=0;iAddObject(param); ++ ++ /*Free ressources:*/ ++ for(i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#include ++ ++/*Matlab includes: */ ++#include "mex.h" ++ ++#include "../../shared/shared.h" ++ ++int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){ ++ ++ int rows,cols; ++ double* mxvector_ptr=NULL; ++ int ierr; ++ int i,j; ++ ++ /*output: */ ++ double* vector=NULL; ++ ++ /*matlab indices: */ ++ mwIndex* ir=NULL; ++ mwIndex* jc=NULL; ++ double* pr=NULL; ++ int count; ++ int nnz; ++ int nz; ++ ++ /*Ok, first check if we are dealing with a sparse or full vector: */ ++ if (mxIsSparse(mxvector)){ ++ ++ /*Dealing with sparse vector: recover size first: */ ++ mxvector_ptr=(double*)mxGetPr(mxvector); ++ rows=mxGetM(mxvector); ++ cols=mxGetN(mxvector); ++ nnz=mxGetNzmax(mxvector); ++ ++ /*Check that input is actualy a vector*/ ++ if (cols!=1) _error_("input vector of size %ix%i should have only one column",rows,cols); ++ ++ nz=(int)((double)nnz/(double)rows); ++ ++ if(rows){ ++ vector=(double*)xcalloc(rows,sizeof(double)); ++ ++ /*Now, get ir,jc and pr: */ ++ pr=mxGetPr(mxvector); ++ ir=mxGetIr(mxvector); ++ jc=mxGetJc(mxvector); ++ ++ /*Now, start inserting data into sparse vector: */ ++ count=0; ++ for(i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../../include/include.h" ++#include "../../shared/shared.h" ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++#include ++ ++/*FUNCTION WriteData(mxArray** pdataref,DataSet* dataset){{{1*/ ++void WriteData(mxArray** pdataref,DataSet* dataset){ ++ ++ mxArray* dataref=NULL; ++ char* marshalled_dataset=NULL; ++ int marshalled_dataset_size; ++ ++ /*Write a dataset: */ ++ if(dataset){ ++ /* marshall the dataset: */ ++ marshalled_dataset=dataset->Marshall(); ++ marshalled_dataset_size=dataset->MarshallSize(); ++ ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(dataref,(mwSize)(marshalled_dataset_size/sizeof(double))); ++ mxSetN(dataref,(mwSize)1); ++ mxSetPr(dataref,(double*)marshalled_dataset); ++ } ++ else{ ++ /* return empty matrix: */ ++ dataref=mxCreateDoubleMatrix(0,0,mxREAL); ++ } ++ *pdataref=dataref; ++ ++} ++/*}}}*/ ++/*FUNCTION WriteData(mxArray** pdataref,Matrix* matrix){{{1*/ ++void WriteData(mxArray** pdataref,Matrix* matrix){ ++ ++ mxArray* dataref=NULL; ++ double* matrix_ptr=NULL; ++ int rows,cols; ++ double* tmatrix_ptr=NULL; ++ ++ if(matrix){ ++ ++ #ifdef _HAVE_PETSC_ ++ PetscMatrixToDoubleMatrix(&tmatrix_ptr,&rows,&cols); ++ #else ++ matrix_ptr=matrix->matrix->ToSerial(); ++ matrix->matrix->GetSize(&rows,cols); ++ #endif ++ ++ /*Now transpose the matrix: */ ++ tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double)); ++ for(i=0;ivector); ++ #else ++ vector_ptr=vector->vector->ToMPISerial(); ++ vector->vector->GetSize(&rows); ++ #endif ++ ++ /*now create the matlab vector: */ ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(dataref,rows); ++ mxSetN(dataref,1); ++ mxSetPr(dataref,vector_ptr); ++ } ++ else{ ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ } ++ *pdataref=dataref; ++ ++} ++/*}}}*/ ++/*FUNCTION WriteData(mxArray** pdataref,double* matrix, int M,int N){{{1*/ ++void WriteData(mxArray** pdataref,double* matrix, int M,int N){ ++ ++ mxArray* dataref=NULL; ++ mxArray* tdataref=NULL; ++ ++ if(matrix){ ++ ++ /*data is a double* pointer. Copy into a matrix: */ ++ tdataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(tdataref,(mwSize)N); ++ mxSetN(tdataref,(mwSize)M); ++ mxSetPr(tdataref,(double*)matrix); ++ ++ //transpose ++ mexCallMATLAB(1,&dataref,1,&tdataref, "transpose"); ++ } ++ else{ ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ } ++ *pdataref=dataref; ++} ++/*}}}*/ ++/*FUNCTION WriteData(mxArray** pdataref,int* matrix, int M,int N){{{1*/ ++void WriteData(mxArray** pdataref,int* matrix, int M,int N){ ++ ++ mxArray* dataref=NULL; ++ mxArray* tdataref=NULL; ++ ++ if(matrix){ ++ ++ /*convert to double matrix*/ ++ double* doublematrix=(double*)mxMalloc(M*N*sizeof(double)); ++ for(int i=0;iSize(); ++ fnames=(char**)mxMalloc(nfields*sizeof(char*)); ++ ++ /*Build structure in matlab workspace with all the parameter fields: */ ++ for(i=0;iGetObjectByOffset(i); ++ param->GetParameterName(&fnames[i]); ++ } ++ /*Initialize structure: */ ++ dataref=mxCreateStructArray( ndim,onebyone,nfields,(const char**)fnames); ++ ++ /*Fill each field: */ ++ for(i=0;iGetObjectByOffset(i); ++ param->SetMatlabField(dataref); ++ } ++ ++ /*Assign output pointers:*/ ++ *pdataref=dataref; ++ ++} ++/*}}}*/ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp (revision 12011) +@@ -0,0 +1,47 @@ ++/*!\file: mxGetAssignedField.c: ++ * \brief: abstract interface on parallel side for i/o, so it ressembles the serial i/o. ++ * ++ * In serial mode, this routine takes care of returning the field coming ++ * from the model. If largesize is 1, we are running out of core models in ++ * matlab, and we need to call the subsref private method from the model object ++ * in order to correctly load the data from disk. ++ */ ++ ++#ifdef HAVE_CONFIG_H ++#include ++#else ++#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++#include "mex.h" ++ ++mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number,const char* field){ ++ ++ //output ++ mxArray* mxfield=NULL; ++ ++ //input ++ mxArray *inputs[2]; ++ mxArray *pindex = NULL; ++ const char *fnames[2]; ++ mwSize ndim = 2; ++ mwSize onebyone[2] = {1,1}; ++ ++ //We want to call the subsasgn method, and get the returned array.This ensures that if we are running ++ //large sized problems, the data is truly loaded from disk by the model subsasgn class method. ++ inputs[0]=(mxArray*)pmxa_array; //this is the model ++ ++ //create index structure used in the assignment (index.type='.' and index.subs='x' for field x for ex) ++ fnames[0] = "type"; ++ fnames[1] = "subs"; ++ pindex=mxCreateStructArray( ndim,onebyone,2,fnames); ++ mxSetField( pindex, 0, "type",mxCreateString(".")); ++ mxSetField( pindex, 0, "subs",mxCreateString(field)); ++ inputs[1]=pindex; ++ ++ mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref"); ++ ++ return mxfield; ++} ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 12011) +@@ -0,0 +1,101 @@ ++/* \file MatlabMatrixToDoubleMatrix.cpp ++ * \brief: convert a sparse or dense matlab matrix to a double* pointer ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++/*Matlab includes: */ ++#include "mex.h" ++ ++#include "../../shared/shared.h" ++ ++int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ ++ ++ int i,j,count,rows,cols; ++ double *pmxdoublematrix = NULL; ++ float *pmxsinglematrix = NULL; ++ ++ /*output: */ ++ double* matrix=NULL; ++ ++ /*matlab indices: */ ++ mwIndex* ir=NULL; ++ mwIndex* jc=NULL; ++ ++ /*Ok, first check if we are dealing with a sparse or full matrix: */ ++ if (mxIsSparse(mxmatrix)){ ++ ++ /*Dealing with sparse matrix: recover size first: */ ++ pmxdoublematrix=(double*)mxGetPr(mxmatrix); ++ rows=mxGetM(mxmatrix); ++ cols=mxGetN(mxmatrix); ++ ++ if(rows*cols){ ++ matrix=(double*)xcalloc(rows*cols,sizeof(double)); ++ ++ /*Now, get ir,jc and pr: */ ++ ir=mxGetIr(mxmatrix); ++ jc=mxGetJc(mxmatrix); ++ ++ /*Now, start inserting data into double* matrix: */ ++ count=0; ++ for(i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++ ++/*Petsc includes: */ ++#include "petscmat.h" ++#include "petscvec.h" ++#include "petscksp.h" ++ ++/*Matlab includes: */ ++#include "mex.h" ++ ++#include "../../../shared/shared.h" ++ ++int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector){ ++ ++ int rows, cols; ++ double* mxvector_ptr=NULL; ++ int ierr; ++ int i,j; ++ ++ /*output: */ ++ Vec vector=NULL; ++ ++ /*matlab indices: */ ++ mwIndex* ir=NULL; ++ mwIndex* jc=NULL; ++ double* pr=NULL; ++ int count; ++ int nnz; ++ int nz; ++ ++ /*petsc indices: */ ++ int* idxm=NULL; ++ ++ /*Ok, first check if we are dealing with a sparse or full vector: */ ++ if (mxIsSparse(mxvector)){ ++ ++ /*Dealing with sparse vector: recover size first: */ ++ mxvector_ptr=(double*)mxGetPr(mxvector); ++ rows=mxGetM(mxvector); ++ cols=mxGetN(mxvector); ++ nnz=mxGetNzmax(mxvector); ++ nz=(int)((double)nnz/(double)rows); ++ ++ ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr); ++ ++ /*Now, get ir,jc and pr: */ ++ pr=mxGetPr(mxvector); ++ ir=mxGetIr(mxvector); ++ jc=mxGetJc(mxvector); ++ ++ /*Now, start inserting data into sparse vector: */ ++ count=0; ++ for(i=0;i ++#include ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++#include "mex.h" ++#endif ++ ++int PrintfFunction(char* format,...){ ++ /*http://linux.die.net/man/3/vsnprintf*/ ++ ++ /*string to be printed: */ ++ char *buffer = NULL; ++ int n,size = 100; ++ int string_size; ++ extern int my_rank; ++ extern int num_procs; ++ ++ //variable list of arguments ++ va_list args; ++ ++ while(true){ ++ ++ /*allocate buffer for given string size*/ ++ buffer=(char*)xmalloc(size*sizeof(char)); ++ ++ /* Try to print in the allocated space. */ ++ va_start(args, format); ++#ifndef WIN32 ++ n=vsnprintf(buffer,size,format,args); ++#else ++ n=vsnprintf(buffer,size,format,args); ++#endif ++ va_end(args); ++ ++ /* If that worked, return the string. */ ++ if(n>-1 && n-1) /* glibc 2.1 */ ++ size=n+1; /* precisely what is needed */ ++ else /* glibc 2.0 */ ++ size*=2; /* twice the old size */ ++ ++ xfree((void**)&buffer); ++ } ++ ++ /*Ok, if we are running in parallel, get node 0 to print*/ ++#if defined(_PARALLEL_) ++ if(my_rank==0)printf(buffer); ++#else ++ mexPrintf(buffer); ++#endif ++ ++ /*Clean up and return*/ ++ xfree((void**)&buffer); ++ return 1; ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp (revision 12011) +@@ -0,0 +1,17 @@ ++ ++Vector* MatlabVectorToVector(const mxArray* mxvector){ ++ ++ int dummy; ++ Vector* vector=NULL; ++ ++ /*allocate vector object: */ ++ vector=new Vector(); ++ ++ #ifdef _HAVE_PETSC_ ++ MatlabVectorToPetscVector(&vector->vector,&dummy,mxvector); ++ #else ++ vector->vector=MatlabVectorToSeqVec(mxvector); ++ #endif ++ ++ return vector; ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp (revision 12011) +@@ -0,0 +1,123 @@ ++/* \file MatlabMatrixToPetscMatrix.cpp ++ * \brief: convert a sparse or dense matlab matrix to a serial Petsc matrix: ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++ ++/*Petsc includes: */ ++#include "petscmat.h" ++#include "petscvec.h" ++#include "petscksp.h" ++ ++/*Matlab includes: */ ++#include "mex.h" ++ ++#include "../../../shared/shared.h" ++ ++int MatlabMatrixToPetscMatrix(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ ++ ++ int rows, cols; ++ double* mxmatrix_ptr=NULL; ++ double* tmatrix=NULL; ++ int ierr; ++ int i,j; ++ ++ /*output: */ ++ Mat matrix=NULL; ++ ++ /*matlab indices: */ ++ mwIndex* ir=NULL; ++ mwIndex* jc=NULL; ++ double* pr=NULL; ++ int count; ++ int nnz; ++ int nz; ++ ++ /*petsc indices: */ ++ int* idxm=NULL; ++ int* idxn=NULL; ++ ++ /*Ok, first check if we are dealing with a sparse or full matrix: */ ++ if (mxIsSparse(mxmatrix)){ ++ ++ /*Dealing with sparse matrix: recover size first: */ ++ mxmatrix_ptr=(double*)mxGetPr(mxmatrix); ++ rows=mxGetM(mxmatrix); ++ cols=mxGetN(mxmatrix); ++ nnz=mxGetNzmax(mxmatrix); ++ if(rows){ ++ nz=(int)((double)nnz/(double)rows); ++ } ++ else{ ++ nz=0; ++ } ++ ++ ierr=MatCreateSeqAIJ(PETSC_COMM_SELF,rows,cols,nz,PETSC_NULL,&matrix);CHKERRQ(ierr); ++ ++ /*Now, get ir,jc and pr: */ ++ pr=mxGetPr(mxmatrix); ++ ir=mxGetIr(mxmatrix); ++ jc=mxGetJc(mxmatrix); ++ ++ /*Now, start inserting data into sparse matrix: */ ++ count=0; ++ for(i=0;imatrix,NULL,NULL,mxmatrix); ++ #else ++ matrix->matrix=MatlabMatrixToSeqMat(mxmatrix); ++ #endif ++ ++ return matrix; ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp (revision 12011) +@@ -0,0 +1,52 @@ ++/* \file PetscVectorToDoubleVector.cpp ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++/*Petsc includes: */ ++#include "petscmat.h" ++#include "petscvec.h" ++#include "petscksp.h" ++ ++/*Petsc includes: */ ++#include "mex.h" ++ ++#include "../../../shared/shared.h" ++#include ++ ++ ++void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){ ++ ++ int i; ++ int rows; ++ int *idxm = NULL; ++ double *vector = NULL; ++ ++ /*output: */ ++ mxArray* dataref=NULL; ++ ++ /*Get size of vector: */ ++ if(vector){ ++ VecGetSize(vector,&rows); ++ if(rows){ ++ idxm=(int*)xmalloc(rows*sizeof(int)); ++ vector=(double*)xmalloc(rows*sizeof(double)); ++ for(i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++/*Petsc includes: */ ++#include "petscmat.h" ++#include "petscvec.h" ++#include "petscksp.h" ++ ++/*Petsc includes: */ ++#include "mex.h" ++ ++#include "../../../shared/shared.h" ++#include ++ ++ ++void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat petsc_matrix){ ++ ++ int i,j,k; ++ ++ /*output: */ ++ double* matrix=NULL; ++ int rows,cols; ++ ++ /*intermediary: */ ++ int* idxm=NULL; ++ int* idxn=NULL; ++ ++ /*Some needed information: */ ++ MatGetSize(petsc_matrix,&rows,&cols); ++ ++ idxm=(int*)xmalloc(rows*sizeof(int)); ++ idxn=(int*)xmalloc(cols*sizeof(int)); ++ ++ for(i=0;ivector,&output->M,dataref); ++ return output; ++ ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 12011) +@@ -0,0 +1,274 @@ ++/* \file MatlabNArrayToNArray.cpp ++ * \brief: convert a sparse or dense matlab n-dimensional array to cpp n-dimensional array ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++ ++#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) ++#include ++ ++/*FUNCTION MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{1*/ ++int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){ ++ ++ int i,j,rows,cols; ++ int numel,ndims; ++ int *size,*dims; ++ double* mxmatrix_ptr=NULL; ++ const mwSize* ipt=NULL; ++ ++ /*output: */ ++ double* matrix=NULL; ++ ++ /*matlab indices: */ ++ mwIndex* ir=NULL; ++ mwIndex* jc=NULL; ++ double* pr=NULL; ++ int count; ++ int nnz; ++ int nz; ++ ++ /*get Matlab matrix information: */ ++ numel=mxGetNumberOfElements(mxmatrix); ++ ndims=mxGetNumberOfDimensions(mxmatrix); ++ ipt =mxGetDimensions(mxmatrix); ++ size =(int *) xcalloc(ndims,sizeof(int)); ++ for (i=0; i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../../objects/objects.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++ ++class DataSet; ++class Parameters; ++ ++#include ++ ++void WriteData(mxArray** pdataref,DataSet* dataset); ++void WriteData(mxArray** pdataref,Matrix* matrix); ++void WriteData(mxArray** pdataref,double* matrix, int M,int N); ++void WriteData(mxArray** pdataref,int* matrix, int M,int N); ++void WriteData(mxArray** pdataref,Vector* vector); ++void WriteData(mxArray** pdataref,double* vector, int M); ++void WriteData(mxArray** pdataref,int integer); ++void WriteData(mxArray** pdataref,bool boolean); ++void WriteData(mxArray** pdataref,double scalar); ++void WriteData(mxArray** pdataref,char* string); ++void WriteData(DataHandle* pdataref,Parameters* parameters); ++ ++void FetchData(DataSet** pdataset,const mxArray* dataref); ++void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref); ++void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); ++void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref); ++void FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref); ++void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); ++void FetchData(Matrix** pmatrix,const mxArray* dataref); ++void FetchData(int** pvector,int* pM,const mxArray* dataref); ++void FetchData(float** pvector,int* pM,const mxArray* dataref); ++void FetchData(double** pvector,int* pM,const mxArray* dataref); ++void FetchData(bool** pvector,int* pM,const mxArray* dataref); ++void FetchData(Vector** pvector,const mxArray* dataref); ++void FetchData(char** pstring,const mxArray* dataref); ++void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); ++void FetchData(double* pscalar,const mxArray* dataref); ++void FetchData(int* pinteger,const mxArray* dataref); ++void FetchData(bool* pbool,const mxArray* dataref); ++void FetchData(Parameters** pparameters, DataHandle dataref); ++ ++Option* OptionParse(char* name, const mxArray* prhs[]); ++OptionDouble* OptionDoubleParse( char* name, const mxArray* prhs[]); ++OptionLogical* OptionLogicalParse( char* name, const mxArray* prhs[]); ++OptionChar* OptionCharParse( char* name, const mxArray* prhs[]); ++OptionStruct* OptionStructParse( char* name, const mxArray* prhs[]); ++OptionCell* OptionCellParse( char* name, const mxArray* prhs[]); ++ ++mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number, const char* field); ++int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* THISFUNCTION, void (*function)( void )); ++ ++/*Matlab to Matrix routines: */ ++Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); ++Vector* MatlabVectorToVector(const mxArray* mxvector); ++ ++/*Matlab to double* routines: */ ++int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector); ++int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix); ++int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); ++int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); ++int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); ++int MatlabMatrixToPetscMatrix(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix); ++ ++/*Matlab to Petsc routines: */ ++int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector); ++void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat matrix); ++void PetscVectorToDoubleVector(double** pvector, int* prows, Vec vector); ++ ++/*Matlab to SeqMat routines: */ ++SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref); ++SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); ++ ++#endif /* _IO_H_ */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgGeom.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgGeom.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgGeom.cpp (revision 12011) +@@ -0,0 +1,105 @@ ++#include ++#include "../objects.h" ++#include "../../io/io.h" ++#include "../../shared/shared.h" ++ ++/*Constructors/Destructors*/ ++/*FUNCTION BamgGeom::BamgGeom(void* module_struct){{{1*/ ++BamgGeom::BamgGeom(void* module_struct){ ++ ++ mxArray* matlab_struct=NULL; ++ ++ /*recover our pointer: */ ++ matlab_struct=(mxArray*)module_struct; ++ ++ FetchData(&this->Vertices, &this->VerticesSize[0], &this->VerticesSize[1], mxGetAssignedField(matlab_struct,0,"Vertices")); ++ FetchData(&this->Edges, &this->EdgesSize[0], &this->EdgesSize[1], mxGetAssignedField(matlab_struct,0,"Edges")); ++ this->TangentAtEdgesSize[0]=0, this->TangentAtEdgesSize[1]=0; this->TangentAtEdges=NULL; ++ FetchData(&this->Corners, &this->CornersSize[0], &this->CornersSize[1], mxGetAssignedField(matlab_struct,0,"Corners")); ++ FetchData(&this->RequiredVertices,&this->RequiredVerticesSize[0],&this->RequiredVerticesSize[1],mxGetAssignedField(matlab_struct,0,"RequiredVertices")); ++ FetchData(&this->RequiredEdges, &this->RequiredEdgesSize[0], &this->RequiredEdgesSize[1], mxGetAssignedField(matlab_struct,0,"RequiredEdges")); ++ FetchData(&this->CrackedEdges, &this->CrackedEdgesSize[0], &this->CrackedEdgesSize[1], mxGetAssignedField(matlab_struct,0,"CrackedEdges")); ++ FetchData(&this->SubDomains, &this->SubDomainsSize[0], &this->SubDomainsSize[1], mxGetAssignedField(matlab_struct,0,"SubDomains")); ++ ++} ++/*}}}*/ ++ ++/*Methods*/ ++/*FUNCTION BamgGeom::SetStructureFields{{{1*/ ++void BamgGeom::SetStructureFields(void* module_struct){ ++ ++ mxArray** matlab_struct=NULL; ++ ++ /*Intermediary*/ ++ int i; ++ mxArray* output=NULL; ++ const int numfields=7; ++ const char* fnames[numfields]; ++ mwSize ndim=2; ++ mwSize dimensions[2]={1,1}; ++ ++ /*recover pointer: */ ++ matlab_struct=(mxArray**)module_struct; ++ ++ /*Initialize field names*/ ++ i=0; ++ fnames[i++] = "Vertices"; ++ fnames[i++] = "Edges"; ++ fnames[i++] = "TangentAtEdges"; ++ fnames[i++] = "RequiredVertices"; ++ fnames[i++] = "RequiredEdges"; ++ fnames[i++] = "CrackedEdges"; ++ fnames[i++] = "SubDomains"; ++ _assert_(i==numfields); ++ ++ /*Initialize Matlab structure*/ ++ output=mxCreateStructArray(ndim,dimensions,numfields,fnames); ++ ++ /*set each matlab each field*/ ++ i=0; ++ i++; SetStructureField(output,"Vertices", this->VerticesSize[0], this->VerticesSize[1], this->Vertices); ++ i++; SetStructureField(output,"Edges", this->EdgesSize[0], this->EdgesSize[1], this->Edges); ++ i++; SetStructureField(output,"TangentAtEdges", this->TangentAtEdgesSize[0], this->TangentAtEdgesSize[1], this->TangentAtEdges); ++ i++; SetStructureField(output,"RequiredVertices",this->RequiredVerticesSize[0],this->RequiredVerticesSize[1],this->RequiredVertices); ++ i++; SetStructureField(output,"RequiredEdges", this->RequiredEdgesSize[0], this->RequiredEdgesSize[1], this->RequiredEdges); ++ i++; SetStructureField(output,"CrackedEdges", this->CrackedEdgesSize[0], this->CrackedEdgesSize[1], this->CrackedEdges); ++ i++; SetStructureField(output,"SubDomains", this->SubDomainsSize[0], this->SubDomainsSize[1], this->SubDomains); ++ _assert_(i==numfields); ++ ++ /*Assign output*/ ++ *matlab_struct=output; ++ ++} ++/*}}}*/ ++/*FUNCTION BamgGeom::SetStructureField{{{1*/ ++void BamgGeom::SetStructureField(void* module_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ ++ ++ /*Intermediary*/ ++ mxArray* matlab_struct=NULL; ++ int i1,i2; ++ mxArray* pfield=NULL; ++ mxArray* pfield2=NULL; ++ ++ /*recover pointer: */ ++ matlab_struct=(mxArray*)module_struct; ++ ++ /*Copy field*/ ++ double* fieldcopy=NULL; ++ if (fieldrows*fieldcols){ ++ fieldcopy=(double*)xmalloc(fieldrows*fieldcols*sizeof(double)); ++ for(i1=0;i1 ++#include "../objects.h" ++#include "../../io/io.h" ++#include "../../shared/shared.h" ++ ++/*Constructors/Destructors*/ ++/*FUNCTION BamgMesh::BamgMesh(void* module_struct){{{1*/ ++BamgMesh::BamgMesh(void* module_struct){ ++ ++ mxArray* matlab_struct=NULL; ++ int lines,cols; ++ ++ /*recover our pointer: */ ++ matlab_struct=(mxArray*)module_struct; ++ ++ ++ FetchData(&this->Vertices, &this->VerticesSize[0], &this->VerticesSize[1], mxGetAssignedField(matlab_struct,0,"Vertices")); ++ FetchData(&this->Edges, &this->EdgesSize[0], &this->EdgesSize[1], mxGetAssignedField(matlab_struct,0,"Edges")); ++ FetchData(&this->Triangles, &this->TrianglesSize[0], &this->TrianglesSize[1], mxGetAssignedField(matlab_struct,0,"Triangles")); ++ this->QuadrilateralsSize[0]=0, this->QuadrilateralsSize[1]=0; this->Quadrilaterals=NULL; ++ ++ this->SubDomainsSize[0]=0, this->SubDomainsSize[1]=0; this->SubDomains=NULL; ++ this->SubDomainsFromGeomSize[0]=0, this->SubDomainsFromGeomSize[1]=0; this->SubDomainsFromGeom=NULL; ++ this->CrackedVerticesSize[0]=0, this->CrackedVerticesSize[1]=0; this->CrackedVertices=NULL; ++ FetchData(&this->CrackedEdges, &this->CrackedEdgesSize[0], &this->CrackedEdgesSize[1], mxGetAssignedField(matlab_struct,0,"CrackedEdges")); ++ ++ FetchData(&this->VerticesOnGeomEdge, &this->VerticesOnGeomEdgeSize[0], &this->VerticesOnGeomEdgeSize[1], mxGetAssignedField(matlab_struct,0,"VerticesOnGeomEdge")); ++ FetchData(&this->VerticesOnGeomVertex,&this->VerticesOnGeomVertexSize[0],&this->VerticesOnGeomVertexSize[1],mxGetAssignedField(matlab_struct,0,"VerticesOnGeomVertex")); ++ FetchData(&this->EdgesOnGeomEdge, &this->EdgesOnGeomEdgeSize[0], &this->EdgesOnGeomEdgeSize[1], mxGetAssignedField(matlab_struct,0,"EdgesOnGeomEdge")); ++ ++ this->IssmEdgesSize[0]=0, this->IssmEdgesSize[1]=0; this->IssmEdges=NULL; ++ FetchData(&this->IssmSegments, &this->IssmSegmentsSize[0], &this->IssmSegmentsSize[1], mxGetAssignedField(matlab_struct,0,"IssmSegments")); ++ ++ this->ElementConnectivitySize[0]=0, this->ElementConnectivitySize[1]=0; this->ElementConnectivity=NULL; ++ this->NodalConnectivitySize[0]=0, this->NodalConnectivitySize[1]=0; this->NodalConnectivity=NULL; ++ this->NodalElementConnectivitySize[0]=0, this->NodalElementConnectivitySize[1]=0; this->NodalElementConnectivity=NULL; ++ ++} ++/*}}}*/ ++ ++/*Methods*/ ++/*FUNCTION BamgMesh::SetStructureFields{{{1*/ ++void BamgMesh::SetStructureFields(void* module_struct){ ++ ++ mxArray** matlab_struct=NULL; ++ ++ /*Intermediary*/ ++ int i; ++ mxArray* output=NULL; ++ const int numfields=16; ++ const char* fnames[numfields]; ++ mwSize ndim=2; ++ mwSize dimensions[2]={1,1}; ++ ++ /*recover pointer: */ ++ matlab_struct=(mxArray**)module_struct; ++ ++ /*Initialize field names*/ ++ i=0; ++ fnames[i++] = "Triangles"; ++ fnames[i++] = "Vertices"; ++ fnames[i++] = "Edges"; ++ fnames[i++] = "IssmSegments"; ++ fnames[i++] = "IssmEdges"; ++ fnames[i++] = "Quadrilaterals"; ++ fnames[i++] = "VerticesOnGeomVertex"; ++ fnames[i++] = "VerticesOnGeomEdge"; ++ fnames[i++] = "EdgesOnGeomEdge"; ++ fnames[i++] = "SubDomains"; ++ fnames[i++] = "SubDomainsFromGeom"; ++ fnames[i++] = "ElementConnectivity"; ++ fnames[i++] = "NodalConnectivity"; ++ fnames[i++] = "NodalElementConnectivity"; ++ fnames[i++] = "CrackedVertices"; ++ fnames[i++] = "CrackedEdges"; ++ _assert_(i==numfields); ++ ++ /*Initialize Matlab structure*/ ++ output=mxCreateStructArray(ndim,dimensions,numfields,fnames); ++ ++ /*set each matlab each field*/ ++ i=0; ++ i++; SetStructureField(output,"Triangles", this->TrianglesSize[0], this->TrianglesSize[1], this->Triangles); ++ i++; SetStructureField(output,"Vertices", this->VerticesSize[0], this->VerticesSize[1], this->Vertices); ++ i++; SetStructureField(output,"Edges", this->EdgesSize[0], this->EdgesSize[1], this->Edges); ++ i++; SetStructureField(output,"IssmSegments", this->IssmSegmentsSize[0], this->IssmSegmentsSize[1], this->IssmSegments); ++ i++; SetStructureField(output,"IssmEdges", this->IssmEdgesSize[0], this->IssmEdgesSize[1], this->IssmEdges); ++ i++; SetStructureField(output,"Quadrilaterals", this->QuadrilateralsSize[0], this->QuadrilateralsSize[1], this->Quadrilaterals); ++ i++; SetStructureField(output,"VerticesOnGeomVertex",this->VerticesOnGeomVertexSize[0],this->VerticesOnGeomVertexSize[1], this->VerticesOnGeomVertex); ++ i++; SetStructureField(output,"VerticesOnGeomEdge", this->VerticesOnGeomEdgeSize[0], this->VerticesOnGeomEdgeSize[1], this->VerticesOnGeomEdge); ++ i++; SetStructureField(output,"EdgesOnGeomEdge", this->EdgesOnGeomEdgeSize[0], this->EdgesOnGeomEdgeSize[1], this->EdgesOnGeomEdge); ++ i++; SetStructureField(output,"SubDomains", this->SubDomainsSize[0], this->SubDomainsSize[1], this->SubDomains); ++ i++; SetStructureField(output,"SubDomainsFromGeom", this->SubDomainsFromGeomSize[0], this->SubDomainsFromGeomSize[1], this->SubDomainsFromGeom); ++ i++; SetStructureField(output,"ElementConnectivity", this->ElementConnectivitySize[0], this->ElementConnectivitySize[1], this->ElementConnectivity); ++ i++; SetStructureField(output,"NodalConnectivity", this->NodalConnectivitySize[0], this->NodalConnectivitySize[1], this->NodalConnectivity); ++ i++; SetStructureField(output,"NodalElementConnectivity", this->NodalElementConnectivitySize[0], this->NodalElementConnectivitySize[1], this->NodalElementConnectivity); ++ i++; SetStructureField(output,"CrackedVertices", this->CrackedVerticesSize[0], this->CrackedVerticesSize[1], this->CrackedVertices); ++ i++; SetStructureField(output,"CrackedEdges", this->CrackedEdgesSize[0], this->CrackedEdgesSize[1], this->CrackedEdges); ++ _assert_(i==numfields); ++ ++ /*Assign output*/ ++ *matlab_struct=output; ++ ++} ++/*}}}*/ ++/*FUNCTION BamgMesh::SetStructureField{{{1*/ ++void BamgMesh::SetStructureField(void* module_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ ++ ++ /*Intermediary*/ ++ mxArray* matlab_struct=NULL; ++ int i1,i2; ++ mxArray* pfield=NULL; ++ mxArray* pfield2=NULL; ++ ++ /*recover pointer: */ ++ matlab_struct=(mxArray*)module_struct; ++ ++ /*Copy field*/ ++ double* fieldcopy=NULL; ++ if (fieldrows*fieldcols){ ++ fieldcopy=(double*)xmalloc(fieldrows*fieldcols*sizeof(double)); ++ for(i1=0;i1 ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++#include "../objects.h" ++#include "../../io/io.h" ++ ++/*Constructors/Destructors*/ ++/*FUNCTION BamgOpts::BamgOpts(void* module_struct){{{1*/ ++BamgOpts::BamgOpts(void* module_struct){ ++ ++ mxArray* matlab_struct=NULL; ++ ++ /*recover pointer: */ ++ matlab_struct=(mxArray*)module_struct; ++ ++ FetchData(&this->anisomax,mxGetField(matlab_struct,0,"anisomax")); ++ FetchData(&this->cutoff,mxGetField(matlab_struct,0,"cutoff")); ++ FetchData(&this->coeff,mxGetField(matlab_struct,0,"coeff")); ++ FetchData(&this->errg,mxGetField(matlab_struct,0,"errg")); ++ FetchData(&this->gradation,mxGetField(matlab_struct,0,"gradation")); ++ FetchData(&this->Hessiantype,mxGetField(matlab_struct,0,"Hessiantype")); ++ FetchData(&this->MaxCornerAngle,mxGetField(matlab_struct,0,"MaxCornerAngle")); ++ FetchData(&this->maxnbv,mxGetField(matlab_struct,0,"maxnbv")); ++ FetchData(&this->maxsubdiv,mxGetField(matlab_struct,0,"maxsubdiv")); ++ FetchData(&this->Metrictype,mxGetField(matlab_struct,0,"Metrictype")); ++ FetchData(&this->nbjacobi,mxGetField(matlab_struct,0,"nbjacobi")); ++ FetchData(&this->nbsmooth,mxGetField(matlab_struct,0,"nbsmooth")); ++ FetchData(&this->omega,mxGetField(matlab_struct,0,"omega")); ++ FetchData(&this->power,mxGetField(matlab_struct,0,"power")); ++ FetchData(&this->verbose,mxGetField(matlab_struct,0,"verbose")); ++ ++ FetchData(&this->Crack,mxGetField(matlab_struct,0,"Crack")); ++ FetchData(&this->geometricalmetric,mxGetField(matlab_struct,0,"geometricalmetric")); ++ FetchData(&this->KeepVertices,mxGetField(matlab_struct,0,"KeepVertices")); ++ FetchData(&this->splitcorners,mxGetField(matlab_struct,0,"splitcorners")); ++ ++ FetchData(&this->hmin,mxGetField(matlab_struct,0,"hmin")); ++ FetchData(&this->hmax,mxGetField(matlab_struct,0,"hmax")); ++ FetchData(&this->hminVertices,&this->hminVerticesSize[0],&this->hminVerticesSize[1],mxGetField(matlab_struct,0,"hminVertices")); ++ FetchData(&this->hmaxVertices,&this->hmaxVerticesSize[0],&this->hmaxVerticesSize[1],mxGetField(matlab_struct,0,"hmaxVertices")); ++ FetchData(&this->hVertices,&this->hVerticesSize[0],&this->hVerticesSize[1],mxGetField(matlab_struct,0,"hVertices")); ++ FetchData(&this->metric,&this->metricSize[0],&this->metricSize[1],mxGetField(matlab_struct,0,"metric")); ++ FetchData(&this->field,&this->fieldSize[0],&this->fieldSize[1],mxGetField(matlab_struct,0,"field")); ++ FetchData(&this->err,&this->errSize[0],&this->errSize[1],mxGetField(matlab_struct,0,"err")); ++ ++ /*Additional checks*/ ++ this->Check(); ++ ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h (revision 12011) +@@ -0,0 +1,56 @@ ++/*\file pythonio.h ++ *\brief: I/O for ISSM in python mode ++ */ ++ ++#ifndef _PYTHON_IO_H_ ++#define _PYTHON_IO_H_ ++ ++#ifdef HAVE_CONFIG_H ++#include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#include "../../objects/objects.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++ ++class DataSet; ++class Parameters; ++ ++//void WriteData(PyObject* py_tuple,DataSet* dataset); ++//void WriteData(PyObject* py_tuple,double* matrix, int M,int N); ++//void WriteData(PyObject* py_tuple,int* matrix, int M,int N); ++//void WriteData(PyObject* py_tuple,double* vector, int M); ++//void WriteData(PyObject* py_tuple,int integer); ++//void WriteData(PyObject* py_tuple,bool boolean); ++//void WriteData(PyObject* py_tuple,double scalar); ++//void WriteData(DataHandle* py_tuple,Parameters* parameters); ++void WriteData(PyObject* py_tuple, int index, char* string); ++void WriteData(PyObject* py_tuple, int index, Matrix* matrix); ++void WriteData(PyObject* py_tuple, int index, Vector* vector); ++ ++ ++//void FetchData(DataSet** pdataset,PyObject* py_ref); ++//void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_ref); ++//void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); ++//void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_ref); ++//void FetchData(bool** pmatrix,int* pM,int *pN,PyObject* py_ref); ++//void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); ++//void FetchData(Matrix** pmatrix,PyObject* py_ref); ++//void FetchData(int** pvector,int* pM,PyObject* py_ref); ++//void FetchData(float** pvector,int* pM,PyObject* py_ref); ++//void FetchData(double** pvector,int* pM,PyObject* py_ref); ++//void FetchData(bool** pvector,int* pM,PyObject* py_ref); ++//void FetchData(Vector** pvector,PyObject* py_ref); ++//void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); ++//void FetchData(Parameters** pparameters, DataHandle py_ref); ++void FetchData(char** pstring,PyObject* py_unicode); ++void FetchData(double* pscalar,PyObject* py_float); ++void FetchData(int* pinteger,PyObject* py_long); ++void FetchData(bool* pbool,PyObject* py_boolean); ++ ++int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )); ++ ++#endif /* _IO_H_ */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp (revision 12011) +@@ -0,0 +1,40 @@ ++/*!\file CheckNumPythonArguments.cpp: ++ * \brief: check number of arguments and report an usage error message. ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) ++ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#define NO_IMPORT ++ ++#include "../../toolkits/toolkits.h" ++#include "../../shared/Exceptions/exceptions.h" ++#include "../../include/include.h" ++ ++int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )){ ++ ++ Py_ssize_t size=0; ++ ++ /*figure out size of tuple in input: */ ++ size=PyTuple_Size(inputs); ++ ++ /*check on requested size: */ ++ if (size==0){ ++ function(); ++ _error_("usage: see above"); ++ } ++ else if (size!=NRHS ) { ++ function(); ++ _error_("usage error."); ++ } ++ return 1; ++} ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12011) +@@ -0,0 +1,74 @@ ++/*\file FetchData.cpp: ++ * \brief: general I/O interface to fetch data in python ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#define NO_IMPORT ++ ++#include "../../toolkits/toolkits.h" ++#include "../../include/include.h" ++#include "../../shared/shared.h" ++ ++#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) ++/*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{1*/ ++void FetchData(char** pstring,PyObject* py_unicode){ ++ ++ PyObject* py_bytes; ++ char* string=NULL; ++ ++ ++ /*convert to bytes format: */ ++ PyUnicode_FSConverter(py_unicode,&py_bytes); ++ ++ /*convert from bytes to string: */ ++ string=PyBytes_AS_STRING(py_bytes); ++ ++ *pstring=string; ++} ++/*FUNCTION FetchData(double* pscalar,PyObject* py_float){{{1*/ ++void FetchData(double* pscalar,PyObject* py_float){ ++ ++ double scalar; ++ ++ /*return internal value: */ ++ scalar=PyFloat_AsDouble(py_float); ++ ++ /*output: */ ++ *pscalar=scalar; ++} ++/*}}}*/ ++/*FUNCTION FetchData(int* pinteger,PyObject* py_long){{{1*/ ++void FetchData(int* pinteger, PyObject* py_long){ ++ ++ int integer; ++ ++ /*return internal value: */ ++ integer=(int)PyLong_AsLong(py_long); ++ ++ /*output: */ ++ *pinteger=integer; ++} ++/*}}}*/ ++/*FUNCTION FetchData(bool* pboolean,PyObject* py_boolean){{{1*/ ++void FetchData(bool* pboolean,PyObject* py_boolean){ ++ ++ bool boolean; ++ ++ /*check this is indeed a subtype of long type: */ ++ if(!PyBool_Check(py_boolean))_error_("expecting a boolean in input!"); ++ ++ /*extract boolean: */ ++ boolean=(bool)PyLong_AsLong(py_boolean); ++ ++ /*simple copy: */ ++ *pboolean=boolean; ++ ++} ++/*}}}*/ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 12011) +@@ -0,0 +1,69 @@ ++/* \file WriteData.c: ++ * \brief: general interface for writing data ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) ++ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#define NO_IMPORT ++ ++#include "../../toolkits/toolkits.h" ++#include "../../include/include.h" ++#include "../../modules/modules.h" ++#include "../../Container/Container.h" ++#include "../../shared/shared.h" ++#include "../../io/io.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++ ++ ++/*FUNCTION WriteData(PyObject* py_tuple,int index,char* string){{{1*/ ++void WriteData(PyObject* py_tuple, int index, char* string){ ++ ++ PyTuple_SetItem(py_tuple, index, PyUnicode_FromString(string)); ++ ++} ++/*}}}*/ ++/*FUNCTION WriteData(PyObject* tuple,int index,Matrix* matrix){{{1*/ ++void WriteData(PyObject* tuple,int index,Matrix* matrix){ ++ ++ int M,N; ++ double* buffer=NULL; ++ npy_intp dims[2]={0,0}; ++ PyObject* array=NULL; ++ ++ buffer=matrix->ToSerial(); ++ matrix->GetSize(&M,&N); ++ dims[0]=(npy_intp)M; ++ dims[1]=(npy_intp)N; ++ array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,buffer); ++ ++ PyTuple_SetItem(tuple, index, array); ++ ++ ++} ++/*FUNCTION WriteData(PyObject* py_tuple,int index,Vector* vector){{{1*/ ++void WriteData(PyObject* tuple,int index,Vector* vector){ ++ ++ int M; ++ double* buffer=NULL; ++ npy_intp dim=10; ++ PyObject* array=NULL; ++ ++ buffer=vector->ToMPISerial(); ++ vector->GetSize(&M); ++ dim=(npy_intp)M; ++ array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer); ++ ++ PyTuple_SetItem(tuple, index, array); ++ ++ ++} ++/*}}}*/ ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgGeom.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgGeom.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgGeom.cpp (revision 12011) +@@ -0,0 +1,27 @@ ++#include ++#include "../objects.h" ++#include "../../io/io.h" ++#include "../../shared/shared.h" ++ ++/*Constructors/Destructors*/ ++/*FUNCTION BamgGeom::BamgGeom(void* module_struct){{{1*/ ++BamgGeom::BamgGeom(void* module_struct){ ++ ++ _error_("not implemented yet!"); ++ ++} ++/*}}}*/ ++ ++/*Methods*/ ++/*FUNCTION BamgGeom::SetStructureFields{{{1*/ ++void BamgGeom::SetStructureFields(void* module_struct){ ++ _error_("not implemented yet!"); ++} ++ ++/*}}}*/ ++/*FUNCTION BamgGeom::SetStructureField{{{1*/ ++void BamgGeom::SetStructureField(void* module_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ ++ _error_("not implemented yet!"); ++} ++ ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgMesh.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgMesh.cpp (revision 12011) +@@ -0,0 +1,23 @@ ++#include ++#include "../objects.h" ++#include "../../io/io.h" ++#include "../../shared/shared.h" ++ ++/*Constructors/Destructors*/ ++/*FUNCTION BamgMesh::BamgMesh(void* module_struct){{{1*/ ++BamgMesh::BamgMesh(void* module_struct){ ++ _error_("not implemented yet!"); ++} ++/*}}}*/ ++ ++/*Methods*/ ++/*FUNCTION BamgMesh::SetStructureFields{{{1*/ ++void BamgMesh::SetStructureFields(void* module_struct){ ++ _error_("not implemented yet!"); ++} ++/*}}}*/ ++/*FUNCTION BamgMesh::SetStructureField{{{1*/ ++void BamgMesh::SetStructureField(void* module_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ ++ _error_("not implemented yet!"); ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgOpts.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgOpts.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgOpts.cpp (revision 12011) +@@ -0,0 +1,12 @@ ++#include ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++#include "../objects.h" ++#include "../../io/io.h" ++ ++/*Constructors/Destructors*/ ++/*FUNCTION BamgOpts::BamgOpts(void* module_struct){{{1*/ ++BamgOpts::BamgOpts(void* module_struct){ ++ _error_("not implemented yet!"); ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h (revision 12011) +@@ -14,9 +14,7 @@ + + /*constructors, destructors*/ + Options(); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- Options(int istart, int nrhs, const mxArray* prhs[]); +- #endif ++ Options(int istart, int nrhs, void* module_references); + ~Options(); + + /*numerics*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Results.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Results.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Results.cpp (revision 12011) +@@ -64,90 +64,6 @@ + } + /*}}}*/ + /*FUNCTION Results::Write{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void Results::Write(mxArray** pdataref){ +- +- int i,j; +- int count; +- +- /*output: */ +- mxArray* dataref=NULL; +- mxArray* processeddataref=NULL; +- mwSize nfields; +- mwSize maxfields; +- mwSize nsteps; +- mwSize step; +- const char **fnames = NULL; +- int *enums = NULL; +- int baseenum; +- mwSize onebyone[2] = {1,1}; +- mwSize ndim = 2; +- +- /*How many time steps do we have? : */ +- nsteps=0; +- for(i=0;iSize();i++){ +- ExternalResult* result=(ExternalResult*)this->GetObjectByOffset(i); +- step=result->GetStep(); +- if(step>nsteps)nsteps=step; +- } +- onebyone[0]=nsteps; +- +- /*How many field names do we have. First, figure out how many result types we have: */ +- maxfields=(mwSize)this->Size(); +- enums=(int*)xmalloc(maxfields*sizeof(int)); +- for(i=0;iGetObjectByOffset(i); +- enums[i]=result->InstanceEnum(); +- } +- /*Now, make result types unique: */ +- for(i=0;i=0){//if <0, it means this enum was found to replicate another one previously +- baseenum=enums[i]; +- /*is the baseenum repeated later on?:*/ +- for(j=i+1;j0)nfields++; +- +- /*Add 2 fields for time and step: */ +- nfields=nfields+2; +- +- /*Fill the names of the structure field: */ +- fnames=(const char**)xmalloc(nfields*sizeof(char*)); +- count=0; +- for(i=0;i0){ +- fnames[count]=EnumToStringx(enums[i]); +- count++; +- } +- } +- /*don't forget the extra fields "time" and "step":*/ +- fnames[nfields-2]="time"; +- fnames[nfields-1]="step"; +- +- /*Initialize structure: */ +- dataref=mxCreateStructArray( ndim,onebyone,nfields,fnames); +- +- /*Fill each field: */ +- for(i=0;iSize();i++){ //do not include the last one used for time +- ExternalResult* result=(ExternalResult*)this->GetObjectByOffset(i); +- result->SetMatlabField(dataref); +- } +- +- /*Now, process the patch in the dataref structure, by calling MatlabProcessPatch.m +- *on the current dataref structure: */ +- mexCallMATLAB(1,&processeddataref,1,&dataref, "MatlabProcessPatch"); +- +- /*Assign output pointers:*/ +- *pdataref=processeddataref; +-} +-#else + void Results::Write(Parameters* parameters){ + + int i; +@@ -166,5 +82,4 @@ + } + + } +-#endif + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Results.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Results.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Results.h (revision 12011) +@@ -25,11 +25,7 @@ + /*}}}*/ + /*numerics: {{{1*/ + Results* SpawnTriaResults(int* indices); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void Write(mxArray** pdataref); +- #else + void Write(Parameters* parameters); +- #endif + /*}}}*/ + }; + #endif //ifndef _RESULTS_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h (revision 12011) +@@ -47,20 +47,6 @@ + * will be trapped. Really nifty!*/ + + #ifdef _SERIAL_ +-#ifdef _HAVE_MATLAB_ //{{{2 +-#define MODULEBOOT(); ModuleBoot(); \ +- try{ +- +-#define MODULEEND(); ModuleEnd(); }\ +- catch(ErrorException &exception){\ +- exception.Report(); \ +- mexErrMsgTxt(""); \ +- }\ +- catch (exception& e) {\ +- _printf_(true,"Standard exception: %s\n",e.what());\ +- mexErrMsgTxt(" ");\ +- } +-#endif //}}} + #ifdef _HAVE_PYTHON_ //{{{2 + #define MODULEBOOT(); ModuleBoot(); \ + PyObject* output = PyTuple_New(NLHS); if (!output) return NULL; +@@ -86,9 +72,6 @@ + #endif + /*}}}*/ + /* WRAPPER {{{1*/ +-#ifdef _HAVE_MATLAB_ +-#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +-#endif + #ifdef _HAVE_PYTHON_ + #define WRAPPER(modulename,...) \ + \ +@@ -119,13 +102,9 @@ + + /*}}}*/ + /* CHECKARGUMENTS {{{1*/ +-#ifdef _HAVE_MATLAB_ +-#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer) +-#endif + #ifdef _HAVE_PYTHON_ + #define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) + #endif + /*}}}*/ + +- + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/types.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/types.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/types.h (revision 12011) +@@ -15,14 +15,6 @@ + #include + + /*Define abstract type for I/O: */ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-typedef const mxArray* ConstDataHandle; //serially, we are reading data from a matlab array. +-typedef mxArray* DataHandle; +-#else +-typedef FILE* ConstDataHandle; //in parallel, we are reading data from a file. +-typedef FILE* DataHandle; +-#endif + enum param_type { STRING, INTEGER, STRINGARRAY, DOUBLE, DOUBLEVEC, DOUBLEMAT, PETSCVEC, PETSCMAT }; + + /*here are our abstracted types: inspired on petsc */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptFunc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptFunc.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptFunc.cpp (revision 12011) +@@ -1,41 +0,0 @@ +-/*!\file: OptFunc.cpp +- * \brief: "C" code wrapper to matlab objectivefunctionC call +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include "../../objects/objects.h" +-#include "../../shared/shared.h" +-#include "../../include/include.h" +- +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "mex.h" +-double OptFunc(double scalar, OptArgs* optargs){ +- +- /*output: */ +- double J; +- +- mxArray* inputs[2]; +- mxArray* psearch_scalar=NULL; +- mxArray* mxJ=NULL; +- +- psearch_scalar=mxCreateDoubleScalar(scalar); +- inputs[0]=psearch_scalar; +- inputs[1]=optargs->femmodel; +- +- mexCallMATLAB(1,&mxJ,2,(mxArray**)inputs, optargs->function_name); +- +- /*extract misfit from mxArray*/ +- J=mxGetScalar(mxJ); +- +- return J; +-} +-#else +-double OptFunc(double scalar, OptArgs* optargs){ +- _error_(" not implemented yet"); +-} +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp (revision 12011) +@@ -38,37 +38,13 @@ + + if(level<0) _error_("vebosity level should be a positive integer (user provided %i)",level); + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- +- mxArray* output=NULL; +- mxArray* input=NULL; +- input=mxCreateDoubleScalar((double)level); +- +- mexCallMATLAB(0,&output,1,&input,"SetVerbosityLevel"); +-#else +- + verbositylevel = level; + +-#endif + }/*}}}*/ + /*FUNCTION GetVerbosityLevel {{{*/ + int GetVerbosityLevel(void){ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) + +- mxArray* output=NULL; +- mxArray* input=NULL; +- double level; +- +- mexCallMATLAB(1,&output,0,&input,"GetVerbosityLevel"); +- level=mxGetScalar(output); +- +- verbositylevel = (int)level; +- return verbositylevel; +- +-#else +- + _assert_(verbositylevel>=0); + return verbositylevel; + +-#endif + }/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.cpp (revision 12011) +@@ -0,0 +1,41 @@ ++/* \file alloc_module.h ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++ ++#include "./allocmodule.h" ++#include "../Exceptions/exceptions.h" ++#include "../../include/include.h" ++#include "../../objects/objects.h" ++ ++void xdelete_module(Matrix** pv){ ++ ++ if (pv && *pv){ ++ /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ ++ * correctly: */ ++ #ifdef _HAVE_PETSC_ ++ MatFree(&(*pv)->matrix); ++ #endif ++ *pv=NULL; ++ } ++} ++ ++void xdelete_module(Vector** pv){ ++ ++ if (pv && *pv){ ++ /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ ++ * correctly: */ ++ #ifdef _HAVE_PETSC_ ++ VecFree(&(*pv)->vector); ++ #endif ++ *pv=NULL; ++ } ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.h (revision 12011) +@@ -0,0 +1,11 @@ ++/* \file alloc.h ++ */ ++ ++#ifndef _ALLOC_MODULE_H_ ++#define _ALLOC_MODULE_H_ ++class Matrix; ++class Vector; ++void xdelete_module(Matrix** pvptr); ++void xdelete_module(Vector** pvptr); ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 12011) +@@ -18,10 +18,6 @@ + #error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_SERIAL_) && defined(_HAVE_MATLAB_) +-#include "mex.h" +-#endif +- + #include + #include + +@@ -36,13 +32,8 @@ + + if(!size)_error_(" attempting to 0 size allocation!"); + +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- /* Use the matlab api to do the allocation: */ +- memptr=mxMalloc(size); +- #else + /* Use the c library to do the allocation: */ + memptr=malloc(size); +- #endif + if(!memptr) _error_("memory allocation failed!"); + + return memptr; +@@ -54,13 +45,8 @@ + + if(!size)_error_("attempting to 0 size allocation!"); + +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- /* Use the matlab api to do the allocation: */ +- memptr=mxCalloc(n,size); +- #else + /* Use the c library to do the allocation: */ + memptr=calloc(n,size); +- #endif + if(!memptr) _error_("memory allocation failed!"); + + return memptr; +@@ -69,11 +55,7 @@ + void xfree(void* *pv){ + + if (pv && *pv){ +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- mxFree(*pv); +- #else +- free(*pv); +- #endif ++ free(*pv); + + *pv=NULL; + } +@@ -82,18 +64,10 @@ + void xdelete(Matrix** pv){ + + if (pv && *pv){ +- #ifdef _PARALLEL_ + /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we + * don't actually free memory in Matlab, we let the memory manager do that. We only + * free in parallel: */ + delete *pv; +- #else +- /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ +- * correctly: */ +- #ifdef _HAVE_PETSC_ +- MatFree(&(*pv)->matrix); +- #endif +- #endif + *pv=NULL; + } + } +@@ -101,18 +75,10 @@ + void xdelete(Vector** pv){ + + if (pv && *pv){ +- #ifdef _PARALLEL_ + /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we + * don't actually free memory in Matlab, we let the memory manager do that. We only + * free in parallel: */ + delete *pv; +- #else +- /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ +- * correctly: */ +- #ifdef _HAVE_PETSC_ +- VecFree(&(*pv)->vector); +- #endif +- #endif + *pv=NULL; + } + } +@@ -123,12 +89,7 @@ + register void* value=NULL; + + if(!size)_error_("attempting to realloc to zero"); +- +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- value = (void*)mxRealloc(pv,size); +- #else + value = (void*)realloc(pv,size); +- #endif + + if (value == NULL) { + _error_("virtual memory exhausted"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Dakotax/SpawnCoreSerial.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Dakotax/SpawnCoreSerial.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Dakotax/SpawnCoreSerial.cpp (revision 12011) +@@ -1,71 +0,0 @@ +-/*!\file: SpawnCoreSerial.cpp +- * \brief: run core ISSM solution using Dakota inputs. Call the Serial core solution, using mexCallMATLAB +- * \sa SpawnCore.cpp SpawnCoreParallel.cpp +- * +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include "../../objects/objects.h" +-#include "../../io/io.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +-#include "../../shared/shared.h" +-#include "./Dakotax.h" +-#include "../../include/include.h" +- +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void SpawnCoreSerial(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, mxArray* femmodel, int counter){ +- +- int i; +- +- //inputs to matlab routine +- mxArray* mxvariables=NULL; +- double* variables_copy=NULL; +- mxArray* mxvariabledescriptors=NULL; +- mxArray* mxcounter=NULL; +- mwSize dims[2]={0}; +- +- //mexCallMATLAB arrays +- mxArray* array[4]; +- +- //output from SpawnCore in matlab routine. +- mxArray* mxresponses=NULL; +- +- /*Create variables and variable descriptors mxArrays that we will feed to the core solution for update of the inputs: */ +- mxvariables=mxCreateDoubleMatrix(numvariables,1,mxREAL); +- variables_copy=(double*)xmalloc(numvariables*sizeof(double)); +- memcpy(variables_copy,variables,numvariables*sizeof(double)); +- mxSetPr(mxvariables,variables_copy); +- +- dims[0]=numvariables; +- dims[1]=1; +- mxvariabledescriptors=mxCreateCellArray(2,dims); +- for(i=0;iparameters; +- #endif + + /*Recover dakota_input_file, dakota_output_file and dakota_error_file, in the parameters dataset in parallel */ + parameters->FindParam(&dakota_input_file,QmuInNameEnum); +@@ -85,11 +77,7 @@ + + // Instantiate/initialize the parallel library and problem description + // database objects. +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- Dakota::ParallelLibrary parallel_lib; //use Dakota's standard library mode constructor +- #else +- Dakota::ParallelLibrary parallel_lib("serial"); //use our own ISSM Dakota library mode constructor, which only fires up Dakota on CPU 0. +- #endif ++ Dakota::ParallelLibrary parallel_lib("serial"); //use our own ISSM Dakota library mode constructor, which only fires up Dakota on CPU 0. + Dakota::ProblemDescDB problem_db(parallel_lib); + + // Manage input file parsing, output redirection, and restart processing +@@ -142,9 +130,5 @@ + xfree((void**)&dakota_error_file); + xfree((void**)&dakota_output_file); + +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- delete parameters; +- #endif +- + #endif //#ifdef _HAVE_DAKOTA_ + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/OutputResultsx/OutputResultsx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/OutputResultsx/OutputResultsx.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/OutputResultsx/OutputResultsx.h (revision 12011) +@@ -13,12 +13,7 @@ + + #include "../../Container/Container.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-void OutputResultsx(mxArray** pdataref, Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, Results* results); +-#else + void OutputResultsx(Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, Results* results); +-#endif + + #endif /* _OUTPUTRESULTS_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/OutputResultsx/OutputResultsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 12011) +@@ -15,11 +15,7 @@ + #include "../../io/io.h" + #include "../../objects/objects.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void OutputResultsx(mxArray** pdataref, Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Results* results){ +-#else + void OutputResultsx( Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Results* results){ +-#endif + + extern int my_rank; + FILE *fid = NULL; +@@ -30,21 +26,11 @@ + char* solutiontypestring = NULL; + bool dakota_analysis = false; + +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- const char **fnames = NULL; +- mwSize onebyone[2] = {0,0}; +- mwSize ndim = 2; +- int nfields=0; +- #endif +- + /*retrieve parameters: */ + parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); + + if(dakota_analysis){ + //no need to output anything, Dakota analysis has different outputs +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- *pdataref=mxCreateStructArray( ndim,onebyone,nfields,fnames); +- #endif + return; + } + +@@ -55,7 +41,6 @@ + + /*Results do not include the type of solution being run . In parallel, we output results to a filename, + *therefore, we need to include the solutiontype into the filename: */ +- #ifdef _PARALLEL_ + if(my_rank==0){ + parameters->FindParam(&solutiontype,SolutionTypeEnum); + EnumToStringx(&solutiontypestring,solutiontype); +@@ -87,27 +72,20 @@ + /*Add file pointer in parameters for further calls to OutputResultsx: */ + parameters->SetParam(fid,OutputFilePointerEnum); + } +- #endif + +- /*Write results to disk (in parallel), or to memory (in serial mode): */ +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- results->Write(pdataref); +- #else +- results->Write(parameters); +- #endif ++ /*Write results to disk: */ ++ results->Write(parameters); + + /*Delete and reinitialize results, in parallel: */ +- #ifdef _PARALLEL_ +- results->clear(); ++ results->clear(); + +- /*Close output file? :*/ +- /*WARNING: issm.cpp is taking care of it for now (quick fix) +- if((step==1) && (time==0)){ +- if(io_gather){ +- if(my_rank==0) pfclose(fid,outputfilename); +- } +- else pfclose(fid,cpu_outputfilename); +- } +- */ +- #endif ++ /*Close output file? :*/ ++ /*WARNING: issm.cpp is taking care of it for now (quick fix) ++ if((step==1) && (time==0)){ ++ if(io_gather){ ++ if(my_rank==0) pfclose(fid,outputfilename); ++ } ++ else pfclose(fid,cpu_outputfilename); ++ } ++ */ + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h (revision 12011) +@@ -39,9 +39,6 @@ + /*}}}*/ + /*SeqMat specific routines {{{1*/ + void Echo(void); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- mxArray* ToMatlabMatrix(void); +- #endif + void Assemble(void); + double Norm(NormMode norm_type); + void GetSize(int* pM,int* pN); +@@ -55,9 +52,4 @@ + + }; + +-/*API :*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref); +-#endif +- + #endif //#ifndef _SEQMAT_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp (revision 12011) +@@ -65,44 +65,6 @@ + } + /*}}}*/ + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-/*FUNCTION SeqVec::ToMatlabVector{{{1*/ +-mxArray* SeqVec::ToMatlabVector(void){ +- +- double* buffer=NULL; +- +- mxArray* dataref=NULL; +- +- /*copy vector into a new buffer: */ +- if(this->M){ +- buffer=(double*)xmalloc(this->M*sizeof(double)); +- memcpy(buffer,vector,M*sizeof(double)); +- +- dataref = mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(dataref,this->M); +- mxSetN(dataref,1); +- mxSetPr(dataref,buffer); +- } +- else dataref = mxCreateDoubleMatrix(0,0,mxREAL); +- +- +- /*do not erase buffer!: */ +- return dataref; +- +-} +-/*}}}*/ +-/*FUNCTION MatlabVectorToSeqVec{{{1*/ +-SeqVec* MatlabVectorToSeqVec(const mxArray* dataref){ +- +- SeqVec* output=NULL; +- +- output=new SeqVec(); +- MatlabVectorToDoubleVector(&output->vector,&output->M,dataref); +- return output; +- +-} +-/*}}}*/ +-#endif + /*FUNCTION SeqVec::Assemble{{{1*/ + void SeqVec::Assemble(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp (revision 12011) +@@ -91,54 +91,6 @@ + } + } + /*}}}*/ +- +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-/*FUNCTION SeqMat::ToMatlabMatrix{{{1*/ +-mxArray* SeqMat::ToMatlabMatrix(void){ +- +- /*Intermediary: */ +- double* buffer=NULL; +- mxArray* pfield=NULL; +- +- /*output: */ +- mxArray* dataref=NULL; +- +- /*copy vector into a new buffer: */ +- if(this->M*this->N){ +- buffer=(double*)xmalloc(this->M*this->N*sizeof(double)); +- memcpy(buffer,this->matrix,M*N*sizeof(double)); +- +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,this->N); +- mxSetN(pfield,this->M); +- mxSetPr(pfield,buffer); +- +- //transpose the matrix, written directly to matlab! from C to matlab. +- mexCallMATLAB(1,&dataref, 1, &pfield, "transpose"); +- } +- else dataref=mxCreateDoubleMatrix(0,0,mxREAL); +- +- /*do not erase buffer!: */ +- return dataref; +- +-} +- +- +- +- +-/*}}}*/ +-/*FUNCTION MatlabMatrixToSeqMat{{{1*/ +-SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ +- +- SeqMat* output=NULL; +- +- output=new SeqMat(); +- MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref); +- return output; +- +-} +-/*}}}*/ +-#endif + /*FUNCTION SeqMat::Assemble{{{1*/ + void SeqMat::Assemble(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h (revision 12011) +@@ -36,9 +36,6 @@ + /*}}}*/ + /*SeqVec specific routines {{{1*/ + void Echo(void); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- mxArray* ToMatlabVector(void); +- #endif + void Assemble(void); + void SetValues(int ssize, int* list, double* values, InsMode mode); + void SetValue(int dof, double value, InsMode mode); +@@ -58,10 +55,4 @@ + /*}}}*/ + }; + +- +-/*API :*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); +-#endif +- + #endif //#ifndef _SEQVEC_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12011) +@@ -3,20 +3,13 @@ + EXEEXT=$(ISSMEXT) + + #Library declaration {{{1 +-#Compile serial library, and then try and compile parallel library +-if NOSERIAL +-if NOPARALLEL +-lib_LIBRARIES = +-else +-lib_LIBRARIES = libpISSM.a libOverload.a ++lib_LIBRARIES = libISSMCore.a libISSMModules.a libISSMOverload.a ++if PYTHON ++lib_LIBRARIES += libISSMPython.a + endif +-else +-if NOPARALLEL +-lib_LIBRARIES = libISSM.a libOverload.a +-else +-lib_LIBRARIES = libISSM.a libpISSM.a libOverload.a ++if MATLAB ++lib_LIBRARIES += libISSMMatlab.a + endif +-endif + #}}} + + #sources +@@ -361,8 +354,8 @@ + ./modules/Dakotax/DescriptorIndex.cpp\ + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ + ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\ +- ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h +-dakota_psources= ./modules/Dakotax/SpawnCoreParallel.cpp ++ ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\ ++ ./modules/Dakotax/SpawnCoreParallel.cpp + #}}} + #Transient sources {{{1 + transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp +@@ -442,8 +435,7 @@ + ./objects/Inputs/ControlInput.h\ + ./objects/Inputs/ControlInput.cpp\ + ./shared/Numerics/BrentSearch.cpp\ +- ./shared/Numerics/OptimalSearch.cpp\ +- ./shared/Numerics/OptFunc.cpp ++ ./shared/Numerics/OptimalSearch.cpp + + control_psources=./solutions/control_core.cpp\ + ./solutions/controltao_core.cpp\ +@@ -693,34 +685,11 @@ + ./objects/KML/KMLFileReadUtils.cpp\ + ./objects/KML/KMLFileReadUtils.h + #}}} +-#Matlab sources {{{1 +-matlab_sources= ./toolkits/matlab/matlabincludes.h\ +- ./toolkits/matlab/MatlabNArrayToNArray.cpp\ +- ./toolkits/double/MatlabVectorToDoubleVector.cpp\ +- ./toolkits/double/double.h\ +- ./toolkits/double/MatlabMatrixToDoubleMatrix.cpp\ +- ./io/Matlab/matlabio.h\ +- ./io/Matlab/CheckNumMatlabArguments.cpp\ +- ./io/Matlab/mxGetAssignedField.cpp\ +- ./io/Matlab/WriteMatlabData.cpp\ +- ./io/Matlab/FetchMatlabData.cpp\ +- ./io/Matlab/OptionParse.cpp +-#}}} +-#Python sources {{{1 +-python_sources= ./io/Python/pythonio.h\ +- ./io/Python/WritePythonData.cpp\ +- ./io/Python/CheckNumPythonArguments.cpp\ +- ./io/Python/FetchPythonData.cpp +-#}}} + #Petsc sources {{{1 + petsc_sources= ./toolkits/petsc\ + ./toolkits/petsc/patches\ + ./toolkits/petsc/patches/SolverEnum.h\ + ./toolkits/petsc/patches/petscpatches.h\ +- ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ +- ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ +- ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ +- ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ + ./toolkits/petsc/patches/VecTranspose.cpp\ + ./toolkits/petsc/patches/VecToMPISerial.cpp\ + ./toolkits/petsc/patches/MatToSerial.cpp\ +@@ -753,8 +722,48 @@ + gsl_sources= ./modules/Solverx/SolverxGsl.cpp + + #}}} +-#Serialsources {{{1 +-serial_sources= ./objects/Options/Option.cpp\ ++#Python sources {{{1 ++python_sources= ./python/io/pythonio.h\ ++ ./python/io/WritePythonData.cpp\ ++ ./python/io/CheckNumPythonArguments.cpp\ ++ ./python/io/FetchPythonData.cpp\ ++ ./python/objects/Bamg/BamgGeom.h\ ++ ./python/objects/Bamg/BamgGeom.cpp\ ++ ./python/objects/Bamg/BamgMesh.h\ ++ ./python/objects/Bamg/BamgMesh.cpp\ ++ ./python/objects/Bamg/BamgOpts.h\ ++ ./python/objects/Bamg/BamgOpts.cpp ++ ++#}}} ++#Matlab sources {{{1 ++matlab_sources= ./toolkits/matlab/matlabincludes.h\ ++ ./matlab/io/matlabio.h\ ++ ./matlab/io/MatlabNArrayToNArray.cpp\ ++ ./matlab/io/CheckNumMatlabArguments.cpp\ ++ ./matlab/io/mxGetAssignedField.cpp\ ++ ./matlab/io/WriteMatlabData.cpp\ ++ ./matlab/io/FetchMatlabData.cpp\ ++ ./matlab/io/OptionParse.cpp\ ++ ./matlab/io/MatlabMatrixToMatrix.cpp\ ++ ./matlab/io/MatlabVectorToVector.cpp\ ++ ./matlab/io/MatlabVectorToDoubleVector.cpp\ ++ ./matlab/io/MatlabMatrixToDoubleMatrix.cpp\ ++ ./matlab/io/Container/Options.cpp\ ++ ./matlab/objects/Bamg/BamgGeom.h\ ++ ./matlab/objects/Bamg/BamgGeom.cpp\ ++ ./matlab/objects/Bamg/BamgMesh.h\ ++ ./matlab/objects/Bamg/BamgMesh.cpp\ ++ ./matlab/objects/Bamg/BamgOpts.h\ ++ ./matlab/objects/Bamg/BamgOpts.cpp\ ++ ./matlab/io/MatlabMatrixToPetscMatrix.cpp\ ++ ./matlab/io/MatlabVectorToPetscVector.cpp\ ++ ./matlab/io/PetscMatrixToDoubleMatrix.cpp\ ++ ./matlab/io/PetscVectorToDoubleVector.cpp\ ++ ./matlab/io/MatlabMatrixToSeqMat.cpp\ ++ ./matlab/io/MatlabVectorToSeqVec.cpp ++#}}} ++#Modules sources{{{1 ++module_sources= ./objects/Options/Option.cpp\ + ./objects/Options/Option.h\ + ./objects/Options/OptionDouble.cpp\ + ./objects/Options/OptionDouble.h\ +@@ -768,6 +777,8 @@ + ./objects/Options/OptionCell.h\ + ./objects/Options/OptionUtilities.cpp\ + ./objects/Options/OptionUtilities.h\ ++ ./shared/Alloc/alloc_module.h\ ++ ./shared/Alloc/alloc_module.cpp\ + ./shared/Threads/issm_threads.h\ + ./shared/Threads/LaunchThread.cpp\ + ./shared/Threads/PartitionRange.cpp\ +@@ -789,7 +800,6 @@ + ./modules/Chacox/input_parse.cpp\ + ./modules/Chacox/chaco_seconds.cpp\ + ./modules/Chacox/user_params.cpp\ +- ./modules/Dakotax/SpawnCoreSerial.cpp\ + ./modules/TriaSearchx/TriaSearchx.h\ + ./modules/TriaSearchx/TriaSearchx.cpp\ + ./modules/TriMeshx/TriMeshx.h\ +@@ -840,69 +850,57 @@ + ./modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.h + #}}} + ++#{{{1 Conditional build-up of sources + #ISSM sources are a combination of core sources and sources related to specific capabilities (which can + #be activated by autotools conditionals +-#{{{1 + ++ + #First the core + issm_sources = $(core_sources) +-issm_psources = + + #Now the optional source + if DAKOTA + issm_sources += $(dakota_sources) +-issm_psources += $(dakota_psources) + endif + + if PETSC + issm_sources += $(petsc_sources) +-issm_psources += $(petsc_psources) + endif + + if GSL + issm_sources += $(gsl_sources) +-issm_psources += $(gsl_psources) + endif + +- + if TRANSIENT + issm_sources += $(transient_sources) +-issm_psources += $(transient_psources) + endif + + if STEADYSTATE + issm_sources += $(steadystate_sources) +-issm_psources += $(steadystate_psources) + endif + + if PROGNOSTIC + issm_sources += $(prognostic_sources) +-issm_psources += $(prognostic_psources) + endif + + if THERMAL + issm_sources += $(thermal_sources) +-issm_psources += $(thermal_psources) + endif + + if CONTROL + issm_sources += $(control_sources) +-issm_psources += $(control_psources) + endif + + if HYDROLOGY + issm_sources += $(hydrology_sources) +-issm_psources += $(hydrology_psources) + endif + + if DIAGNOSTIC + issm_sources += $(diagnostic_sources) +-issm_psources += $(diagnostic_psources) + endif + + if BALANCED + issm_sources += $(balanced_sources) +-issm_psources += $(balanced_psources) + endif + + if RESPONSES +@@ -911,7 +909,6 @@ + + if SLOPE + issm_sources += $(slope_sources) +-issm_psources += $(slope_psources) + endif + + if GROUNDINGLINE +@@ -926,71 +923,61 @@ + issm_sources += $(threed_sources) + endif + #}}} ++#Library flags and sources {{{1 ++ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) + +-#ISSM serial library {{{1 +-if SERIAL +-libISSM_a_SOURCES = $(issm_sources) +-libISSM_a_SOURCES += $(serial_sources) +-libISSM_a_SOURCES += $(bamg_sources) +-libISSM_a_SOURCES += $(kml_sources) +-libISSM_a_CXXFLAGS = -fPIC -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) +-#libISSM_a_CXXFLAGS = -D_SERIAL_ -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER $(CXXFLAGS) $(CXXOPTFLAGS) ++libISSMCore_a_SOURCES = $(issm_sources) ++libISSMCore_a_CXXFLAGS = $(ALLCXXFLAGS) + ++libISSMModules_a_SOURCES = $(module_sources) ++libISSMModules_a_SOURCES += $(bamg_sources) ++libISSMModules_a_SOURCES += $(kml_sources) ++libISSMModules_a_CXXFLAGS = $(ALLCXXFLAGS) ++ + if PYTHON +-libISSM_a_CXXFLAGS+= -DNPY_NO_DEPRECATED_API +-libISSM_a_SOURCES += $(python_sources) ++libISSMPython_a_SOURCES = $(python_sources) ++libISSMPython_a_CXXFLAGS= $(ALLCXXFLAGS) ++libISSMPython_a_CXXFLAGS+= -DNPY_NO_DEPRECATED_API + endif + + if MATLAB +-libISSM_a_SOURCES += $(matlab_sources) ++libISSMMatlab_a_SOURCES = $(matlab_sources) ++libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS) + endif + +-endif + #}}} +-#ISSM parallel library {{{1 +-if PARALLEL +-libpISSM_a_SOURCES = $(issm_sources) +-libpISSM_a_SOURCES += $(issm_psources) +-libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXFLAGS) $(CXXOPTFLAGS) +-endif +-#}}} + #Overload library, to overload any non-standard symbols. {{{1 +-libOverload_a_SOURCES = ./shared/String/stricmp.c +-libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) $(CFLAGS) ++libISSMOverload_a_SOURCES = ./shared/String/stricmp.c ++libISSMOverload_a_CFLAGS = -fPIC -D_C_ $(COPTFLAGS) $(CFLAGS) + #}}} + + #Executable {{{1 +-if NOPARALLEL +-bin_PROGRAMS = +-else + bin_PROGRAMS = issm +-endif + + #Standard libraries +-LDADD = ./libpISSM.a ./libOverload.a ++LDADD = ./libISSMCore.a ./libISSMOverload.a + + #External packages + LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) + + issm_SOURCES = solutions/issm.cpp +-issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) ++issm_CXXFLAGS= -fPIC $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) + #}}} + #Automatic differentiation: append this fold to the end of the src/c/Makefile.am to get this Makefile.am {{{ + if ADIC2 +-lib_LIBRARIES += libAD.a libpISSMRose.a ++lib_LIBRARIES += libAD.a libISSMRose.a + + #ADIC2 library, for automatic differentiation + #libAD_a_SOURCES = ./mini1.ad.c + libAD_a_SOURCES = +-libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) ++libAD_a_CFLAGS = -fPIC -D_C_ $(COPTFLAGS) + + +- + #test rose preprocessing + %.r2cpp.cpp : %.cpp + testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< +-libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) +-libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) ++libISSMRose_a_SOURCES = $(libISSMCore_a_SOURCES:.cpp=.r2cpp.cpp) ++libISSMRose_a_CXXFLAGS= -fPIC -D_C_ $(CXXOPTFLAGS) + + + +@@ -1002,9 +989,9 @@ + + #Executable + bin_PROGRAMS += issmRose.exe +-issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) ++issmRose_exe_LDADD = ./libISSMRose.a $(LDADD) + issmRose_exe_SOURCES = solutions/issm.cpp +-issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) ++issmRose_exe_CXXFLAGS= -fPIC $(CXXOPTFLAGS) $(COPTFLAGS) + LDADD += $(ADIC2LIB) + + endif #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h (revision 12011) +@@ -81,9 +81,6 @@ + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + /*}}}*/ + }; + #endif /* _DOUBLEVECPARAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h (revision 12011) +@@ -81,9 +81,6 @@ + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.cpp (revision 12011) +@@ -100,14 +100,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION FileParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void FileParam::SetMatlabField(mxArray* dataref){ +- +- _error_("FileParam is a pointer and cannot be converted into a matlab object"); +-} +-#endif +-/*}}}*/ + /*FUNCTION FileParam::UnitConversion{{{1*/ + void FileParam::UnitConversion(int direction_enum){ + /*do nothing, no unit conversion*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h (revision 12011) +@@ -83,9 +83,6 @@ + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h (revision 12011) +@@ -83,9 +83,6 @@ + double* GetPointer(void); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h (revision 12011) +@@ -59,8 +59,5 @@ + virtual void SetValue(double** array, int M, int* mdim_array, int* ndim_array)=0; + virtual void UnitConversion(int direction_enum)=0; + virtual void GetParameterName(char**pname)=0; +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- virtual void SetMatlabField(mxArray* dataref)=0; +- #endif + }; + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h (revision 12011) +@@ -80,9 +80,6 @@ + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.cpp (revision 12011) +@@ -184,35 +184,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION IntVecParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void IntVecParam::SetMatlabField(mxArray* dataref){ +- +- char *name = NULL; +- double *doublevec = NULL; +- int *intvec = NULL; +- mxArray *pfield = NULL; +- +- this->GetParameterValue(&intvec,NULL); +- this->GetParameterName(&name); +- +- /*cast intvec into doublevec for Matlab*/ +- if(M){ +- doublevec=(double*)xmalloc(M*sizeof(double)); +- for(int i=0;ienum_type); + } + /*}}}*/ +-/*FUNCTION IntParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void IntParam::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- this->GetParameterName(&name); +- mxSetField( dataref, 0, name,mxCreateDoubleScalar((double)value)); +-} +-#endif +-/*}}}*/ + /*FUNCTION IntParam::UnitConversion{{{1*/ + void IntParam::UnitConversion(int direction_enum){ + /*do nothing, no unit conversion*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.cpp (revision 12011) +@@ -133,15 +133,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION BoolParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void BoolParam::SetMatlabField(mxArray* dataref){ +- char* name=NULL; +- this->GetParameterName(&name); +- mxSetField( dataref, 0, name,mxCreateDoubleScalar((double)value)); +-} +-#endif +-/*}}}*/ + /*FUNCTION BoolParam::UnitConversion{{{1*/ + void BoolParam::UnitConversion(int direction_enum){ + /*do nothing, no unit conversion*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.cpp (revision 12011) +@@ -171,35 +171,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION IntMatParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void IntMatParam::SetMatlabField(mxArray* dataref){ +- +- char *name = NULL; +- double *doublearray = NULL; +- int *intarray = NULL; +- mxArray *pfield = NULL; +- mxArray *pfield2 = NULL; +- +- this->GetParameterValue(&intarray,NULL,NULL); +- this->GetParameterName(&name); +- +- /*cast intarray into doublearray for Matlab*/ +- doublearray=(double*)xmalloc(M*N*sizeof(double)); +- for(int i=0;ienum_type); + } + /*}}}*/ +-/*FUNCTION VectorParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void VectorParam::SetMatlabField(mxArray* dataref){ +- +- mxArray* pfield=NULL; +- char* name=NULL; +- double* doublevec=NULL; +- int M; +- +- doublevec=value->ToMPISerial(); +- value->GetSize(&M); +- this->GetParameterName(&name); +- +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,M); +- mxSetN(pfield,1); +- mxSetPr(pfield,doublevec); +- +- mxSetField( dataref, 0, name, pfield); +-} +-#endif +-/*}}}*/ + /*FUNCTION VectorParam::SetValue{{{1*/ + void VectorParam::SetValue(Vector* vector){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp (revision 12011) +@@ -189,27 +189,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION MatrixParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void MatrixParam::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- int M,N; +- double* doublemat=NULL; +- mxArray* pfield=NULL; +- +- doublemat=value->ToSerial(); +- value->GetSize(&M,&N); +- this->GetParameterName(&name); +- +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,M); +- mxSetN(pfield,N); +- mxSetPr(pfield,doublemat); +- mxSetField( dataref, 0, name, pfield); +-} +-#endif +-/*}}}*/ + /*FUNCTION MatrixParam::SetValue{{{1*/ + void MatrixParam::SetValue(Matrix* matrix){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.cpp (revision 12011) +@@ -235,28 +235,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION StringArrayParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void StringArrayParam::SetMatlabField(mxArray* dataref){ +- +- int i; +- char* name=NULL; +- mwSize dims[2]={0}; +- mxArray* pfield=NULL; +- +- this->GetParameterName(&name); +- +- dims[0]=this->numstrings; +- dims[1]=1; +- pfield=mxCreateCellArray(2,dims); +- for(i=0;inumstrings;i++){ +- char* string=value[i]; +- mxSetCell(pfield,i,mxCreateString(string)); +- } +- mxSetField( dataref, 0, name,pfield); +-} +-#endif +-/*}}}*/ + /*FUNCTION StringArrayParam::SetValue{{{1*/ + void StringArrayParam::SetValue(char** stringarray,int M){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.cpp (revision 12011) +@@ -163,17 +163,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION StringParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void StringParam::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- +- this->GetParameterName(&name); +- mxSetField( dataref, 0, name, mxCreateString(value)); +-} +-#endif +-/*}}}*/ + /*FUNCTION StringParam::SetValue{{{1*/ + void StringParam::SetValue(char* string){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h (revision 12011) +@@ -81,9 +81,6 @@ + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp (revision 12011) +@@ -201,26 +201,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION DoubleVecParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void DoubleVecParam::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- double* doublevec=NULL; +- mxArray* pfield=NULL; +- +- this->GetParameterValue(&doublevec,NULL); +- this->GetParameterName(&name); +- +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,M); +- mxSetN(pfield,1); +- mxSetPr(pfield,doublevec); +- +- mxSetField( dataref, 0, name, pfield); +-} +-#endif +-/*}}}*/ + /*FUNCTION DoubleVecParam::SetValue{{{1*/ + void DoubleVecParam::SetValue(double* doublearray,int in_M){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h (revision 12011) +@@ -81,9 +81,6 @@ + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.cpp (revision 12011) +@@ -218,16 +218,6 @@ + #endif + } + /*}}}*/ +-/*FUNCTION DoubleParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void DoubleParam::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- this->GetParameterName(&name); +- mxSetField( dataref, 0, name,mxCreateDoubleScalar(value)); +-} +-#endif +-/*}}}*/ + /*FUNCTION DoubleParam::UnitConversion{{{1*/ + void DoubleParam::UnitConversion(int direction_enum){ + ::UnitConversion(&this->value,1,direction_enum,this->enum_type); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h (revision 12011) +@@ -83,9 +83,6 @@ + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + /*}}}*/ + }; + #endif /* _STRINGARRAYPARAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.cpp (revision 12011) +@@ -307,46 +307,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION StringArrayParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void DoubleMatArrayParam::SetMatlabField(mxArray* dataref){ +- +- int i,m,n; +- double* matrix=NULL; +- double* outmatrix=NULL; +- char* name=NULL; +- mwSize dims[2]={0}; +- mxArray* pfield=NULL; +- mxArray* pfield2=NULL; +- mxArray* pfield3=NULL; +- +- this->GetParameterName(&name); +- dims[0]=this->M; +- dims[1]=1; +- pfield=mxCreateCellArray(2,dims); +- +- for(i=0;iM;i++){ +- matrix=this->array[i]; +- m=this->mdim_array[i]; +- n=this->ndim_array[i]; +- outmatrix=(double*)xmalloc(m*n*sizeof(double)); +- memcpy(outmatrix,matrix,m*n*sizeof(double)); +- +- pfield2=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield2,n); +- mxSetN(pfield2,m); +- mxSetPr(pfield2,outmatrix); +- +- //transpose the outmatrix, written directly to matlab! from C to matlab. +- mexCallMATLAB(1,&pfield3, 1, &pfield2, "transpose"); +- +- mxSetCell(pfield,i,pfield3); +- } +- +- mxSetField( dataref, 0, name,pfield); +-} +-#endif +-/*}}}*/ + /*FUNCTION DoubleMatArrayParam::SetValue(double** array, int M, int* mdim_array, int* ndim_array){{{1*/ + void DoubleMatArrayParam::SetValue(double** in_array, int in_M, int* in_mdim_array, int* in_ndim_array){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h (revision 12011) +@@ -81,9 +81,6 @@ + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp (revision 12011) +@@ -189,29 +189,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION DoubleMatParam::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void DoubleMatParam::SetMatlabField(mxArray* dataref){ +- +- mxArray* pfield=NULL; +- mxArray* pfield2=NULL; +- double* doublemat=NULL; +- char* name=NULL; +- +- this->GetParameterName(&name); +- this->GetParameterValue(&doublemat,NULL,NULL); +- +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,N); +- mxSetN(pfield,M); +- mxSetPr(pfield,doublemat); +- +- //transpose the matrix, written directly to matlab! from C to matlab. +- mexCallMATLAB(1,&pfield2, 1, &pfield, "transpose"); +- mxSetField( dataref, 0, name,pfield2); +-} +-#endif +-/*}}}*/ + /*FUNCTION DoubleMatParam::SetValue{{{1*/ + void DoubleMatParam::SetValue(double* doublearray,int in_M,int in_N){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 12011) +@@ -131,40 +131,6 @@ + #endif + } + /*}}}*/ +- +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-/*FUNCTION Vector::ToMatlabVector{{{1*/ +-mxArray* Vector::ToMatlabVector(void){ +- +- mxArray* dataref=NULL; +- #ifdef _HAVE_PETSC_ +- PetscVectorToMatlabVector(&dataref,this->vector); +- #else +- dataref=this->vector->ToMatlabVector(); +- #endif +- return dataref; +- +-} +-/*}}}*/ +-/*FUNCTION MatlabVectorToVector{{{1*/ +-Vector* MatlabVectorToVector(const mxArray* mxvector){ +- +- int dummy; +- Vector* vector=NULL; +- +- /*allocate vector object: */ +- vector=new Vector(); +- +- #ifdef _HAVE_PETSC_ +- MatlabVectorToPetscVector(&vector->vector,&dummy,mxvector); +- #else +- vector->vector=MatlabVectorToSeqVec(mxvector); +- #endif +- +- return vector; +-} +-/*}}}*/ +-#endif + /*FUNCTION Vector::Assemble{{{1*/ + void Vector::Assemble(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 12011) +@@ -139,40 +139,6 @@ + #endif + } + /*}}}*/ +- +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-/*FUNCTION Matrix::ToMatlabMatrix{{{1*/ +-mxArray* Matrix::ToMatlabMatrix(void){ +- +- mxArray* dataref=NULL; +- #ifdef _HAVE_PETSC_ +- PetscMatrixToMatlabMatrix(&dataref,this->matrix); +- #else +- dataref=this->matrix->ToMatlabMatrix(); +- #endif +- return dataref; +- +-} +-/*}}}*/ +-/*FUNCTION MatlabMatrixToMatrix{{{1*/ +-Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ +- +- int dummy; +- Matrix* matrix=NULL; +- +- /*allocate matrix object: */ +- matrix=new Matrix(); +- +- #ifdef _HAVE_PETSC_ +- MatlabMatrixToPetscMatrix(&matrix->matrix,NULL,NULL,mxmatrix); +- #else +- matrix->matrix=MatlabMatrixToSeqMat(mxmatrix); +- #endif +- +- return matrix; +-} +-/*}}}*/ +-#endif + /*FUNCTION Matrix::Assemble{{{1*/ + void Matrix::Assemble(void){ + #ifdef _HAVE_PETSC_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 12011) +@@ -53,9 +53,6 @@ + /*}}}*/ + /*Vector specific routines {{{1*/ + void Echo(void); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- mxArray* ToMatlabVector(void); +- #endif + void AXPY(Vector *X, double a); + void AYPX(Vector *X, double a); + void Assemble(void); +@@ -76,9 +73,5 @@ + /*}}}*/ + }; + +-/*API: */ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-Vector* MatlabVectorToVector(const mxArray* mxvector); +-#endif + + #endif //#ifndef _VECTOR_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 12011) +@@ -50,9 +50,6 @@ + /*}}}*/ + /*Matrix specific routines {{{1*/ + void Echo(void); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- mxArray* ToMatlabMatrix(void); +- #endif + void Assemble(void); + double Norm(NormMode norm_type); + void GetSize(int* pM,int* pN); +@@ -65,9 +62,5 @@ + /*}}}*/ + + }; +-/*API: */ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); +-#endif + + #endif //#ifndef _MATRIX_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 12011) +@@ -221,39 +221,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION DoubleMatExternalResult::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void DoubleMatExternalResult::SetMatlabField(mxArray* dataref){ +- +- mxArray* pfield=NULL; +- mxArray* pfield2=NULL; +- char* name=NULL; +- double* doublemat=NULL; +- +- /*Make a copy of the value, to be used by matlab: */ +- doublemat=(double*)xmalloc(M*N*sizeof(double)); +- memcpy(doublemat,values,M*N*sizeof(double)); +- +- /*recover name: */ +- this->GetResultName(&name); +- +- /*create matlab matrix: */ +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,N); +- mxSetN(pfield,M); +- mxSetPr(pfield,doublemat); +- +- /*transpose the matrix, from c to matlab format */ +- mexCallMATLAB(1,&pfield2, 1, &pfield, "transpose"); +- +- /*set tranpose matrix inside the dataref structure: */ +- mxSetField( dataref, this->step-1, name,pfield2); +- mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); +- mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); +- +-} +-#endif +-/*}}}*/ + /*FUNCTION DoubleMatExternalResult::GetStep{{{1*/ + int DoubleMatExternalResult::GetStep(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 12011) +@@ -243,31 +243,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION PetscVecExternalResult::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void PetscVecExternalResult::SetMatlabField(mxArray* dataref){ +- +- mxArray* pfield=NULL; +- char* name=NULL; +- double* doublevec=NULL; +- int M; +- +- VecToMPISerial(&doublevec,value); +- VecGetSize(value,&M); +- this->GetResultName(&name); +- +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,M); +- mxSetN(pfield,1); +- mxSetPr(pfield,doublevec); +- +- mxSetField( dataref, this->step-1, name, pfield); +- mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); +- mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); +- +-} +-#endif +-/*}}}*/ + /*FUNCTION PetscVecExternalResult::GetStep{{{1*/ + int PetscVecExternalResult::GetStep(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.h (revision 12011) +@@ -59,9 +59,6 @@ + int InstanceEnum(){return enum_type;} + void WriteData(FILE* fid,bool io_gather); + void GetResultName(char**); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + int GetStep(void); + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 12011) +@@ -59,9 +59,6 @@ + int InstanceEnum(){return enum_type;} + void WriteData(FILE* fid,bool io_gather); + void GetResultName(char**); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + int GetStep(void); + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.h (revision 12011) +@@ -57,9 +57,6 @@ + int InstanceEnum(){return enum_type;} + void WriteData(FILE* fid,bool io_gather); + void GetResultName(char**); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + int GetStep(void); + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.h (revision 12011) +@@ -58,9 +58,6 @@ + int InstanceEnum(){return enum_type;} + void WriteData(FILE* fid,bool io_gather); + void GetResultName(char**); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + int GetStep(void); + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 12011) +@@ -60,9 +60,6 @@ + int InstanceEnum(){return enum_type;} + void WriteData(FILE* fid,bool io_gather); + void GetResultName(char**); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + int GetStep(void); + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 12011) +@@ -59,9 +59,6 @@ + int InstanceEnum(){return enum_type;} + void WriteData(FILE* fid,bool io_gather); + void GetResultName(char**); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + int GetStep(void); + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/ExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/ExternalResult.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/ExternalResult.h (revision 12011) +@@ -32,9 +32,6 @@ + virtual int InstanceEnum()=0; + virtual void WriteData(FILE* fid,bool io_gather)=0; + virtual void GetResultName(char**)=0; +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- virtual void SetMatlabField(mxArray* dataref)=0; +- #endif + virtual int GetStep(void)=0; + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 12011) +@@ -196,21 +196,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION StringExternalResult::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void StringExternalResult::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- +- this->GetResultName(&name); +- +- mxSetField( dataref, this->step-1, name, mxCreateString(value)); +- mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); +- mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); +- +-} +-#endif +-/*}}}*/ + /*FUNCTION StringExternalResult::GetStep{{{1*/ + int StringExternalResult::GetStep(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 12011) +@@ -205,34 +205,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION DoubleVecExternalResult::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void DoubleVecExternalResult::SetMatlabField(mxArray* dataref){ +- +- mxArray *pfield = NULL; +- double *doublemat = NULL; +- char *name = NULL; +- double *doublevec = NULL; +- +- /*Make a copy of the value, to be used by matlab: */ +- doublevec=(double*)xmalloc(M*sizeof(double)); +- memcpy(doublevec,values,M*sizeof(double)); +- +- /*recover name: */ +- this->GetResultName(&name); +- +- /*create matlab matrix: */ +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,M); +- mxSetN(pfield,1); +- mxSetPr(pfield,doublevec); +- +- mxSetField( dataref, this->step-1, name,pfield); +- mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); +- mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); +-} +-#endif +-/*}}}*/ + /*FUNCTION DoubleVecExternalResult::GetStep{{{1*/ + int DoubleVecExternalResult::GetStep(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 12011) +@@ -180,19 +180,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION DoubleExternalResult::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void DoubleExternalResult::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- this->GetResultName(&name); +- mxSetField( dataref,this->step-1, name,mxCreateDoubleScalar(value)); +- mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); +- mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); +- +-} +-#endif +-/*}}}*/ + /*FUNCTION DoubleExternalResult::GetStep{{{1*/ + int DoubleExternalResult::GetStep(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 12011) +@@ -184,20 +184,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION IntExternalResult::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void IntExternalResult::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- this->GetResultName(&name); +- +- mxSetField( dataref, this->step-1, name,mxCreateDoubleScalar(value)); +- mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); +- mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); +- +-} +-#endif +-/*}}}*/ + /*FUNCTION IntExternalResult::GetStep{{{1*/ + int IntExternalResult::GetStep(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 12011) +@@ -184,19 +184,6 @@ + EnumToStringx(pname,this->enum_type); + } + /*}}}*/ +-/*FUNCTION BoolExternalResult::SetMatlabField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void BoolExternalResult::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- this->GetResultName(&name); +- +- mxSetField( dataref, this->step-1, name,mxCreateDoubleScalar((double)value)); +- mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); +- mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); +-} +-#endif +-/*}}}*/ + /*FUNCTION BoolExternalResult::GetStep{{{1*/ + int BoolExternalResult::GetStep(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.h (revision 12011) +@@ -59,9 +59,6 @@ + int InstanceEnum(){return enum_type;} + void WriteData(FILE* fid,bool io_gather); + void GetResultName(char**); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabField(mxArray* dataref); +- #endif + int GetStep(void); + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/OptArgs.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/OptArgs.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/OptArgs.h (revision 12011) +@@ -5,20 +5,9 @@ + #ifndef _OPTARGS_H_ + #define _OPTARGS_H_ + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- +-#include "mex.h" +-struct OptArgs{ +- char* function_name; +- mxArray* femmodel; +-}; +- +-#else +- + class Model; + struct OptArgs{ + FemModel* femmodel; + }; +-#endif + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgOpts.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgOpts.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgOpts.cpp (revision 12011) +@@ -40,46 +40,6 @@ + + } + /*}}}*/ +-/*FUNCTION BamgOpts::BamgOpts(mxArray* matlab_struct){{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-BamgOpts::BamgOpts(mxArray* matlab_struct){ +- +- FetchData(&this->anisomax,mxGetField(matlab_struct,0,"anisomax")); +- FetchData(&this->cutoff,mxGetField(matlab_struct,0,"cutoff")); +- FetchData(&this->coeff,mxGetField(matlab_struct,0,"coeff")); +- FetchData(&this->errg,mxGetField(matlab_struct,0,"errg")); +- FetchData(&this->gradation,mxGetField(matlab_struct,0,"gradation")); +- FetchData(&this->Hessiantype,mxGetField(matlab_struct,0,"Hessiantype")); +- FetchData(&this->MaxCornerAngle,mxGetField(matlab_struct,0,"MaxCornerAngle")); +- FetchData(&this->maxnbv,mxGetField(matlab_struct,0,"maxnbv")); +- FetchData(&this->maxsubdiv,mxGetField(matlab_struct,0,"maxsubdiv")); +- FetchData(&this->Metrictype,mxGetField(matlab_struct,0,"Metrictype")); +- FetchData(&this->nbjacobi,mxGetField(matlab_struct,0,"nbjacobi")); +- FetchData(&this->nbsmooth,mxGetField(matlab_struct,0,"nbsmooth")); +- FetchData(&this->omega,mxGetField(matlab_struct,0,"omega")); +- FetchData(&this->power,mxGetField(matlab_struct,0,"power")); +- FetchData(&this->verbose,mxGetField(matlab_struct,0,"verbose")); +- +- FetchData(&this->Crack,mxGetField(matlab_struct,0,"Crack")); +- FetchData(&this->geometricalmetric,mxGetField(matlab_struct,0,"geometricalmetric")); +- FetchData(&this->KeepVertices,mxGetField(matlab_struct,0,"KeepVertices")); +- FetchData(&this->splitcorners,mxGetField(matlab_struct,0,"splitcorners")); +- +- FetchData(&this->hmin,mxGetField(matlab_struct,0,"hmin")); +- FetchData(&this->hmax,mxGetField(matlab_struct,0,"hmax")); +- FetchData(&this->hminVertices,&this->hminVerticesSize[0],&this->hminVerticesSize[1],mxGetField(matlab_struct,0,"hminVertices")); +- FetchData(&this->hmaxVertices,&this->hmaxVerticesSize[0],&this->hmaxVerticesSize[1],mxGetField(matlab_struct,0,"hmaxVertices")); +- FetchData(&this->hVertices,&this->hVerticesSize[0],&this->hVerticesSize[1],mxGetField(matlab_struct,0,"hVertices")); +- FetchData(&this->metric,&this->metricSize[0],&this->metricSize[1],mxGetField(matlab_struct,0,"metric")); +- FetchData(&this->field,&this->fieldSize[0],&this->fieldSize[1],mxGetField(matlab_struct,0,"field")); +- FetchData(&this->err,&this->errSize[0],&this->errSize[1],mxGetField(matlab_struct,0,"err")); +- +- /*Additional checks*/ +- this->Check(); +- +-} +-#endif +-/*}}}*/ + /*FUNCTION BamgOpts::~BamgOpts() {{{1*/ + BamgOpts::~BamgOpts(){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.cpp (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.cpp (revision 12011) +@@ -18,22 +18,6 @@ + + } + /*}}}*/ +-/*FUNCTION BamgGeom::BamgGeom(mxArray* matlab_struct){{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-BamgGeom::BamgGeom(mxArray* matlab_struct){ +- +- FetchData(&this->Vertices, &this->VerticesSize[0], &this->VerticesSize[1], mxGetAssignedField(matlab_struct,0,"Vertices")); +- FetchData(&this->Edges, &this->EdgesSize[0], &this->EdgesSize[1], mxGetAssignedField(matlab_struct,0,"Edges")); +- this->TangentAtEdgesSize[0]=0, this->TangentAtEdgesSize[1]=0; this->TangentAtEdges=NULL; +- FetchData(&this->Corners, &this->CornersSize[0], &this->CornersSize[1], mxGetAssignedField(matlab_struct,0,"Corners")); +- FetchData(&this->RequiredVertices,&this->RequiredVerticesSize[0],&this->RequiredVerticesSize[1],mxGetAssignedField(matlab_struct,0,"RequiredVertices")); +- FetchData(&this->RequiredEdges, &this->RequiredEdgesSize[0], &this->RequiredEdgesSize[1], mxGetAssignedField(matlab_struct,0,"RequiredEdges")); +- FetchData(&this->CrackedEdges, &this->CrackedEdgesSize[0], &this->CrackedEdgesSize[1], mxGetAssignedField(matlab_struct,0,"CrackedEdges")); +- FetchData(&this->SubDomains, &this->SubDomainsSize[0], &this->SubDomainsSize[1], mxGetAssignedField(matlab_struct,0,"SubDomains")); +- +-} +-#endif +-/*}}}*/ + /*FUNCTION BamgGeom::~BamgGeom(){{{1*/ + BamgGeom::~BamgGeom(){ + +@@ -48,78 +32,3 @@ + + } + /*}}}*/ +- +-/*Methods*/ +-/*FUNCTION BamgGeom::SetMatlabStructureFields{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void BamgGeom::SetMatlabStructureFields(mxArray** matlab_struct){ +- +- /*Intermediary*/ +- int i; +- mxArray* output=NULL; +- const int numfields=7; +- const char* fnames[numfields]; +- mwSize ndim=2; +- mwSize dimensions[2]={1,1}; +- +- /*Initialize field names*/ +- i=0; +- fnames[i++] = "Vertices"; +- fnames[i++] = "Edges"; +- fnames[i++] = "TangentAtEdges"; +- fnames[i++] = "RequiredVertices"; +- fnames[i++] = "RequiredEdges"; +- fnames[i++] = "CrackedEdges"; +- fnames[i++] = "SubDomains"; +- _assert_(i==numfields); +- +- /*Initialize Matlab structure*/ +- output=mxCreateStructArray(ndim,dimensions,numfields,fnames); +- +- /*set each matlab each field*/ +- i=0; +- i++; SetMatlabStructureField(output,"Vertices", this->VerticesSize[0], this->VerticesSize[1], this->Vertices); +- i++; SetMatlabStructureField(output,"Edges", this->EdgesSize[0], this->EdgesSize[1], this->Edges); +- i++; SetMatlabStructureField(output,"TangentAtEdges", this->TangentAtEdgesSize[0], this->TangentAtEdgesSize[1], this->TangentAtEdges); +- i++; SetMatlabStructureField(output,"RequiredVertices",this->RequiredVerticesSize[0],this->RequiredVerticesSize[1],this->RequiredVertices); +- i++; SetMatlabStructureField(output,"RequiredEdges", this->RequiredEdgesSize[0], this->RequiredEdgesSize[1], this->RequiredEdges); +- i++; SetMatlabStructureField(output,"CrackedEdges", this->CrackedEdgesSize[0], this->CrackedEdgesSize[1], this->CrackedEdges); +- i++; SetMatlabStructureField(output,"SubDomains", this->SubDomainsSize[0], this->SubDomainsSize[1], this->SubDomains); +- _assert_(i==numfields); +- +- /*Assign output*/ +- *matlab_struct=output; +- +-} +-#endif +-/*}}}*/ +-/*FUNCTION BamgGeom::SetMatlabStructureField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void BamgGeom::SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ +- +- /*Intermediary*/ +- int i1,i2; +- mxArray* pfield=NULL; +- mxArray* pfield2=NULL; +- +- /*Copy field*/ +- double* fieldcopy=NULL; +- if (fieldrows*fieldcols){ +- fieldcopy=(double*)xmalloc(fieldrows*fieldcols*sizeof(double)); +- for(i1=0;i1Vertices, &this->VerticesSize[0], &this->VerticesSize[1], mxGetAssignedField(matlab_struct,0,"Vertices")); +- FetchData(&this->Edges, &this->EdgesSize[0], &this->EdgesSize[1], mxGetAssignedField(matlab_struct,0,"Edges")); +- FetchData(&this->Triangles, &this->TrianglesSize[0], &this->TrianglesSize[1], mxGetAssignedField(matlab_struct,0,"Triangles")); +- this->QuadrilateralsSize[0]=0, this->QuadrilateralsSize[1]=0; this->Quadrilaterals=NULL; +- +- this->SubDomainsSize[0]=0, this->SubDomainsSize[1]=0; this->SubDomains=NULL; +- this->SubDomainsFromGeomSize[0]=0, this->SubDomainsFromGeomSize[1]=0; this->SubDomainsFromGeom=NULL; +- this->CrackedVerticesSize[0]=0, this->CrackedVerticesSize[1]=0; this->CrackedVertices=NULL; +- FetchData(&this->CrackedEdges, &this->CrackedEdgesSize[0], &this->CrackedEdgesSize[1], mxGetAssignedField(matlab_struct,0,"CrackedEdges")); +- +- FetchData(&this->VerticesOnGeomEdge, &this->VerticesOnGeomEdgeSize[0], &this->VerticesOnGeomEdgeSize[1], mxGetAssignedField(matlab_struct,0,"VerticesOnGeomEdge")); +- FetchData(&this->VerticesOnGeomVertex,&this->VerticesOnGeomVertexSize[0],&this->VerticesOnGeomVertexSize[1],mxGetAssignedField(matlab_struct,0,"VerticesOnGeomVertex")); +- FetchData(&this->EdgesOnGeomEdge, &this->EdgesOnGeomEdgeSize[0], &this->EdgesOnGeomEdgeSize[1], mxGetAssignedField(matlab_struct,0,"EdgesOnGeomEdge")); +- +- this->IssmEdgesSize[0]=0, this->IssmEdgesSize[1]=0; this->IssmEdges=NULL; +- FetchData(&this->IssmSegments, &this->IssmSegmentsSize[0], &this->IssmSegmentsSize[1], mxGetAssignedField(matlab_struct,0,"IssmSegments")); +- +- this->ElementConnectivitySize[0]=0, this->ElementConnectivitySize[1]=0; this->ElementConnectivity=NULL; +- this->NodalConnectivitySize[0]=0, this->NodalConnectivitySize[1]=0; this->NodalConnectivity=NULL; +- this->NodalElementConnectivitySize[0]=0, this->NodalElementConnectivitySize[1]=0; this->NodalElementConnectivity=NULL; +- +-} +-#endif +-/*}}}*/ + /*FUNCTION BamgMesh::~BamgMesh(){{{1*/ + BamgMesh::~BamgMesh(){ + +@@ -88,96 +58,3 @@ + + } + /*}}}*/ +- +-/*Methods*/ +-/*FUNCTION BamgMesh::SetMatlabStructureFields{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void BamgMesh::SetMatlabStructureFields(mxArray** matlab_struct){ +- +- /*Intermediary*/ +- int i; +- mxArray* output=NULL; +- const int numfields=16; +- const char* fnames[numfields]; +- mwSize ndim=2; +- mwSize dimensions[2]={1,1}; +- +- /*Initialize field names*/ +- i=0; +- fnames[i++] = "Triangles"; +- fnames[i++] = "Vertices"; +- fnames[i++] = "Edges"; +- fnames[i++] = "IssmSegments"; +- fnames[i++] = "IssmEdges"; +- fnames[i++] = "Quadrilaterals"; +- fnames[i++] = "VerticesOnGeomVertex"; +- fnames[i++] = "VerticesOnGeomEdge"; +- fnames[i++] = "EdgesOnGeomEdge"; +- fnames[i++] = "SubDomains"; +- fnames[i++] = "SubDomainsFromGeom"; +- fnames[i++] = "ElementConnectivity"; +- fnames[i++] = "NodalConnectivity"; +- fnames[i++] = "NodalElementConnectivity"; +- fnames[i++] = "CrackedVertices"; +- fnames[i++] = "CrackedEdges"; +- _assert_(i==numfields); +- +- /*Initialize Matlab structure*/ +- output=mxCreateStructArray(ndim,dimensions,numfields,fnames); +- +- /*set each matlab each field*/ +- i=0; +- i++; SetMatlabStructureField(output,"Triangles", this->TrianglesSize[0], this->TrianglesSize[1], this->Triangles); +- i++; SetMatlabStructureField(output,"Vertices", this->VerticesSize[0], this->VerticesSize[1], this->Vertices); +- i++; SetMatlabStructureField(output,"Edges", this->EdgesSize[0], this->EdgesSize[1], this->Edges); +- i++; SetMatlabStructureField(output,"IssmSegments", this->IssmSegmentsSize[0], this->IssmSegmentsSize[1], this->IssmSegments); +- i++; SetMatlabStructureField(output,"IssmEdges", this->IssmEdgesSize[0], this->IssmEdgesSize[1], this->IssmEdges); +- i++; SetMatlabStructureField(output,"Quadrilaterals", this->QuadrilateralsSize[0], this->QuadrilateralsSize[1], this->Quadrilaterals); +- i++; SetMatlabStructureField(output,"VerticesOnGeomVertex",this->VerticesOnGeomVertexSize[0],this->VerticesOnGeomVertexSize[1], this->VerticesOnGeomVertex); +- i++; SetMatlabStructureField(output,"VerticesOnGeomEdge", this->VerticesOnGeomEdgeSize[0], this->VerticesOnGeomEdgeSize[1], this->VerticesOnGeomEdge); +- i++; SetMatlabStructureField(output,"EdgesOnGeomEdge", this->EdgesOnGeomEdgeSize[0], this->EdgesOnGeomEdgeSize[1], this->EdgesOnGeomEdge); +- i++; SetMatlabStructureField(output,"SubDomains", this->SubDomainsSize[0], this->SubDomainsSize[1], this->SubDomains); +- i++; SetMatlabStructureField(output,"SubDomainsFromGeom", this->SubDomainsFromGeomSize[0], this->SubDomainsFromGeomSize[1], this->SubDomainsFromGeom); +- i++; SetMatlabStructureField(output,"ElementConnectivity", this->ElementConnectivitySize[0], this->ElementConnectivitySize[1], this->ElementConnectivity); +- i++; SetMatlabStructureField(output,"NodalConnectivity", this->NodalConnectivitySize[0], this->NodalConnectivitySize[1], this->NodalConnectivity); +- i++; SetMatlabStructureField(output,"NodalElementConnectivity", this->NodalElementConnectivitySize[0], this->NodalElementConnectivitySize[1], this->NodalElementConnectivity); +- i++; SetMatlabStructureField(output,"CrackedVertices", this->CrackedVerticesSize[0], this->CrackedVerticesSize[1], this->CrackedVertices); +- i++; SetMatlabStructureField(output,"CrackedEdges", this->CrackedEdgesSize[0], this->CrackedEdgesSize[1], this->CrackedEdges); +- _assert_(i==numfields); +- +- /*Assign output*/ +- *matlab_struct=output; +- +-} +-#endif +-/*}}}*/ +-/*FUNCTION BamgMesh::SetMatlabStructureField{{{1*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-void BamgMesh::SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ +- +- /*Intermediary*/ +- int i1,i2; +- mxArray* pfield=NULL; +- mxArray* pfield2=NULL; +- +- /*Copy field*/ +- double* fieldcopy=NULL; +- if (fieldrows*fieldcols){ +- fieldcopy=(double*)xmalloc(fieldrows*fieldcols*sizeof(double)); +- for(i1=0;i1 +-#endif +- + class BamgOpts{ + + public: +@@ -53,9 +49,7 @@ + double* err; + + BamgOpts(); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- BamgOpts(mxArray* matlab_struct); +- #endif ++ BamgOpts(void* module_struct); + ~BamgOpts(); + + void Check(void); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.h (revision 12011) +@@ -4,10 +4,6 @@ + #ifndef _BAMGGEOM_H_ + #define _BAMGGEOM_H_ + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + class BamgGeom{ + + public: +@@ -29,15 +25,11 @@ + double* SubDomains; + + BamgGeom(); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- BamgGeom(mxArray* matlab_struct); +- #endif ++ BamgGeom(void* module_struct); + ~BamgGeom(); + +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabStructureFields(mxArray** matlab_struct); +- void SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); +- #endif ++ void SetStructureFields(void* matlab_struct); ++ void SetStructureField(void* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); + }; + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgMesh.h (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgMesh.h (revision 12011) +@@ -4,10 +4,6 @@ + #ifndef _BAMGMESH_H_ + #define _BAMGMESH_H_ + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + class BamgMesh{ + + public: +@@ -50,15 +46,11 @@ + double* NodalElementConnectivity; + + BamgMesh(); +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- BamgMesh(mxArray* matlab_struct); +- #endif ++ BamgMesh(void* module_struct); + ~BamgMesh(); + +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- void SetMatlabStructureFields(mxArray** matlab_struct); +- void SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); +- #endif ++ void SetStructureFields(void* module_struct); ++ void SetStructureField(void* module_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); + + }; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12010) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12011) +@@ -78,7 +78,6 @@ + from hydrology import * + from miscellaneous import * + from private import * +-from TriMesh import * + + #}}} + Index: /issm/oecreview/Archive/12010-12040/ISSM-12011-12012.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12011-12012.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12011-12012.diff (revision 12325) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp (revision 12011) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp (revision 12012) +@@ -1,4 +1,3 @@ +-#include "../../io/Matlab/matlabio.h" + #include "../Alloc/alloc.h" + #include "../../include/include.h" + #include "../Exceptions/exceptions.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.cpp (revision 12011) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc_module.cpp (revision 12012) +@@ -11,7 +11,7 @@ + #include + #include + +-#include "./allocmodule.h" ++#include "./alloc_module.h" + #include "../Exceptions/exceptions.h" + #include "../../include/include.h" + #include "../../objects/objects.h" Index: /issm/oecreview/Archive/12010-12040/ISSM-12012-12013.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12012-12013.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12012-12013.diff (revision 12325) @@ -0,0 +1,1370 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12013) +@@ -22,6 +22,7 @@ + AC_MSG_RESULT($MODULES_VALUE) + dnl }}} + dnl Extensions{{{ ++ ISSMEXT=".exe" + AC_SUBST([ISSMEXT]) + dnl }}} + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/Container/Options.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/Container/Options.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/Container/Options.cpp (revision 12013) +@@ -12,16 +12,15 @@ + + #include + #include ++#include + +-#include "./DataSet.h" +-#include "../shared/shared.h" +-#include "../io/io.h" +-#include "../include/include.h" +-#include "../shared/shared.h" +-#include "../EnumDefinitions/EnumDefinitions.h" +-#if _SERIAL_ +-#include "../io/io.h" +-#endif ++#include "../../Container/DataSet.h" ++#include "../../shared/shared.h" ++#include "../../io/io.h" ++#include "../io/matlabio.h" ++#include "../../include/include.h" ++#include "../../shared/shared.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" + /*}}}*/ + + /*Object constructors and destructor*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12013) +@@ -6,8 +6,6 @@ + #ifndef _MATLAB_MACROS_H_ + #define _MATLAB_MACROS_H_ + +-#include "./typedefs.h" +- + #ifdef HAVE_CONFIG_H + #include + #else +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp (revision 12013) +@@ -1,3 +1,23 @@ ++/*!\file MatlabMatrixToSeqMat.cpp ++ */ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include ++#include "../../toolkits/toolkits.h" ++#include "../../shared/shared.h" ++#include "./matlabio.h" ++ ++/*}}}*/ ++ + SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ + + SeqMat* output=NULL; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp (revision 12013) +@@ -12,7 +12,6 @@ + #include "../../include/include.h" + #include "./matlabio.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) + #include + + /*FUNCTION OptionDoubleParse {{{1*/ +@@ -190,5 +189,3 @@ + + return(option); + }/*}}}*/ +- +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 12013) +@@ -9,8 +9,6 @@ + #endif + + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- + #include "../../shared/Exceptions/exceptions.h" + #include "../../include/include.h" + #include "mex.h" +@@ -31,5 +29,3 @@ + } + return 1; + } +- +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12013) +@@ -8,45 +8,11 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + ++#include + #include "../../shared/shared.h" + #include "../../include/include.h" ++#include "./matlabio.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-/*FUNCTION FetchData(DataSet** pdataset,const mxArray* dataref){{{1*/ +-void FetchData(DataSet** pdataset,const mxArray* dataref){ +- +- /*output*/ +- DataSet* outdataset=NULL; +- char* outdataset_buffer=NULL; +- int outdataset_size; +- +- /*First, check that our reference is a double, otherwise, error out: */ +- if (mxIsClass(dataref,"double")){ +- +- /*We need to copy the data pointed by dataref, so that our dataset is not actually a pointer!:*/ +- if (!mxIsEmpty(dataref)){ +- outdataset_buffer=(char*)mxGetPr(dataref); +- outdataset_size=mxGetM(dataref)*mxGetN(dataref); +- if(outdataset_size)outdataset=DataSetDemarshall(outdataset_buffer); +- } +- } +- else{ +- if (mxIsEmpty(dataref)){ +- /*Nothing to pick up. Just initialize pointer to NULL, and warn the server we are not uploading anything: */ +- outdataset_size=0; +- outdataset=NULL; +- } +- else{ +- /*This is an error: we don't have the correct input!: */ +- _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); +- } +- } +- +- /*Assign output pointers:*/ +- *pdataset=outdataset; +-} +-/*}}}*/ + /*FUNCTION FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/ + void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){ + +@@ -559,186 +525,3 @@ + *pboolean=*mxbool_ptr; + } + /*}}}*/ +-/*FUNCTION FetchData(Parameters** pparameters, DataHandle dataref){{{1*/ +-void FetchData(Parameters** pparameters, DataHandle dataref){ +- +- int i,j; +- int count; +- +- /*output: */ +- Param* param=NULL; +- Parameters* parameters=NULL; +- +- /*intermediary: */ +- int M,N; +- double* tmatrix=NULL; +- double* matrix=NULL; +- char** stringarray=NULL; +- double** array=NULL; +- int* mdims_array=NULL; +- int* ndims_array=NULL; +- int nfields; +- char* name=NULL; +- mxArray* pfield=NULL; +- mxArray* pfield2=NULL; +- int enum_type; +- +- +- /*First, create parameters : */ +- parameters=new Parameters(); +- +- /*go through matlab params structure, and create Param object for each field: */ +- +- nfields=mxGetNumberOfFields(dataref); +- +- for(count=0;countAddObject(param); +- +- } +- else{ +- if (N==1){ +- +- /*vector: */ +- param= new DoubleVecParam(enum_type,mxGetPr(pfield),M); +- parameters->AddObject(param); +- +- } +- else{ +- /*matrix: first, transpose, then plug into Param */ +- matrix=mxGetPr(pfield); +- tmatrix=(double*)xmalloc(M*N*sizeof(double)); +- for (i=0;iAddObject(param); +- +- /*Free ressources:*/ +- xfree((void**)&tmatrix); +- } +- } +- +- } +- else if (mxIsClass(pfield,"logical")){ +- +- M=mxGetM(pfield); +- N=mxGetN(pfield); +- +- if (M==0 | N==0){ +- _error_("array in parameters structure field %s is of size 0",name); +- } +- if (M==1 && N==1){ +- /*we have a simple bool: */ +- param= new BoolParam(enum_type,*mxGetLogicals(pfield)); +- parameters->AddObject(param); +- +- } +- else{ +- _error_("Matrices of Booleans not supported yet in parameters"); +- } +- } +- else if (mxIsClass(pfield,"char")){ +- /* we have a string parameter:*/ +- +- int stringlen; +- char* string=NULL; +- +- stringlen = mxGetM(pfield)*mxGetN(pfield)+1; +- string = (char*)xmalloc(sizeof(mxChar)*stringlen); +- mxGetString(pfield,string,stringlen); +- +- param= new StringParam(enum_type,string); +- parameters->AddObject(param); +- +- xfree((void**)&string); +- } +- else if (mxIsClass(pfield,"cell")){ +- +- /*This can be a string array, or a matrix array. Check the first +- *element type to decide: */ +- pfield2=mxGetCell(pfield,0); +- if (mxIsClass(pfield2,"char")){ +- +- /*string array: */ +- M=mxGetM(pfield); +- stringarray=(char**)xmalloc(M*sizeof(char*)); +- +- for(i=0;iAddObject(param); +- +- /*Free ressources:*/ +- for(i=0;iAddObject(param); +- +- /*Free ressources:*/ +- for(i=0;i + +-/*FUNCTION WriteData(mxArray** pdataref,DataSet* dataset){{{1*/ +-void WriteData(mxArray** pdataref,DataSet* dataset){ +- +- mxArray* dataref=NULL; +- char* marshalled_dataset=NULL; +- int marshalled_dataset_size; +- +- /*Write a dataset: */ +- if(dataset){ +- /* marshall the dataset: */ +- marshalled_dataset=dataset->Marshall(); +- marshalled_dataset_size=dataset->MarshallSize(); +- +- dataref = mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(dataref,(mwSize)(marshalled_dataset_size/sizeof(double))); +- mxSetN(dataref,(mwSize)1); +- mxSetPr(dataref,(double*)marshalled_dataset); +- } +- else{ +- /* return empty matrix: */ +- dataref=mxCreateDoubleMatrix(0,0,mxREAL); +- } +- *pdataref=dataref; +- +-} +-/*}}}*/ + /*FUNCTION WriteData(mxArray** pdataref,Matrix* matrix){{{1*/ + void WriteData(mxArray** pdataref,Matrix* matrix){ + ++ int i,j; + mxArray* dataref=NULL; + double* matrix_ptr=NULL; + int rows,cols; +@@ -51,7 +26,7 @@ + if(matrix){ + + #ifdef _HAVE_PETSC_ +- PetscMatrixToDoubleMatrix(&tmatrix_ptr,&rows,&cols); ++ PetscMatrixToDoubleMatrix(&tmatrix_ptr,&rows,&cols,matrix->matrix); + #else + matrix_ptr=matrix->matrix->ToSerial(); + matrix->matrix->GetSize(&rows,cols); +@@ -207,43 +182,3 @@ + *pdataref=mxCreateString(string); + } + /*}}}*/ +-/*FUNCTION WriteData(mxArray** pdataref,Parameters* parameters){{{1*/ +-void WriteData(mxArray** pdataref,Parameters* parameters){ +- +- int i; +- +- /*output: */ +- mxArray *dataref = NULL; +- mwSize nfields; +- char **fnames = NULL; +- mwSize onebyone[2] = {1,1}; +- mwSize ndim = 2; +- +- /*intermediary: */ +- Param* param=NULL; +- +- /*Recover data from the parameters dataset: */ +- nfields=(mwSize)parameters->Size(); +- fnames=(char**)mxMalloc(nfields*sizeof(char*)); +- +- /*Build structure in matlab workspace with all the parameter fields: */ +- for(i=0;iGetObjectByOffset(i); +- param->GetParameterName(&fnames[i]); +- } +- /*Initialize structure: */ +- dataref=mxCreateStructArray( ndim,onebyone,nfields,(const char**)fnames); +- +- /*Fill each field: */ +- for(i=0;iGetObjectByOffset(i); +- param->SetMatlabField(dataref); +- } +- +- /*Assign output pointers:*/ +- *pdataref=dataref; +- +-} +-/*}}}*/ +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp (revision 12013) +@@ -13,7 +13,6 @@ + #error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) + #include "mex.h" + + mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number,const char* field){ +@@ -44,4 +43,3 @@ + + return mxfield; + } +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToPetscVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToPetscVector.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToPetscVector.cpp (revision 12013) +@@ -9,9 +9,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +- +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- + /*Petsc includes: */ + #include "petscmat.h" + #include "petscvec.h" +@@ -20,7 +17,7 @@ + /*Matlab includes: */ + #include "mex.h" + +-#include "../../../shared/shared.h" ++#include "../../shared/shared.h" + + int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector){ + +@@ -99,4 +96,3 @@ + + return 1; + } +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PrintfFunction.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PrintfFunction.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PrintfFunction.cpp (revision 12013) +@@ -8,9 +8,7 @@ + #include "../../shared/shared.h" + #include "../../include/include.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) + #include "mex.h" +-#endif + + int PrintfFunction(char* format,...){ + /*http://linux.die.net/man/3/vsnprintf*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp (revision 12013) +@@ -1,4 +1,26 @@ ++/*!\file MatlabVectorToVector.cpp ++ */ + ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include ++#include "./matlabio.h" ++#include "../../objects/objects.h" ++#include "../../shared/shared.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++#include "../../toolkits/toolkits.h" ++ ++/*}}}*/ ++ + Vector* MatlabVectorToVector(const mxArray* mxvector){ + + int dummy; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp (revision 12013) +@@ -10,8 +10,6 @@ + #endif + + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- + /*Petsc includes: */ + #include "petscmat.h" + #include "petscvec.h" +@@ -20,7 +18,7 @@ + /*Matlab includes: */ + #include "mex.h" + +-#include "../../../shared/shared.h" ++#include "../../shared/shared.h" + + int MatlabMatrixToPetscMatrix(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ + +@@ -120,4 +118,3 @@ + + return 1; + } +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToMatrix.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabMatrixToMatrix.cpp (revision 12013) +@@ -1,3 +1,26 @@ ++/*!\file MatlabMatrixToMatrix.cpp ++ */ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include ++#include "./matlabio.h" ++#include "../../objects/objects.h" ++#include "../../shared/shared.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++#include "../../toolkits/toolkits.h" ++ ++/*}}}*/ ++ + Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ + + int dummy; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp (revision 12013) +@@ -17,7 +17,7 @@ + /*Petsc includes: */ + #include "mex.h" + +-#include "../../../shared/shared.h" ++#include "../../shared/shared.h" + #include + + +@@ -33,13 +33,13 @@ + + /*Get size of vector: */ + if(vector){ +- VecGetSize(vector,&rows); ++ VecGetSize(petsc_vector,&rows); + if(rows){ + idxm=(int*)xmalloc(rows*sizeof(int)); + vector=(double*)xmalloc(rows*sizeof(double)); + for(i=0;i + + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToSeqVec.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToSeqVec.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabVectorToSeqVec.cpp (revision 12013) +@@ -1,3 +1,23 @@ ++/*!\file MatlabVectorToSeqVec.cpp ++ */ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include ++#include "../../toolkits/toolkits.h" ++#include "../../shared/shared.h" ++#include "./matlabio.h" ++ ++/*}}}*/ ++ + SeqVec* MatlabVectorToSeqVec(const mxArray* dataref){ + + SeqVec* output=NULL; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 12013) +@@ -12,7 +12,6 @@ + #include "../../shared/shared.h" + #include "../../include/include.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) + #include + + /*FUNCTION MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{1*/ +@@ -271,4 +270,3 @@ + return 1; + } + /*}}}*/ +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h (revision 12013) +@@ -15,12 +15,8 @@ + #include "../../Container/Container.h" + #include "../../include/include.h" + +-class DataSet; +-class Parameters; +- + #include + +-void WriteData(mxArray** pdataref,DataSet* dataset); + void WriteData(mxArray** pdataref,Matrix* matrix); + void WriteData(mxArray** pdataref,double* matrix, int M,int N); + void WriteData(mxArray** pdataref,int* matrix, int M,int N); +@@ -30,9 +26,7 @@ + void WriteData(mxArray** pdataref,bool boolean); + void WriteData(mxArray** pdataref,double scalar); + void WriteData(mxArray** pdataref,char* string); +-void WriteData(DataHandle* pdataref,Parameters* parameters); + +-void FetchData(DataSet** pdataset,const mxArray* dataref); + void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref); + void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); + void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref); +@@ -49,7 +43,6 @@ + void FetchData(double* pscalar,const mxArray* dataref); + void FetchData(int* pinteger,const mxArray* dataref); + void FetchData(bool* pbool,const mxArray* dataref); +-void FetchData(Parameters** pparameters, DataHandle dataref); + + Option* OptionParse(char* name, const mxArray* prhs[]); + OptionDouble* OptionDoubleParse( char* name, const mxArray* prhs[]); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgGeom.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgGeom.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgGeom.cpp (revision 12013) +@@ -1,7 +1,12 @@ ++/*!\file BamgGeom.cpp ++ */ ++ + #include +-#include "../objects.h" +-#include "../../io/io.h" +-#include "../../shared/shared.h" ++#include "../../../objects/objects.h" ++#include "../../../io/io.h" ++#include "../../../shared/shared.h" ++#include "../../io/matlabio.h" ++#include + + /*Constructors/Destructors*/ + /*FUNCTION BamgGeom::BamgGeom(void* module_struct){{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgMesh.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgMesh.cpp (revision 12013) +@@ -1,7 +1,11 @@ ++/*!\file BamgMesh.cpp ++ */ ++ + #include +-#include "../objects.h" +-#include "../../io/io.h" +-#include "../../shared/shared.h" ++#include "../../../objects/objects.h" ++#include "../../../io/io.h" ++#include "../../../shared/shared.h" ++#include "../../io/matlabio.h" + + /*Constructors/Destructors*/ + /*FUNCTION BamgMesh::BamgMesh(void* module_struct){{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgOpts.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgOpts.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/objects/Bamg/BamgOpts.cpp (revision 12013) +@@ -1,8 +1,12 @@ ++/*!\file BamgOpts.cpp ++ */ ++ + #include +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../objects.h" +-#include "../../io/io.h" ++#include "../../../objects/objects.h" ++#include "../../../io/io.h" ++#include "../../../shared/shared.h" ++#include "../../io/matlabio.h" ++#include "../../../include/include.h" + + /*Constructors/Destructors*/ + /*FUNCTION BamgOpts::BamgOpts(void* module_struct){{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/matlab-binding.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/matlab-binding.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/matlab-binding.h (revision 12013) +@@ -0,0 +1,6 @@ ++#ifndef _MATLAB_BINDING_H_ ++#define _MATLAB_BINDING_H_ ++ ++#include "./io/matlabio.h" ++#include "./include/matlab_macros.h" ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Wrapper/wrappershared.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Wrapper/wrappershared.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Wrapper/wrappershared.h (revision 12013) +@@ -7,9 +7,7 @@ + + #include "../../objects/objects.h" + +-#ifdef _SERIAL_ + int ModuleBoot(void); + int ModuleEnd(void); +-#endif + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h (revision 12013) +@@ -110,9 +110,7 @@ + #include "./CreateJacobianMatrixx/CreateJacobianMatrixx.h" + #include "./TimeAdaptx/TimeAdaptx.h" + #include "./TriaSearchx/TriaSearchx.h" +-#ifdef _SERIAL_ + #include "./TriMeshx/TriMeshx.h" +-#endif + #include "./ThicknessAbsMisfitx/ThicknessAbsMisfitx.h" + #include "./ThicknessAbsGradientx/ThicknessAbsGradientx.h" + #include "./UpdateVertexPositionsx/UpdateVertexPositionsx.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12013) +@@ -14,7 +14,9 @@ + + #sources + #Core sources{{{1 +-core_sources = ./include/macros.h\ ++core_sources = ./issm.h\ ++ ./issm-binding.h\ ++ ./include/macros.h\ + ./include/typedefs.h\ + ./include/types.h\ + ./include/include.h\ +@@ -748,7 +750,7 @@ + ./matlab/io/MatlabVectorToVector.cpp\ + ./matlab/io/MatlabVectorToDoubleVector.cpp\ + ./matlab/io/MatlabMatrixToDoubleMatrix.cpp\ +- ./matlab/io/Container/Options.cpp\ ++ ./matlab/Container/Options.cpp\ + ./matlab/objects/Bamg/BamgGeom.h\ + ./matlab/objects/Bamg/BamgGeom.cpp\ + ./matlab/objects/Bamg/BamgMesh.h\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/issm-binding.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/issm-binding.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/issm-binding.h (revision 12013) +@@ -0,0 +1,18 @@ ++#ifndef _ISSM_BINDING_H_ ++#define _ISSM_BINDING_H_ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#ifdef _HAVE_MATLAB_ ++#include "./matlab/matlab-binding.h" ++#endif ++ ++#ifdef _HAVE_PYTHON_ ++#include "./python/python-binding.h" ++#endif ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 12013) +@@ -20,9 +20,6 @@ + #include "adolc.h" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "mex.h" +-#endif + class Vector; + + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Scotch/Scotch.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Scotch/Scotch.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Scotch/Scotch.h (revision 12013) +@@ -16,6 +16,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "Scotch" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgConvertMesh/BamgConvertMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgConvertMesh/BamgConvertMesh.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgConvertMesh/BamgConvertMesh.cpp (revision 12013) +@@ -63,8 +63,8 @@ + BamgConvertMeshx(bamgmesh,bamggeom,index,x,y,nods,nels); + + /*Generate output Matlab Structures*/ +- bamggeom->SetMatlabStructureFields(BAMGGEOMOUT); +- bamgmesh->SetMatlabStructureFields(BAMGMESHOUT); ++ bamggeom->SetStructureFields((void*)BAMGGEOMOUT); ++ bamgmesh->SetStructureFields((void*)BAMGMESHOUT); + + /*Clean up*/ + delete bamggeom; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgConvertMesh/BamgConvertMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgConvertMesh/BamgConvertMesh.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgConvertMesh/BamgConvertMesh.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "BamgConvertMesh" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLOverlay/KMLOverlay.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLOverlay/KMLOverlay.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLOverlay/KMLOverlay.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "KMLOverlay" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "ContourToNodes" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/HoleFiller/HoleFiller.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/HoleFiller/HoleFiller.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/HoleFiller/HoleFiller.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "HoleFiller" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/MeshProfileIntersection/MeshProfileIntersection.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/MeshProfileIntersection/MeshProfileIntersection.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/MeshProfileIntersection/MeshProfileIntersection.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "MeshProfileIntersection" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshRefine/TriMeshRefine.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshRefine/TriMeshRefine.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshRefine/TriMeshRefine.h (revision 12013) +@@ -13,6 +13,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + void TriMeshRefineUsage(void); + #undef __FUNCT__ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "InterpFromMeshToMesh3d" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Ll2xy/Ll2xy.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Ll2xy/Ll2xy.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Ll2xy/Ll2xy.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "Ll2xy" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgMesher/BamgMesher.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgMesher/BamgMesher.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgMesher/BamgMesher.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "BamgMesher" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgMesher/BamgMesher.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgMesher/BamgMesher.cpp (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgMesher/BamgMesher.cpp (revision 12013) +@@ -35,8 +35,8 @@ + Bamgx(bamgmesh_out,bamggeom_out,bamgmesh_in,bamggeom_in,bamgopts); + + /*Generate output Matlab Structures*/ +- bamggeom_out->SetMatlabStructureFields(BAMGGEOMOUT); +- bamgmesh_out->SetMatlabStructureFields(BAMGMESHOUT); ++ bamggeom_out->SetStructureFields((void*)BAMGGEOMOUT); ++ bamgmesh_out->SetStructureFields((void*)BAMGMESHOUT); + + /*Free ressources: */ + delete bamgopts; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "InterpFromGridToMesh" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToGrid/InterpFromMeshToGrid.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "InterpFromMeshToGrid" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLFileRead/KMLFileRead.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLFileRead/KMLFileRead.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLFileRead/KMLFileRead.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "KMLFileRead" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Shp2Kml/Shp2Kml.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Shp2Kml/Shp2Kml.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Shp2Kml/Shp2Kml.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "Shp2Kml" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/AverageFilter/AverageFilter.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/AverageFilter/AverageFilter.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/AverageFilter/AverageFilter.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "AverageFilter" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshProcessRifts/TriMeshProcessRifts.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshProcessRifts/TriMeshProcessRifts.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshProcessRifts/TriMeshProcessRifts.h (revision 12013) +@@ -13,6 +13,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + #include "../../c/EnumDefinitions/EnumDefinitions.h" + + void TriMeshProcessRiftsUsage(void); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Exp2Kml/Exp2Kml.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Exp2Kml/Exp2Kml.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Exp2Kml/Exp2Kml.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "Exp2Kml" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Kml2Exp/Kml2Exp.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Kml2Exp/Kml2Exp.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Kml2Exp/Kml2Exp.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "Kml2Exp" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "PointCloudFindNeighbors" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "PropagateFlagsFromConnectivity" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshRifts/TriMeshRifts.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshRifts/TriMeshRifts.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshRifts/TriMeshRifts.h (revision 12013) +@@ -13,6 +13,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + void TriMeshRiftsUsage(void); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriaSearch/TriaSearch.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriaSearch/TriaSearch.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriaSearch/TriaSearch.h (revision 12013) +@@ -11,6 +11,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "TriaSearch" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InternalFront/InternalFront.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InternalFront/InternalFront.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InternalFront/InternalFront.h (revision 12013) +@@ -12,6 +12,7 @@ + + #include "../../c/include/globals.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + #include "../../c/io/io.h" + + #undef __FUNCT__ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/MeshPartition/MeshPartition.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/MeshPartition/MeshPartition.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/MeshPartition/MeshPartition.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef CLEANUP + #define CLEANUP MeshPartitionLocalCleanup(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "InterpFromMesh2d" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ElementConnectivity/ElementConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ElementConnectivity/ElementConnectivity.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ElementConnectivity/ElementConnectivity.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "ElementConnectivity" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/EnumToString/EnumToString.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/EnumToString/EnumToString.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/EnumToString/EnumToString.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + /* serial input macros: */ + #define ENUMIN (mxArray*)prhs[0] +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/StringToEnum/StringToEnum.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/StringToEnum/StringToEnum.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/StringToEnum/StringToEnum.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + /* serial input macros: */ + #define NAME (mxArray*)prhs[0] +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgTriangulate/BamgTriangulate.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgTriangulate/BamgTriangulate.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/BamgTriangulate/BamgTriangulate.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "BamgTriangulate" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "InterpFromMeshToMesh2d" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshNoDensity/TriMeshNoDensity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshNoDensity/TriMeshNoDensity.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMeshNoDensity/TriMeshNoDensity.h (revision 12013) +@@ -13,6 +13,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + void TriMeshNoDensityUsage(void); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 12013) +@@ -54,14 +54,14 @@ + + if MATLAB + AM_LDFLAGS = $(MEXLINK) +-AM_CXXFLAGS += -DMATLAB -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread ++AM_CXXFLAGS += -D_HAVE_MATLAB_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread + LDADD += $(MEXLIB) ../c/libISSMMatlab.a + + endif + + if PYTHON + AM_LDFLAGS = $(PYTHONLINK) +-AM_CXXFLAGS += -DNPY_NO_DEPRECATED_API ++AM_CXXFLAGS += -D_HAVE_PYTHON_ -DNPY_NO_DEPRECATED_API + LDADD += $(BOOSTLIB) $(PYTHONLIB) ../c/libISSMPython.a + endif + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.h (revision 12013) +@@ -14,6 +14,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "ContourToMesh" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Xy2ll/Xy2ll.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Xy2ll/Xy2ll.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Xy2ll/Xy2ll.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "Xy2ll" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h (revision 12013) +@@ -24,6 +24,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + #include "../../c/io/io.h" + #include "../../c/EnumDefinitions/EnumDefinitions.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLMeshWrite/KMLMeshWrite.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLMeshWrite/KMLMeshWrite.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/KMLMeshWrite/KMLMeshWrite.h (revision 12013) +@@ -12,6 +12,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + #undef __FUNCT__ + #define __FUNCT__ "KMLMeshWrite" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Chaco/Chaco.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Chaco/Chaco.h (revision 12012) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Chaco/Chaco.h (revision 12013) +@@ -16,6 +16,7 @@ + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" + + /* serial input macros: */ + #define A_IN (mxArray*)prhs[0] Index: /issm/oecreview/Archive/12010-12040/ISSM-12013-12014.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12013-12014.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12013-12014.diff (revision 12325) @@ -0,0 +1,5511 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.h (revision 12014) +@@ -33,11 +33,6 @@ + void DeepEcho(void); + int Id(void); + int MyRank(void); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(void); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(void); + Object* copy(void); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/DofIndexing.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/DofIndexing.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/DofIndexing.cpp (revision 12014) +@@ -207,129 +207,4 @@ + printf("\n"); + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DofIndexing::Marshall{{{1*/ +-void DofIndexing::Marshall(char** pmarshalled_dataset){ + +- char* marshalled_dataset=NULL; +- int enum_type=0; +- bool flagdoftype; //to indicate if there are some doftype or if NULL +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*preliminary: */ +- if(this->doftype)flagdoftype=true; +- else flagdoftype=false; +- +- /*get enum type of DofIndexing: */ +- enum_type=DofIndexingEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall DofIndexing data: */ +- memcpy(marshalled_dataset,&gsize,sizeof(gsize));marshalled_dataset+=sizeof(gsize); +- memcpy(marshalled_dataset,&fsize,sizeof(fsize));marshalled_dataset+=sizeof(fsize); +- memcpy(marshalled_dataset,&ssize,sizeof(ssize));marshalled_dataset+=sizeof(ssize); +- memcpy(marshalled_dataset,&flagdoftype,sizeof(flagdoftype));marshalled_dataset+=sizeof(flagdoftype); +- memcpy(marshalled_dataset,&clone,sizeof(clone));marshalled_dataset+=sizeof(clone); +- +- if(this->gsize>0){ +- memcpy(marshalled_dataset,f_set,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); +- memcpy(marshalled_dataset,s_set,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); +- memcpy(marshalled_dataset,svalues,gsize*sizeof(double)); marshalled_dataset+=gsize*sizeof(double); +- if(flagdoftype){ memcpy(marshalled_dataset,doftype,gsize*sizeof(int)); marshalled_dataset+=gsize*sizeof(int); } +- memcpy(marshalled_dataset,gdoflist,gsize*sizeof(int)); marshalled_dataset+=gsize*sizeof(int); +- } +- if(this->fsize>0 && this->fsize!=UNDEF){ memcpy(marshalled_dataset,fdoflist,fsize*sizeof(int)); marshalled_dataset+=fsize*sizeof(int);} +- if(this->ssize>0 && this->ssize!=UNDEF){ memcpy(marshalled_dataset,sdoflist,ssize*sizeof(int)); marshalled_dataset+=ssize*sizeof(int);} +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION DofIndexing::MarshallSize{{{1*/ +-int DofIndexing::MarshallSize(){ +- +- int size=0; +- +- size+=4*sizeof(int)+sizeof(bool); +- if(this->gsize>0){ +- size+= 2*this->gsize*sizeof(bool)+ +- this->gsize*sizeof(double)+ +- this->gsize*sizeof(int); +- if(this->doftype)size+=this->gsize*sizeof(int); +- } +- if(this->fsize>0 && this->fsize!=UNDEF)size+=this->fsize*sizeof(int); +- if(this->ssize>0 && this->ssize!=UNDEF)size+=this->ssize*sizeof(int); +- +- size+=sizeof(int); //sizeof(int) for enum type +- +- return size; +-} +-/*}}}*/ +-/*FUNCTION DofIndexing::Demarshall{{{1*/ +-void DofIndexing::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type; +- bool flagdoftype; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of object since DofIndexing is not directly called by DataSet: */ +- memcpy(&enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- +- /*easy part: */ +- memcpy(&gsize,marshalled_dataset,sizeof(gsize));marshalled_dataset+=sizeof(gsize); +- memcpy(&fsize,marshalled_dataset,sizeof(fsize));marshalled_dataset+=sizeof(fsize); +- memcpy(&ssize,marshalled_dataset,sizeof(ssize));marshalled_dataset+=sizeof(ssize); +- memcpy(&flagdoftype,marshalled_dataset,sizeof(flagdoftype));marshalled_dataset+=sizeof(flagdoftype); +- memcpy(&clone,marshalled_dataset,sizeof(clone));marshalled_dataset+=sizeof(clone); +- +- /*Allocate: */ +- if(this->gsize>0){ +- this->f_set=(bool*)xmalloc(this->gsize*sizeof(bool)); +- this->s_set=(bool*)xmalloc(this->gsize*sizeof(bool)); +- this->svalues=(double*)xmalloc(this->gsize*sizeof(double)); +- if(flagdoftype)this->doftype=(int*)xmalloc(this->gsize*sizeof(int)); +- else this->doftype=NULL; +- this->gdoflist=(int*)xmalloc(this->gsize*sizeof(int)); +- } +- else{ +- this->f_set=NULL; +- this->s_set=NULL; +- this->svalues=NULL; +- this->doftype=NULL; +- this->gdoflist=NULL; +- } +- if(this->fsize>0) +- this->fdoflist=(int*)xmalloc(this->fsize*sizeof(int)); +- else +- this->fdoflist=NULL; +- if(this->ssize>0) +- this->sdoflist=(int*)xmalloc(this->ssize*sizeof(int)); +- else +- this->sdoflist=NULL; +- +- /*Copy arrays: */ +- if(this->gsize>0){ +- memcpy(f_set,marshalled_dataset,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); +- memcpy(s_set,marshalled_dataset,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); +- memcpy(svalues,marshalled_dataset,gsize*sizeof(double));marshalled_dataset+=gsize*sizeof(double); +- if(flagdoftype){memcpy(doftype,marshalled_dataset,gsize*sizeof(int));marshalled_dataset+=gsize*sizeof(int); } +- memcpy(gdoflist,marshalled_dataset,gsize*sizeof(int));marshalled_dataset+=gsize*sizeof(int); +- } +- +- if(this->fsize>0 && this->fsize!=UNDEF){ memcpy(this->fdoflist,marshalled_dataset,this->fsize*sizeof(int));marshalled_dataset+=this->fsize*sizeof(int); } +- if(this->ssize>0 && this->ssize!=UNDEF){ memcpy(this->sdoflist,marshalled_dataset,this->ssize*sizeof(int));marshalled_dataset+=this->ssize*sizeof(int); } +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.cpp (revision 12014) +@@ -87,76 +87,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION Matice::Marshall {{{1*/ +-void Matice::Marshall(char** pmarshalled_dataset){ +- +- /*Intermediaries*/ +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Matice: */ +- enum_type=MaticeEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Matice data: */ +- memcpy(marshalled_dataset,&mid,sizeof(mid));marshalled_dataset+=sizeof(mid); +- +- /*Marshall hooks: */ +- helement->Marshall(&marshalled_dataset); +- +- /*Marshall inputs: */ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- *pmarshalled_dataset=marshalled_dataset; +- +- /*clean up and return*/ +- xfree((void**)&marshalled_inputs); +-} +-/*}}}*/ +-/*FUNCTION Matice::MarshallSize{{{1*/ +-int Matice::MarshallSize(){ +- +- return sizeof(mid) +- +helement->MarshallSize() +- +inputs->MarshallSize() +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Matice::Demarshall {{{1*/ +-void Matice::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&mid,marshalled_dataset,sizeof(mid));marshalled_dataset+=sizeof(mid); +- +- /*demarshall hooks: */ +- helement=new Hook(); helement->Demarshall(&marshalled_dataset); +- +- /*demarshall inputs: */ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION Matice::ObjectEnum{{{1*/ + int Matice::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.cpp (revision 12014) +@@ -101,91 +101,6 @@ + return my_rank; + } + /*}}}1*/ +-#ifdef _SERIAL_ +-/*FUNCTION Matpar::Marshall {{{1*/ +-void Matpar::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Matpar: */ +- enum_type=MatparEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Matpar data: */ +- memcpy(marshalled_dataset,&mid,sizeof(mid));marshalled_dataset+=sizeof(mid); +- memcpy(marshalled_dataset,&rho_ice,sizeof(rho_ice));marshalled_dataset+=sizeof(rho_ice); +- memcpy(marshalled_dataset,&rho_water,sizeof(rho_water));marshalled_dataset+=sizeof(rho_water); +- memcpy(marshalled_dataset,&mu_water,sizeof(mu_water));marshalled_dataset+=sizeof(mu_water); +- memcpy(marshalled_dataset,&heatcapacity,sizeof(heatcapacity));marshalled_dataset+=sizeof(heatcapacity); +- memcpy(marshalled_dataset,&thermalconductivity,sizeof(thermalconductivity));marshalled_dataset+=sizeof(thermalconductivity); +- memcpy(marshalled_dataset,&latentheat,sizeof(latentheat));marshalled_dataset+=sizeof(latentheat); +- memcpy(marshalled_dataset,&beta,sizeof(beta));marshalled_dataset+=sizeof(beta); +- memcpy(marshalled_dataset,&meltingpoint,sizeof(meltingpoint));marshalled_dataset+=sizeof(meltingpoint); +- memcpy(marshalled_dataset,&referencetemperature,sizeof(referencetemperature));marshalled_dataset+=sizeof(referencetemperature); +- memcpy(marshalled_dataset,&mixed_layer_capacity,sizeof(mixed_layer_capacity));marshalled_dataset+=sizeof(mixed_layer_capacity); +- memcpy(marshalled_dataset,&thermal_exchange_velocity,sizeof(thermal_exchange_velocity));marshalled_dataset+=sizeof(thermal_exchange_velocity); +- memcpy(marshalled_dataset,&g,sizeof(g));marshalled_dataset+=sizeof(g); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-/*FUNCTION Matpar::MarshallSize {{{1*/ +-int Matpar::MarshallSize(){ +- +- return sizeof(mid)+ +- sizeof(rho_ice)+ +- sizeof(rho_water)+ +- sizeof(mu_water)+ +- sizeof(heatcapacity)+ +- sizeof(thermalconductivity)+ +- sizeof(latentheat)+ +- sizeof(beta)+ +- sizeof(meltingpoint)+ +- sizeof(referencetemperature)+ +- sizeof(mixed_layer_capacity)+ +- sizeof(thermal_exchange_velocity)+ +- sizeof(g)+ +- sizeof(int); //sizeof(int) for enum type +-} +-/*}}}1*/ +-/*FUNCTION Matpar::Demarshall {{{1*/ +-void Matpar::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&mid,marshalled_dataset,sizeof(mid));marshalled_dataset+=sizeof(mid); +- memcpy(&rho_ice,marshalled_dataset,sizeof(rho_ice));marshalled_dataset+=sizeof(rho_ice); +- memcpy(&rho_water,marshalled_dataset,sizeof(rho_water));marshalled_dataset+=sizeof(rho_water); +- memcpy(&mu_water,marshalled_dataset,sizeof(mu_water));marshalled_dataset+=sizeof(mu_water); +- memcpy(&heatcapacity,marshalled_dataset,sizeof(heatcapacity));marshalled_dataset+=sizeof(heatcapacity); +- memcpy(&thermalconductivity,marshalled_dataset,sizeof(thermalconductivity));marshalled_dataset+=sizeof(thermalconductivity); +- memcpy(&latentheat,marshalled_dataset,sizeof(latentheat));marshalled_dataset+=sizeof(latentheat); +- memcpy(&beta,marshalled_dataset,sizeof(beta));marshalled_dataset+=sizeof(beta); +- memcpy(&meltingpoint,marshalled_dataset,sizeof(meltingpoint));marshalled_dataset+=sizeof(meltingpoint); +- memcpy(&referencetemperature,marshalled_dataset,sizeof(referencetemperature));marshalled_dataset+=sizeof(referencetemperature); +- memcpy(&mixed_layer_capacity,marshalled_dataset,sizeof(mixed_layer_capacity));marshalled_dataset+=sizeof(mixed_layer_capacity); +- memcpy(&thermal_exchange_velocity,marshalled_dataset,sizeof(thermal_exchange_velocity));marshalled_dataset+=sizeof(thermal_exchange_velocity); +- memcpy(&g,marshalled_dataset,sizeof(g));marshalled_dataset+=sizeof(g); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-#endif + /*FUNCTION Matpar::ObjectEnum{{{1*/ + int Matpar::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.h (revision 12014) +@@ -34,11 +34,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.h (revision 12014) +@@ -45,11 +45,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -41,11 +37,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -41,11 +37,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.cpp (revision 12014) +@@ -61,24 +61,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION FileParam::Marshall{{{1*/ +-void FileParam::Marshall(char** pmarshalled_dataset){ +- +- _error_("FileParam is a pointer and cannot be marshalled"); +-} +-/*}}}*/ +-/*FUNCTION FileParam::MarshallSize{{{1*/ +-int FileParam::MarshallSize(){ +- _error_("FileParam is a pointer and cannot be marshalled"); +-} +-/*}}}*/ +-/*FUNCTION FileParam::Demarshall{{{1*/ +-void FileParam::Demarshall(char** pmarshalled_dataset){ +- _error_("FileParam is a pointer and cannot be marshalled"); +-} +-/*}}}*/ +-#endif + /*FUNCTION FileParam::ObjectEnum{{{1*/ + int FileParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -43,11 +39,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -42,11 +38,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h (revision 12014) +@@ -15,10 +15,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "../Object.h" + #include "../Node.h" + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -40,11 +36,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.cpp (revision 12014) +@@ -90,65 +90,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION IntVecParam::Marshall{{{1*/ +-void IntVecParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of IntVecParam: */ +- enum_value=IntVecParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall IntVecParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- if(M)memcpy(marshalled_dataset,values,M*sizeof(int));marshalled_dataset+=M*sizeof(int); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION IntVecParam::MarshallSize{{{1*/ +-int IntVecParam::MarshallSize(){ +- +- return sizeof(M)+ +- +M*sizeof(int) +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION IntVecParam::Demarshall{{{1*/ +-void IntVecParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- if(M) { +- values=(int*)xmalloc(M*sizeof(int)); +- memcpy(values,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); +- } +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION IntVecParam::ObjectEnum{{{1*/ + int IntVecParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.cpp (revision 12014) +@@ -61,57 +61,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION IntParam::Marshall{{{1*/ +-void IntParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of IntParam: */ +- enum_value=IntParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall IntParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION IntParam::MarshallSize{{{1*/ +-int IntParam::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION IntParam::Demarshall{{{1*/ +-void IntParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION IntParam::ObjectEnum{{{1*/ + int IntParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.cpp (revision 12014) +@@ -61,57 +61,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION BoolParam::Marshall{{{1*/ +-void BoolParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of BoolParam: */ +- enum_value=BoolParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall BoolParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION BoolParam::MarshallSize{{{1*/ +-int BoolParam::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION BoolParam::Demarshall{{{1*/ +-void BoolParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION BoolParam::ObjectEnum{{{1*/ + int BoolParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.cpp (revision 12014) +@@ -77,66 +77,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION IntMatParam::Marshall{{{1*/ +-void IntMatParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of IntMatParam: */ +- enum_value=IntMatParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall IntMatParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); +- memcpy(marshalled_dataset,value,M*N*sizeof(int));marshalled_dataset+=M*N*sizeof(int); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION IntMatParam::MarshallSize{{{1*/ +-int IntMatParam::MarshallSize(){ +- +- return sizeof(M) +- +sizeof(N) +- +M*N*sizeof(int) +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION IntMatParam::Demarshall{{{1*/ +-void IntMatParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); +- value=(int*)xmalloc(M*N*sizeof(int)); +- memcpy(value,marshalled_dataset,M*N*sizeof(int));marshalled_dataset+=M*N*sizeof(int); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION IntMatParam::ObjectEnum{{{1*/ + int IntMatParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -42,11 +38,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -41,11 +37,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -40,11 +36,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -42,11 +38,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.cpp (revision 12014) +@@ -71,90 +71,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION VectorParam::Marshall{{{1*/ +-void VectorParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int M; +- double* serial_value=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of VectorParam: */ +- enum_value=VectorParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall VectorParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- if(value){ +- value->GetSize(&M); +- serial_value=value->ToMPISerial(); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); +- } +- else{ +- M=0; +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- } +- /*Free ressources:*/ +- xfree((void**)&serial_value); +- +- /*return:*/ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION VectorParam::MarshallSize{{{1*/ +-int VectorParam::MarshallSize(){ +- +- int M=0; +- if(value)value->GetSize(&M); +- +- return sizeof(M)+M*sizeof(double) +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION VectorParam::Demarshall{{{1*/ +-void VectorParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- double* serial_vec=NULL; +- int M; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- if(M){ +- serial_vec=(double*)xmalloc(M*sizeof(double)); +- memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); +- +- value=new Vector(serial_vec,M); +- } +- else{ +- value=NULL; +- } +- +- /*Free ressources:*/ +- xfree((void**)&serial_vec); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-#endif + /*FUNCTION VectorParam::ObjectEnum{{{1*/ + int VectorParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp (revision 12014) +@@ -69,95 +69,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION MatrixParam::Marshall{{{1*/ +-void MatrixParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int M,N; +- double* serial_mat=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of MatrixParam: */ +- enum_value=MatrixParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall MatrixParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- if(value){ +- value->GetSize(&M,&N); +- serial_mat=value->ToSerial(); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); +- memcpy(marshalled_dataset,serial_mat,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); +- } +- else{ +- M=0; +- N=0; +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); +- } +- +- /*Free ressources:*/ +- xfree((void**)&serial_mat); +- +- /*return:*/ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION MatrixParam::MarshallSize{{{1*/ +-int MatrixParam::MarshallSize(){ +- +- int M=0; +- int N=0; +- if(value)value->GetSize(&M,&N); +- +- return sizeof(M)+ +- sizeof(N)+ +- M*N*sizeof(double)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION MatrixParam::Demarshall{{{1*/ +-void MatrixParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int M,N; +- double* serial_mat=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); +- if(M!=0 && N!=0){ +- serial_mat=(double*)xmalloc(M*N*sizeof(double)); +- memcpy(serial_mat,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); +- value=new Matrix(serial_mat,M,N,.001); +- } +- else{ +- value=NULL; +- } +- +- /*Free ressources:*/ +- xfree((void**)&serial_mat); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-#endif + /*FUNCTION MatrixParam::ObjectEnum{{{1*/ + int MatrixParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.cpp (revision 12014) +@@ -91,98 +91,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION StringArrayParam::Marshall{{{1*/ +-void StringArrayParam::Marshall(char** pmarshalled_dataset){ +- +- int i; +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int stringsize; +- char* string=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of StringArrayParam: */ +- enum_value=StringArrayParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&numstrings,sizeof(numstrings));marshalled_dataset+=sizeof(numstrings); +- for(i=0;ivalue[i]; +- stringsize=strlen(string)+1; +- +- memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); +- memcpy(marshalled_dataset,string,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); +- } +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION StringArrayParam::MarshallSize{{{1*/ +-int StringArrayParam::MarshallSize(){ +- +- int i; +- int marshallsize=0; +- int stringsize; +- char* string=NULL; +- +- marshallsize+=sizeof(numstrings); +- +- for(i=0;ivalue[i]; +- stringsize=strlen(string)+1; +- marshallsize+=sizeof(stringsize); +- marshallsize+=stringsize*sizeof(char); +- } +- +- marshallsize+=sizeof(enum_type); +- marshallsize+=sizeof(int); //sizeof(int) for enum value +- +- return marshallsize; +-} +-/*}}}*/ +-/*FUNCTION StringArrayParam::Demarshall{{{1*/ +-void StringArrayParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- int stringsize; +- char* string=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- memcpy(&numstrings,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- if(numstrings){ +- this->value=(char**)xmalloc(numstrings*sizeof(char*)); +- +- for(i=0;ivalue[i]=string; +- } +- } +- else this->value=NULL; +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION StringArrayParam::ObjectEnum{{{1*/ + int StringArrayParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.cpp (revision 12014) +@@ -63,70 +63,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION StringParam::Marshall{{{1*/ +-void StringParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int stringsize; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of StringParam: */ +- enum_value=StringParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- stringsize=strlen(this->value)+1; +- +- memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); +- memcpy(marshalled_dataset,this->value,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION StringParam::MarshallSize{{{1*/ +-int StringParam::MarshallSize(){ +- +- int stringsize; +- stringsize=strlen(this->value)+1; +- +- return sizeof(int)+ +- stringsize*sizeof(char)+ +- sizeof(enum_type)+ +- sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION StringParam::Demarshall{{{1*/ +-void StringParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- int stringsize; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- memcpy(&stringsize,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- +- this->value=(char*)xmalloc(stringsize*sizeof(char)); +- memcpy(this->value,marshalled_dataset,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION StringParam::ObjectEnum{{{1*/ + int StringParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -41,11 +37,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp (revision 12014) +@@ -74,63 +74,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleVecParam::Marshall{{{1*/ +-void DoubleVecParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleVecParam: */ +- enum_value=DoubleVecParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleVecParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleVecParam::MarshallSize{{{1*/ +-int DoubleVecParam::MarshallSize(){ +- +- return sizeof(M) +- +M*sizeof(double) +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION DoubleVecParam::Demarshall{{{1*/ +-void DoubleVecParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- values=(double*)xmalloc(M*sizeof(double)); +- memcpy(values,marshalled_dataset,M*sizeof(double));marshalled_dataset+=M*sizeof(double); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleVecParam::ObjectEnum{{{1*/ + int DoubleVecParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleTransientMatParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleTransientMatParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleTransientMatParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -41,11 +37,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.cpp (revision 12014) +@@ -58,57 +58,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleParam::Marshall{{{1*/ +-void DoubleParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleParam: */ +- enum_value=DoubleParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleParam::MarshallSize{{{1*/ +-int DoubleParam::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION DoubleParam::Demarshall{{{1*/ +-void DoubleParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleParam::ObjectEnum{{{1*/ + int DoubleParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -43,11 +39,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.cpp (revision 12014) +@@ -126,113 +126,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleMatArrayParam::Marshall{{{1*/ +-void DoubleMatArrayParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleMatArrayParam: */ +- enum_value=DoubleMatArrayParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleMatArrayParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- if(M){ +- memcpy(marshalled_dataset,mdim_array,M*sizeof(int));marshalled_dataset+=M*sizeof(int); +- memcpy(marshalled_dataset,ndim_array,M*sizeof(int));marshalled_dataset+=M*sizeof(int); +- for(i=0;iarray[i]; +- int m=this->mdim_array[i]; +- int n=this->ndim_array[i]; +- memcpy(marshalled_dataset,&m,sizeof(m));marshalled_dataset+=sizeof(m); +- memcpy(marshalled_dataset,&n,sizeof(n));marshalled_dataset+=sizeof(n); +- if(m*n)memcpy(marshalled_dataset,matrix,m*n*sizeof(double));marshalled_dataset+=m*n*sizeof(double); +- } +- } +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleMatArrayParam::MarshallSize{{{1*/ +-int DoubleMatArrayParam::MarshallSize(){ +- +- int size=0; +- int i; +- +- size+=sizeof(enum_type)+ +- sizeof(M)+ +- M*sizeof(int)+ +- M*sizeof(int); +- +- for(i=0;imdim_array[i]; +- int n=this->ndim_array[i]; +- size+=sizeof(m)+sizeof(n)+m*n*sizeof(double); +- } +- size+=sizeof(int); //sizeof(int) for enum value +- +- return size; +-} +-/*}}}*/ +-/*FUNCTION DoubleMatArrayParam::Demarshall{{{1*/ +-void DoubleMatArrayParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- double* matrix=NULL; +- int m,n; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum value, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- /*data: */ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- if(M){ +- this->mdim_array=(int*)xmalloc(M*sizeof(int)); +- this->ndim_array=(int*)xmalloc(M*sizeof(int)); +- memcpy(this->mdim_array,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); +- memcpy(this->ndim_array,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); +- +- this->array=(double**)xmalloc(M*sizeof(double*)); +- for(i=0;iarray[i]=matrix; +- } +- } +- else{ +- this->array=NULL; +- this->mdim_array=NULL; +- this->ndim_array=NULL; +- } +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleMatArrayParam::ObjectEnum{{{1*/ + int DoubleMatArrayParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h (revision 12014) +@@ -14,10 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./Param.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -41,11 +37,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp (revision 12014) +@@ -77,66 +77,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleMatParam::Marshall{{{1*/ +-void DoubleMatParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleMatParam: */ +- enum_value=DoubleMatParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleMatParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); +- memcpy(marshalled_dataset,value,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleMatParam::MarshallSize{{{1*/ +-int DoubleMatParam::MarshallSize(){ +- +- return sizeof(M) +- +sizeof(N) +- +M*N*sizeof(double) +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION DoubleMatParam::Demarshall{{{1*/ +-void DoubleMatParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); +- value=(double*)xmalloc(M*N*sizeof(double)); +- memcpy(value,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleMatParam::ObjectEnum{{{1*/ + int DoubleMatParam::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Segment.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Segment.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Segment.cpp (revision 12014) +@@ -70,24 +70,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION Segment::Marshall{{{1*/ +-void Segment::Marshall(char** pmarshalled_dataset){ +- +- _error_(" not supported yet!"); +-} +-/*}}}*/ +-/*FUNCTION Segment::MarshallSize{{{1*/ +-int Segment::MarshallSize(){ +- _error_(" not supported yet!"); +-} +-/*}}}*/ +-/*FUNCTION Segment::Demarshall{{{1*/ +-void Segment::Demarshall(char** pmarshalled_dataset){ +- _error_(" not supported yet!"); +-} +-/*}}}*/ +-#endif + /*FUNCTION Segment::ObjectEnum{{{1*/ + int Segment::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 12014) +@@ -20,10 +20,6 @@ + #include "adolc.h" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "mex.h" +-#endif +- + /*}}}*/ + + class Vector{ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Hook.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Hook.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Hook.h (revision 12014) +@@ -33,11 +33,6 @@ + /*Object like functionality:{{{1*/ + void Echo(void); + void DeepEcho(void); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + Object* copy(void); + /*}}}*/ + /*Hook management: {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionStruct.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionStruct.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionStruct.h (revision 12014) +@@ -29,11 +29,6 @@ + void DeepEcho(char* indent); + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- int MarshallSize(){_error_("Not implemented yet");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- #endif + int ObjectEnum(){return OptionStructEnum;}; + Object* copy(){_error_("Not implemented yet");}; + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionDouble.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionDouble.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionDouble.h (revision 12014) +@@ -29,11 +29,6 @@ + void DeepEcho(char* indent); + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- int MarshallSize(){_error_("Not implemented yet");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- #endif + int ObjectEnum(){return OptionDoubleEnum;}; + Object* copy(){_error_("Not implemented yet");}; + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionLogical.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionLogical.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionLogical.h (revision 12014) +@@ -29,11 +29,6 @@ + void DeepEcho(char* indent); + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- int MarshallSize(){_error_("Not implemented yet");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- #endif + int ObjectEnum(){return OptionLogicalEnum;}; + Object* copy(){_error_("Not implemented yet");}; + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionChar.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionChar.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionChar.h (revision 12014) +@@ -29,11 +29,6 @@ + void DeepEcho(char* indent); + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- int MarshallSize(){_error_("Not implemented yet");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- #endif + int ObjectEnum(){return OptionCharEnum;}; + Object* copy(){_error_("Not implemented yet");}; + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/Option.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/Option.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/Option.h (revision 12014) +@@ -32,11 +32,6 @@ + virtual void DeepEcho(char* indent); + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- int MarshallSize(){_error_("Not implemented yet");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- #endif + int ObjectEnum(){return OptionEnum;}; + Object* copy(){_error_("Not implemented yet");}; + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionCell.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionCell.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionCell.h (revision 12014) +@@ -29,11 +29,6 @@ + void DeepEcho(char* indent); + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- int MarshallSize(){_error_("Not implemented yet");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; +- #endif + int ObjectEnum(){return OptionCellEnum;}; + Object* copy(){_error_("Not implemented yet");}; + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.cpp (revision 12014) +@@ -91,80 +91,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION Vertex::Marshall {{{1*/ +-void Vertex::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Vertex: */ +- enum_type=VertexEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Vertex data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(marshalled_dataset,&x,sizeof(x));marshalled_dataset+=sizeof(x); +- memcpy(marshalled_dataset,&y,sizeof(y));marshalled_dataset+=sizeof(y); +- memcpy(marshalled_dataset,&z,sizeof(z));marshalled_dataset+=sizeof(z); +- memcpy(marshalled_dataset,&sigma,sizeof(sigma));marshalled_dataset+=sizeof(sigma); +- memcpy(marshalled_dataset,&connectivity,sizeof(connectivity));marshalled_dataset+=sizeof(connectivity); +- memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); +- memcpy(marshalled_dataset,&clone,sizeof(clone));marshalled_dataset+=sizeof(clone); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Vertex::MarshallSize {{{1*/ +-int Vertex::MarshallSize(){ +- +- return sizeof(id)+ +- sizeof(sid)+ +- sizeof(x)+ +- sizeof(y)+ +- sizeof(z)+ +- sizeof(sigma)+ +- sizeof(connectivity)+ +- sizeof(dof)+ +- sizeof(clone)+ +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Vertex::Demarshall {{{1*/ +-void Vertex::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(&x,marshalled_dataset,sizeof(x));marshalled_dataset+=sizeof(x); +- memcpy(&y,marshalled_dataset,sizeof(y));marshalled_dataset+=sizeof(y); +- memcpy(&z,marshalled_dataset,sizeof(z));marshalled_dataset+=sizeof(z); +- memcpy(&sigma,marshalled_dataset,sizeof(sigma));marshalled_dataset+=sizeof(sigma); +- memcpy(&connectivity,marshalled_dataset,sizeof(connectivity));marshalled_dataset+=sizeof(connectivity); +- memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); +- memcpy(&clone,marshalled_dataset,sizeof(clone));marshalled_dataset+=sizeof(clone); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION Vertex::ObjectEnum{{{1*/ + int Vertex::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.h (revision 12014) +@@ -48,11 +48,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.cpp (revision 12014) +@@ -188,89 +188,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION Numericalflux::Marshall {{{1*/ +-void Numericalflux::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Numericalflux: */ +- enum_type=NumericalfluxEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Numericalflux data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- /*Marshall hooks: */ +- hnodes->Marshall(&marshalled_dataset); +- helement->Marshall(&marshalled_dataset); +- +- /*Marshall inputs: */ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ +- +- xfree((void**)&marshalled_inputs); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Numericalflux::MarshallSize{{{1*/ +-int Numericalflux::MarshallSize(){ +- +- return sizeof(id) +- +sizeof(analysis_type) +- +hnodes->MarshallSize() +- +helement->MarshallSize() +- +inputs->MarshallSize() +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Numericalflux::Demarshall {{{1*/ +-void Numericalflux::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- /*demarshall hooks: */ +- hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); +- helement=new Hook(); helement->Demarshall(&marshalled_dataset); +- +- /*demarshall inputs: */ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*parameters: may not exist even yet, so let Configure handle it: */ +- this->parameters=NULL; +- this->element=NULL; +- this->nodes=NULL; +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION Numericalflux::ObjectEnum{{{1*/ + int Numericalflux::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.cpp (revision 12014) +@@ -84,69 +84,6 @@ + return my_rank; + } + /*}}}1*/ +-#ifdef _SERIAL_ +-/*FUNCTION Penpair::Marshall {{{1*/ +-void Penpair::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Penpair: */ +- enum_type=PenpairEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Penpair data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- /*Marshall hooks*/ +- hnodes->Marshall(&marshalled_dataset); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-/*FUNCTION Penpair::MarshallSize {{{1*/ +-int Penpair::MarshallSize(){ +- +- return sizeof(id)+ +- +sizeof(analysis_type) +- +hnodes->MarshallSize() +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}1*/ +-/*FUNCTION Penpair::Demarshall {{{1*/ +-void Penpair::Demarshall(char** pmarshalled_dataset){ +- +- int i; +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- /*demarshall hooks: */ +- hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); +- +- /*pointers are garbabe, until configuration is carried out: */ +- nodes=NULL; +- parameters=NULL; +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-#endif + /*FUNCTION Penpair::ObjectEnum{{{1*/ + int Penpair::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.h (revision 12014) +@@ -56,11 +56,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.h (revision 12014) +@@ -44,11 +44,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.h (revision 12014) +@@ -36,11 +36,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp (revision 12014) +@@ -131,100 +131,6 @@ + return my_rank; + } + /*}}}1*/ +-#ifdef _SERIAL_ +-/*FUNCTION Pengrid::Marshall {{{1*/ +-void Pengrid::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Tria: */ +- enum_type=PengridEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Tria data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- memcpy(marshalled_dataset,&active,sizeof(active));marshalled_dataset+=sizeof(active); +- memcpy(marshalled_dataset,&zigzag_counter,sizeof(zigzag_counter));marshalled_dataset+=sizeof(zigzag_counter); +- +- /*Marshall hooks: */ +- hnode->Marshall(&marshalled_dataset); +- helement->Marshall(&marshalled_dataset); +- hmatpar->Marshall(&marshalled_dataset); +- +- /*Marshall inputs: */ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ +- +- xfree((void**)&marshalled_inputs); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Pengrid::MarshallSize {{{1*/ +-int Pengrid::MarshallSize(){ +- +- return sizeof(id) +- +sizeof(analysis_type) +- +sizeof(active) +- +sizeof(zigzag_counter) +- +hnode->MarshallSize() +- +helement->MarshallSize() +- +hmatpar->MarshallSize() +- +inputs->MarshallSize() +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Pengrid::Demarshall {{{1*/ +-void Pengrid::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- memcpy(&active,marshalled_dataset,sizeof(active));marshalled_dataset+=sizeof(active); +- memcpy(&zigzag_counter,marshalled_dataset,sizeof(zigzag_counter));marshalled_dataset+=sizeof(zigzag_counter); +- +- /*demarshall hooks: */ +- hnode=new Hook(); hnode->Demarshall(&marshalled_dataset); +- helement=new Hook(); helement->Demarshall(&marshalled_dataset); +- hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); +- +- /*demarshall inputs: */ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*parameters: may not exist even yet, so let Configure handle it: */ +- this->parameters=NULL; +- this->node=NULL; +- this->element=NULL; +- this->matpar=NULL; +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION Pengrid::ObjectEnum{{{1*/ + int Pengrid::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.cpp (revision 12014) +@@ -162,94 +162,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION Icefront::Marshall {{{1*/ +-void Icefront::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Icefront: */ +- enum_type=IcefrontEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Icefront data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- /*Marshall hooks: */ +- hnodes->Marshall(&marshalled_dataset); +- helement->Marshall(&marshalled_dataset); +- hmatpar->Marshall(&marshalled_dataset); +- +- /*Marshall inputs: */ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ +- +- xfree((void**)&marshalled_inputs); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION Icefront::MarshallSize {{{1*/ +-int Icefront::MarshallSize(){ +- +- return sizeof(id) +- +sizeof(analysis_type) +- +hnodes->MarshallSize() +- +helement->MarshallSize() +- +hmatpar->MarshallSize() +- +inputs->MarshallSize() +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Icefront::Demarshall {{{1*/ +-void Icefront::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- /*demarshall hooks: */ +- hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); +- helement=new Hook(); helement->Demarshall(&marshalled_dataset); +- hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); +- +- /*pointers are garbabe, until configuration is carried out: */ +- nodes=NULL; +- element=NULL; +- matpar=NULL; +- +- /*demarshall inputs: */ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*parameters: may not exist even yet, so let Configure handle it: */ +- this->parameters=NULL; +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION Icefront::ObjectEnum{{{1*/ + int Icefront::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h (revision 12014) +@@ -49,11 +49,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.cpp (revision 12014) +@@ -191,125 +191,6 @@ + return my_rank; + } + /*}}}1*/ +-#ifdef _SERIAL_ +-/*FUNCTION Riftfront::Marshall {{{1*/ +-void Riftfront::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Riftfront: */ +- enum_type=RiftfrontEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Riftfront data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- memcpy(marshalled_dataset,&active,sizeof(active));marshalled_dataset+=sizeof(active); +- memcpy(marshalled_dataset,&normal,sizeof(normal));marshalled_dataset+=sizeof(normal); +- memcpy(marshalled_dataset,&length,sizeof(length));marshalled_dataset+=sizeof(length); +- memcpy(marshalled_dataset,&fraction,sizeof(fraction));marshalled_dataset+=sizeof(fraction); +- memcpy(marshalled_dataset,&frozen,sizeof(frozen));marshalled_dataset+=sizeof(frozen); +- memcpy(marshalled_dataset,&state,sizeof(state));marshalled_dataset+=sizeof(state); +- memcpy(marshalled_dataset,&counter,sizeof(counter));marshalled_dataset+=sizeof(counter); +- memcpy(marshalled_dataset,&prestable,sizeof(prestable));marshalled_dataset+=sizeof(prestable); +- memcpy(marshalled_dataset,&penalty_lock,sizeof(penalty_lock));marshalled_dataset+=sizeof(penalty_lock); +- memcpy(marshalled_dataset,&material_converged,sizeof(material_converged));marshalled_dataset+=sizeof(material_converged); +- +- /*Marshall hooks: */ +- hnodes->Marshall(&marshalled_dataset); +- helements->Marshall(&marshalled_dataset); +- hmatpar->Marshall(&marshalled_dataset); +- +- /*Marshall inputs: */ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ +- +- xfree((void**)&marshalled_inputs); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Riftfront::MarshallSize {{{1*/ +-int Riftfront::MarshallSize(){ +- +- return sizeof(id) +- +sizeof(analysis_type) +- +sizeof(active) +- +sizeof(normal) +- +sizeof(length) +- +sizeof(fraction) +- +sizeof(frozen) +- +sizeof(state) +- +sizeof(counter) +- +sizeof(prestable) +- +sizeof(penalty_lock) +- +sizeof(material_converged) +- +hnodes->MarshallSize() +- +helements->MarshallSize() +- +hmatpar->MarshallSize() +- +inputs->MarshallSize() +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Riftfront::Demarshall {{{1*/ +-void Riftfront::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- memcpy(&active,marshalled_dataset,sizeof(active));marshalled_dataset+=sizeof(active); +- memcpy(&normal,marshalled_dataset,sizeof(normal));marshalled_dataset+=sizeof(normal); +- memcpy(&length,marshalled_dataset,sizeof(length));marshalled_dataset+=sizeof(length); +- memcpy(&fraction,marshalled_dataset,sizeof(fraction));marshalled_dataset+=sizeof(fraction); +- memcpy(&frozen,marshalled_dataset,sizeof(frozen));marshalled_dataset+=sizeof(frozen); +- memcpy(&state,marshalled_dataset,sizeof(state));marshalled_dataset+=sizeof(state); +- memcpy(&counter,marshalled_dataset,sizeof(counter));marshalled_dataset+=sizeof(counter); +- memcpy(&prestable,marshalled_dataset,sizeof(prestable));marshalled_dataset+=sizeof(prestable); +- memcpy(&penalty_lock,marshalled_dataset,sizeof(penalty_lock));marshalled_dataset+=sizeof(penalty_lock); +- memcpy(&material_converged,marshalled_dataset,sizeof(material_converged));marshalled_dataset+=sizeof(material_converged); +- +- /*demarshall hooks: */ +- hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); +- helements=new Hook(); helements->Demarshall(&marshalled_dataset); +- hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); +- +- /*pointers are garbabe, until configuration is carried out: */ +- nodes=NULL; +- elements=NULL; +- matpar=NULL; +- +- /*demarshall inputs: */ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*parameters: may not exist even yet, so let Configure handle it: */ +- this->parameters=NULL; +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-#endif + /*FUNCTION Riftfront::ObjectEnum{{{1*/ + int Riftfront::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 12014) +@@ -95,75 +95,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleMatExternalResult::Marshall{{{1*/ +-void DoubleMatExternalResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleMatExternalResult: */ +- enum_value=DoubleMatExternalResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleMatExternalResult data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); +- memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleMatExternalResult::MarshallSize{{{1*/ +-int DoubleMatExternalResult::MarshallSize(){ +- +- return sizeof(M) +- +sizeof(N) +- +M*N*sizeof(double) +- +sizeof(id) +- +sizeof(enum_type) +- +sizeof(step) +- +sizeof(time) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION DoubleMatExternalResult::Demarshall{{{1*/ +-void DoubleMatExternalResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); +- values=(double*)xmalloc(M*N*sizeof(double)); +- memcpy(values,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleMatExternalResult::ObjectEnum{{{1*/ + int DoubleMatExternalResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 12014) +@@ -79,110 +79,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION PetscVecExternalResult::Marshall{{{1*/ +-void PetscVecExternalResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int M; +- double* serial_value=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of PetscVecExternalResult: */ +- enum_value=PetscVecExternalResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall PetscVecExternalResult data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- +- if(value){ +- VecGetSize(value,&M); +- VecToMPISerial(&serial_value,value); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); +- } +- else{ +- M=0; +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- } +- /*Free ressources:*/ +- xfree((void**)&serial_value); +- +- /*return:*/ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION PetscVecExternalResult::MarshallSize{{{1*/ +-int PetscVecExternalResult::MarshallSize(){ +- +- int M=0; +- if(value)VecGetSize(value,&M); +- +- return sizeof(M)+M*sizeof(double) +- +sizeof(id) +- +sizeof(enum_type) +- +sizeof(step) +- +sizeof(time) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION PetscVecExternalResult::Demarshall{{{1*/ +-void PetscVecExternalResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- int M; +- double* serial_vec=NULL; +- int* idxm=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- if(M){ +- serial_vec=(double*)xmalloc(M*sizeof(double)); +- memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); +- +- value=NewVec(M); +- idxm=(int*)xmalloc(M*sizeof(int)); +- for(i=0;i +-#endif +- +- + #include "./ExternalResult.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -47,11 +42,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 12014) +@@ -15,11 +15,7 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif + +- + #include "./ExternalResult.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -47,11 +43,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.h (revision 12014) +@@ -15,10 +15,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "./ExternalResult.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -45,11 +41,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.h (revision 12014) +@@ -15,11 +15,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- +- + #include "./ExternalResult.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -46,11 +41,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +@@ -61,4 +51,4 @@ + int GetStep(void); + /*}}}*/ + }; +-#endif /* _BOOLEXTERNALRESULT_H */ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 12014) +@@ -14,11 +14,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- +- + #include "./ExternalResult.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -48,11 +43,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 12014) +@@ -15,11 +15,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- +- + #include "./ExternalResult.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -47,11 +42,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/ExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/ExternalResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/ExternalResult.h (revision 12014) +@@ -15,10 +15,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- + #include "../Object.h" + #include "../Node.h" + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 12014) +@@ -70,79 +70,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION StringExternalResult::Marshall{{{1*/ +-void StringExternalResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int stringsize; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of StringExternalResult: */ +- enum_value=StringExternalResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- stringsize=strlen(this->value)+1; +- +- memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); +- memcpy(marshalled_dataset,this->value,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION StringExternalResult::MarshallSize{{{1*/ +-int StringExternalResult::MarshallSize(){ +- +- int stringsize; +- stringsize=strlen(this->value)+1; +- +- return sizeof(int)+ +- +stringsize*sizeof(char) +- +sizeof(id) +- +sizeof(enum_type) +- +sizeof(step) +- +sizeof(time) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION StringExternalResult::Demarshall{{{1*/ +-void StringExternalResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- int stringsize; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- memcpy(&stringsize,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- +- this->value=(char*)xmalloc(stringsize*sizeof(char)); +- memcpy(value,marshalled_dataset,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION StringExternalResult::ObjectEnum{{{1*/ + int StringExternalResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 12014) +@@ -86,72 +86,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleVecExternalResult::Marshall{{{1*/ +-void DoubleVecExternalResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleVecExternalResult: */ +- enum_value=DoubleVecExternalResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleVecExternalResult data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleVecExternalResult::MarshallSize{{{1*/ +-int DoubleVecExternalResult::MarshallSize(){ +- +- return sizeof(M) +- +M*sizeof(double) +- +sizeof(id) +- +sizeof(enum_type) +- +sizeof(step) +- +sizeof(time) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION DoubleVecExternalResult::Demarshall{{{1*/ +-void DoubleVecExternalResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- values=(double*)xmalloc(M*sizeof(double)); +- memcpy(values,marshalled_dataset,M*sizeof(double));marshalled_dataset+=M*sizeof(double); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleVecExternalResult::ObjectEnum{{{1*/ + int DoubleVecExternalResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 12014) +@@ -67,66 +67,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleExternalResult::Marshall{{{1*/ +-void DoubleExternalResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleExternalResult: */ +- enum_value=DoubleExternalResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleExternalResult data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleExternalResult::MarshallSize{{{1*/ +-int DoubleExternalResult::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(id) +- +sizeof(enum_type) +- +sizeof(step) +- +sizeof(time) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION DoubleExternalResult::Demarshall{{{1*/ +-void DoubleExternalResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleExternalResult::ObjectEnum{{{1*/ + int DoubleExternalResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 12014) +@@ -67,66 +67,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION IntExternalResult::Marshall{{{1*/ +-void IntExternalResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of IntExternalResult: */ +- enum_value=IntExternalResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall IntExternalResult data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION IntExternalResult::MarshallSize{{{1*/ +-int IntExternalResult::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(id) +- +sizeof(enum_type) +- +sizeof(step) +- +sizeof(time) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION IntExternalResult::Demarshall{{{1*/ +-void IntExternalResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION IntExternalResult::ObjectEnum{{{1*/ + int IntExternalResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 12014) +@@ -67,66 +67,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION BoolExternalResult::Marshall{{{1*/ +-void BoolExternalResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of BoolExternalResult: */ +- enum_value=BoolExternalResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall BoolExternalResult data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION BoolExternalResult::MarshallSize{{{1*/ +-int BoolExternalResult::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(id) +- +sizeof(enum_type) +- +sizeof(step) +- +sizeof(time) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION BoolExternalResult::Demarshall{{{1*/ +-void BoolExternalResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION BoolExternalResult::ObjectEnum{{{1*/ + int BoolExternalResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/StringExternalResult.h (revision 12014) +@@ -15,11 +15,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif +- +- + #include "./ExternalResult.h" + #include "../../include/include.h" + #include "../../shared/shared.h" +@@ -47,11 +42,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h (revision 12014) +@@ -32,11 +32,6 @@ + void DeepEcho(){_error_("not implemented yet");}; + int Id(){_error_("not implemented yet");}; + int MyRank(){_error_("not implemented yet");}; +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset){_error_("not implemented yet");}; +- int MarshallSize(){_error_("not implemented yet");}; +- void Demarshall(char** pmarshalled_dataset){_error_("not implemented yet");}; +- #endif + int ObjectEnum(){_error_("not implemented yet");}; + Object* copy(){_error_("not implemented yet");}; + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.cpp (revision 12014) +@@ -78,73 +78,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION Contour::Marshall{{{1*/ +-void Contour::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputssize; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Contour: */ +- enum_type=ContourEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Contour data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&nods,sizeof(nods));marshalled_dataset+=sizeof(nods); +- memcpy(marshalled_dataset,&closed,sizeof(closed));marshalled_dataset+=sizeof(closed); +- memcpy(marshalled_dataset,x,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); +- memcpy(marshalled_dataset,y,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Contour::MarshallSize{{{1*/ +-int Contour::MarshallSize(){ +- +- return sizeof(id)+ +- sizeof(nods)+ +- sizeof(closed)+ +- 2*nods*sizeof(double)+ +- sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Contour::Demarshall{{{1*/ +-void Contour::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&nods,marshalled_dataset,sizeof(nods));marshalled_dataset+=sizeof(nods); +- memcpy(&closed,marshalled_dataset,sizeof(closed));marshalled_dataset+=sizeof(closed); +- +- if(nods){ +- this->x=(double*)xmalloc(nods*sizeof(double)); +- this->y=(double*)xmalloc(nods*sizeof(double)); +- memcpy(x,marshalled_dataset,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); +- memcpy(y,marshalled_dataset,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); +- } +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION Contour::ObjectEnum{{{1*/ + int Contour::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 12014) +@@ -32,11 +32,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 12014) +@@ -66,63 +66,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION PentaP1ElementResult::Marshall{{{1*/ +-void PentaP1ElementResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of PentaP1ElementResult: */ +- enum_value=PentaP1ElementResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall PentaP1ElementResult data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION PentaP1ElementResult::MarshallSize{{{1*/ +-int PentaP1ElementResult::MarshallSize(){ +- +- return sizeof(values)+ +- +sizeof(enum_type) +- +sizeof(time) +- +sizeof(step) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION PentaP1ElementResult::Demarshall{{{1*/ +-void PentaP1ElementResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION PentaP1ElementResult::ObjectEnum{{{1*/ + int PentaP1ElementResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.cpp (revision 12014) +@@ -63,63 +63,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleElementResult::Marshall{{{1*/ +-void DoubleElementResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleElementResult: */ +- enum_value=DoubleElementResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleElementResult data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleElementResult::Demarshall{{{1*/ +-void DoubleElementResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION DoubleElementResult::MarshallSize{{{1*/ +-int DoubleElementResult::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(enum_type) +- +sizeof(time) +- +sizeof(step) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleElementResult::ObjectEnum{{{1*/ + int DoubleElementResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.cpp (revision 12014) +@@ -63,63 +63,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION BoolElementResult::Marshall{{{1*/ +-void BoolElementResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of BoolElementResult: */ +- enum_value=BoolElementResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall BoolElementResult data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION BoolElementResult::Demarshall{{{1*/ +-void BoolElementResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION BoolElementResult::MarshallSize{{{1*/ +-int BoolElementResult::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(enum_type) +- +sizeof(time) +- +sizeof(step) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-#endif + /*FUNCTION BoolElementResult::ObjectEnum{{{1*/ + int BoolElementResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 12014) +@@ -33,11 +33,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.h (revision 12014) +@@ -34,11 +34,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.h (revision 12014) +@@ -34,11 +34,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 12014) +@@ -65,64 +65,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION TriaP1ElementResult::Marshall{{{1*/ +-void TriaP1ElementResult::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of TriaP1ElementResult: */ +- enum_value=TriaP1ElementResultEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall TriaP1ElementResult data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); +- memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); +- memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION TriaP1ElementResult::MarshallSize{{{1*/ +-int TriaP1ElementResult::MarshallSize(){ +- +- return sizeof(values) +- +sizeof(enum_type) +- +sizeof(time) +- +sizeof(step) +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION TriaP1ElementResult::Demarshall{{{1*/ +-void TriaP1ElementResult::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); +- memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); +- memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION TriaP1ElementResult::ObjectEnum{{{1*/ + int TriaP1ElementResult::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h (revision 12014) +@@ -43,11 +43,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(){_error_("Not implemented yet (similar to Elements)");}; + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 12014) +@@ -122,160 +122,6 @@ + } + /*}}}*/ + +-/*Marshall*/ +-#ifdef _SERIAL_ +-/*FUNCTION Tria::Marshall {{{1*/ +-void Tria::Marshall(char** pmarshalled_dataset){ +- +- int i; +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- char* marshalled_results=NULL; +- int marshalled_results_size; +- int flaghook; //to indicate if hook is NULL or exists +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Tria: */ +- enum_type=TriaEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Tria data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(marshalled_dataset,&numanalyses,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); +- +- /*Mershall Ref: */ +- for(i=0;iMarshall(&marshalled_dataset); +- } +- else{ +- /*Set flag to 0 and do not marshall flag as there is no Hook */ +- flaghook=0; +- memcpy(marshalled_dataset,&flaghook,sizeof(flaghook));marshalled_dataset+=sizeof(flaghook); +- } +- } +- hmatice->Marshall(&marshalled_dataset); +- hmatpar->Marshall(&marshalled_dataset); +- +- /*Marshall inputs: */ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- /*Marshall results: */ +- marshalled_results_size=results->MarshallSize(); +- marshalled_results=results->Marshall(); +- memcpy(marshalled_dataset,marshalled_results,marshalled_results_size*sizeof(char)); +- marshalled_dataset+=marshalled_results_size; +- +- /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ +- +- xfree((void**)&marshalled_inputs); +- xfree((void**)&marshalled_results); +- +- /*marshall horizontal neighbors: */ +- memcpy(marshalled_dataset,horizontalneighborsids,3*sizeof(int));marshalled_dataset+=3*sizeof(int); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Tria::MarshallSize {{{1*/ +-int Tria::MarshallSize(){ +- +- int i; +- int hnodes_size=0;; +- +- for(i=0;iMarshallSize(); +- } +- +- return sizeof(id) +- +sizeof(sid) +- +hnodes_size +- +sizeof(numanalyses) +- +numanalyses*sizeof(int) //element_type_lists +- +hmatice->MarshallSize() +- +hmatpar->MarshallSize() +- +inputs->MarshallSize() +- +results->MarshallSize() +- +3*sizeof(int) +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Tria::Demarshall {{{1*/ +-void Tria::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- int flaghook; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(&numanalyses,marshalled_dataset,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); +- +- /*demarshall Ref: */ +- this->element_type_list=(int*)xmalloc(this->numanalyses*sizeof(int)); +- for(i=0;ihnodes=new Hook*[this->numanalyses]; +- /*demarshall hooks: */ +- for(i=0;iDemarshall(&marshalled_dataset); +- } +- else hnodes[i]=NULL; //There is no hook so it is NULL +- } +- hmatice=new Hook(); hmatice->Demarshall(&marshalled_dataset); +- hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); +- +- /*pointers are garbabe, until configuration is carried out: */ +- nodes=NULL; +- matice=NULL; +- matpar=NULL; +- +- /*demarshall inputs: */ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- results=(Results*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*parameters: may not exist even yet, so let Configure handle it: */ +- this->parameters=NULL; +- +- /*neighbors: */ +- memcpy(&this->horizontalneighborsids,marshalled_dataset,3*sizeof(int));marshalled_dataset+=3*sizeof(int); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif +- + /*Other*/ + /*FUNCTION Tria::AverageOntoPartition {{{1*/ + void Tria::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 12014) +@@ -50,11 +50,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 12014) +@@ -142,163 +142,6 @@ + } + /*}}}*/ + +-/*Marshall*/ +-#ifdef _SERIAL_ +-/*FUNCTION Penta::Marshall {{{1*/ +-void Penta::Marshall(char** pmarshalled_dataset){ +- +- int i; +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- char* marshalled_results=NULL; +- int marshalled_results_size; +- int flaghook; //to indicate if hook is NULL or exists +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Penta: */ +- enum_type=PentaEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Penta data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(marshalled_dataset,&numanalyses,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); +- +- /*Mershall Ref: */ +- for(i=0;iMarshall(&marshalled_dataset); +- } +- else{ +- /*Set flag to 0 and do not marshall flag as there is no Hook */ +- flaghook=0; +- memcpy(marshalled_dataset,&flaghook,sizeof(flaghook));marshalled_dataset+=sizeof(flaghook); +- } +- } +- hmatice->Marshall(&marshalled_dataset); +- hmatpar->Marshall(&marshalled_dataset); +- hneighbors->Marshall(&marshalled_dataset); +- +- /*Marshall inputs and results: */ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- marshalled_results_size=results->MarshallSize(); +- marshalled_results=results->Marshall(); +- memcpy(marshalled_dataset,marshalled_results,marshalled_results_size*sizeof(char)); +- marshalled_dataset+=marshalled_results_size; +- +- /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ +- +- xfree((void**)&marshalled_inputs); +- xfree((void**)&marshalled_results); +- +- /*marshall horizontal neighbors: */ +- memcpy(marshalled_dataset,horizontalneighborsids,3*sizeof(int));marshalled_dataset+=3*sizeof(int); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Penta::MarshallSize {{{1*/ +-int Penta::MarshallSize(){ +- +- int i; +- int hnodes_size=0;; +- +- for(i=0;iMarshallSize(); +- } +- +- return sizeof(id) +- +sizeof(sid) +- +hnodes_size +- +sizeof(numanalyses) +- +numanalyses*sizeof(int) //element_type_lists +- +hmatice->MarshallSize() +- +hmatpar->MarshallSize() +- +hneighbors->MarshallSize() +- +inputs->MarshallSize() +- +results->MarshallSize() +- +3*sizeof(int) +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Penta::Demarshall {{{1*/ +-void Penta::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- int flaghook; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(&numanalyses,marshalled_dataset,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); +- +- /*demarshall Ref: */ +- this->element_type_list=(int*)xmalloc(this->numanalyses*sizeof(int)); +- for(i=0;ihnodes=new Hook*[this->numanalyses]; +- /*demarshall hooks: */ +- for(i=0;iDemarshall(&marshalled_dataset); +- } +- else hnodes[i]=NULL; //There is no hook so it is NULL +- } +- hmatice=new Hook(); hmatice->Demarshall(&marshalled_dataset); +- hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); +- hneighbors=new Hook(); hneighbors->Demarshall(&marshalled_dataset); +- +- /*pointers are garbage, until configuration is carried out: */ +- nodes=NULL; +- matice=NULL; +- matpar=NULL; +- verticalneighbors=NULL; +- +- /*demarshall inputs and results: */ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- results=(Results*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*parameters: may not exist even yet, so let Configure handle it: */ +- this->parameters=NULL; +- +- /*neighbors: */ +- memcpy(&this->horizontalneighborsids,marshalled_dataset,3*sizeof(int));marshalled_dataset+=3*sizeof(int); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif +- + /*Other*/ + /*FUNCTION Penta::AverageOntoPartition {{{1*/ + void Penta::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 12014) +@@ -54,11 +54,6 @@ + void Echo(); + int ObjectEnum(); + int Id(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int MyRank(); + /*}}}*/ + /*Update virtual functions definitions: {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Patch.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Patch.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Patch.cpp (revision 12014) +@@ -121,10 +121,6 @@ + double *total_values = NULL; + MPI_Status status; + +- #ifdef _SERIAL_ +- return; //nothing to be done +- #endif +- + /*First, figure out total number of rows combining all the cpus: */ + MPI_Reduce(&this->numrows,&total_numrows,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&total_numrows,1,MPI_INT,0,MPI_COMM_WORLD); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Hook.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Hook.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Hook.cpp (revision 12014) +@@ -117,93 +117,6 @@ + } + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION Hook::Marshall{{{1*/ +-void Hook::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Hook: */ +- enum_type=HookEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Hook data: */ +- memcpy(marshalled_dataset,&num,sizeof(num));marshalled_dataset+=sizeof(num); +- for(i=0;iids[i],sizeof(int));marshalled_dataset+=sizeof(int); +- memcpy(marshalled_dataset,&this->offsets[i],sizeof(int));marshalled_dataset+=sizeof(int); +- } +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Hook::MarshallSize{{{1*/ +-int Hook::MarshallSize(){ +- +- return +- sizeof(num)+ +- num*sizeof(int)+ +- num*sizeof(int)+ +- sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Hook::Demarshall{{{1*/ +-void Hook::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- int enum_type; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of object since Hook is not directly called by DataSet: */ +- memcpy(&enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- +- memcpy(&num,marshalled_dataset,sizeof(num));marshalled_dataset+=sizeof(num); +- +- /*allocate: */ +- if (num<0){ +- _error_("cannot demarshall Hook as num<=0"); +- } +- else if (num==0){ +- this->ids=NULL; +- this->offsets=NULL; +- this->objects=NULL; +- } +- else{ +- +- this->ids=(int*)xmalloc(num*sizeof(int)); +- this->offsets=(int*)xmalloc(num*sizeof(int)); +- +- /*demarshall allocated ids and offsets: */ +- _assert_(num<1000); +- for (i=0;iids[i],marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- memcpy(&this->offsets[i],marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- } +- +- /*nullify object pointers */ +- this->objects=(Object**)xmalloc(num*sizeof(Object*)); +- for (i=0;iobjects[i]=NULL; +- } +- } +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION Hook::copy {{{1*/ + Object* Hook::copy(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.h (revision 12014) +@@ -29,11 +29,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.cpp (revision 12014) +@@ -89,214 +89,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION ControlInput::Marshall{{{1*/ +-void ControlInput::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int flag; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of ControlInput: */ +- enum_value=ControlInputEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall enum_type: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&control_id,sizeof(control_id));marshalled_dataset+=sizeof(control_id); +- +- /*marshal values*/ +- if(!values){ +- flag=0; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- } +- else{ +- flag=1; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- this->values->Marshall(&marshalled_dataset); +- } +- +- /*marshal savedvalues*/ +- if(!savedvalues){ +- flag=0; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- } +- else{ +- flag=1; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- this->savedvalues->Marshall(&marshalled_dataset); +- } +- +- /*marshal minvalues*/ +- if(!minvalues){ +- flag=0; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- } +- else{ +- flag=1; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- this->minvalues->Marshall(&marshalled_dataset); +- } +- +- /*marshal maxvalues*/ +- if(!maxvalues){ +- flag=0; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- } +- else{ +- flag=1; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- this->maxvalues->Marshall(&marshalled_dataset); +- } +- +- /*marshal gradient*/ +- if(!gradient){ +- flag=0; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- } +- else{ +- flag=1; +- memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); +- this->gradient->Marshall(&marshalled_dataset); +- } +- +- /*clean up and assign output pointer*/ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION ControlInput::MarshallSize{{{1*/ +-int ControlInput::MarshallSize(){ +- +- int size=0; +- +- size=sizeof(enum_type)+ +- +sizeof(control_id) +- +5*sizeof(int) //5 flags +- +sizeof(int); //sizeof(int) for enum value +- +- if(values) size+=values->MarshallSize(); +- if(savedvalues)size+=savedvalues->MarshallSize(); +- if(minvalues)size+=minvalues->MarshallSize(); +- if(maxvalues)size+=maxvalues->MarshallSize(); +- if(gradient) size+=gradient->MarshallSize(); +- return size; +-} +-/*}}}*/ +-/*FUNCTION ControlInput::Demarshall{{{1*/ +-void ControlInput::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int flag,input_enum_type; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&control_id,marshalled_dataset,sizeof(control_id));marshalled_dataset+=sizeof(control_id); +- +- /*Demarshal values*/ +- memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- if(flag){ +- memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- if(input_enum_type==PentaP1InputEnum){ +- values=new PentaP1Input(); +- values->Demarshall(&marshalled_dataset); +- } +- else if(input_enum_type==TriaP1InputEnum){ +- values=new TriaP1Input(); +- values->Demarshall(&marshalled_dataset); +- } +- else _error_("Not supported yet"); +- } +- else{ +- values=NULL; +- } +- +- /*Demarshal savedvalues*/ +- memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- if(flag){ +- memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- if(input_enum_type==PentaP1InputEnum){ +- savedvalues=new PentaP1Input(); +- savedvalues->Demarshall(&marshalled_dataset); +- } +- else if(input_enum_type==TriaP1InputEnum){ +- savedvalues=new TriaP1Input(); +- savedvalues->Demarshall(&marshalled_dataset); +- } +- else _error_("Not supported yet"); +- } +- else{ +- savedvalues=NULL; +- } +- +- /*Demarshal minvalues*/ +- memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- if(flag){ +- memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- if(input_enum_type==PentaP1InputEnum){ +- minvalues=new PentaP1Input(); +- minvalues->Demarshall(&marshalled_dataset); +- } +- else if(input_enum_type==TriaP1InputEnum){ +- minvalues=new TriaP1Input(); +- minvalues->Demarshall(&marshalled_dataset); +- } +- else _error_("Not supported yet"); +- } +- else{ +- minvalues=NULL; +- } +- +- /*Demarshal maxvalues*/ +- memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- if(flag){ +- memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- if(input_enum_type==PentaP1InputEnum){ +- maxvalues=new PentaP1Input(); +- maxvalues->Demarshall(&marshalled_dataset); +- } +- else if(input_enum_type==TriaP1InputEnum){ +- maxvalues=new TriaP1Input(); +- maxvalues->Demarshall(&marshalled_dataset); +- } +- else _error_("Not supported yet"); +- } +- else{ +- maxvalues=NULL; +- } +- +- /*Demarshal gradient*/ +- memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); +- if(flag){ +- memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- if(input_enum_type==PentaP1InputEnum){ +- gradient=new PentaP1Input(); +- gradient->Demarshall(&marshalled_dataset); +- } +- else if(input_enum_type==TriaP1InputEnum){ +- gradient=new TriaP1Input(); +- gradient->Demarshall(&marshalled_dataset); +- } +- else _error_("Not supported yet"); +- } +- else{ +- gradient=NULL; +- } +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION ControlInput::ObjectEnum{{{1*/ + int ControlInput::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.h (revision 12014) +@@ -34,11 +34,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.cpp (revision 12014) +@@ -60,70 +60,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DatasetInput::Marshall{{{1*/ +-void DatasetInput::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DatasetInput: */ +- enum_value=DatasetInputEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall enum_type: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshal inputs*/ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- /*clean up and assign output pointer*/ +- xfree((void**)&marshalled_inputs); +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DatasetInput::MarshallSize{{{1*/ +-int DatasetInput::MarshallSize(){ +- +- int size=0; +- +- size=sizeof(enum_type)+ +- +inputs->MarshallSize() +- +sizeof(int); //sizeof(int) for enum value +- +- return size; +-} +-/*}}}*/ +-/*FUNCTION DatasetInput::Demarshall{{{1*/ +-void DatasetInput::Demarshall(char** pmarshalled_dataset){ +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*Demarshal values*/ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DatasetInput::ObjectEnum{{{1*/ + int DatasetInput::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.h (revision 12014) +@@ -30,11 +30,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.cpp (revision 12014) +@@ -53,57 +53,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION IntInput::Marshall{{{1*/ +-void IntInput::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of IntInput: */ +- enum_value=IntInputEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall IntInput data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION IntInput::MarshallSize{{{1*/ +-int IntInput::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION IntInput::Demarshall{{{1*/ +-void IntInput::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION IntInput::ObjectEnum{{{1*/ + int IntInput::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.cpp (revision 12014) +@@ -58,57 +58,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION BoolInput::Marshall{{{1*/ +-void BoolInput::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of BoolInput: */ +- enum_value=BoolInputEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall BoolInput data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION BoolInput::MarshallSize{{{1*/ +-int BoolInput::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION BoolInput::Demarshall{{{1*/ +-void BoolInput::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION BoolInput::ObjectEnum{{{1*/ + int BoolInput::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.h (revision 12014) +@@ -30,11 +30,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.h (revision 12014) +@@ -30,11 +30,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.cpp (revision 12014) +@@ -69,57 +69,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION TriaP1Input::Marshall{{{1*/ +-void TriaP1Input::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of TriaP1Input: */ +- enum_value=TriaP1InputEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall TriaP1Input data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION TriaP1Input::MarshallSize{{{1*/ +-int TriaP1Input::MarshallSize(){ +- +- return sizeof(values)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION TriaP1Input::Demarshall{{{1*/ +-void TriaP1Input::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION TriaP1Input::ObjectEnum{{{1*/ + int TriaP1Input::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.h (revision 12014) +@@ -30,11 +30,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.cpp (revision 12014) +@@ -113,79 +113,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION TransientInput::Marshall{{{1*/ +-void TransientInput::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- char* marshalled_inputs=NULL; +- int marshalled_inputs_size; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of TransientInput: */ +- enum_value=TransientInputEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall TransientInput data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&numtimesteps,sizeof(numtimesteps));marshalled_dataset+=sizeof(numtimesteps); +- memcpy(marshalled_dataset,timesteps,numtimesteps*sizeof(double));marshalled_dataset+=numtimesteps*sizeof(double); +- +- /*marshal inputs*/ +- marshalled_inputs_size=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); +- marshalled_dataset+=marshalled_inputs_size; +- +- /*clean up and assign output pointer*/ +- xfree((void**)&marshalled_inputs); +- *pmarshalled_dataset=marshalled_dataset; +- +-} +-/*}}}* +-/*FUNCTION TransientInput::MarshallSize{{{1*/ +-int TransientInput::MarshallSize(){ +- +- return +- +sizeof(enum_type)+ +- +sizeof(numtimesteps)+ +- +inputs->MarshallSize() +- +numtimesteps*sizeof(double)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION TransientInput::Demarshall{{{1*/ +-void TransientInput::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&numtimesteps,marshalled_dataset,sizeof(numtimesteps));marshalled_dataset+=sizeof(numtimesteps); +- +- /*allocate: */ +- timesteps=(double*)xmalloc(numtimesteps*sizeof(double)); +- memcpy(timesteps,marshalled_dataset,numtimesteps*sizeof(double));marshalled_dataset+=numtimesteps*sizeof(double); +- +- /*Demarshal values*/ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +- +-} +-/*}}}*/ +-#endif + /*FUNCTION TransientInput::ObjectEnum{{{1*/ + int TransientInput::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.cpp (revision 12014) +@@ -69,57 +69,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION PentaP1Input::Marshall{{{1*/ +-void PentaP1Input::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of PentaP1Input: */ +- enum_value=PentaP1InputEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall PentaP1Input data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION PentaP1Input::MarshallSize{{{1*/ +-int PentaP1Input::MarshallSize(){ +- +- return sizeof(values)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION PentaP1Input::Demarshall{{{1*/ +-void PentaP1Input::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION PentaP1Input::ObjectEnum{{{1*/ + int PentaP1Input::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp (revision 12014) +@@ -58,57 +58,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION DoubleInput::Marshall{{{1*/ +-void DoubleInput::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of DoubleInput: */ +- enum_value=DoubleInputEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall DoubleInput data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DoubleInput::MarshallSize{{{1*/ +-int DoubleInput::MarshallSize(){ +- +- return sizeof(value)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION DoubleInput::Demarshall{{{1*/ +-void DoubleInput::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION DoubleInput::ObjectEnum{{{1*/ + int DoubleInput::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.h (revision 12014) +@@ -33,11 +33,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.h (revision 12014) +@@ -30,11 +30,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/DofIndexing.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/DofIndexing.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/DofIndexing.h (revision 12014) +@@ -42,11 +42,6 @@ + /*Object like functionality: {{{1*/ + void Echo(void); + void DeepEcho(void); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + void copy(DofIndexing* properties); + /*}}}*/ + /*DofIndexing management: {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Segment.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Segment.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Segment.h (revision 12014) +@@ -29,11 +29,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Object.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Object.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Object.h (revision 12014) +@@ -20,11 +20,6 @@ + virtual void DeepEcho()=0; + virtual int Id()=0; + virtual int MyRank()=0; +- #ifdef _SERIAL_ +- virtual void Marshall(char** pmarshalled_dataset)=0; +- virtual int MarshallSize()=0; +- virtual void Demarshall(char** pmarshalled_dataset)=0; +- #endif + virtual int ObjectEnum()=0; + virtual Object* copy()=0; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.h (revision 12014) +@@ -46,11 +46,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp (revision 12014) +@@ -192,89 +192,6 @@ + return my_rank; + } + /*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION Node::Marshall{{{1*/ +-void Node::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- char* marshalled_inputs=NULL; +- int marshalled_inputssize; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of Node: */ +- enum_type=NodeEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall Node data: */ +- memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- memcpy(marshalled_dataset,&coord_system,9*sizeof(double));marshalled_dataset+=9*sizeof(double); +- +- /*marshall objects: */ +- indexing.Marshall(&marshalled_dataset); +- hvertex->Marshall(&marshalled_dataset); +- +- /*Marshall inputs: */ +- marshalled_inputssize=inputs->MarshallSize(); +- marshalled_inputs=inputs->Marshall(); +- memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputssize*sizeof(char)); +- marshalled_dataset+=marshalled_inputssize; +- +- /*Free ressources:*/ +- xfree((void**)&marshalled_inputs); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-/*FUNCTION Node::MarshallSize{{{1*/ +-int Node::MarshallSize(){ +- +- return sizeof(id)+ +- sizeof(sid)+ +- indexing.MarshallSize()+ +- hvertex->MarshallSize()+ +- inputs->MarshallSize()+ +- sizeof(analysis_type)+ +- 9*sizeof(double)+ +- sizeof(int); //sizeof(int) for enum type +-} +-/*}}}*/ +-/*FUNCTION Node::Demarshall{{{1*/ +-void Node::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); +- memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- memcpy(&coord_system,marshalled_dataset,9*sizeof(double));marshalled_dataset+=9*sizeof(double); +- +- /*demarshall objects: */ +- indexing.Demarshall(&marshalled_dataset); +- hvertex=new Hook(); hvertex->Demarshall(&marshalled_dataset); +- +- /*demarshall inputs: */ +- inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}*/ +-#endif + /*FUNCTION Node::ObjectEnum{{{1*/ + int Node::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcDynamic.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcDynamic.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcDynamic.h (revision 12014) +@@ -33,11 +33,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcStatic.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcStatic.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcStatic.h (revision 12014) +@@ -32,11 +32,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcTransient.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcTransient.h (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcTransient.h (revision 12014) +@@ -34,11 +34,6 @@ + void DeepEcho(); + int Id(); + int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcDynamic.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcDynamic.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcDynamic.cpp (revision 12014) +@@ -71,70 +71,6 @@ + return my_rank; + } + /*}}}1*/ +-#ifdef _SERIAL_ +-/*FUNCTION SpcDynamic::Marshall {{{1*/ +-void SpcDynamic::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of SpcDynamic: */ +- enum_type=SpcDynamicEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall SpcDynamic data: */ +- memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); +- memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(marshalled_dataset,&isset,sizeof(isset));marshalled_dataset+=sizeof(isset); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-/*FUNCTION SpcDynamic::MarshallSize {{{1*/ +-int SpcDynamic::MarshallSize(){ +- +- return sizeof(sid) +- +sizeof(nodeid) +- +sizeof(dof) +- +sizeof(value) +- +sizeof(isset) +- +sizeof(analysis_type) +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}1*/ +-/*FUNCTION SpcDynamic::Demarshall {{{1*/ +-void SpcDynamic::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); +- memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(&isset,marshalled_dataset,sizeof(isset));marshalled_dataset+=sizeof(isset); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-#endif + /*FUNCTION SpcDynamic::ObjectEnum{{{1*/ + int SpcDynamic::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcStatic.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcStatic.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcStatic.cpp (revision 12014) +@@ -74,67 +74,6 @@ + return my_rank; + } + /*}}}1*/ +-#ifdef _SERIAL_ +-/*FUNCTION SpcStatic::Marshall {{{1*/ +-void SpcStatic::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of SpcStatic: */ +- enum_type=SpcStaticEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall SpcStatic data: */ +- memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); +- memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); +- memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-/*FUNCTION SpcStatic::MarshallSize {{{1*/ +-int SpcStatic::MarshallSize(){ +- +- return sizeof(sid) +- +sizeof(nodeid) +- +sizeof(dof) +- +sizeof(value) +- +sizeof(analysis_type) +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}1*/ +-/*FUNCTION SpcStatic::Demarshall {{{1*/ +-void SpcStatic::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); +- memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); +- memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-#endif + /*FUNCTION SpcStatic::ObjectEnum{{{1*/ + int SpcStatic::ObjectEnum(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcTransient.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcTransient.cpp (revision 12013) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/SpcTransient.cpp (revision 12014) +@@ -86,78 +86,6 @@ + return my_rank; + } + /*}}}1*/ +-#ifdef _SERIAL_ +-/*FUNCTION SpcTransient::Marshall {{{1*/ +-void SpcTransient::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_type=0; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum type of SpcTransient: */ +- enum_type=SpcTransientEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*marshall SpcTransient data: */ +- memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); +- memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); +- memcpy(marshalled_dataset,&nsteps,sizeof(nsteps));marshalled_dataset+=sizeof(nsteps); +- memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- if(nsteps){ +- memcpy(marshalled_dataset,values,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); +- memcpy(marshalled_dataset,times,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); +- } +- +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-/*FUNCTION SpcTransient::MarshallSize {{{1*/ +-int SpcTransient::MarshallSize(){ +- +- return sizeof(sid) +- +sizeof(nodeid) +- +sizeof(dof) +- +sizeof(nsteps) +- +nsteps*2*sizeof(double) +- +sizeof(analysis_type) +- +sizeof(int); //sizeof(int) for enum type +-} +-/*}}}1*/ +-/*FUNCTION SpcTransient::Demarshall {{{1*/ +-void SpcTransient::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- +- memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); +- memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); +- memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); +- memcpy(&nsteps,marshalled_dataset,sizeof(nsteps));marshalled_dataset+=sizeof(nsteps); +- memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); +- if(nsteps){ +- values=(double*)xmalloc(nsteps*sizeof(double)); +- times=(double*)xmalloc(nsteps*sizeof(double)); +- memcpy(values,marshalled_dataset,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); +- memcpy(times,marshalled_dataset,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); +- } +- +- /*return: */ +- *pmarshalled_dataset=marshalled_dataset; +- return; +-} +-/*}}}1*/ +-#endif + /*FUNCTION SpcTransient::ObjectEnum{{{1*/ + int SpcTransient::ObjectEnum(void){ + Index: /issm/oecreview/Archive/12010-12040/ISSM-12014-12015.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12014-12015.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12014-12015.diff (revision 12325) @@ -0,0 +1,623 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12014) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12015) +@@ -1,5 +1,5 @@ +-/* \file macros.h +- * \brief: global macros used in the whole code ++/* \file matlab macros.h ++ * \brief: macros used for the matlab bindings + */ + + /*Header {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/python-binding.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/python-binding.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/python-binding.h (revision 12015) +@@ -0,0 +1,6 @@ ++#ifndef _PYTHON_BINDING_H_ ++#define _PYTHON_BINDING_H_ ++ ++#include "./io/pythonio.h" ++#include "./include/python_macros.h" ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h (revision 12015) +@@ -0,0 +1,59 @@ ++/* \file python_macros.h ++ * \brief: macros used for the python bindings ++ */ ++ ++#ifndef _PYTHON_MACROS_H_ ++#define _PYTHON_MACROS_H_ ++ ++/*Header {{{1*/ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++/*}}}*/ ++ ++/* MODULEBOOT/MODULEEND {{{1*/ ++ ++/*The following macros hide the error exception handling in a matlab module. Just put ++ * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions ++ * will be trapped. Really nifty!*/ ++ ++#define MODULEBOOT(); ModuleBoot(); \ ++ PyObject* output = PyTuple_New(NLHS); if (!output) return NULL; ++ ++#define MODULEEND(); ModuleEnd(); \ ++ return output; ++//}}} ++/* WRAPPER {{{1*/ ++#define WRAPPER(modulename,...) \ ++\ ++static PyObject* modulename(PyObject* self,PyObject* args);\ ++static PyMethodDef modulename##_funcs[] = {\ ++ {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ ++ {NULL,NULL,0,NULL}\ ++};\ ++\ ++static struct PyModuleDef modulename##module= {\ ++ PyModuleDef_HEAD_INIT,\ ++ #modulename, /* name of module */\ ++ NULL, /* module documentation, may be NULL */\ ++ -1, /* size of per-interpreter state of the module,\ ++ or -1 if the module keeps state in global variables. */\ ++ modulename##_funcs\ ++};\ ++\ ++PyMODINIT_FUNC PyInit_##modulename(void){\ ++\ ++ import_array();\ ++ return PyModule_Create(&modulename##module);\ ++}\ ++\ ++static PyObject* modulename(PyObject* self,PyObject* args) ++/*}}}*/ ++/* CHECKARGUMENTS {{{1*/ ++#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) ++/*}}}*/ ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.cpp (revision 12014) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.cpp (revision 12015) +@@ -83,331 +83,6 @@ + } + /*}}}*/ + +-/*I/O*/ +-#ifdef _SERIAL_ +-/*FUNCTION DataSet::Marshall{{{1*/ +-char* DataSet::Marshall(){ +- +- vector::iterator object; +- int object_size; +- int marshalled_dataset_size=0; +- char* marshalled_dataset=NULL; +- char* old_marshalled_dataset=NULL; +- +- /*First get size of marshalled dataset: */ +- object_size=(int)objects.size(); +- +- marshalled_dataset_size=MarshallSize(); +- +- /*Allocate marshalled dataset: */ +- marshalled_dataset=(char*)xmalloc(marshalled_dataset_size*sizeof(char)); +- +- /*Keep track of old_marshalled_dataset: */ +- old_marshalled_dataset=marshalled_dataset; +- +- /*Store internals of dataset first: */ +- memcpy(marshalled_dataset,&object_size,sizeof(int)); marshalled_dataset+=sizeof(int); +- memcpy(marshalled_dataset,&sorted,sizeof(int)); marshalled_dataset+=sizeof(int); +- if(sorted){ +- if(object_size)memcpy(marshalled_dataset,sorted_ids,object_size*sizeof(int)); marshalled_dataset+=object_size*sizeof(int); +- if(object_size)memcpy(marshalled_dataset,id_offsets,object_size*sizeof(int)); marshalled_dataset+=object_size*sizeof(int); +- } +- +- for ( object=objects.begin() ; object < objects.end(); object++ ){ +- (*object)->Marshall(&marshalled_dataset); +- } +- +- /* Ok, marshalled_dataset now points to the end of the original marshalled_dataset pointer +- * before we started the loop on objects. Get object to point right again: */ +- marshalled_dataset-=marshalled_dataset_size; +- +- /*We should be back to old_marshalled_dataset: check and abort if that's not the case, +- * because this is a nasty error: */ +- if (marshalled_dataset!=old_marshalled_dataset){ +- _error_("final marshalled dataset \"%s\" is different from initial one!",EnumToStringx(enum_type)); +- abort(); +- } +- +- /*Return: */ +- return marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION DataSet::MarshallSize{{{1*/ +-int DataSet::MarshallSize(){ +- +- vector::iterator object; +- int marshalled_dataset_size=0; +- +- +- for ( object=objects.begin() ; object < objects.end(); object++ ){ +- marshalled_dataset_size+= (*object)->MarshallSize(); +- } +- +- marshalled_dataset_size+=sizeof(int); //objects size +- marshalled_dataset_size+=sizeof(int); //sorted size +- if(sorted){ +- marshalled_dataset_size+=(int)objects.size()*sizeof(int); //sorted ids +- marshalled_dataset_size+=(int)objects.size()*sizeof(int); //id offsets +- } +- +- return marshalled_dataset_size; +-} +-/*}}}*/ +-/*FUNCTION DataSet::Demarshall{{{1*/ +-DataSet* DataSetDemarshall(char* marshalled_dataset){ +- +- return DataSetDemarshallRaw(&marshalled_dataset); +- +-} +-/*}}}*/ +-/*FUNCTION DataSet::DemarshallRaw{{{1*/ +-DataSet* DataSetDemarshallRaw(char** pmarshalled_dataset){ +- +- int i; +- +- DataSet* dataset=NULL; +- int numobjects=0; +- int enum_type; +- Object* object=NULL; +- int sorted; +- int* sorted_ids=NULL; +- int* id_offsets=NULL; +- char* marshalled_dataset=NULL; +- +- /*recover marshalled_dataset pointer: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*initialize dataset: */ +- dataset=new DataSet(); +- +- /*Get internals first: */ +- memcpy(&numobjects,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- memcpy(&sorted,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); +- if(sorted){ +- if(numobjects){ +- sorted_ids=(int*)xmalloc(numobjects*sizeof(int)); +- id_offsets=(int*)xmalloc(numobjects*sizeof(int)); +- memcpy(sorted_ids,marshalled_dataset,numobjects*sizeof(int)); marshalled_dataset+=numobjects*sizeof(int); +- memcpy(id_offsets,marshalled_dataset,numobjects*sizeof(int)); marshalled_dataset+=numobjects*sizeof(int); +- } +- dataset->SetSorting(sorted_ids,id_offsets); +- } +- +- for(i=0;iDemarshall(&marshalled_dataset); +- dataset->AddObject(node);} +- break; +- case VertexEnum:{ +- Vertex* vertex=NULL; +- vertex=new Vertex(); +- vertex->Demarshall(&marshalled_dataset); +- dataset->AddObject(vertex);} +- break; +- case DoubleParamEnum:{ +- DoubleParam* doubleparam=NULL; +- doubleparam=new DoubleParam(); +- doubleparam->Demarshall(&marshalled_dataset); +- dataset->AddObject(doubleparam);} +- break; +- case TriaEnum:{ +- Tria* tria=NULL; +- tria=new Tria(); +- tria->Demarshall(&marshalled_dataset); +- dataset->AddObject(tria);} +- break; +- case TriaP1InputEnum:{ +- TriaP1Input* triavertexinput=NULL; +- triavertexinput=new TriaP1Input(); +- triavertexinput->Demarshall(&marshalled_dataset); +- dataset->AddObject(triavertexinput);} +- break; +- #ifdef _HAVE_3D_ +- case PentaP1InputEnum:{ +- PentaP1Input* pentavertexinput=NULL; +- pentavertexinput=new PentaP1Input(); +- pentavertexinput->Demarshall(&marshalled_dataset); +- dataset->AddObject(pentavertexinput);} +- break; +- #endif +- case TransientInputEnum:{ +- TransientInput* transientinput=NULL; +- transientinput=new TransientInput(); +- transientinput->Demarshall(&marshalled_dataset); +- dataset->AddObject(transientinput);} +- break; +- #ifdef _HAVE_CONTROL_ +- case ControlInputEnum:{ +- ControlInput* controlinputinput=NULL; +- controlinputinput=new ControlInput(); +- controlinputinput->Demarshall(&marshalled_dataset); +- dataset->AddObject(controlinputinput);} +- break; +- #endif +- case DatasetInputEnum:{ +- DatasetInput* datasetinputinput=NULL; +- datasetinputinput=new DatasetInput(); +- datasetinputinput->Demarshall(&marshalled_dataset); +- dataset->AddObject(datasetinputinput);} +- break; +- case TriaP1ElementResultEnum:{ +- TriaP1ElementResult* triavertexelementresult=NULL; +- triavertexelementresult=new TriaP1ElementResult(); +- triavertexelementresult->Demarshall(&marshalled_dataset); +- dataset->AddObject(triavertexelementresult);} +- break; +- #ifdef _HAVE_3D_ +- case PentaP1ElementResultEnum:{ +- PentaP1ElementResult* pentavertexelementresult=NULL; +- pentavertexelementresult=new PentaP1ElementResult(); +- pentavertexelementresult->Demarshall(&marshalled_dataset); +- dataset->AddObject(pentavertexelementresult);} +- break; +- case PentaEnum:{ +- Penta* penta=NULL; +- penta=new Penta(); +- penta->Demarshall(&marshalled_dataset); +- dataset->AddObject(penta);} +- break; +- #endif +- case MaticeEnum:{ +- Matice* matice=NULL; +- matice=new Matice(); +- matice->Demarshall(&marshalled_dataset); +- dataset->AddObject(matice);} +- break; +- case MatparEnum:{ +- Matpar* matpar=NULL; +- matpar=new Matpar(); +- matpar->Demarshall(&marshalled_dataset); +- dataset->AddObject(matpar);} +- break; +- case SpcStaticEnum:{ +- SpcStatic* spcstatic=NULL; +- spcstatic=new SpcStatic(); +- spcstatic->Demarshall(&marshalled_dataset); +- dataset->AddObject(spcstatic);} +- break; +- case SpcDynamicEnum:{ +- SpcDynamic* spcdynamic=NULL; +- spcdynamic=new SpcDynamic(); +- spcdynamic->Demarshall(&marshalled_dataset); +- dataset->AddObject(spcdynamic);} +- break; +- case SpcTransientEnum:{ +- SpcTransient* spctransient=NULL; +- spctransient=new SpcTransient(); +- spctransient->Demarshall(&marshalled_dataset); +- dataset->AddObject(spctransient);} +- break; +- case PengridEnum:{ +- Pengrid* pengrid=NULL; +- pengrid=new Pengrid(); +- pengrid->Demarshall(&marshalled_dataset); +- dataset->AddObject(pengrid);} +- break; +- case PenpairEnum:{ +- Penpair* penpair=NULL; +- penpair=new Penpair(); +- penpair->Demarshall(&marshalled_dataset); +- dataset->AddObject(penpair);} +- break; +- case IcefrontEnum:{ +- Icefront* icefront=NULL; +- icefront=new Icefront(); +- icefront->Demarshall(&marshalled_dataset); +- dataset->AddObject(icefront);} +- break; +- case NumericalfluxEnum:{ +- Numericalflux* numericalflux=NULL; +- numericalflux=new Numericalflux(); +- numericalflux->Demarshall(&marshalled_dataset); +- dataset->AddObject(numericalflux);} +- break; +- #ifdef _HAVE_RIFTS_ +- case RiftfrontEnum:{ +- Riftfront* riftfront=NULL; +- riftfront=new Riftfront(); +- riftfront->Demarshall(&marshalled_dataset); +- dataset->AddObject(riftfront);} +- break; +- #endif +- case DoubleInputEnum:{ +- DoubleInput* doubleinput=NULL; +- doubleinput=new DoubleInput(); +- doubleinput->Demarshall(&marshalled_dataset); +- dataset->AddObject(doubleinput);} +- break; +- case IntInputEnum:{ +- IntInput* intinput=NULL; +- intinput=new IntInput(); +- intinput->Demarshall(&marshalled_dataset); +- dataset->AddObject(intinput);} +- break; +- case BoolInputEnum:{ +- BoolInput* boolinput=NULL; +- boolinput=new BoolInput(); +- boolinput->Demarshall(&marshalled_dataset); +- dataset->AddObject(boolinput);} +- break; +- case IntParamEnum:{ +- IntParam* intparam=NULL; +- intparam=new IntParam(); +- intparam->Demarshall(&marshalled_dataset); +- dataset->AddObject(intparam);} +- break; +- case BoolParamEnum:{ +- BoolParam* boolparam=NULL; +- boolparam=new BoolParam(); +- boolparam->Demarshall(&marshalled_dataset); +- dataset->AddObject(boolparam);} +- break; +- case StringParamEnum:{ +- StringParam* stringparam=NULL; +- stringparam=new StringParam(); +- stringparam->Demarshall(&marshalled_dataset); +- dataset->AddObject(stringparam);} +- break; +- case DoubleVecExternalResultEnum:{ +- DoubleVecExternalResult* doublevecexternalresult=NULL; +- doublevecexternalresult=new DoubleVecExternalResult(); +- doublevecexternalresult->Demarshall(&marshalled_dataset); +- dataset->AddObject(doublevecexternalresult);} +- break; +- case DoubleExternalResultEnum:{ +- DoubleExternalResult* doubleexternalresult=NULL; +- doubleexternalresult=new DoubleExternalResult(); +- doubleexternalresult->Demarshall(&marshalled_dataset); +- dataset->AddObject(doubleexternalresult);} +- break; +- #ifdef _HAVE_GROUNDINGLINE_ +- case BoolElementResultEnum:{ +- BoolElementResult* boolelementresult=NULL; +- boolelementresult=new BoolElementResult(); +- boolelementresult->Demarshall(&marshalled_dataset); +- dataset->AddObject(boolelementresult);} +- break; +- #endif +- default: +- _error_("could not recognize enum type: %s",EnumToStringx(enum_type)); +- } +- } +- +- /*Assign output pointers:*/ +- *pmarshalled_dataset=marshalled_dataset; +- +- return dataset; +-} +-/*}}}*/ +-#endif +- + /*Specific methods*/ + /*FUNCTION DataSet::AddObject{{{1*/ + int DataSet::AddObject(Object* object){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.h (revision 12014) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.h (revision 12015) +@@ -48,10 +48,6 @@ + int GetEnum(int offset); + void Echo(); + void DeepEcho(); +- #ifdef _SERIAL_ +- char* Marshall(); +- int MarshallSize(); +- #endif + int AddObject(Object* object); + int DeleteObject(int id); + int Size(); +@@ -68,12 +64,4 @@ + + }; + +-/*This routine cannot be object oriented, but need for demarshalling: */ +-#ifdef _SERIAL_ +-DataSet* DataSetDemarshall(char* marshalled_dataset); +-DataSet* DataSetDemarshallRaw(char** pmarshalled_dataset); + #endif +- +- +- +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp (revision 12014) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp (revision 12015) +@@ -19,9 +19,7 @@ + #include "../include/include.h" + #include "../shared/shared.h" + #include "../EnumDefinitions/EnumDefinitions.h" +-#if _SERIAL_ + #include "../io/io.h" +-#endif + /*}}}*/ + + /*Object constructors and destructor*/ +@@ -30,32 +28,6 @@ + return; + } + /*}}}*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-/*FUNCTION Options::Options(int istart, int nrhs, const mxArray* prhs[]){{{1*/ +-Options::Options(int istart, int nrhs, const mxArray* prhs[]){ +- +- int i; +- char *name = NULL; +- Option *option = NULL; +- +- /*loop over each name and value*/ +- for (i=istart; iAddOption(option); +- option=NULL; +- } +- +- /*echo the dataset */ +- //if (this->Size()) for(i=0;iSize();i++) ((Option*)this->GetObjectByOffset(i))->Echo(); +-} +-/*}}}*/ +-#endif + /*FUNCTION Options::~Options(){{{1*/ + Options::~Options(){ + return; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h (revision 12014) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h (revision 12015) +@@ -39,23 +39,12 @@ + ((void) 0) + #endif + /*}}}*/ +- + /* MODULEBOOT/MODULEEND {{{1*/ + + /*The following macros hide the error exception handling in a matlab module. Just put + * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ + +-#ifdef _SERIAL_ +-#ifdef _HAVE_PYTHON_ //{{{2 +-#define MODULEBOOT(); ModuleBoot(); \ +- PyObject* output = PyTuple_New(NLHS); if (!output) return NULL; +- +-#define MODULEEND(); ModuleEnd(); \ +- return output; +-#endif //}}} +-#else +-//{{{2 + #define MODULEBOOT(); \ + try{ + +@@ -68,43 +57,6 @@ + _printf_(true,"Standard exception: %s\n",e.what());\ + return 1;\ + } +-//}}} +-#endif + /*}}}*/ +-/* WRAPPER {{{1*/ +-#ifdef _HAVE_PYTHON_ +-#define WRAPPER(modulename,...) \ +-\ +-static PyObject* modulename(PyObject* self,PyObject* args);\ +-static PyMethodDef modulename##_funcs[] = {\ +- {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ +- {NULL,NULL,0,NULL}\ +-};\ +-\ +-static struct PyModuleDef modulename##module= {\ +- PyModuleDef_HEAD_INIT,\ +- #modulename, /* name of module */\ +- NULL, /* module documentation, may be NULL */\ +- -1, /* size of per-interpreter state of the module,\ +- or -1 if the module keeps state in global variables. */\ +- modulename##_funcs\ +-};\ +-\ +-PyMODINIT_FUNC PyInit_##modulename(void){\ +-\ +- import_array();\ +- return PyModule_Create(&modulename##module);\ +-}\ +-\ +-static PyObject* modulename(PyObject* self,PyObject* args) + + #endif +- +-/*}}}*/ +-/* CHECKARGUMENTS {{{1*/ +-#ifdef _HAVE_PYTHON_ +-#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) +-#endif +-/*}}}*/ +- +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/shared.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/shared.h (revision 12014) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/shared.h (revision 12015) +@@ -7,6 +7,7 @@ + + + #include "Alloc/alloc.h" ++#include "Alloc/alloc_module.h" + #include "Exceptions/exceptions.h" + #include "Exp/exp.h" + #include "TriMesh/trimesh.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12014) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12015) +@@ -726,6 +726,7 @@ + #}}} + #Python sources {{{1 + python_sources= ./python/io/pythonio.h\ ++ ./python/python-binding.h\ + ./python/io/WritePythonData.cpp\ + ./python/io/CheckNumPythonArguments.cpp\ + ./python/io/FetchPythonData.cpp\ +@@ -739,6 +740,7 @@ + #}}} + #Matlab sources {{{1 + matlab_sources= ./toolkits/matlab/matlabincludes.h\ ++ ./matlab/matlab-binding.h\ + ./matlab/io/matlabio.h\ + ./matlab/io/MatlabNArrayToNArray.cpp\ + ./matlab/io/CheckNumMatlabArguments.cpp\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.cpp (revision 12014) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.cpp (revision 12015) +@@ -49,11 +49,11 @@ + + /*free ressources: */ + delete domain; +- xdelete(&index); +- xdelete(&x); +- xdelete(&y); +- xdelete(&segments); +- xdelete(&segmentmarkerlist); ++ xdelete_module(&index); ++ xdelete_module(&x); ++ xdelete_module(&y); ++ xdelete_module(&segments); ++ xdelete_module(&segmentmarkerlist); + + /*end module: */ + MODULEEND(); Index: /issm/oecreview/Archive/12010-12040/ISSM-12015-12016.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12015-12016.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12015-12016.diff (revision 12325) @@ -0,0 +1,757 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 12016) +@@ -36,10 +36,6 @@ + + MODULEBOOT(); + +- #ifndef _PARALLEL_ +- _error_(" parallel executable was compiled without support of parallel libraries!"); +- #endif +- + /*Initialize environments: Petsc, MPI, etc...: */ + #ifdef _HAVE_PETSC_ + ierr=PetscInitialize(&argc,&argv,(char*)0,""); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PrintfFunction.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PrintfFunction.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PrintfFunction.cpp (revision 12016) +@@ -50,11 +50,7 @@ + } + + /*Ok, if we are running in parallel, get node 0 to print*/ +-#if defined(_PARALLEL_) + if(my_rank==0)printf(buffer); +-#else +- mexPrintf(buffer); +-#endif + + /*Clean up and return*/ + xfree((void**)&buffer); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Loads.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Loads.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Loads.cpp (revision 12016) +@@ -62,12 +62,8 @@ + localloads=this->Size(); + + /*figure out total number of loads combining all the cpus (no clones here)*/ +- #ifdef _PARALLEL_ + MPI_Reduce(&localloads,&numberofloads,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&numberofloads,1,MPI_INT,0,MPI_COMM_WORLD); +- #else +- numberofloads=localloads; +- #endif + + return numberofloads; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Constraints.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Constraints.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Constraints.cpp (revision 12016) +@@ -47,12 +47,8 @@ + localconstraints=this->Size(); + + /*figure out total number of constraints combining all the cpus (no clones here)*/ +- #ifdef _PARALLEL_ + MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); +- #else +- numberofconstraints=localconstraints; +- #endif + + return numberofconstraints; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp (revision 12016) +@@ -203,11 +203,9 @@ + } + } + +-#ifdef _PARALLEL_ + /*Grab max of all cpus: */ + MPI_Allreduce ( (void*)&max,(void*)&allmax,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + max=allmax; +-#endif + + return max; + } +@@ -287,11 +285,9 @@ + } + } + +- #ifdef _PARALLEL_ +- MPI_Reduce (&max_sid,&node_max_sid,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); +- MPI_Bcast(&node_max_sid,1,MPI_INT,0,MPI_COMM_WORLD); +- max_sid=node_max_sid; +- #endif ++ MPI_Reduce (&max_sid,&node_max_sid,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); ++ MPI_Bcast(&node_max_sid,1,MPI_INT,0,MPI_COMM_WORLD); ++ max_sid=node_max_sid; + + if(max_sid==1){ + return 0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp (revision 12016) +@@ -123,7 +123,6 @@ + if(element_numnodes>numnodes)numnodes=element_numnodes; + } + +- #ifdef _PARALLEL_ + /*Synchronize across cluster, so as to not end up with different sizes for each patch on each cpu: */ + MPI_Reduce (&numvertices,&max_numvertices,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&max_numvertices,1,MPI_INT,0,MPI_COMM_WORLD); +@@ -132,7 +131,6 @@ + MPI_Reduce (&numnodes,&max_numnodes,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&max_numnodes,1,MPI_INT,0,MPI_COMM_WORLD); + numnodes=max_numnodes; +- #endif + + /*Ok, initialize Patch object: */ + patch=new Patch(numrows,numvertices,numnodes); +@@ -249,9 +247,7 @@ + patch=this->ResultsToPatch(); + + /*Gather onto master cpu 0, if needed: */ +-#ifdef _PARALLEL_ + if(io_gather)patch->Gather(); +-#endif + + /*create result object and add to results dataset:*/ + if (patch->maxvertices && patch->maxnodes){ +@@ -275,12 +271,8 @@ + int local_nelem=0; + int numberofelements; + +- #ifdef _PARALLEL_ + local_nelem=this->Size(); + MPI_Allreduce ( (void*)&local_nelem,(void*)&numberofelements,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); +- #else +- numberofelements=this->Size(); +- #endif + + return numberofelements; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.cpp (revision 12016) +@@ -148,11 +148,9 @@ + if (sid>max_sid)max_sid=sid; + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&max_sid,&vertex_max_sid,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&vertex_max_sid,1,MPI_INT,0,MPI_COMM_WORLD); + max_sid=vertex_max_sid; +- #endif + + /*sid starts at 0*/ + max_sid++; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp (revision 12016) +@@ -30,12 +30,10 @@ + minvz=INFINITY; + } + +- #ifdef _PARALLEL_ + /*Figure out minimum across the cluster: */ + MPI_Reduce (&minvz,&node_minvz,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_minvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + minvz=node_minvz; +- #endif + + /*Assign output pointers:*/ + *pminvz=minvz; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12016) +@@ -30,12 +30,10 @@ + maxvx=-INFINITY; + } + +- #ifdef _PARALLEL_ + /*Figure out minimum across the cluster: */ + MPI_Reduce (&maxvx,&node_maxvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxvx=node_maxvx; +- #endif + + /*Assign output pointers:*/ + *pmaxvx=maxvx; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TimeAdaptx/TimeAdaptx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TimeAdaptx/TimeAdaptx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TimeAdaptx/TimeAdaptx.cpp (revision 12016) +@@ -30,12 +30,10 @@ + if(dtFindParam(&dakota_output_file,QmuOutNameEnum); + parameters->FindParam(&dakota_error_file,QmuErrNameEnum); + +- #ifdef _PARALLEL_ + if(my_rank==0){ +- #endif + + // Instantiate/initialize the parallel library and problem description + // database objects. +@@ -110,12 +108,9 @@ + problem_db.lock(); // prevent run-time DB queries + selected_strategy.run_strategy(); + +- #ifdef _PARALLEL_ + //Warn other cpus that we are done running the dakota iterator, by setting the counter to -1: + SpawnCore(NULL,0, NULL,NULL,0,femmodel,-1); +- #endif + +- #ifdef _PARALLEL_ + } + else{ + +@@ -123,7 +118,6 @@ + if(!SpawnCore(NULL,0, NULL,NULL,0,femmodel,0))break; //counter came in at -1 on cpu0, bail out. + } + } +- #endif //#ifdef _PARALLEL_ + + /*Free ressources:*/ + xfree((void**)&dakota_input_file); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12016) +@@ -30,12 +30,10 @@ + maxvy=-INFINITY; + } + +- #ifdef _PARALLEL_ + /*Figure out minimum across the cluster: */ + MPI_Reduce (&maxvy,&node_maxvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxvy=node_maxvy; +- #endif + + /*Assign output pointers:*/ + *pmaxvy=maxvy; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12016) +@@ -31,12 +31,10 @@ + maxabsvy=-INFINITY; + } + +- #ifdef _PARALLEL_ + /*Figure out maximum across the cluster: */ + MPI_Reduce (&maxabsvy,&node_maxabsvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxabsvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxabsvy=node_maxabsvy; +- #endif + + /*Assign output pointers:*/ + *pmaxabsvy=maxabsvy; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (revision 12016) +@@ -62,7 +62,6 @@ + if(dim==2) elements_width=3; //tria elements + else elements_width=6; //penta elements + +- #ifdef _PARALLEL_ + /*Determine parallel partitioning of elements: we use Metis for now. First load the data, then partition*/ + if(dim==2){ + /*load elements: */ +@@ -79,11 +78,6 @@ + xfree((void**)&elements); + xfree((void**)&elements2d); + +- #else +- /*In serial mode, epart is full of 0: all elements belong to cpu 0: */ +- epart=(int*)xcalloc(numberofelements,sizeof(int)); +- #endif +- + /*Deal with rifts, they have to be included into one partition only, not several: */ + if(numrifts){ + iomodel->FetchData(&riftinfo,&numrifts,NULL,RiftsRiftstructEnum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp (revision 12016) +@@ -30,12 +30,10 @@ + minvx=INFINITY; + } + +- #ifdef _PARALLEL_ + /*Figure out minimum across the cluster: */ + MPI_Reduce (&minvx,&node_minvx,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_minvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + minvx=node_minvx; +- #endif + + /*Assign output pointers:*/ + *pminvx=minvx; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12016) +@@ -31,12 +31,10 @@ + maxvz=-INFINITY; + } + +- #ifdef _PARALLEL_ + /*Figure out minimum across the cluster: */ + MPI_Reduce (&maxvz,&node_maxvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxvz=node_maxvz; +- #endif + + /*Assign output pointers:*/ + *pmaxvz=maxvz; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12016) +@@ -35,11 +35,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); + num_unstable_constraints=sum_num_unstable_constraints; +- #endif + + /*Have we converged? : */ + if (num_unstable_constraints==0) converged=1; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12016) +@@ -27,11 +27,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; +- #endif + + return found; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12016) +@@ -31,11 +31,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; +- #endif + + return found; + } +@@ -94,11 +92,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); + num_unstable_constraints=sum_num_unstable_constraints; +- #endif + + /*Assign output pointers: */ + *pnum_unstable_constraints=num_unstable_constraints; +@@ -134,11 +130,9 @@ + } + + /*Is there just one found? that would mean we have frozen! : */ +- #ifdef _PARALLEL_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; +- #endif + + return found; + } +@@ -194,11 +188,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; +- #endif + + return found; + } +@@ -227,11 +219,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; +- #endif + + if (found){ + /*We found an unstable constraint. : */ +@@ -288,11 +278,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); + num_unstable_constraints=sum_num_unstable_constraints; +- #endif + + /*Assign output pointers: */ + *pnum_unstable_constraints=num_unstable_constraints; +@@ -328,11 +316,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&max_penetration,&mpi_max_penetration,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_max_penetration,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + max_penetration=mpi_max_penetration; +- #endif + + /*feed max_penetration to inputs: */ + for(i=0;iSize();i++){ +@@ -367,11 +353,9 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); + num_unstable_constraints=sum_num_unstable_constraints; +- #endif + + return num_unstable_constraints; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp (revision 12016) +@@ -122,7 +122,7 @@ + KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); + KSPSetFromOptions(ksp); + +- #if defined(_SERIAL_) && _PETSC_MAJOR_==3 ++ #if _PETSC_MAJOR_==3 + /*Specific solver?: */ + KSPGetPC(ksp,&pc); + if (solver_type==MUMPSPACKAGE_LU){ +@@ -132,9 +132,7 @@ + PCFactorSetMatSolverPackage(pc,MATSOLVERMUMPS); + #endif + } +- #endif + +- #if defined(_PARALLEL_) && _PETSC_MAJOR_==3 + /*Stokes: */ + if (solver_type==StokesSolverEnum){ + /*Make indices out of doftypes: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12016) +@@ -29,10 +29,8 @@ + } + + /*In parallel, we need to gather the converged status: */ +- #ifdef _PARALLEL_ + MPI_Allreduce ( (void*)&num_notconverged,(void*)&total_notconverged,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); + num_notconverged=total_notconverged; +- #endif + _printf_(VerboseConvergence()," #elements above convergence criterion = %i\n",num_notconverged); + + /*Free ressources:*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12016) +@@ -91,7 +91,6 @@ + } + } + +- #ifdef _PARALLEL_ + /*Ok, broadcast to other cpus: */ + MPI_Bcast(&numanalyses,1,MPI_INT,0,MPI_COMM_WORLD); + if(my_rank!=0){ +@@ -110,7 +109,6 @@ + MPI_Bcast(string,stringlength,MPI_CHAR,0,MPI_COMM_WORLD); + if(my_rank!=0)strings[i]=string; + } +- #endif + + /*Ok, out of strings and analyses and numanalyses, create parameters, and plug them into parameters container: */ + parameters->AddObject(new StringArrayParam(PetscOptionsStringsEnum,strings,numanalyses)); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp (revision 12016) +@@ -30,12 +30,10 @@ + maxabsvz=-INFINITY; + } + +- #ifdef _PARALLEL_ + /*Figure out minimum across the cluster: */ + MPI_Reduce (&maxabsvz,&node_maxabsvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxabsvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxabsvz=node_maxabsvz; +- #endif + + /*Assign output pointers:*/ + *pmaxabsvz=maxabsvz; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp (revision 12015) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp (revision 12016) +@@ -58,10 +58,8 @@ + } + } + +- #ifdef _PARALLEL_ + MPI_Allreduce ( (void*)&mass_flux,(void*)&all_mass_flux,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD); + mass_flux=all_mass_flux; +- #endif + + /*Free ressources:*/ + for(j=0;jparameters->AddObject(new StringParam(OutputfilenameEnum,outputfilename)); + +-#endif +- + } + + /*}}}1*/ Index: /issm/oecreview/Archive/12010-12040/ISSM-12016-12017.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12016-12017.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12016-12017.diff (revision 12325) @@ -0,0 +1,165 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12017) +@@ -1,5 +1,5 @@ + from model import * +-from TriMesh.Python import * ++from TriMesh import * + + #md=model() + #md=triangle(md,'../Exp/Square.exp',150000); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/python-binding.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/python-binding.h (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/python-binding.h (revision 12017) +@@ -3,4 +3,5 @@ + + #include "./io/pythonio.h" + #include "./include/python_macros.h" ++ + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp (revision 12017) +@@ -9,8 +9,6 @@ + #endif + + +-#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) +- + #define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol + #define NO_IMPORT + +@@ -36,5 +34,3 @@ + } + return 1; + } +- +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12017) +@@ -15,7 +15,6 @@ + #include "../../include/include.h" + #include "../../shared/shared.h" + +-#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) + /*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{1*/ + void FetchData(char** pstring,PyObject* py_unicode){ + +@@ -71,4 +70,3 @@ + + } + /*}}}*/ +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 12017) +@@ -8,8 +8,6 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) +- + #define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol + #define NO_IMPORT + +@@ -65,5 +63,3 @@ + + } + /*}}}*/ +- +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgGeom.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgGeom.cpp (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgGeom.cpp (revision 12017) +@@ -1,8 +1,13 @@ ++/*!\file BamgGeom.cpp ++ */ ++ + #include +-#include "../objects.h" +-#include "../../io/io.h" +-#include "../../shared/shared.h" ++#include "../../../objects/objects.h" ++#include "../../../io/io.h" ++#include "../../../shared/shared.h" ++#include "../../io/pythonio.h" + ++ + /*Constructors/Destructors*/ + /*FUNCTION BamgGeom::BamgGeom(void* module_struct){{{1*/ + BamgGeom::BamgGeom(void* module_struct){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgMesh.cpp (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgMesh.cpp (revision 12017) +@@ -1,8 +1,13 @@ ++/*!\file BamgMesh.cpp ++ */ ++ + #include +-#include "../objects.h" +-#include "../../io/io.h" +-#include "../../shared/shared.h" ++#include "../../../objects/objects.h" ++#include "../../../io/io.h" ++#include "../../../shared/shared.h" ++#include "../../io/pythonio.h" + ++ + /*Constructors/Destructors*/ + /*FUNCTION BamgMesh::BamgMesh(void* module_struct){{{1*/ + BamgMesh::BamgMesh(void* module_struct){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgOpts.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgOpts.cpp (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/objects/Bamg/BamgOpts.cpp (revision 12017) +@@ -1,8 +1,12 @@ ++/*!\file BamgOpts.cpp ++ */ ++ + #include +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../objects.h" +-#include "../../io/io.h" ++#include "../../../objects/objects.h" ++#include "../../../io/io.h" ++#include "../../../shared/shared.h" ++#include "../../io/pythonio.h" ++#include "../../../include/include.h" + + /*Constructors/Destructors*/ + /*FUNCTION BamgOpts::BamgOpts(void* module_struct){{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/python/pythonincludes.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/python/pythonincludes.h (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/python/pythonincludes.h (revision 12017) +@@ -9,8 +9,6 @@ + #include "Python.h" + #include "arrayobject.h" + +- +- + #ifdef _HAVE_BOOST_ + using namespace std; + #include +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 12016) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 12017) +@@ -11,7 +11,7 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) ++#ifdef _HAVE_PYTHON_ + #include "./python/pythonincludes.h" + #endif + Index: /issm/oecreview/Archive/12010-12040/ISSM-12017-12018.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12017-12018.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12017-12018.diff (revision 12325) @@ -0,0 +1,437 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp (revision 12018) +@@ -10,9 +10,6 @@ + + #include "../shared.h" + #include "../../include/include.h" +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "mex.h" +-#endif + + ErrorException::ErrorException(const string &what_arg){ + +@@ -44,13 +41,8 @@ + printf("%s%s","Error message: ",what()); + } + else{ +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- mexErrMsgTxt(exprintf("\n??? Error using ==> %s at %i\n%s error message: %s\n", +- file_name.c_str(),file_line,function_name.c_str(),what())); +- #else +- printf("\n[%i] ??? Error using ==> %s:%i\n",my_rank,file_name.c_str(),file_line); +- printf("[%i] %s error message: %s\n\n",my_rank,function_name.c_str(),what()); +- #endif ++ printf("\n[%i] ??? Error using ==> %s:%i\n",my_rank,file_name.c_str(),file_line); ++ printf("[%i] %s error message: %s\n\n",my_rank,function_name.c_str(),what()); + } + return; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Synchronize.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Synchronize.sh (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Synchronize.sh (revision 12018) +@@ -28,9 +28,6 @@ + #include "./Verbosity.h" + #include "../../include/macros.h" + #include "../Exceptions/exceptions.h" +-#ifdef _SERIAL_ +-#include +-#endif + /*}}}*/ + + /*Verbosityt levels*/ +@@ -139,39 +136,13 @@ + + if(level<0) _error_("vebosity level should be a positive integer (user provided %i)",level); + +-#ifdef _SERIAL_ +- +- mxArray* output=NULL; +- mxArray* input=NULL; +- input=mxCreateDoubleScalar((double)level); +- +- mexCallMATLAB(0,&output,1,&input,"SetVerbosityLevel"); +-#else +- + verbositylevel = level; + +-#endif + }/*}}}*/ + /*FUNCTION GetVerbosityLevel {{{*/ + int GetVerbosityLevel(void){ +-#ifdef _SERIAL_ +- +- mxArray* output=NULL; +- mxArray* input=NULL; +- double level; +- +- mexCallMATLAB(1,&output,0,&input,"GetVerbosityLevel"); +- level=mxGetScalar(output); +- +- verbositylevel = (int)level; +- return verbositylevel; +- +-#else +- + _assert_(verbositylevel>=0); + return verbositylevel; +- +-#endif + }/*}}}*/ + END + #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 12018) +@@ -29,13 +29,7 @@ + numanalyses=0; + parameters->FindParam(&strings,&numanalyses,PetscOptionsStringsEnum); + +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) //do not take this away, because ISSM loads analyses as a Double Param instead of a DoubleVec Param when running with only 1 analysis +- if(numanalyses==1){ analyses=(double*)xmalloc(1*sizeof(double)); parameters->FindParam(analyses,PetscOptionsAnalysesEnum); +- } +- else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); +- #else + parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); +- #endif + + if(numanalyses==0)return NULL; //we did not find petsc options, don't bother. + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp (revision 12018) +@@ -17,9 +17,6 @@ + #include "./Verbosity.h" + #include "../../include/macros.h" + #include "../Exceptions/exceptions.h" +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include +-#endif + /*}}}*/ + + /*Verbosityt levels*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/PrintfFunction.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/PrintfFunction.cpp (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/PrintfFunction.cpp (revision 12018) +@@ -8,10 +8,6 @@ + #include "../shared/shared.h" + #include "../include/include.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "mex.h" +-#endif +- + int PrintfFunction(const char* format,...){ + /*http://linux.die.net/man/3/vsnprintf*/ + +@@ -52,11 +48,7 @@ + } + + /*Ok, if we are running in parallel, get node 0 to print*/ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- mexPrintf(buffer); +-#else + if(my_rank==0)printf(buffer); +-#endif + + /*Clean up and return*/ + xfree((void**)&buffer); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp (revision 12018) +@@ -77,35 +77,6 @@ + /*Process petsc options to see if we are using special types of external solvers: {{{1*/ + PetscOptionsDetermineSolverType(&solver_type); + +- /*In serial mode, the matrices have been loaded as MPIAIJ or AIJ matrices. +- We need to convert them if we are going to run the solvers successfully: */ +- #ifdef _SERIAL_ +- #if _PETSC_MAJOR_ == 2 +- if (solver_type==MUMPSPACKAGE_LU){ +- /*Convert Kff to MATTAIJMUMPS: */ +- MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==MUMPSPACKAGE_CHOL){ +- /*Convert Kff to MATTSBAIJMUMPS: */ +- MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==SPOOLESPACKAGE_LU){ +- /*Convert Kff to MATTSBAIJMUMPS: */ +- MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==SPOOLESPACKAGE_CHOL){ +- /*Convert Kff to MATTSBAIJMUMPS: */ +- MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==SUPERLUDISTPACKAGE){ +- /*Convert Kff to MATTSBAIJMUMPS: */ +- MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==StokesSolverEnum){ +- _error_("Petsc 2 does not support multi-physics solvers"); +- } +- #endif +- #endif + /*}}}*/ + /*Check the solver is available: {{{1*/ + if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 12018) +@@ -33,10 +33,6 @@ + if(df) df_vector = df->vector; + + /*In serial mode, the Petsc Options database has not been initialized properly: */ +- #ifdef _SERIAL_ +- parameters->FindParam(&analysis_type,AnalysisTypeEnum); +- PetscOptionsFromAnalysis(parameters,analysis_type); +- #endif + + SolverxPetsc(&uf_vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/triangle/triangleincludes.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/triangle/triangleincludes.h (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/triangle/triangleincludes.h (revision 12018) +@@ -5,14 +5,10 @@ + #ifndef _TRIANGLE_INCLUDES_H_ + #define _TRIANGLE_INCLUDES_H_ + +-#ifdef _SERIAL_ +- + #ifdef _C_ //only valid for iso C, not C++ + /*Triangle includes: */ + #include "triangle.h" + #endif //#ifdef _C_ + +-#endif //ifdef _SERIAL_ + +- + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h (revision 12018) +@@ -15,10 +15,6 @@ + + #include "../toolkitsenums.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "mex.h" +-#endif +- + /*}}}*/ + class SeqVec; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h (revision 12018) +@@ -15,10 +15,6 @@ + + #include "../toolkitsenums.h" + +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +-#include "mex.h" +-#endif +- + /*}}}*/ + + class SeqVec{ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatInvert.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatInvert.cpp (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatInvert.cpp (revision 12018) +@@ -54,12 +54,8 @@ + /*Assemble inverse: */ + MatAssemblyBegin(inv,MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(inv,MAT_FINAL_ASSEMBLY); +- +- #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- MatConvert(inv, MATSEQAIJ,MAT_REUSE_MATRIX,&inv); +- #else +- MatConvert(inv, MATMPIAIJ,MAT_REUSE_MATRIX,&inv); +- #endif ++ ++ MatConvert(inv, MATMPIAIJ,MAT_REUSE_MATRIX,&inv); + + /*Free ressources:*/ + MatFree(&identity); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp (revision 12017) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp (revision 12018) +@@ -123,20 +123,7 @@ + /*}}}*/ + /*FUNCTION DoubleVecParam::GetParameterValue(int** pintarray,int* pM){{{1*/ + void DoubleVecParam::GetParameterValue(int** pintarray,int* pM){ +-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) +- int* output=NULL; +- int i; +- +- /*Cast values into integers*/ +- output=(int*)xmalloc(M*sizeof(int)); +- for(i=0;i= 3 + PetscOptionsGetString(PETSC_NULL,"-ksp_type",ksp_type,49,&flg); +@@ -73,22 +72,20 @@ + else{ + MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,fromlocalsize); + } +- /*}}}*/ +- /*Process petsc options to see if we are using special types of external solvers: {{{1*/ ++ ++ /*Process petsc options to see if we are using special types of external solvers*/ + PetscOptionsDetermineSolverType(&solver_type); + +- /*}}}*/ +- /*Check the solver is available: {{{1*/ ++ /*Check the solver is available*/ + if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ +- #if _PETSC_MAJOR_ >=3 +- #ifndef _HAVE_MUMPS_ +- _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); ++ #if _PETSC_MAJOR_ >=3 ++ #ifndef _HAVE_MUMPS_ ++ _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); ++ #endif + #endif +- +- #endif + } +- /*}}}*/ +- /*Prepare solver:{{{1*/ ++ ++ /*Prepare solver*/ + KSPCreate(MPI_COMM_WORLD,&ksp); + KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); + KSPSetFromOptions(ksp); +@@ -123,18 +120,17 @@ + } + #endif + +- /*}}}*/ +- /*If there is an initial guess for the solution, use it, except if we are using the MUMPS direct solver, where any initial guess will crash Petsc: {{{1*/ ++ /*If there is an initial guess for the solution, use it ++ * except if we are using the MUMPS direct solver ++ * where any initial guess will crash Petsc*/ + if (uf0){ +- if( (solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ ++ if((solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ + KSPSetInitialGuessNonzero(ksp,PETSC_TRUE); + } + } +- /*}}}*/ +- +- if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); + + /*Solve: */ ++ if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); + KSPSolve(ksp,pf,uf); + + /*Check convergence*/ Index: /issm/oecreview/Archive/12010-12040/ISSM-12021-12022.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12021-12022.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12021-12022.diff (revision 12325) @@ -0,0 +1,88 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 12021) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 12022) +@@ -34,7 +34,7 @@ + double start_init, finish_init; + int ierr; + +- MODULEBOOT(); ++ ISSMBOOT(); + + /*Initialize environments: Petsc, MPI, etc...: */ + #ifdef _HAVE_PETSC_ +@@ -140,8 +140,7 @@ + #endif + + /*end module: */ +- MODULEEND(); ++ ISSMEND(); + + return 0; //unix success return; + } +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12021) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12022) +@@ -19,7 +19,6 @@ + * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ + +-//Module Boot //{{{ + #define MODULEBOOT(); ModuleBoot(); \ + try{ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 12021) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 12022) +@@ -26,7 +26,7 @@ + if(matrix){ + + #ifdef _HAVE_PETSC_ +- PetscMatrixToDoubleMatrix(&tmatrix_ptr,&rows,&cols,matrix->matrix); ++ PetscMatrixToDoubleMatrix(&matrix_ptr,&rows,&cols,matrix->matrix); + #else + matrix_ptr=matrix->matrix->ToSerial(); + matrix->matrix->GetSize(&rows,cols); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h (revision 12021) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h (revision 12022) +@@ -39,16 +39,16 @@ + ((void) 0) + #endif + /*}}}*/ +-/* MODULEBOOT/MODULEEND {{{1*/ ++/* ISSMBOOT/ISSMEND {{{1*/ + + /*The following macros hide the error exception handling in a matlab module. Just put +- * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions ++ * ISSMBOOT(); and ISSMEND(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ + +-#define MODULEBOOT(); \ ++#define ISSMBOOT(); \ + try{ + +-#define MODULEEND(); }\ ++#define ISSMEND(); }\ + catch(ErrorException &exception){\ + exception.Report(); \ + return 1;\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12021) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12022) +@@ -15,8 +15,8 @@ + #sources + #Core sources{{{1 + core_sources = ./issm.h\ +- ./issm-binding.h\ +- ./include/macros.h\ ++ ./issm-binding.h\ ++ ./include/macros.h\ + ./include/typedefs.h\ + ./include/types.h\ + ./include/include.h\ Index: /issm/oecreview/Archive/12010-12040/ISSM-12022-12023.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12022-12023.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12022-12023.diff (revision 12325) @@ -0,0 +1,41 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 12022) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 12023) +@@ -1,7 +1,6 @@ + INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ + EXEEXT=$(WRAPPEREXT) + #Bin programs {{{1 +- + if MODULES + if MATLAB + bin_PROGRAMS = AverageFilter\ +@@ -53,18 +52,18 @@ + AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER + + if MATLAB +-AM_LDFLAGS = $(MEXLINK) ++AM_LDFLAGS = $(MEXLINK) + AM_CXXFLAGS += -D_HAVE_MATLAB_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread +-LDADD += $(MEXLIB) ../c/libISSMMatlab.a +- ++LDADD += $(MEXLIB) ../c/libISSMMatlab.a + endif + + if PYTHON +-AM_LDFLAGS = $(PYTHONLINK) ++AM_LDFLAGS = $(PYTHONLINK) + AM_CXXFLAGS += -D_HAVE_PYTHON_ -DNPY_NO_DEPRECATED_API + LDADD += $(BOOSTLIB) $(PYTHONLIB) ../c/libISSMPython.a + endif + ++LDADD += ../c/libISSMCore.a ../c/libISSMModules.a + + #Optimization flags: + AM_CXXFLAGS += $(CXXOPTFLAGS) +@@ -177,5 +176,4 @@ + + TriMeshRefine_SOURCES = TriMeshRefine/TriMeshRefine.cpp\ + TriMeshRefine/TriMeshRefine.h +- + #}}} Index: /issm/oecreview/Archive/12010-12040/ISSM-12023-12024.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12023-12024.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12023-12024.diff (revision 12325) @@ -0,0 +1,40 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp (revision 12023) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp (revision 12024) +@@ -1,26 +1,21 @@ + /* \file PetscVectorToDoubleVector.cpp + */ + +- + #ifdef HAVE_CONFIG_H + #include + #else + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +- + /*Petsc includes: */ + #include "petscmat.h" + #include "petscvec.h" + #include "petscksp.h" + +-/*Petsc includes: */ + #include "mex.h" +- + #include "../../shared/shared.h" + #include + +- + void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){ + + int i; +@@ -32,7 +27,7 @@ + mxArray* dataref=NULL; + + /*Get size of vector: */ +- if(vector){ ++ if(petsc_vector){ + VecGetSize(petsc_vector,&rows); + if(rows){ + idxm=(int*)xmalloc(rows*sizeof(int)); Index: /issm/oecreview/Archive/12010-12040/ISSM-12024-12025.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12024-12025.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12024-12025.diff (revision 12325) @@ -0,0 +1,81 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h (revision 12024) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h (revision 12025) +@@ -5,7 +5,6 @@ + #ifndef _TRIMESH_H + #define _TRIMESH_H + +- + #ifdef HAVE_CONFIG_H + #include + #else +@@ -30,27 +29,27 @@ + + #ifdef _HAVE_MATLAB_ + /* serial input macros: */ +-#define DOMAINOUTLINE (mxArray *)prhs[0] +-#define AREA (mxArray *)prhs[1] +-#define ORDER (mxArray *)prhs[2] ++#define DOMAINOUTLINE (mxArray *)prhs[0] ++#define AREA (mxArray *)prhs[1] ++#define ORDER (mxArray *)prhs[2] + /* serial output macros: */ +-#define INDEX (mxArray**)&plhs[0] +-#define X (mxArray**)&plhs[1] +-#define Y (mxArray**)&plhs[2] +-#define SEGMENTS (mxArray**)&plhs[3] ++#define INDEX (mxArray**)&plhs[0] ++#define X (mxArray**)&plhs[1] ++#define Y (mxArray**)&plhs[2] ++#define SEGMENTS (mxArray**)&plhs[3] + #define SEGMENTMARKERLIST (mxArray**)&plhs[4] + #endif + + #ifdef _HAVE_PYTHON_ + /* serial input macros: */ +-#define DOMAINOUTLINE PyTuple_GetItem(args,0) +-#define AREA PyTuple_GetItem(args,1) +-#define ORDER PyTuple_GetItem(args,2) ++#define DOMAINOUTLINE PyTuple_GetItem(args,0) ++#define AREA PyTuple_GetItem(args,1) ++#define ORDER PyTuple_GetItem(args,2) + /* serial output macros: */ +-#define INDEX output,0 +-#define X output,1 +-#define Y output,2 +-#define SEGMENTS output,3 ++#define INDEX output,0 ++#define X output,1 ++#define Y output,2 ++#define SEGMENTS output,3 + #define SEGMENTMARKERLIST output,4 + #endif + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.cpp (revision 12024) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.cpp (revision 12025) +@@ -32,14 +32,12 @@ + FetchData(&area,AREA); + FetchData(&order,ORDER); + +- + /*Read domain outline: */ + domain=DomainOutlineRead(domainname,false); + + /*call x core: */ + TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,area,order); + +- + /*write outputs: */ + WriteData(INDEX,index); + WriteData(X,x); +@@ -57,7 +55,6 @@ + + /*end module: */ + MODULEEND(); +- + } + + void TriMeshUsage(void) //{{{1 Index: /issm/oecreview/Archive/12010-12040/ISSM-12025-12026.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12025-12026.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12025-12026.diff (revision 12325) @@ -0,0 +1,133 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/AnalysisConfiguration.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/AnalysisConfiguration.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/AnalysisConfiguration.m (revision 12026) +@@ -0,0 +1,58 @@ ++function [analyses,numanalyses]=AnalysisConfiguration(solutiontype), ++%ANALYSISCONFIGURATION - return type of analyses, number of analyses ++% ++% Usage: ++% [analyses, numanalyses]=AnalysisConfiguration(solutiontype); ++ ++ ++ ++switch solutiontype, ++ ++ case DiagnosticSolutionEnum, ++ numanalyses=5; ++ analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum]; ++ ++ case SteadystateSolutionEnum, ++ numanalyses=7; ++ analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum;ThermalAnalysisEnum;MeltingAnalysisEnum]; ++ ++ case ThermalSolutionEnum, ++ numanalyses=2; ++ analyses=[ThermalAnalysisEnum;MeltingAnalysisEnum]; ++ ++ case EnthalpySolutionEnum, ++ numanalyses=1; ++ analyses=[EnthalpyAnalysisEnum]; ++ ++ case PrognosticSolutionEnum, ++ numanalyses=1; ++ analyses=[PrognosticAnalysisEnum]; ++ ++ case BalancethicknessSolutionEnum, ++ numanalyses=1; ++ analyses=[BalancethicknessAnalysisEnum]; ++ ++ case SurfaceSlopeSolutionEnum, ++ numanalyses=1; ++ analyses=[SurfaceSlopeAnalysisEnum]; ++ ++ case BedSlopeSolutionEnum, ++ numanalyses=1; ++ analyses=[BedSlopeAnalysisEnum]; ++ ++ case TransientSolutionEnum, ++ numanalyses=9; ++ analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum;ThermalAnalysisEnum;MeltingAnalysisEnum;EnthalpyAnalysisEnum;PrognosticAnalysisEnum]; ++ ++ case FlaimSolutionEnum, ++ numanalyses=1; ++ analyses=[FlaimAnalysisEnum]; ++ ++ case HydrologySolutionEnum, ++ numanalyses=3; ++ analyses=[BedSlopeAnalysisEnum;SurfaceSlopeAnalysisEnum;HydrologyAnalysisEnum]; ++ ++ otherwise ++ error('%s%s%s',' solution type: ',EnumToString(solutiontype),' not supported yet!'); ++ ++end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/MatlabProcessPatch.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/MatlabProcessPatch.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/MatlabProcessPatch.m (revision 12026) +@@ -0,0 +1,65 @@ ++function structure=MatlabProcessPatch(structure); ++%PROCESSPATCH - create a structure from a patch ++% ++% Usage: ++% Result=ProcessPatch(Result); ++ ++%return if there is no fiel Patch ++if (~isfield(structure,'Patch')), ++ return; ++end ++ ++%loop over steps ++for i=1:length(structure), ++ ++ %Get Patch for current step ++ Patch=structure(i).Patch; ++ numvertices=structure(i).PatchVertices; ++ ++ %check that Patch is not empty ++ if length(Patch)==0 continue; end ++ ++ %Get number of fields; ++ fields=unique(Patch(:,1)); ++ steps=unique(Patch(:,2)); ++ ++ %parse steps ++ for j=1:length(steps), ++ ++ posstep=find(Patch(:,2)==steps(j)); ++ ++ %Take all the lines of the Patch for this timestep ++ temporarypatch=Patch(posstep,:); ++ time=temporarypatch(1,3); ++ step=temporarypatch(1,2); ++ ++ %parse fields ++ for i=1:length(fields), ++ ++ %get name ++ fieldname=EnumToString(fields(i)); ++ ++ %get line positions ++ pos=find(temporarypatch(:,1)==fields(i)); ++ ++ %Fill Result structure ++ structure(step).steps=step; ++ structure(step).time=time; ++ structure(step).(fieldname).element=temporarypatch(pos,4); ++ structure(step).(fieldname).interpolation=temporarypatch(pos,5); ++ structure(step).(fieldname).index=temporarypatch(pos,6:5+numvertices); ++ if structure(step).(fieldname).interpolation==P1Enum, ++ structure(step).(fieldname).value=temporarypatch(pos,6+numvertices:end); ++ end ++ if structure(step).(fieldname).interpolation==P0Enum, ++ structure(step).(fieldname).value=temporarypatch(pos,6+numvertices); ++ end ++ ++ end ++ end ++end ++ ++%remove fields ++structure=rmfield(structure,'Patch'); ++structure=rmfield(structure,'PatchVertices'); ++structure=rmfield(structure,'PatchNodes'); Index: /issm/oecreview/Archive/12010-12040/ISSM-12026-12027.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12026-12027.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12026-12027.diff (revision 12325) @@ -0,0 +1,4829 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test401.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test401.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test401.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test141.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test141.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test141.m (revision 12027) +@@ -1,30 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +-md.cluster=none; +-md.transient.isdiagnostic=0; +-md.transient.isprognostic=0; +-md.transient.isthermal=1; +-md.transient.isgroundingline=0; +-md.thermal.isenthalpy=1; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Enthalpy1','Waterfraction1','Temperature1',... +- 'Enthalpy2','Waterfraction2','Temperature2',... +- 'Enthalpy3','Waterfraction3','Temperature3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Enthalpy),... +- (md.results.TransientSolution(1).Waterfraction),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(2).Enthalpy),... +- (md.results.TransientSolution(2).Waterfraction),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(3).Enthalpy),... +- (md.results.TransientSolution(3).Waterfraction),... +- (md.results.TransientSolution(3).Temperature),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test303.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test303.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test303.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'hutter','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test205.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test205.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test205.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test107.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test107.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test107.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,2); +-md.cluster=none; +-md=setflowequation(md,'stokes','all'); +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test605.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test605.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test605.m (revision 12027) +@@ -1,14 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=extrude(md,6,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test443.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test443.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test443.m (revision 12027) +@@ -1,19 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,5,1); +-md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','tiling'); +-md.cluster=none; +-md.diagnostic.reltol=0.4; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-06,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test345.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test345.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test345.m (revision 12027) +@@ -1,35 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.timestepping.time_adapt=1; +-md.timestepping.final_time=600; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test507.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test507.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test507.m (revision 12027) +@@ -1,26 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',20000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test409.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test409.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test409.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,5,1); +-md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','penalties'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test247.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test247.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test247.m (revision 12027) +@@ -1,46 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.prognostic.hydrostatic_adjustment='Incremental'; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test133.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test133.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test133.m (revision 12027) +@@ -1,17 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,5,1); +-%Add boundary conditions on thickness on the border +-pos=find(md.mesh.vertexonboundary); +-md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.BalancethicknessSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test435.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test435.m (revision 12027) +@@ -1,21 +0,0 @@ +-%test partitioning, and partition averaging +-md=triangle(model,'../Exp/Square.exp',30000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-%partitioning +-md.qmu.numberofpartitions=100; +-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions); +-md.qmu.partition=md.qmu.partition-1; +- +-vector=(1:1:md.mesh.numberofvertices)'; +-vector_on_partition=AreaAverageOntoPartition(md,vector); +-vector_on_nodes=vector_on_partition(md.qmu.partition+1); +- +-field_names ={'vector_on_nodes'}; +-field_tolerances={1e-11}; +-field_values={... +- vector_on_nodes,... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test337.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test337.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test337.m (revision 12027) +@@ -1,33 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'FrictionCoefficient'}; +-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=0*2*10^-7; +-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.FrictionCoefficient),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test239.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test239.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test239.m (revision 12027) +@@ -1,17 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',120000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,2,1); +-md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','pattyn'); +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test321.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test321.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test321.m (revision 12027) +@@ -1,14 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md=extrude(md,5,0.5); +-md.cluster=none; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test223.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test223.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test223.m (revision 12027) +@@ -1,33 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'MaterialsRheologyBbar'}; +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); +-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.MaterialsRheologyBbar),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test125.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test125.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test125.m (revision 12027) +@@ -1,15 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,5,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,SurfaceSlopeSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'SurfaceSlopeX','SurfaceSlopeY'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.SurfaceSlopeSolution.SurfaceSlopeX),... +- (md.results.SurfaceSlopeSolution.SurfaceSlopeY),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test623.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test623.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test623.m (revision 12027) +@@ -1,32 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=meshconvert(md); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +- +-%control parameters +-md.inversion.nsteps=2; +-md.balancethickness.stabilization=3; +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'BalancethicknessThickeningRate'}; +-md.inversion.thickness_obs=md.geometry.thickness; +-md.inversion.min_parameters=-50*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=50*ones(md.mesh.numberofvertices,1); +-md.inversion.cost_functions=201*ones(md.inversion.nsteps,1); +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); +-md.inversion.gradient_scaling=10/md.constants.yts*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); +- +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'BalancethicknessThickeningRate' 'Thickness'}; +-field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; +-field_values={... +- (md.results.BalancethicknessSolution.Gradient1),... +- md.results.BalancethicknessSolution.J,... +- (md.results.BalancethicknessSolution.BalancethicknessThickeningRate),... +- (md.results.BalancethicknessSolution.Thickness) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m (revision 12027) +@@ -1,24 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md.thermal.isenthalpy=1; +-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; +-field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; +-field_values={... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.Waterfraction),... +- (md.results.SteadystateSolution.Enthalpy),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test525.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test525.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test525.m (revision 12027) +@@ -1,39 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',30000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'FrictionCoefficient'}; +-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; +-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +-md.timestepping.time_step=0; +- +-md.thermal.penalty_lock=5; +-md.cluster=none; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.SteadystateSolution.Gradient1),... +- md.results.SteadystateSolution.J,... +- (md.results.SteadystateSolution.FrictionCoefficient),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test265.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test265.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test265.m (revision 12027) +@@ -1,62 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.thermal.spctemperature=[md.thermal.spctemperature, md.thermal.spctemperature+5; 1 2]; +-md.timestepping.time_step=0.5; +-md.timestepping.final_time=2; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3',... +- 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','Temperature4','BasalforcingsMeltingRate4'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ... +- 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ... +- 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ... +- 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(4).Vx),... +- (md.results.TransientSolution(4).Vy),... +- (md.results.TransientSolution(4).Vz),... +- (md.results.TransientSolution(4).Vel),... +- (md.results.TransientSolution(4).Pressure),... +- (md.results.TransientSolution(4).Bed),... +- (md.results.TransientSolution(4).Surface),... +- (md.results.TransientSolution(4).Thickness),... +- (md.results.TransientSolution(4).Temperature),... +- (md.results.TransientSolution(4).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test427.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test427.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test427.m (revision 12027) +@@ -1,71 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.materials.rho_ice=10^7; %involved in the mass flux, make it easy +-md.geometry.thickness(:)=1; %make it easy +- +-%constrain all velocities to 1 m/yr, in the y-direction +-md.diagnostic.spcvx(:)=0; +-md.diagnostic.spcvy(:)=1; +-md.diagnostic.spcvz(:)=0; +- +-%Dakota options +- +-%partitioning +-md.qmu.numberofpartitions=20; +-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); +-md.qmu.partition=md.qmu.partition-1; +- +-%variables +-md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,0.01); +- +-%responses +-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux6=response_function('indexed_MassFlux_6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux7=response_function('indexed_MassFlux_7',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +- +-%mass flux profiles +-md.qmu.mass_flux_profiles={'../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp','../Exp/Square.exp'}; +-md.qmu.mass_flux_profile_directory=pwd; +- +-%method +-md.qmu.method =dakota_method('nond_l'); +- +-%parameters +-md.qmu.params.direct=true; +-md.qmu.params.analysis_driver='diagnostic'; +-md.qmu.params.evaluation_concurrency=1; +-md.qmu.params.interval_type='forward'; +-md.qmu.isdakota=1; +-md.diagnostic.reltol=10^-5; %tighten for qmu analyses +- +-%solve +-md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); +-md=tres(md,'dakota'); +- +-%Fields and tolerances to track changes +- +-%ok, mass flux of 3 profiles should be -3 Gt/yr -3 Gt/yr and the sum, which is -6 Gt/yr +-%we recover those mass fluxes through the mean of the response. +-%also, we recover the max velo, which should be 1m/yr. +-%we put all that data in the importancefactors, which we will use to test for success. +-%also, check that the stddev are 0. +-md.results.dakota.importancefactors=[]; +-for i=1:8, +- md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean]; +-end +-for i=1:8, +- md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev]; +-end +-field_names ={'importancefactors'}; +-field_tolerances={1e-11}; +-field_values={... +- md.results.dakota.importancefactors,... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test329.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test329.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test329.m (revision 12027) +@@ -1,47 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,5,1.2); +-md=setflowequation(md,'hutter','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test411.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test411.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test411.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,4,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md=solve(md,ThermalSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.ThermalSolution.Temperature),... +- (md.results.ThermalSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test313.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test313.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test313.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test215.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test215.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test215.m (revision 12027) +@@ -1,33 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test117.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test117.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test117.m (revision 12027) +@@ -1,19 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.transient.isdiagnostic=0; +-md.transient.isprognostic=0; +-md.transient.isthermal=1; +-md.transient.isgroundingline=0; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test453.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test453.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test453.m (revision 12027) +@@ -1,41 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md.initialization.vx(:)=0; +-md.initialization.vy(:)=0; +-md.initialization.vel(:)=0; +-md.geometry.bed=-700-abs(md.mesh.y-500000)/1000; +-md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000; +-md.geometry.thickness(:)=1300; +-md.geometry.surface=md.geometry.bed+md.geometry.thickness; +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +- +-md.surfaceforcings.mass_balance(:)=-150; +-md.transient.isdiagnostic=0; +-md.transient.isgroundingline=1; +-md.groundingline.migration='SoftMigration'; +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1',... +- 'Bed2','Surface2','Thickness2','Floatingice2',... +- 'Bed3','Surface3','Thickness3','Floatingice3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).MaskElementonfloatingice),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).MaskElementonfloatingice),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).MaskElementonfloatingice),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test615.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test615.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test615.m (revision 12027) +@@ -1,13 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.BalancethicknessSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test517.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test517.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test517.m (revision 12027) +@@ -1,22 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',30000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 +-}; +-field_values={... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test419.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test419.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test419.m (revision 12027) +@@ -1,22 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 +-}; +-field_values={... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test257.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test257.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test257.m (revision 12027) +@@ -1,64 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-md.timestepping.time_step=1; +-md.settings.output_frequency=1; +-md.timestepping.final_time=4; +- +-%Set up transient +-smb = ones(md.mesh.numberofvertices,1)*3.6; +-smb=[ smb smb*2 ]; +- +-md.surfaceforcings.mass_balance= smb; +-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; +-md.transient.isthermal=0; +- +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ... +- 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ... +- 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3', ... +- 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceforcingsMassBalance4'}; +-field_tolerances={1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; +- +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(4).Vx),... +- (md.results.TransientSolution(4).Vy),... +- (md.results.TransientSolution(4).Vel),... +- (md.results.TransientSolution(4).Pressure),... +- (md.results.TransientSolution(4).Bed),... +- (md.results.TransientSolution(4).Surface),... +- (md.results.TransientSolution(4).Thickness),... +- (md.results.TransientSolution(4).SurfaceforcingsMassBalance),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test501.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test501.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test501.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',20000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test403.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test403.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test403.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,4,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test241.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test241.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test241.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',120000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,2,1); +-md.diagnostic.viscosity_overshoot=0.0; +-md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','macayeal'); +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test305.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test305.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test305.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'hutter','../Exp/SquareHalfRight.exp','fill','macayeal'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test143.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test143.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test143.m (revision 12027) +@@ -1,53 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +-md.thermal.isenthalpy=1; +-md.thermal.stabilization=2; +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','Enthalpy1','Waterfraction1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','Enthalpy2','Waterfraction2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','Enthalpy3','Waterfraction3'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).Enthalpy),... +- (md.results.TransientSolution(1).Waterfraction),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).Enthalpy),... +- (md.results.TransientSolution(2).Waterfraction),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).Enthalpy),... +- (md.results.TransientSolution(3).Waterfraction),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test207.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test207.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test207.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,2); +-md.cluster=none; +-md=setflowequation(md,'stokes','all'); +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test109.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test109.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test109.m (revision 12027) +@@ -1,13 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test445.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test445.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test445.m (revision 12027) +@@ -1,37 +0,0 @@ +-radius=1e6; +-shelfextent=2e5; +- +-md=roundmesh(model,radius,200000); +-%fix center node to 0,0 +-rad=sqrt(md.mesh.x.^2+md.mesh.y.^2); +-pos=find(rad==min(rad)); +-md.mesh.x(pos)=0; md.mesh.y(pos)=0; %the closest node to the center is changed to be exactly at the center +-xelem=md.mesh.x(md.mesh.elements)*[1;1;1]/3; +-yelem=md.mesh.y(md.mesh.elements)*[1;1;1]/3; +-rad=sqrt(xelem.^2+yelem.^2); +-flags=zeros(md.mesh.numberofelements,1); +-pos=find(rad>=(radius-shelfextent)); +-flags(pos)=1; +-md=setmask(md,flags,''); +-md=parameterize(md,'../Par/RoundSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-md.transient.isthermal=0; +-md.transient.isprognostic=0; +-md.transient.isdiagnostic=0; +-md.transient.isgroundingline=1; +- +-%test different grounding line dynamics +-md.groundingline.migration='AgressiveMigration'; +-md=solve(md,TransientSolutionEnum); +-element_on_iceshelf_agressive=(md.results.TransientSolution.MaskElementonfloatingice); +- +-md.groundingline.migration='SoftMigration'; +-md=solve(md,TransientSolutionEnum); +-element_on_iceshelf_soft=(md.results.TransientSolution.MaskElementonfloatingice); +- +-%Fields and tolerances to track changes +-field_names ={'ElementOnIceShelfAgressive','ElementOnIceShelfSoft'}; +-field_tolerances={1e-13,1e-13}; +-field_values={element_on_iceshelf_agressive,element_on_iceshelf_soft}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test607.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test607.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test607.m (revision 12027) +@@ -1,14 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,SurfaceSlopeSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'SurfaceSlopeX','SurfaceSlopeY'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.SurfaceSlopeSolution.SurfaceSlopeX),... +- (md.results.SurfaceSlopeSolution.SurfaceSlopeY),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test347.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test347.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test347.m (revision 12027) +@@ -1,49 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,4,1.2); +-md=setflowequation(md,'hutter','all'); +-md.cluster=none; +-md.timestepping.time_adapt=1; +-md.timestepping.final_time=500; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'}; +- %'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +-% (md.results.TransientSolution(3).Vx),... +-% (md.results.TransientSolution(3).Vy),... +-% (md.results.TransientSolution(3).Vz),... +-% (md.results.TransientSolution(3).Vel),... +-% (md.results.TransientSolution(3).Pressure),... +-% (md.results.TransientSolution(3).Bed),... +-% (md.results.TransientSolution(3).Surface),... +-% (md.results.TransientSolution(3).Thickness),... +-% (md.results.TransientSolution(3).Temperature),... +-% (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test509.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test509.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test509.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',30000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'}; +-field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test249.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test249.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test249.m (revision 12027) +@@ -1,47 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; +-md.cluster=none; +-md.prognostic.hydrostatic_adjustment='Incremental'; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test331.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test331.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test331.m (revision 12027) +@@ -1,33 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test233.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test233.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test233.m (revision 12027) +@@ -1,69 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-%redo the parameter file for this special shelf. +-%constant thickness, constrained (vy=0) flow into an icefront, +-%from 0 m/yr at the grounding line. +- +-%tighten +-md.diagnostic.restol=10^-4; +- +-%needed later +-ymin=min(md.mesh.y); +-ymax=max(md.mesh.y); +-xmin=min(md.mesh.x); +-xmax=max(md.mesh.x); +- +-di=md.materials.rho_ice/md.materials.rho_water; +- +-h=1000; +-md.geometry.thickness=h*ones(md.mesh.numberofvertices,1); +-md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +-md.geometry.surface=md.geometry.bed+md.geometry.thickness; +- +-%Initial velocity and pressure +-md.initialization.vx=zeros(md.mesh.numberofvertices,1); +-md.initialization.vy=zeros(md.mesh.numberofvertices,1); +-md.initialization.vz=zeros(md.mesh.numberofvertices,1); +-md.initialization.pressure=zeros(md.mesh.numberofvertices,1); +- +-%Materials +-md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1); +-md.materials.rheology_B=paterson(md.initialization.temperature); +-md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +- +-%Boundary conditions: +-md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); +-md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); +-md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); +- +-%constrain flanks to 0 normal velocity +-pos=find(md.mesh.x==xmin | md.mesh.x==xmax); +-md.diagnostic.spcvx(pos)=0; +-md.diagnostic.spcvz(pos)=NaN; +- +-%constrain grounding line to 0 velocity +-pos=find(md.mesh.y==ymin); +-md.diagnostic.spcvx(pos)=0; +-md.diagnostic.spcvy(pos)=0; +- +-%icefront +-nodeonicefront=zeros(md.mesh.numberofvertices,1); +-pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1; +-pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:); +-diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))]; +-md.diagnostic.icefront=diagnostic.icefront; +- +-md=solve(md,DiagnosticSolutionEnum); +- +-%create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. +-%ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; +-%vy_c=ey_c.*md.mesh.y*md.constants.yts; +- +-%Fields and tolerances to track changes +-field_names ={'Vy'}; +-field_tolerances={1e-13}; +-field_values={(md.results.DiagnosticSolution.Vy)}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test135.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test135.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test135.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=meshconvert(md); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md.balancethickness.stabilization=3; +-md.initialization.vy=md.initialization.vy+400; +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.BalancethicknessSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test437.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test437.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test437.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,5,1); +-md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','tiling'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test339.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test339.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test339.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'FrictionCoefficient'}; +-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; +-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.FrictionCoefficient),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test421.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test421.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test421.m (revision 12027) +@@ -1,21 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06}; +-field_values={... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test323.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test323.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test323.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.timestepping.time_step=0; +-md.cluster=none; +-md=solve(md,ThermalSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.ThermalSolution.Temperature),... +- (md.results.ThermalSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test225.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test225.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test225.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'MaterialsRheologyBbar'}; +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); +-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.MaterialsRheologyB),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test127.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test127.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test127.m (revision 12027) +@@ -1,14 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BedSlopeSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'BedSlopeX','BedSlopeY'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.BedSlopeSolution.BedSlopeX),... +- (md.results.BedSlopeSolution.BedSlopeY),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test625.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test625.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test625.m (revision 12027) +@@ -1,40 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=meshconvert(md); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +- +-%Ice sheet only +-md=modelextract(md,md.mask.elementongroundedice); +-pos=find(md.mesh.vertexonboundary); +-md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); +- +-%control parameters +-md.inversion.thickness_obs=md.geometry.thickness; +-md.inversion.iscontrol=1; +-md.inversion.thickness_obs=md.geometry.thickness; +-md.inversion.nsteps=2; +-md.inversion.control_parameters={'Vx' 'Vy'}; +-md.balancethickness.stabilization=1; +-md.inversion.gradient_scaling=[10/md.constants.yts*ones(md.inversion.nsteps,1) 10/md.constants.yts*ones(md.inversion.nsteps,1)]; +-md.inversion.min_parameters=[-2000*ones(md.mesh.numberofvertices,1) -2000*ones(md.mesh.numberofvertices,1)]; +-md.inversion.max_parameters=[+2000*ones(md.mesh.numberofvertices,1) +2000*ones(md.mesh.numberofvertices,1)]; +-md.inversion.cost_functions=201*ones(md.inversion.nsteps,1); +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); +-md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); +- +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient1' 'Gradient2' 'Misfits' 'Vx' 'Vy' 'Thickness'}; +-field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; +-field_values={... +- (md.results.BalancethicknessSolution.Gradient1),... +- (md.results.BalancethicknessSolution.Gradient2),... +- md.results.BalancethicknessSolution.J,... +- (md.results.BalancethicknessSolution.Vx),... +- (md.results.BalancethicknessSolution.Vy),... +- (md.results.BalancethicknessSolution.Thickness) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m (revision 12027) +@@ -1,24 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md.thermal.isenthalpy=1; +-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; +-field_tolerances={1e-09,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; +-field_values={... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.Waterfraction),... +- (md.results.SteadystateSolution.Enthalpy),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test527.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test527.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test527.m (revision 12027) +@@ -1,56 +0,0 @@ +-%Simple mesh 1 +-hVertices=10000*ones(27,1); +-hVertices(1:5)=1000; +-md=bamg(model,'domain','../Exp/Pig.exp','hmax',20000,'hVertices',hVertices,'gradation',3,'geometricalmetric',1); +-x1=md.mesh.x; +-y1=md.mesh.y; +- +-%Simple mesh 2 +-md=bamg(model,'domain','../Exp/Pig.exp','hmax',10000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-x2=md.mesh.x; +-y2=md.mesh.y; +- +-%refine existing mesh 1 +-hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vy_obs,'node'); +-metric=ComputeMetric(hessian,2/9,1,1000,25*10^3,[]); +-md.miscellaneous.dummy=metric; +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1); +-x3=md2.mesh.x; +-y3=md2.mesh.y; +- +-%refine existing mesh 2 +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1); +-x4=md2.mesh.x; +-y4=md2.mesh.y; +- +-%refine existing mesh 3 +-hVertices=NaN*ones(md.mesh.numberofvertices,1); +-hVertices(find(md.mesh.vertexonboundary))=500; +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1,'hVertices',hVertices); +-x5=md2.mesh.x; +-y5=md2.mesh.y; +- +-%refine existing mesh 4 +-md2=bamg(md,'field',md.inversion.vy_obs,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',0,'err',1); +-x6=md2.mesh.x; +-y6=md2.mesh.y; +- +-%refine existing mesh 5 +-md2=bamg(md,'field',[md.inversion.vy_obs md.geometry.thickness],'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',1,'err',[10 100]); +-x7=md2.mesh.x; +-y7=md2.mesh.y; +- +-%Fields and tolerances to track changes +-field_names ={'x1' 'y1' 'x2' 'y2' 'x3' 'y3' 'x4' 'y4' 'x5' 'y5' 'x6' 'y6' 'x7' 'y7' }; +-field_tolerances={1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13}; +-field_values={... +- x1, y1,... +- y2, y2,... +- y3, y3,... +- y4, y4,... +- y5, y5,... +- y6, y6,... +- y7, y7,... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test267.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test267.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test267.m (revision 12027) +@@ -1,72 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=generic('name',oshostname(),'np',3); +- +-md.timestepping.time_step=1; +-md.settings.output_frequency=1; +-md.timestepping.final_time=4; +- +-smb = ones(md.mesh.numberofvertices,1)*3.6; +-smb=[ smb smb*-1 ]; +- +-md.surfaceforcings.mass_balance= smb; +-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; +-md.transient.isthermal=0; +-%Dakota options +- +-%partitioning +-md.qmu.numberofpartitions=20; +-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); +-md.qmu.partition=md.qmu.partition-1; +- +-%variables +-md.qmu.variables.surface_mass_balance=normal_uncertain('scaled_SurfaceforcingsMassBalance',1,0.1); +- +-%responses +-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.IceVolume=response_function('IceVolume',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +-md.qmu.responses.massFlux6=response_function('indexed_MassFlux_6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +- +-%mass flux profiles +-md.qmu.mass_flux_profiles={'../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp'}; +-md.qmu.mass_flux_profile_directory=pwd; +- +-%% nond_sampling study +-md.qmu.method=dakota_method('nond_samp'); +-md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),'seed',1234,'samples',20,'sample_type','lhs'); +- +-%parameters +-md.qmu.params.direct=true; +-md.qmu.params.analysis_driver=''; +-md.qmu.params.analysis_components=''; +-md.qmu.params.evaluation_concurrency=1; +-md.qmu.params.interval_type='forward'; +-md.qmu.isdakota=1; +- +-md.diagnostic.reltol=10^-5; %tighten for qmu analyses +-md.transient.requested_outputs=IceVolumeEnum(); +- +-%solve +-md=solve(md,TransientSolutionEnum,'overwrite','y'); +-md=tres(md,'dakota'); +- +-%Fields and tolerances to track changes +-md.results.dakota.importancefactors=[]; +-for i=1:8, +- md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean]; +-end +-for i=1:8, +- md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev]; +-end +-field_names ={'importancefactors'}; +-field_tolerances={1e-11}; +-field_values={... +- md.results.dakota.importancefactors,... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test429.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test429.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test429.m (revision 12027) +@@ -1,38 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',170000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'FrictionCoefficient'}; +-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; +-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.timestepping.time_step=0; +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.SteadystateSolution.Gradient1),... +- md.results.SteadystateSolution.J,... +- (md.results.SteadystateSolution.FrictionCoefficient),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test111.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test111.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test111.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=meshconvert(md); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.prognostic.stabilization=3; +-md.prognostic.spcthickness=md.geometry.thickness; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test511.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test511.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test511.m (revision 12027) +@@ -1,35 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',30000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,2,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-12,1e-12,1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test251.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test251.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test251.m (revision 12027) +@@ -1,35 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.timestepping.time_adapt=1; +-md.timestepping.final_time=10; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test413.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test413.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test413.m (revision 12027) +@@ -1,19 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,4,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.transient.isdiagnostic=0; +-md.transient.isprognostic=0; +-md.transient.isthermal=1; +-md.transient.isgroundingline=0; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test315.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test315.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test315.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md.cluster=none; +-md=setflowequation(md,'stokes','all'); +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test217.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test217.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test217.m (revision 12027) +@@ -1,45 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test119.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test119.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test119.m (revision 12027) +@@ -1,39 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +- +- +- +- +- +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test617.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test617.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test617.m (revision 12027) +@@ -1,15 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=meshconvert(md); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +-md.balancethickness.stabilization=3; +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.BalancethicknessSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test455.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test455.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test455.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.diagnostic.isnewton=1; +-md.diagnostic.restol=0.0001; +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test519.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test519.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test519.m (revision 12027) +@@ -1,22 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',20000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,2,1); +-md=setflowequation(md,'stokes','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06 +-}; +-field_values={... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test259.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test259.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test259.m (revision 12027) +@@ -1,69 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',350000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-md.timestepping.time_step=1; +-md.settings.output_frequency=1; +-md.timestepping.final_time=4; +- +-%Set up transient +-smb = ones(md.mesh.numberofvertices,1)*3.6; +-smb=[ smb smb*-1 ]; +- +-md.surfaceforcings.mass_balance= smb; +-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; +-md.transient.isthermal=0; +- +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3',... +- 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceMassbalance4'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +- +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(4).Vx),... +- (md.results.TransientSolution(4).Vy),... +- (md.results.TransientSolution(4).Vz),... +- (md.results.TransientSolution(4).Vel),... +- (md.results.TransientSolution(4).Pressure),... +- (md.results.TransientSolution(4).Bed),... +- (md.results.TransientSolution(4).Surface),... +- (md.results.TransientSolution(4).Thickness),... +- (md.results.TransientSolution(4).SurfaceforcingsMassBalance),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test201.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test201.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test201.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test103.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test103.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test103.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test601.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test601.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test601.m (revision 12027) +@@ -1,13 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test503.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test503.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test503.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',20000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,3,0.9); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test341.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test341.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test341.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'FrictionCoefficient'}; +-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=[102*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; +-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.FrictionCoefficient),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test243.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test243.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test243.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.prognostic.hydrostatic_adjustment='Incremental'; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test405.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test405.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test405.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,5,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test307.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test307.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test307.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test209.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test209.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test209.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','penalties'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test609.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test609.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test609.m (revision 12027) +@@ -1,15 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=extrude(md,5,1.5); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,SurfaceSlopeSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'SurfaceSlopeX','SurfaceSlopeY'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.SurfaceSlopeSolution.SurfaceSlopeX),... +- (md.results.SurfaceSlopeSolution.SurfaceSlopeY),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test447.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test447.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test447.m (revision 12027) +@@ -1,39 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.initialization.vx(:)=0; +-md.initialization.vy(:)=0; +-md.initialization.vel(:)=0; +-md.geometry.bed=-700-abs(md.mesh.y-500000)/1000; +-md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000; +-md.geometry.thickness(:)=1000; +-md.geometry.surface=md.geometry.bed+md.geometry.thickness; +-md.surfaceforcings.mass_balance(:)=100; +-md.transient.isdiagnostic=0; +-md.transient.isgroundingline=1; +-md.groundingline.migration='AgressiveMigration'; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1',... +- 'Bed2','Surface2','Thickness2','Floatingice2',... +- 'Bed3','Surface3','Thickness3','Floatingice3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).MaskElementonfloatingice),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).MaskElementonfloatingice),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).MaskElementonfloatingice),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test349.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test349.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test349.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +-md.timestepping.time_step=0; +-md.cluster=none; +-md=solve(md,EnthalpySolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Enthalpy','Waterfraction','Temperature'}; +-field_tolerances={1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.EnthalpySolution.Enthalpy),... +- (md.results.EnthalpySolution.Waterfraction),... +- (md.results.EnthalpySolution.Temperature),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test431.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test431.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test431.m (revision 12027) +@@ -1,38 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',170000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'FrictionCoefficient'}; +-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=[102*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; +-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.timestepping.time_step=0; +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'}; +-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06}; +-field_values={... +- (md.results.SteadystateSolution.Gradient1),... +- md.results.SteadystateSolution.J,... +- (md.results.SteadystateSolution.FrictionCoefficient),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test333.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test333.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test333.m (revision 12027) +@@ -1,47 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test235.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test235.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test235.m (revision 12027) +@@ -1,92 +0,0 @@ +-md=squaremesh(model,1000000,1000000,5,5); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-%redo the parameter file for this special shelf. +-%constant thickness, constrained (vy=0) flow into an icefront, +-%from 0 m/yr at the grounding line. +- +-%needed later +-ymin=min(md.mesh.y); +-ymax=max(md.mesh.y); +-xmin=min(md.mesh.x); +-xmax=max(md.mesh.x); +- +-di=md.materials.rho_ice/md.materials.rho_water; +- +-h=1000; +-md.geometry.thickness=h*ones(md.mesh.numberofvertices,1); +-md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +-md.geometry.surface=md.geometry.bed+md.geometry.thickness; +- +-%Initial velocity and pressure +-md.initialization.vx=zeros(md.mesh.numberofvertices,1); +-md.initialization.vy=zeros(md.mesh.numberofvertices,1); +-md.initialization.vz=zeros(md.mesh.numberofvertices,1); +-md.initialization.pressure=zeros(md.mesh.numberofvertices,1); +- +-%Materials +-md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1); +-md.materials.rheology_B=paterson(md.initialization.temperature); +-md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +- +-%Boundary conditions: +-md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); +-md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); +-md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); +- +-%constrain flanks to 0 normal velocity +-pos=find(md.mesh.x==xmin | md.mesh.x==xmax); +-md.diagnostic.spcvx(pos)=0; +-md.diagnostic.spcvz(pos)=NaN; +- +-%constrain grounding line to 0 velocity +-pos=find(md.mesh.y==ymin); +-md.diagnostic.spcvx(pos)=0; +-md.diagnostic.spcvy(pos)=0; +- +-%icefront +-nodeonicefront=zeros(md.mesh.numberofvertices,1); +-pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1; +-pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:); +-diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))]; +-md.diagnostic.icefront=diagnostic.icefront; +- +-%partitioning +-md.qmu.numberofpartitions=md.mesh.numberofvertices; +-md=partitioner(md,'package','linear','npart',md.qmu.numberofpartitions); +-md.qmu.partition=md.qmu.partition-1; +- +-%Dakota options +-%variables +-md.qmu.variables.rheology_B=normal_uncertain('scaled_MaterialsRheologyB',1,.5); +- +-%responses +-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +- +-%method +-md.qmu.method =dakota_method('nond_l'); +- +-%parameters +-md.qmu.params.direct=true; +-md.qmu.params.analysis_driver='diagnostic'; +-md.qmu.params.evaluation_concurrency=1; +-md.qmu.params.interval_type='forward'; +- +-%imperative! +-md.diagnostic.reltol=10^-10; %tighten for qmu analysese +-md.qmu.isdakota=1; +- +-%solve +-md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); +- +-%Fields and tolerances to track changes +-md=tres(md,'dakota'); +-md.results.dakota.importancefactors=importancefactors(md,'scaled_MaterialsRheologyB','MaxVel')'; +-field_names ={'importancefactors'}; +-field_tolerances={1e-10}; +-field_values={... +- md.results.dakota.importancefactors,... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test137.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test137.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test137.m (revision 12027) +@@ -1,25 +0,0 @@ +- +-%Simple mesh +-md=bamg(model,'domain','../Exp/Square.exp','hmax',100000); +-x1=md.mesh.x; +-y1=md.mesh.y; +- +-%hVertices +-md=bamg(model,'domain','../Exp/Square.exp','hmax',300000,'hvertices',[10000 100000 400000 100000]'); +-x2=md.mesh.x; +-y2=md.mesh.y; +- +-%big mesh +-t0=clock; +-md=bamg(model,'domain','../Exp/Square.exp','hmax',3000); +-nbelements=md.mesh.numberofelements; +-elapsedtime=etime(clock,t0); +- +-%Fields and tolerances to track changes +-field_names ={'x1' 'y1' 'x2' 'y2' 'nbelements' 'elapsed time'}; +-field_tolerances={1e-13 1e-13 1e-13 1e-13 1e-13 0.5}; +-field_values={... +- x1, y1,... +- x2, y2,... +- nbelements,elapsedtime... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test439.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test439.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test439.m (revision 12027) +@@ -1,49 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-%partitioning +-md.qmu.numberofpartitions=10; +-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions); +-md.qmu.partition=md.qmu.partition-1; +-md.qmu.isdakota=1; +- +-%Dakota options +-%variables +-md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01); +- +-%responses +-md.qmu.responses.MaxVel=response_function('scaled_Thickness',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +- +-%method +-md.qmu.method =dakota_method('nond_l'); +- +-%parameters +-md.qmu.params.direct=true; +-md.qmu.params.analysis_driver='diagnostic'; +-md.qmu.params.evaluation_concurrency=1; +-md.qmu.params.interval_type='forward'; +- +- +-%imperative! +-md.diagnostic.reltol=10^-5; %tighten for qmu analysese +- +-%solve +-md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); +-md=tres(md,'dakota'); +- +-%test on thickness +-h=zeros(md.qmu.numberofpartitions,1); +-for i=1:md.qmu.numberofpartitions, +- h(i)=md.qmu.results.dresp_out(i).mean; +-end +- +-%project onto grid +-thickness=h(md.qmu.partition+1); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-11}; +-field_values={thickness}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test121.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test121.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test121.m (revision 12027) +@@ -1,45 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test521.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test521.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test521.m (revision 12027) +@@ -1,39 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',10000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +- +-%impose hydrostatic equilibrium (required by Stokes) +-md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +-md.geometry.surface=md.geometry.bed+md.geometry.thickness; +-md=extrude(md,3,1); +-md=setflowequation(md,'stokes','all'); +-md=modelextract(md,md.mask.elementonfloatingice); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'MaterialsRheologyBbar'}; +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); +-md.inversion.gradient_scaling=10^8*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'MaterialsRheologyB' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.MaterialsRheologyB),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test261.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test261.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test261.m (revision 12027) +@@ -1,69 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',350000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-md.timestepping.time_step=1; +-md.settings.output_frequency=1; +-md.timestepping.final_time=4; +- +-%Set up transient +-smb = ones(md.mesh.numberofvertices,1)*3.6; +-smb=[ smb smb*2 ]; +- +-md.surfaceforcings.mass_balance= smb; +-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; +-md.transient.isthermal=0; +- +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3',... +- 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceMassbalance4'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +- +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(4).Vx),... +- (md.results.TransientSolution(4).Vy),... +- (md.results.TransientSolution(4).Vz),... +- (md.results.TransientSolution(4).Vel),... +- (md.results.TransientSolution(4).Pressure),... +- (md.results.TransientSolution(4).Bed),... +- (md.results.TransientSolution(4).Surface),... +- (md.results.TransientSolution(4).Thickness),... +- (md.results.TransientSolution(4).SurfaceforcingsMassBalance),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test423.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test423.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test423.m (revision 12027) +@@ -1,45 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',300000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-%partitioning +-md.qmu.numberofpartitions=md.mesh.numberofvertices; +-md=partitioner(md,'package','linear','npart',md.qmu.numberofpartitions); +-md.qmu.partition=md.qmu.partition-1; +-md.qmu.isdakota=1; +- +-%Dakota options +-%variables +-md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01); +-md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,.01); +-%md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,.01*ones(md.qmu.numberofpartitions,1)); +- +-%responses +-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +- +-%method +-md.qmu.method =dakota_method('nond_l'); +- +-%parameters +-md.qmu.params.direct=true; +-md.qmu.params.analysis_driver='diagnostic'; +-md.qmu.params.evaluation_concurrency=1; +-md.qmu.params.interval_type='forward'; +- +- +-%imperative! +-md.diagnostic.reltol=10^-5; %tighten for qmu analysese +- +-%solve +-md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); +- +-%Fields and tolerances to track changes +-md=tres(md,'dakota'); +-md.results.dakota.importancefactors=importancefactors(md,'scaled_FrictionCoefficient','MaxVel')'; +-field_names ={'importancefactors'}; +-field_tolerances={1e-10}; +-field_values={... +- md.results.dakota.importancefactors,... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test325.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test325.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test325.m (revision 12027) +@@ -1,19 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.transient.isdiagnostic=0; +-md.transient.isprognostic=0; +-md.transient.isthermal=1; +-md.transient.isgroundingline=0; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test227.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test227.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test227.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'MaterialsRheologyBbar'}; +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); +-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.MaterialsRheologyB),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test129.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test129.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test129.m (revision 12027) +@@ -1,15 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,5,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BedSlopeSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'BedSlopeX','BedSlopeY'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.BedSlopeSolution.BedSlopeX),... +- (md.results.BedSlopeSolution.BedSlopeY),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test529.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test529.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test529.m (revision 12027) +@@ -1,22 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',30000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.thermal.stabilization=2; +-md.transient.isdiagnostic=0; +-md.transient.isprognostic=0; +-md.transient.isthermal=1; +-md.transient.isgroundingline=0; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature1','BasalforcingsMeltingRate1', ... +- 'Temperature2','BasalforcingsMeltingRate2'}; +-field_tolerances={1e-13,1e-9,1e-13,1e-9}; +-field_values={... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test211.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test211.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test211.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.timestepping.time_step=0; +-md.cluster=none; +-md=solve(md,ThermalSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.ThermalSolution.Temperature),... +- (md.results.ThermalSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test113.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test113.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test113.m (revision 12027) +@@ -1,14 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md=extrude(md,5,3); +-md.cluster=none; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test611.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test611.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test611.m (revision 12027) +@@ -1,14 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BedSlopeSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'BedSlopeX','BedSlopeY'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.BedSlopeSolution.BedSlopeX),... +- (md.results.BedSlopeSolution.BedSlopeY),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test513.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test513.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test513.m (revision 12027) +@@ -1,35 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',30000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,2,1); +-md=setflowequation(md,'stokes','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-%The thickness wants to be lower than 1 so we contrain it to 1 +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'}; +-field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test351.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test351.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test351.m (revision 12027) +@@ -1,30 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +-md.cluster=none; +-md.transient.isdiagnostic=0; +-md.transient.isprognostic=0; +-md.transient.isthermal=1; +-md.transient.isgroundingline=0; +-md.thermal.isenthalpy=1; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Enthalpy1','Waterfraction1','Temperature1',... +- 'Enthalpy2','Waterfraction2','Temperature2',... +- 'Enthalpy3','Waterfraction3','Temperature3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Enthalpy),... +- (md.results.TransientSolution(1).Waterfraction),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(2).Enthalpy),... +- (md.results.TransientSolution(2).Waterfraction),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(3).Enthalpy),... +- (md.results.TransientSolution(3).Waterfraction),... +- (md.results.TransientSolution(3).Temperature),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test253.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test253.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test253.m (revision 12027) +@@ -1,49 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.timestepping.time_adapt=1; +-md.timestepping.final_time=10; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,... +- 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,... +- 1e-09,1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test415.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test415.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test415.m (revision 12027) +@@ -1,33 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test317.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test317.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test317.m (revision 12027) +@@ -1,13 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test219.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test219.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test219.m (revision 12027) +@@ -1,45 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test619.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test619.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test619.m (revision 12027) +@@ -1,14 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.BalancethicknessSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test457.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test457.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test457.m (revision 12027) +@@ -1,20 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,5,1); +-md=setflowequation(md,'pattyn','all'); +-md.diagnostic.isnewton=1; +-md.diagnostic.restol=0.0001; +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test301.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test301.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test301.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test203.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test203.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test203.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test105.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test105.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test105.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test603.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test603.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test603.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=meshconvert(md); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +-md.prognostic.stabilization=3; +-md.prognostic.spcthickness=md.geometry.thickness; +-md.cluster=none; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test441.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test441.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test441.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,5,1); +-md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','tiling'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test505.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test505.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test505.m (revision 12027) +@@ -1,17 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',20000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,3,0.9); +-md=setflowequation(md,'stokes','all'); +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test343.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test343.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test343.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'stokes','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'FrictionCoefficient'}; +-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=[104*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; +-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.FrictionCoefficient),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test407.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test407.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test407.m (revision 12027) +@@ -1,17 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'stokes','all'); +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test245.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test245.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test245.m (revision 12027) +@@ -1,35 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; +-md.cluster=none; +-md.prognostic.hydrostatic_adjustment='Incremental'; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test309.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test309.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test309.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,5,2); +-md=setflowequation(md,'hutter','all'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test449.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test449.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test449.m (revision 12027) +@@ -1,39 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.initialization.vx(:)=0; +-md.initialization.vy(:)=0; +-md.initialization.vel(:)=0; +-md.geometry.bed=-700-abs(md.mesh.y-500000)/1000; +-md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000; +-md.geometry.thickness(:)=1300; +-md.geometry.surface=md.geometry.bed+md.geometry.thickness; +-md.surfaceforcings.mass_balance(:)=-150; +-md.transient.isdiagnostic=0; +-md.transient.isgroundingline=1; +-md.groundingline.migration='SoftMigration'; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1',... +- 'Bed2','Surface2','Thickness2','Floatingice2',... +- 'Bed3','Surface3','Thickness3','Floatingice3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).MaskElementonfloatingice),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).MaskElementonfloatingice),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).MaskElementonfloatingice),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test131.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test131.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test131.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-%Add boundary conditions on thickness on the border +-pos=find(md.mesh.vertexonboundary); +-md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.BalancethicknessSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test531.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test531.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test531.m (revision 12027) +@@ -1,17 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',30000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.thermal.stabilization=2; +-md.timestepping.time_step=0; +-md.thermal.penalty_threshold=40; +-md=solve(md,ThermalSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-12}; +-field_values={... +- (md.results.ThermalSolution.Temperature),... +- (md.results.ThermalSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test335.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test335.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test335.m (revision 12027) +@@ -1,23 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,4,1); +-md=setflowequation(md,'hutter','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +- +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 +-}; +-field_values={... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test237.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test237.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test237.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,2); +-md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test139.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test139.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test139.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.timestepping.time_step=0; +-md.cluster=none; +-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +-md=solve(md,EnthalpySolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Enthalpy','Waterfraction','Temperature'}; +-field_tolerances={1e-13,1e-10,1e-13}; +-field_values={... +- (md.results.EnthalpySolution.Enthalpy),... +- (md.results.EnthalpySolution.Waterfraction),... +- (md.results.EnthalpySolution.Temperature),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test221.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test221.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test221.m (revision 12027) +@@ -1,48 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'stokes','all'); +-md.diagnostic.reltol=NaN; +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,... +- 1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,... +- 1e-08,1e-08,1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test123.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test123.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test123.m (revision 12027) +@@ -1,14 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,SurfaceSlopeSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'SurfaceSlopeX','SurfaceSlopeY'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.SurfaceSlopeSolution.SurfaceSlopeX),... +- (md.results.SurfaceSlopeSolution.SurfaceSlopeY),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test621.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test621.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test621.m (revision 12027) +@@ -1,31 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=setflowequation(md,'macayeal','all'); +- +-%control parameters +-md.inversion.nsteps=2; +-md.prognostic.stabilization=1; +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'BalancethicknessThickeningRate'}; +-md.inversion.thickness_obs=md.geometry.thickness; +-md.inversion.min_parameters=-50*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=50*ones(md.mesh.numberofvertices,1); +-md.inversion.cost_functions=201*ones(md.inversion.nsteps,1); +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); +-md.inversion.gradient_scaling=10/md.constants.yts*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); +- +-md.cluster=none; +-md=solve(md,BalancethicknessSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'BalancethicknessThickeningRate' 'Thickness'}; +-field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; +-field_values={... +- (md.results.BalancethicknessSolution.Gradient1),... +- md.results.BalancethicknessSolution.J,... +- (md.results.BalancethicknessSolution.BalancethicknessThickeningRate),... +- (md.results.BalancethicknessSolution.Thickness) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test523.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test523.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test523.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',20000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'FrictionCoefficient'}; +-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1) 501*ones(md.inversion.nsteps,1)]; +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7; +-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.FrictionCoefficient),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test425.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test425.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test425.m (revision 12027) +@@ -1,45 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-%Dakota options +- +-%partitioning +-md.qmu.numberofpartitions=20; +-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); +-md.qmu.partition=md.qmu.partition-1; +- +-%variables +-md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01); +-md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,0.01); +- +-%responses +-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); +- +-%method +-md.qmu.method =dakota_method('nond_l'); +- +-%parameters +-md.qmu.params.direct=true; +-md.qmu.params.analysis_driver='diagnostic'; +-md.qmu.params.evaluation_concurrency=1; +-md.qmu.params.interval_type='forward'; +- +- +-%imperative! +-md.diagnostic.reltol=10^-5; %tighten for qmu analyses +-md.qmu.isdakota=1; +- +-%solve +-md=solve(md,DiagnosticSolutionEnum,'overwrite','y'); +- +-%Fields and tolerances to track changes +-md=tres(md,'dakota'); +-md.results.dakota.importancefactors=importancefactors(md,'scaled_FrictionCoefficient','MaxVel')'; +-field_names ={'importancefactors'}; +-field_tolerances={1e-10}; +-field_values={... +- md.results.dakota.importancefactors,... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test263.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test263.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test263.m (revision 12027) +@@ -1,28 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.thermal.spctemperature=[md.thermal.spctemperature, md.thermal.spctemperature+5, md.thermal.spctemperature+10, md.thermal.spctemperature+15; 1.5 2.5 3.5 4]; +-md.timestepping.time_step=1; +-md.timestepping.final_time=4; +-md.transient.isdiagnostic=0; +-md.transient.isprognostic=0; +-md.transient.isthermal=1; +-md.transient.isgroundingline=0; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature1','BasalforcingsMeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3','Temperature4','BasalforcingsMeltingRate4'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(4).Temperature),... +- (md.results.TransientSolution(4).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test327.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test327.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test327.m (revision 12027) +@@ -1,37 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'hutter','all'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1',... +- 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2',... +- 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test229.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test229.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test229.m (revision 12027) +@@ -1,34 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'stokes','all'); +- +-%control parameters +-md.inversion.iscontrol=1; +-md.inversion.control_parameters={'MaterialsRheologyBbar'}; +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1); +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1); +-md.inversion.nsteps=2; +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1); +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1); +-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1); +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1); +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1); +-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy; +- +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'}; +-field_tolerances={1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; +-field_values={... +- (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... +- (md.results.DiagnosticSolution.MaterialsRheologyB),... +- (md.results.DiagnosticSolution.Pressure),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy) +-}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test311.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test311.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test311.m (revision 12027) +@@ -1,18 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,4,2); +-md=setflowequation(md,'hutter','../Exp/SquareHalfRight.exp','fill','macayeal'); +-md.cluster=none; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test213.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test213.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test213.m (revision 12027) +@@ -1,23 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.transient.isdiagnostic=0; +-md.transient.isprognostic=0; +-md.transient.isthermal=1; +-md.transient.isgroundingline=0; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature1','MeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test115.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test115.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test115.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +-md.timestepping.time_step=0; +-md.cluster=none; +-md=solve(md,ThermalSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.ThermalSolution.Temperature),... +- (md.results.ThermalSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test451.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test451.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test451.m (revision 12027) +@@ -1,42 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',350000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md.cluster=none; +-md.initialization.vx(:)=0; +-md.initialization.vy(:)=0; +-md.initialization.vel(:)=0; +-md.geometry.bed=-700-abs(md.mesh.y-500000)/1000; +-md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000; +-md.geometry.thickness(:)=1000; +-md.geometry.surface=md.geometry.bed+md.geometry.thickness; +-md.surfaceforcings.mass_balance(:)=100; +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','all'); +- +-md.transient.isdiagnostic=0; +-md.transient.isgroundingline=1; +-md.groundingline.migration='AgressiveMigration'; +- +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1',... +- 'Bed2','Surface2','Thickness2','Floatingice2',... +- 'Bed3','Surface3','Thickness3','Floatingice3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).MaskElementonfloatingice),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).MaskElementonfloatingice),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).MaskElementonfloatingice),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test613.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test613.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test613.m (revision 12027) +@@ -1,15 +0,0 @@ +-md=triangle(model,'../Exp/79North.exp',10000); +-md=setmask(md,'../Exp/79NorthShelf.exp',''); +-md=parameterize(md,'../Par/79North.par'); +-md=extrude(md,2,1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md=solve(md,BedSlopeSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'BedSlopeX','BedSlopeY'}; +-field_tolerances={1e-13,1e-13}; +-field_values={... +- (md.results.BedSlopeSolution.BedSlopeX),... +- (md.results.BedSlopeSolution.BedSlopeY),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test353.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test353.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test353.m (revision 12027) +@@ -1,55 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',200000); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'pattyn','all'); +-md.cluster=none; +-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +-md.initialization.temperature(:)=272; +-md.thermal.spctemperature(find(md.mesh.vertexonsurface))=272; +-md.thermal.isenthalpy=1; +-md.basalforcings.geothermalflux(:)=5; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','Enthalpy1','Waterfraction1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','Enthalpy2','Waterfraction2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','Enthalpy3','Waterfraction3'}; +-field_tolerances={1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).Enthalpy),... +- (md.results.TransientSolution(1).Waterfraction),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).Enthalpy),... +- (md.results.TransientSolution(2).Waterfraction),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).Enthalpy),... +- (md.results.TransientSolution(3).Waterfraction),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test515.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test515.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test515.m (revision 12027) +@@ -1,22 +0,0 @@ +-md=triangle(model,'../Exp/Pig.exp',30000); +-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +-md=parameterize(md,'../Par/Pig.par'); +-md=extrude(md,4,1.1); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +-md.timestepping.time_step=0; +-md=solve(md,SteadystateSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 +-}; +-field_values={... +- (md.results.SteadystateSolution.Vx),... +- (md.results.SteadystateSolution.Vy),... +- (md.results.SteadystateSolution.Vz),... +- (md.results.SteadystateSolution.Vel),... +- (md.results.SteadystateSolution.Pressure),... +- (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test417.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test417.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test417.m (revision 12027) +@@ -1,45 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','penalties'); +-md.cluster=none; +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ... +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ... +- 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05}; +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vz),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).Temperature),... +- (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vz),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).Temperature),... +- (md.results.TransientSolution(2).BasalforcingsMeltingRate),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vz),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).Temperature),... +- (md.results.TransientSolution(3).BasalforcingsMeltingRate),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test255.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test255.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test255.m (revision 12027) +@@ -1,64 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelf.par'); +-md=setflowequation(md,'macayeal','all'); +-md.cluster=none; +- +-md.timestepping.time_step=1; +-md.settings.output_frequency=1; +-md.timestepping.final_time=4; +- +-%Set up transient +-smb = ones(md.mesh.numberofvertices,1)*3.6; +-smb=[ smb smb*-1 ]; +- +-md.surfaceforcings.mass_balance= smb; +-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3]; +-md.transient.isthermal=0; +- +-md=solve(md,TransientSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ... +- 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ... +- 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3', ... +- 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceforcingsMassBalance4'}; +-field_tolerances={1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; +- +-field_values={... +- (md.results.TransientSolution(1).Vx),... +- (md.results.TransientSolution(1).Vy),... +- (md.results.TransientSolution(1).Vel),... +- (md.results.TransientSolution(1).Pressure),... +- (md.results.TransientSolution(1).Bed),... +- (md.results.TransientSolution(1).Surface),... +- (md.results.TransientSolution(1).Thickness),... +- (md.results.TransientSolution(1).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(2).Vx),... +- (md.results.TransientSolution(2).Vy),... +- (md.results.TransientSolution(2).Vel),... +- (md.results.TransientSolution(2).Pressure),... +- (md.results.TransientSolution(2).Bed),... +- (md.results.TransientSolution(2).Surface),... +- (md.results.TransientSolution(2).Thickness),... +- (md.results.TransientSolution(2).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(3).Vx),... +- (md.results.TransientSolution(3).Vy),... +- (md.results.TransientSolution(3).Vel),... +- (md.results.TransientSolution(3).Pressure),... +- (md.results.TransientSolution(3).Bed),... +- (md.results.TransientSolution(3).Surface),... +- (md.results.TransientSolution(3).Thickness),... +- (md.results.TransientSolution(3).SurfaceforcingsMassBalance),... +- (md.results.TransientSolution(4).Vx),... +- (md.results.TransientSolution(4).Vy),... +- (md.results.TransientSolution(4).Vel),... +- (md.results.TransientSolution(4).Pressure),... +- (md.results.TransientSolution(4).Bed),... +- (md.results.TransientSolution(4).Surface),... +- (md.results.TransientSolution(4).Thickness),... +- (md.results.TransientSolution(4).SurfaceforcingsMassBalance),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test319.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test319.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test319.m (revision 12027) +@@ -1,16 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',150000); +-md=meshconvert(md); +-md=setmask(md,'',''); +-md=parameterize(md,'../Par/SquareSheetConstrained.par'); +-md=setflowequation(md,'macayeal','all'); +-md.prognostic.stabilization=3; +-md.prognostic.spcthickness=md.geometry.thickness; +-md.cluster=none; +-md=solve(md,PrognosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Thickness'}; +-field_tolerances={1e-13}; +-field_values={... +- (md.results.PrognosticSolution.Thickness),... +- }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test459.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test459.m (revision 12026) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test459.m (revision 12027) +@@ -1,19 +0,0 @@ +-md=triangle(model,'../Exp/Square.exp',180000); +-md=setmask(md,'../Exp/SquareShelf.exp',''); +-md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md=extrude(md,3,1); +-md=setflowequation(md,'stokes','all'); +-md.diagnostic.isnewton=1; +-md.diagnostic.restol=0.0001; +-md=solve(md,DiagnosticSolutionEnum); +- +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.DiagnosticSolution.Vx),... +- (md.results.DiagnosticSolution.Vy),... +- (md.results.DiagnosticSolution.Vz),... +- (md.results.DiagnosticSolution.Vel),... +- (md.results.DiagnosticSolution.Pressure),... +- }; Index: /issm/oecreview/Archive/12010-12040/ISSM-12027-12028.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12027-12028.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12027-12028.diff (revision 12325) @@ -0,0 +1,178 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/nodeconnectivity.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/nodeconnectivity.m (revision 12027) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/nodeconnectivity.m (revision 12028) +@@ -1,58 +0,0 @@ +-% +-% create a node connectivity table for the elements in the model. +-% +-% [nodecon]=edgeadjacency(elem,nnodes,mxepg) +-% +-% where the required input is: +-% elem (numeric, element connectivity array (elems x nodes)) +-% +-% and the required output is: +-% nodecon (numeric, node connectivity array (nnodes x mxepg+1)) +-% +-% the optional input is: +-% nnodes (numeric, number of nodes) +-% mxepg (numeric, max elements per node) +-% +-function [nodecon]=nodeconnectivity(elem,nnodes,mxepg) +- +-if ~nargin +- help nodeconnectivity +- return +-end +- +-if ~exist('nnodes','var') || isempty(nnodes) +- nnodes=max(max(elem)); +-end +-if ~exist('mxepg','var') || isempty(mxepg) +- mxepg=25; +-end +- +-%% create the node connectivity array +- +-nodecon=zeros(nnodes,mxepg+1); +- +-% loop over the elements +- +-for i=1:size(elem,1) +- +-% loop over the nodes for each element +- +- for j=1:size(elem,2) +- if elem(i,j) +- nodecon(elem(i,j),nodecon(elem(i,j),end)+1)=i; +- nodecon(elem(i,j),end)=nodecon(elem(i,j),end)+1; +- end +- end +-end +- +-%% sort the node connectivity array +- +-% loop over the nodes +- +-for i=1:size(nodecon,1) +- if (nodecon(i,end) > 1) +- nodecon(i,1:nodecon(i,end))=sort(nodecon(i,1:nodecon(i,end))); +- end +-end +- +-end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_unsh_edges.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_unsh_edges.m (revision 12027) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_unsh_edges.m (revision 12028) +@@ -73,7 +73,7 @@ + + if (~exist('prtplt','var') || strncmpi(prtplt,'on' ,2) || strncmpi(prtplt,'y',1)) && ... + md.qmu.numberofpartitions +- [edgeadj]=edgeadjacency(md.mesh.elements,md.nodeconnectivity); ++ [edgeadj]=edgeadjacency(md.mesh.elements,md.kmlnodeconnectivity); + [icol,irow]=find(edgeadj'==0); + edgeuns=zeros(length(irow),2); + for i=1:length(irow) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kmlnodeconnectivity.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kmlnodeconnectivity.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kmlnodeconnectivity.m (revision 12028) +@@ -0,0 +1,58 @@ ++% ++% create a node connectivity table for the elements in the model. ++% ++% [nodecon]=edgeadjacency(elem,nnodes,mxepg) ++% ++% where the required input is: ++% elem (numeric, element connectivity array (elems x nodes)) ++% ++% and the required output is: ++% nodecon (numeric, node connectivity array (nnodes x mxepg+1)) ++% ++% the optional input is: ++% nnodes (numeric, number of nodes) ++% mxepg (numeric, max elements per node) ++% ++function [nodecon]=kmlnodeconnectivity(elem,nnodes,mxepg) ++ ++if ~nargin ++ help kmlnodeconnectivity ++ return ++end ++ ++if ~exist('nnodes','var') || isempty(nnodes) ++ nnodes=max(max(elem)); ++end ++if ~exist('mxepg','var') || isempty(mxepg) ++ mxepg=25; ++end ++ ++%% create the node connectivity array ++ ++nodecon=zeros(nnodes,mxepg+1); ++ ++% loop over the elements ++ ++for i=1:size(elem,1) ++ ++% loop over the nodes for each element ++ ++ for j=1:size(elem,2) ++ if elem(i,j) ++ nodecon(elem(i,j),nodecon(elem(i,j),end)+1)=i; ++ nodecon(elem(i,j),end)=nodecon(elem(i,j),end)+1; ++ end ++ end ++end ++ ++%% sort the node connectivity array ++ ++% loop over the nodes ++ ++for i=1:size(nodecon,1) ++ if (nodecon(i,end) > 1) ++ nodecon(i,1:nodecon(i,end))=sort(nodecon(i,1:nodecon(i,end))); ++ end ++end ++ ++end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_partitions.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_partitions.m (revision 12027) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_partitions.m (revision 12028) +@@ -150,7 +150,7 @@ + irow=unique(irow); + elemp=md.mesh.elements(irow,:); + epartp=epart(irow,:); +- nodeconp=nodeconnectivity(elemp,md.mesh.numberofvertices); ++ nodeconp=kmlnodeconnectivity(elemp,md.mesh.numberofvertices); + [edgeadjp]=edgeadjacency(elemp,nodeconp); + [edgeper,elemper,iloop]=edgeperimeter(elemp,nodeconp,edgeadjp); + iloop(end+1)=size(edgeper,1)+1; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/README.txt +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/README.txt (revision 12027) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/README.txt (revision 12028) +@@ -60,7 +60,7 @@ + + There are some other utilities that are used in the construction of topological tables for the kml writing. + +-nodeconnectivity.m - create a node connectivity table (nnodes x mxepg+1) ++kmlnodeconnectivity.m - create a node connectivity table (nnodes x mxepg+1) + edgeadjacency.m - create an edge adjacency array (elems x edges) + edgeperimeter.m - create an edge perimeter (edgeper x 2) and element perimeter (edgeper x 1) list + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_part_edges.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_part_edges.m (revision 12027) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml/kml_part_edges.m (revision 12028) +@@ -149,7 +149,7 @@ + irow=unique(irow); + elemp=md.mesh.elements(irow,:); + epartp=epart(irow,:); +- nodeconp=nodeconnectivity(elemp,md.mesh.numberofvertices); ++ nodeconp=kmlnodeconnectivity(elemp,md.mesh.numberofvertices); + [edgeadjp]=edgeadjacency(elemp,nodeconp); + [edgeper,elemper,iloop]=edgeperimeter(elemp,nodeconp,edgeadjp); + iloop(end+1)=size(edgeper,1)+1; Index: /issm/oecreview/Archive/12010-12040/ISSM-12028-12029.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12028-12029.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12028-12029.diff (revision 12325) @@ -0,0 +1,159 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/NodeConnectivity/NodeConnectivity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/NodeConnectivity/NodeConnectivity.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/NodeConnectivity/NodeConnectivity.cpp (revision 12029) +@@ -0,0 +1,44 @@ ++/*\file NodeConnectivity.c ++ *\brief: build node connectivity from elements. ++ */ ++ ++#include "./NodeConnectivity.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*inputs: */ ++ double* elements=NULL; ++ int nel,nods; ++ ++ /*outputs: */ ++ double* connectivity=NULL; ++ int width; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&NodeConnectivityUsage); ++ ++ /*Input datasets: */ ++ FetchData(&elements,&nel,NULL,ELEMENTS); ++ FetchData(&nods,NUMNODES); ++ ++ /*!Generate internal degree of freedom numbers: */ ++ NodeConnectivityx(&connectivity, &width,elements,nel, nods); ++ ++ /*write output datasets: */ ++ WriteData(CONNECTIVITY,connectivity,nods,width); ++ ++ /*Free ressources: */ ++ xfree((void**)&elements); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void NodeConnectivityUsage(void) { ++ _printf_(true,"\n"); ++ _printf_(true," usage: connectivity = %s(elements, numnodes);\n",__FUNCT__); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/NodeConnectivity/NodeConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/NodeConnectivity/NodeConnectivity.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/NodeConnectivity/NodeConnectivity.h (revision 12029) +@@ -0,0 +1,33 @@ ++/* ++ NodeConnectivity.h ++*/ ++ ++#ifndef _NODECONNECTIVITY_H ++#define _NODECONNECTIVITY_H ++ ++/* local prototypes: */ ++void NodeConnectivityUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "NodeConnectivity" ++ ++/* serial input macros: */ ++#define ELEMENTS (mxArray*)prhs[0] ++#define NUMNODES (mxArray*)prhs[1] ++ ++/* serial output macros: */ ++#define CONNECTIVITY (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 2 ++ ++#endif /* _NODECONNECTIVITY_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ElementConnectivity/ElementConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ElementConnectivity/ElementConnectivity.h (revision 12028) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ElementConnectivity/ElementConnectivity.h (revision 12029) +@@ -1,9 +1,7 @@ +- + /* + ElementConnectivity.h + */ + +- + #ifndef _ELEMENTCONNECTIVITY_H + #define _ELEMENTCONNECTIVITY_H + +@@ -32,6 +30,4 @@ + #undef NRHS + #define NRHS 2 + +- + #endif /* _ELEMENTCONNECTIVITY_H */ +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 12028) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 12029) +@@ -12,7 +12,7 @@ + ContourToNodes \ + ElementConnectivity\ + EnumToString\ +- StringToEnum\ ++ Exp2Kml \ + HoleFiller \ + InternalFront\ + InterpFromGridToMesh \ +@@ -23,22 +23,23 @@ + KMLFileRead \ + KMLMeshWrite \ + KMLOverlay \ +- Xy2ll \ ++ Kml2Exp \ + Ll2xy \ +- Exp2Kml \ +- Kml2Exp \ ++ NodeConnectivity \ + MeshPartition\ + MeshProfileIntersection\ + PointCloudFindNeighbors\ + PropagateFlagsFromConnectivity\ + Scotch\ + Shp2Kml\ ++ StringToEnum\ + TriaSearch\ + TriMesh\ + TriMeshRifts\ + TriMeshNoDensity\ + TriMeshProcessRifts\ +- TriMeshRefine ++ TriMeshRefine\ ++ Xy2ll + endif + if PYTHON + bin_PROGRAMS = TriMesh +@@ -147,6 +148,9 @@ + MeshProfileIntersection_SOURCES = MeshProfileIntersection/MeshProfileIntersection.cpp\ + MeshProfileIntersection/MeshProfileIntersection.h + ++NodeConnectivity_SOURCES = NodeConnectivity/NodeConnectivity.cpp\ ++ NodeConnectivity/NodeConnectivity.h ++ + PointCloudFindNeighbors_SOURCES = PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\ + PointCloudFindNeighbors/PointCloudFindNeighbors.h + Index: /issm/oecreview/Archive/12010-12040/ISSM-12029-12030.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12029-12030.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12029-12030.diff (revision 12325) @@ -0,0 +1,75 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/modellist.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/modellist.m (revision 12029) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/modellist.m (revision 12030) +@@ -6,7 +6,7 @@ + classdef modellist + properties (SetAccess=public) + models = cell(0,1); +- cluster = none(); ++ cluster = generic(); + end + methods + function obj = modellist(varargin) % {{{ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m (revision 12029) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m (revision 12030) +@@ -378,7 +378,7 @@ + else + md.solver = addoptions(md.solver,DiagnosticVertAnalysisEnum,iluasmoptions); + end +- md.cluster = none(); ++ md.cluster = generic(); + md.balancethickness = balancethickness(); + md.diagnostic = diagnostic(); + md.hydrology = hydrology(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.m (revision 12029) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.m (revision 12030) +@@ -1,7 +1,6 @@ + %GENERIC cluster class definition + % + % Usage: +-% cluster=generic('name','astrid',); + % cluster=generic('name','astrid','np',3); + % cluster=generic('name',oshostname(),'np',3,'login','username'); + +@@ -27,8 +26,7 @@ + options=pairoptions(varargin{:}); + + %get name +- if ~exist(options,'name'), error('option ''name'' has not been provided'); end +- cluster.name=getfieldvalue(options,'name'); ++ cluster.name=getfieldvalue(options,'name',oshostname()); + + %initialize cluster using user settings if provided + if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/none.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/none.m (revision 12029) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/none.m (revision 12030) +@@ -11,21 +11,8 @@ + end + methods + function cluster=none(varargin) % {{{1 +- cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); ++ error('Cannot assign md.cluster to ''none'': ISSM is not available in serial model anymore'); + end + %}}} +- function disp(cluster) % {{{1 +- % display the object +- disp(sprintf('cluster class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); +- disp(sprintf(' name: %s',cluster.name)); +- end +- %}}} +- function checkconsistency(cluster,md,solution,analyses) % {{{1 +- end +- %}}} +- function BuildQueueScript(cluster,md) % {{{1 +- error('none.BuildQueueScript error message: serial cluster cannot build queue script'); +- end +- %}}} + end + end Index: /issm/oecreview/Archive/12010-12040/ISSM-12030-12031.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12030-12031.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12030-12031.diff (revision 12325) @@ -0,0 +1,592 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12031) +@@ -201,8 +201,8 @@ + + AC_SUBST([MATLABINCL]) + AC_SUBST([MEX]) +- WRAPPEREXT=$MEXEXT +- AC_SUBST([WRAPPEREXT]) ++ MATLABWRAPPEREXT=$MEXEXT ++ AC_SUBST([MATLABWRAPPEREXT]) + AC_SUBST([MEXLIB]) + AC_SUBST([MEXLINK]) + fi +@@ -319,8 +319,8 @@ + AC_DEFINE([_HAVE_PYTHON_],[1],[with Python in ISSM src]) + AC_SUBST([PYTHONINCL]) + AC_SUBST([PYTHONLIB]) +- WRAPPEREXT=$PYTHONEXT +- AC_SUBST([WRAPPEREXT]) ++ PYTHONWRAPPEREXT=$PYTHONEXT ++ AC_SUBST([PYTHONWRAPPEREXT]) + AC_SUBST([PYTHONLINK]) + else + HAVE_PYTHON=no +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12031) +@@ -13,6 +13,7 @@ + #endif + /*}}}*/ + ++#ifdef _HAVE_MATLAB_ + /* MODULEBOOT/MODULEEND {{{1*/ + + /*The following macros hide the error exception handling in a matlab module. Just put +@@ -33,15 +34,12 @@ + } + //}}} + /* WRAPPER {{{1*/ +-#ifdef _HAVE_MATLAB_ + #define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +-#endif + + /*}}}*/ + /* CHECKARGUMENTS {{{1*/ +-#ifdef _HAVE_MATLAB_ + #define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer) +-#endif + /*}}}*/ ++#endif + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/matlab-binding.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/matlab-binding.h (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/matlab-binding.h (revision 12031) +@@ -3,4 +3,5 @@ + + #include "./io/matlabio.h" + #include "./include/matlab_macros.h" ++ + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h (revision 12031) +@@ -14,6 +14,7 @@ + #endif + /*}}}*/ + ++#ifdef _HAVE_PYTHON_ + /* MODULEBOOT/MODULEEND {{{1*/ + + /*The following macros hide the error exception handling in a matlab module. Just put +@@ -55,5 +56,6 @@ + /* CHECKARGUMENTS {{{1*/ + #define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) + /*}}}*/ ++#endif + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/issm-binding.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/issm-binding.h (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/issm-binding.h (revision 12031) +@@ -7,11 +7,11 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#ifdef _HAVE_MATLAB_ ++#ifdef _HAVE_MATLAB_MODULES_ + #include "./matlab/matlab-binding.h" + #endif + +-#ifdef _HAVE_PYTHON_ ++#ifdef _HAVE_PYTHON_MODULES_ + #include "./python/python-binding.h" + #endif + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/python/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/python/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/python/Makefile.am (revision 12031) +@@ -0,0 +1,27 @@ ++INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ ++EXEEXT=$(PYTHONWRAPPEREXT) ++#Bin programs {{{1 ++if MODULES ++bin_PROGRAMS = TriMesh ++endif ++#}}} ++#Flags and libraries {{{1 ++LDADD = ../../c/libISSMCore.a ../../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) ++ ++#Triangle library ++AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER ++ ++#Python part ++AM_LDFLAGS = $(PYTHONLINK) ++AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_ -DNPY_NO_DEPRECATED_API ++LDADD += $(BOOSTLIB) $(PYTHONLIB) ../../c/libISSMPython.a ++ ++LDADD += ../../c/libISSMCore.a ../../c/libISSMModules.a ++ ++#Optimization flags: ++AM_CXXFLAGS += $(CXXOPTFLAGS) ++#}}} ++#Bin sources {{{1 ++TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\ ++ ../TriMesh/TriMesh.h ++#}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/matlab/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/matlab/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/matlab/Makefile.am (revision 12031) +@@ -0,0 +1,171 @@ ++INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ ++EXEEXT=$(MATLABWRAPPEREXT) ++#Bin programs {{{1 ++if MODULES ++bin_PROGRAMS = AverageFilter\ ++ BamgMesher\ ++ BamgConvertMesh\ ++ BamgTriangulate\ ++ Chaco\ ++ ContourToMesh \ ++ ContourToNodes \ ++ ElementConnectivity\ ++ EnumToString\ ++ Exp2Kml \ ++ HoleFiller \ ++ InternalFront\ ++ InterpFromGridToMesh \ ++ InterpFromMeshToMesh2d \ ++ InterpFromMeshToMesh3d \ ++ InterpFromMeshToGrid \ ++ InterpFromMesh2d \ ++ KMLFileRead \ ++ KMLMeshWrite \ ++ KMLOverlay \ ++ Kml2Exp \ ++ Ll2xy \ ++ NodeConnectivity \ ++ MeshPartition\ ++ MeshProfileIntersection\ ++ PointCloudFindNeighbors\ ++ PropagateFlagsFromConnectivity\ ++ Scotch\ ++ Shp2Kml\ ++ StringToEnum\ ++ TriaSearch\ ++ TriMesh\ ++ TriMeshRifts\ ++ TriMeshNoDensity\ ++ TriMeshProcessRifts\ ++ TriMeshRefine\ ++ Xy2ll ++endif ++#}}} ++#Flags and libraries {{{1 ++LDADD = ../../c/libISSMCore.a ../../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) ++ ++#Triangle library ++AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER ++ ++#Matlab part ++AM_LDFLAGS = $(MEXLINK) ++AM_CXXFLAGS += -D_HAVE_MATLAB_MODULES_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread ++LDADD += $(MEXLIB) ../../c/libISSMMatlab.a ++ ++LDADD += ../../c/libISSMCore.a ../../c/libISSMModules.a ++ ++#Optimization flags: ++AM_CXXFLAGS += $(CXXOPTFLAGS) ++#}}} ++#Bin sources {{{1 ++AverageFilter_SOURCES = ../AverageFilter/AverageFilter.cpp\ ++ ../AverageFilter/AverageFilter.h ++ ++BamgMesher_SOURCES = ../BamgMesher/BamgMesher.cpp\ ++ ../BamgMesher/BamgMesher.h ++ ++BamgConvertMesh_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\ ++ ../BamgConvertMesh/BamgConvertMesh.h ++ ++BamgTriangulate_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp\ ++ ../BamgTriangulate/BamgTriangulate.h ++ ++Chaco_SOURCES = ../Chaco/Chaco.cpp\ ++ ../Chaco/Chaco.h ++ ++ContourToMesh_SOURCES = ../ContourToMesh/ContourToMesh.cpp\ ++ ../ContourToMesh/ContourToMesh.h ++ ++ContourToNodes_SOURCES = ../ContourToNodes/ContourToNodes.cpp\ ++ ../ContourToNodes/ContourToNodes.h ++ ++ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\ ++ ../ElementConnectivity/ElementConnectivity.h ++ ++EnumToString_SOURCES = ../EnumToString/EnumToString.cpp\ ++ ../EnumToString/EnumToString.h ++ ++StringToEnum_SOURCES = ../StringToEnum/StringToEnum.cpp\ ++ ../StringToEnum/StringToEnum.h ++ ++HoleFiller_SOURCES = ../HoleFiller/HoleFiller.cpp\ ++ ../HoleFiller/HoleFiller.h ++ ++InternalFront_SOURCES = ../InternalFront/InternalFront.cpp\ ++ ../InternalFront/InternalFront.h ++ ++InterpFromGridToMesh_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\ ++ ../InterpFromGridToMesh/InterpFromGridToMesh.h ++ ++InterpFromMeshToMesh2d_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\ ++ ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h ++ ++InterpFromMeshToMesh3d_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\ ++ ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h ++ ++InterpFromMeshToGrid_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\ ++ ../InterpFromMeshToGrid/InterpFromMeshToGrid.h ++ ++InterpFromMesh2d_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp\ ++ ../InterpFromMesh2d/InterpFromMesh2d.h ++ ++KMLFileRead_SOURCES = ../KMLFileRead/KMLFileRead.cpp\ ++ ../KMLFileRead/KMLFileRead.h ++ ++KMLMeshWrite_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp\ ++ ../KMLMeshWrite/KMLMeshWrite.h ++ ++KMLOverlay_SOURCES = ../KMLOverlay/KMLOverlay.cpp\ ++ ../KMLOverlay/KMLOverlay.h ++ ++Xy2ll_SOURCES = ../Xy2ll/Xy2ll.cpp\ ++ ../Xy2ll/Xy2ll.h ++ ++Ll2xy_SOURCES = ../Ll2xy/Ll2xy.cpp\ ++ ../Ll2xy/Ll2xy.h ++ ++Exp2Kml_SOURCES = ../Exp2Kml/Exp2Kml.cpp\ ++ ../Exp2Kml/Exp2Kml.h ++ ++Kml2Exp_SOURCES = ../Kml2Exp/Kml2Exp.cpp\ ++ ../Kml2Exp/Kml2Exp.h ++ ++MeshPartition_SOURCES = ../MeshPartition/MeshPartition.cpp\ ++ ../MeshPartition/MeshPartition.h ++ ++MeshProfileIntersection_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\ ++ ../MeshProfileIntersection/MeshProfileIntersection.h ++ ++NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\ ++ ../NodeConnectivity/NodeConnectivity.h ++ ++PointCloudFindNeighbors_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\ ++ ../PointCloudFindNeighbors/PointCloudFindNeighbors.h ++ ++PropagateFlagsFromConnectivity_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\ ++ ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h ++ ++Scotch_SOURCES = ../Scotch/Scotch.cpp\ ++ ../Scotch/Scotch.h ++ ++Shp2Kml_SOURCES = ../Shp2Kml/Shp2Kml.cpp\ ++ ../Shp2Kml/Shp2Kml.h ++ ++TriaSearch_SOURCES = ../TriaSearch/TriaSearch.cpp\ ++ ../TriaSearch/TriaSearch.h ++ ++TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\ ++ ../TriMesh/TriMesh.h ++ ++TriMeshRifts_SOURCES = ../TriMeshRifts/TriMeshRifts.cpp\ ++ ../TriMeshRifts/TriMeshRifts.h ++ ++TriMeshNoDensity_SOURCES = ../TriMeshNoDensity/TriMeshNoDensity.cpp\ ++ ../TriMeshNoDensity/TriMeshNoDensity.h ++ ++TriMeshProcessRifts_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\ ++ ../TriMeshProcessRifts/TriMeshProcessRifts.h ++ ++TriMeshRefine_SOURCES = ../TriMeshRefine/TriMeshRefine.cpp\ ++ ../TriMeshRefine/TriMeshRefine.h ++#}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 12031) +@@ -1,183 +1,8 @@ +-INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ +-EXEEXT=$(WRAPPEREXT) +-#Bin programs {{{1 +-if MODULES ++SUBDIRS = + if MATLAB +-bin_PROGRAMS = AverageFilter\ +- BamgMesher\ +- BamgConvertMesh\ +- BamgTriangulate\ +- Chaco\ +- ContourToMesh \ +- ContourToNodes \ +- ElementConnectivity\ +- EnumToString\ +- Exp2Kml \ +- HoleFiller \ +- InternalFront\ +- InterpFromGridToMesh \ +- InterpFromMeshToMesh2d \ +- InterpFromMeshToMesh3d \ +- InterpFromMeshToGrid \ +- InterpFromMesh2d \ +- KMLFileRead \ +- KMLMeshWrite \ +- KMLOverlay \ +- Kml2Exp \ +- Ll2xy \ +- NodeConnectivity \ +- MeshPartition\ +- MeshProfileIntersection\ +- PointCloudFindNeighbors\ +- PropagateFlagsFromConnectivity\ +- Scotch\ +- Shp2Kml\ +- StringToEnum\ +- TriaSearch\ +- TriMesh\ +- TriMeshRifts\ +- TriMeshNoDensity\ +- TriMeshProcessRifts\ +- TriMeshRefine\ +- Xy2ll ++SUBDIRS += matlab + endif +-if PYTHON +-bin_PROGRAMS = TriMesh +-endif +-endif +-#}}} +-#Flags and libraries {{{1 +-LDADD = ../c/libISSMCore.a ../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) + +-#Triangle library +-AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER +- +-if MATLAB +-AM_LDFLAGS = $(MEXLINK) +-AM_CXXFLAGS += -D_HAVE_MATLAB_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread +-LDADD += $(MEXLIB) ../c/libISSMMatlab.a +-endif +- + if PYTHON +-AM_LDFLAGS = $(PYTHONLINK) +-AM_CXXFLAGS += -D_HAVE_PYTHON_ -DNPY_NO_DEPRECATED_API +-LDADD += $(BOOSTLIB) $(PYTHONLIB) ../c/libISSMPython.a ++SUBDIRS += python + endif +- +-LDADD += ../c/libISSMCore.a ../c/libISSMModules.a +- +-#Optimization flags: +-AM_CXXFLAGS += $(CXXOPTFLAGS) +-#}}} +-#Bin sources {{{1 +-AverageFilter_SOURCES = AverageFilter/AverageFilter.cpp\ +- AverageFilter/AverageFilter.h +- +-BamgMesher_SOURCES = BamgMesher/BamgMesher.cpp\ +- BamgMesher/BamgMesher.h +- +-BamgConvertMesh_SOURCES = BamgConvertMesh/BamgConvertMesh.cpp\ +- BamgConvertMesh/BamgConvertMesh.h +- +-BamgTriangulate_SOURCES = BamgTriangulate/BamgTriangulate.cpp\ +- BamgTriangulate/BamgTriangulate.h +- +-Chaco_SOURCES = Chaco/Chaco.cpp\ +- Chaco/Chaco.h +- +-ContourToMesh_SOURCES = ContourToMesh/ContourToMesh.cpp\ +- ContourToMesh/ContourToMesh.h +- +-ContourToNodes_SOURCES = ContourToNodes/ContourToNodes.cpp\ +- ContourToNodes/ContourToNodes.h +- +-ElementConnectivity_SOURCES = ElementConnectivity/ElementConnectivity.cpp\ +- ElementConnectivity/ElementConnectivity.h +- +-EnumToString_SOURCES = EnumToString/EnumToString.cpp\ +- EnumToString/EnumToString.h +- +-StringToEnum_SOURCES = StringToEnum/StringToEnum.cpp\ +- StringToEnum/StringToEnum.h +- +-HoleFiller_SOURCES = HoleFiller/HoleFiller.cpp\ +- HoleFiller/HoleFiller.h +- +-InternalFront_SOURCES = InternalFront/InternalFront.cpp\ +- InternalFront/InternalFront.h +- +-InterpFromGridToMesh_SOURCES = InterpFromGridToMesh/InterpFromGridToMesh.cpp\ +- InterpFromGridToMesh/InterpFromGridToMesh.h +- +-InterpFromMeshToMesh2d_SOURCES = InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\ +- InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h +- +-InterpFromMeshToMesh3d_SOURCES = InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\ +- InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h +- +-InterpFromMeshToGrid_SOURCES = InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\ +- InterpFromMeshToGrid/InterpFromMeshToGrid.h +- +-InterpFromMesh2d_SOURCES = InterpFromMesh2d/InterpFromMesh2d.cpp\ +- InterpFromMesh2d/InterpFromMesh2d.h +- +-KMLFileRead_SOURCES = KMLFileRead/KMLFileRead.cpp\ +- KMLFileRead/KMLFileRead.h +- +-KMLMeshWrite_SOURCES = KMLMeshWrite/KMLMeshWrite.cpp\ +- KMLMeshWrite/KMLMeshWrite.h +- +-KMLOverlay_SOURCES = KMLOverlay/KMLOverlay.cpp\ +- KMLOverlay/KMLOverlay.h +- +-Xy2ll_SOURCES = Xy2ll/Xy2ll.cpp\ +- Xy2ll/Xy2ll.h +- +-Ll2xy_SOURCES = Ll2xy/Ll2xy.cpp\ +- Ll2xy/Ll2xy.h +- +-Exp2Kml_SOURCES = Exp2Kml/Exp2Kml.cpp\ +- Exp2Kml/Exp2Kml.h +- +-Kml2Exp_SOURCES = Kml2Exp/Kml2Exp.cpp\ +- Kml2Exp/Kml2Exp.h +- +-MeshPartition_SOURCES = MeshPartition/MeshPartition.cpp\ +- MeshPartition/MeshPartition.h +- +-MeshProfileIntersection_SOURCES = MeshProfileIntersection/MeshProfileIntersection.cpp\ +- MeshProfileIntersection/MeshProfileIntersection.h +- +-NodeConnectivity_SOURCES = NodeConnectivity/NodeConnectivity.cpp\ +- NodeConnectivity/NodeConnectivity.h +- +-PointCloudFindNeighbors_SOURCES = PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\ +- PointCloudFindNeighbors/PointCloudFindNeighbors.h +- +-PropagateFlagsFromConnectivity_SOURCES = PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\ +- PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h +- +-Scotch_SOURCES = Scotch/Scotch.cpp\ +- Scotch/Scotch.h +- +-Shp2Kml_SOURCES = Shp2Kml/Shp2Kml.cpp\ +- Shp2Kml/Shp2Kml.h +- +-TriaSearch_SOURCES = TriaSearch/TriaSearch.cpp\ +- TriaSearch/TriaSearch.h +- +-TriMesh_SOURCES = TriMesh/TriMesh.cpp\ +- TriMesh/TriMesh.h +- +-TriMeshRifts_SOURCES = TriMeshRifts/TriMeshRifts.cpp\ +- TriMeshRifts/TriMeshRifts.h +- +-TriMeshNoDensity_SOURCES = TriMeshNoDensity/TriMeshNoDensity.cpp\ +- TriMeshNoDensity/TriMeshNoDensity.h +- +-TriMeshProcessRifts_SOURCES = TriMeshProcessRifts/TriMeshProcessRifts.cpp\ +- TriMeshProcessRifts/TriMeshProcessRifts.h +- +-TriMeshRefine_SOURCES = TriMeshRefine/TriMeshRefine.cpp\ +- TriMeshRefine/TriMeshRefine.h +-#}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/TriMesh/TriMesh.h (revision 12031) +@@ -27,7 +27,7 @@ + #include "../../c/io/io.h" + #include "../../c/EnumDefinitions/EnumDefinitions.h" + +-#ifdef _HAVE_MATLAB_ ++#ifdef _HAVE_MATLAB_MODULES_ + /* serial input macros: */ + #define DOMAINOUTLINE (mxArray *)prhs[0] + #define AREA (mxArray *)prhs[1] +@@ -40,7 +40,7 @@ + #define SEGMENTMARKERLIST (mxArray**)&plhs[4] + #endif + +-#ifdef _HAVE_PYTHON_ ++#ifdef _HAVE_PYTHON_MODULES_ + /* serial input macros: */ + #define DOMAINOUTLINE PyTuple_GetItem(args,0) + #define AREA PyTuple_GetItem(args,1) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh (revision 12031) +@@ -0,0 +1,30 @@ ++#!/bin/sh ++ ++#petsc 3.2 ++#mpich 1.4 ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-python-dir=$ISSM_TIER/externalpackages/python/install\ ++ --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ ++ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ ++ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ ++ --with-math-lib="/usr/lib/libm.dylib" \ ++ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ ++ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ ++ --with-numthreads=8 \ ++ --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ ++ #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ #--with-boost-dir=$ISSM_TIER/externalpackages/boost/install/ \ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 12031) +@@ -37,6 +37,8 @@ + src/Makefile + src/c/Makefile + src/mex/Makefile ++ src/mex/python/Makefile ++ src/mex/matlab/Makefile + src/m/Makefile + bin/Makefile]) + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 12030) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 12031) +@@ -258,8 +258,8 @@ + + #PYTHON + export PATH="$PYTHON_DIR/bin:$PATH" +-export PYTHONPATH="$PYTHONPATH:$ISSM_TIER/src/mex" +-export LD_LIBRARY_PATH=$ISSM_TIER/src/mex:$LD_LIBRARY_PATH ++export PYTHONPATH="$PYTHONPATH:$ISSM_TIER/src/mex/python" ++export LD_LIBRARY_PATH=$ISSM_TIER/src/mex/python:$LD_LIBRARY_PATH + + #MODELE + export PATH="$MODELE_DIR/src/exec:$PATH" Index: /issm/oecreview/Archive/12010-12040/ISSM-12031-12032.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12031-12032.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12031-12032.diff (revision 12325) @@ -0,0 +1,6688 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am (revision 12032) +@@ -0,0 +1,27 @@ ++INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ ++EXEEXT=$(PYTHONWRAPPEREXT) ++#Bin programs {{{1 ++if MODULES ++bin_PROGRAMS = TriMesh ++endif ++#}}} ++#Flags and libraries {{{1 ++LDADD = ../../c/libISSMCore.a ../../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) ++ ++#Triangle library ++AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER ++ ++#Python part ++AM_LDFLAGS = $(PYTHONLINK) ++AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_ -DNPY_NO_DEPRECATED_API ++LDADD += $(BOOSTLIB) $(PYTHONLIB) ../../c/libISSMPython.a ++ ++LDADD += ../../c/libISSMCore.a ../../c/libISSMModules.a ++ ++#Optimization flags: ++AM_CXXFLAGS += $(CXXOPTFLAGS) ++#}}} ++#Bin sources {{{1 ++TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\ ++ ../TriMesh/TriMesh.h ++#}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Scotch/Scotch.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Scotch/Scotch.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Scotch/Scotch.cpp (revision 12032) +@@ -0,0 +1,267 @@ ++/*\file Scotch.c ++ *\brief: Scotch partitioner mex module ++ */ ++ ++#ifdef HAVE_CONFIG_H ++#include "config.h" ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#include "./Scotch.h" ++ ++/******************************/ ++/* */ ++/* This is the main function. */ ++/* */ ++/******************************/ ++ ++void mexFunction( int nlhs, ++ mxArray *plhs[], ++ int nrhs, ++ const mxArray *prhs[] ) ++{ ++ ++#ifndef _HAVE_SCOTCH_ //only works if scotch library has been compiled in. ++ _error_(" Scotch not available! Cannot carry out Scotch partitioning!"); ++ #else ++ ++ int argcm; ++ char **argvm=NULL; ++ int nvert =0,nedge2=0,napar =0; ++ mwIndex *ir=NULL,*jc=NULL; ++ int *adjir=NULL,*adjjc=NULL; ++ double *vld=NULL,*vwd=NULL,*ewd=NULL,*apd=NULL; ++ int *vli=NULL,*vwi=NULL,*ewi=NULL,*api=NULL; ++ char *archtyp=NULL; ++ int (*maptabi)[2]=NULL; ++ double* maptabd=NULL; ++ int i,j,k,imi=0,imo=0,isi=0,ierr; ++ ++ /* Check for proper number of arguments */ ++ ++ if (nrhs == 0 && nlhs == 0) { ++ GmapUsage(); ++ return; ++ } ++ else if (nrhs < 6 || nlhs > 1) { ++ GmapUsage(); ++ mexErrMsgTxt(" "); ++ } ++ ++/* load matlab argument list and convert to integer (note that converting here ++ and in the x-layer is inefficient, but it makes the x-layer more general) */ ++ ++ argvm = (char **) calloc(nrhs,sizeof(char *)); ++ ++ if (!(mxIsNumeric(prhs[imi]) && ++ (mxGetM(prhs[imi]) == 1 && mxGetN(prhs[imi]) == 1))) { ++ argvm[isi] = (char *) calloc(4+1,sizeof(char)); ++ strcpy(argvm[isi],"gmap"); ++ mexPrintf("%s -- Using \"%s\" entry point.\n", ++ __FUNCT__,argvm[isi]); ++ isi++; ++ } ++ else { ++ argvm[isi] = (char *) calloc(5+1,sizeof(char)); ++ strcpy(argvm[isi],"gpart"); ++ mexPrintf("%s -- Using \"%s\" entry point.\n", ++ __FUNCT__,argvm[isi]); ++ isi++; ++ ++ argvm[isi] = (char *) calloc(17,sizeof(char)); ++ sprintf(argvm[isi],"%d",(int)mxGetScalar(prhs[imi])); ++ mexPrintf("%s -- Number of parts is %s.\n", ++ __FUNCT__,argvm[isi]); ++ isi++; ++ imi++; ++ } ++ ++ if (!mxIsNumeric(prhs[imi]) || (!mxIsEmpty(prhs[imi]) && !mxIsSparse(prhs[imi]))) { ++ mexPrintf("%s -- Adjacency matrix must be numeric and sparse.\n",__FUNCT__); ++ mexErrMsgTxt(" "); ++ } ++ else { ++ nvert =mxGetM(prhs[imi]); ++ nedge2=mxGetNzmax(prhs[imi]); ++ if (mxGetNzmax(prhs[imi])) { ++ ir =mxGetIr(prhs[imi]); ++ adjir = (int *) malloc(mxGetNzmax(prhs[imi])*sizeof(int)); ++ for (i=0; i= 5) && ++ (strncmp (argvm[0] + strlen (argvm[0]) - 5, "gpart", 5) == 0))) { ++ if (!mxIsChar(prhs[imi])) { ++ mexPrintf("%s -- Architecture type must be character.\n",__FUNCT__); ++ mexErrMsgTxt(" "); ++ } ++ else { ++ if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { ++ archtyp = (char *) calloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])+1,sizeof(char)); ++ mxGetString(prhs[imi],archtyp,mxGetM(prhs[imi])*mxGetN(prhs[imi])+1); ++ } ++ mexPrintf("%s -- Architecture type is \"%s\".\n", ++ __FUNCT__,archtyp); ++ } ++ imi++; ++ ++ if (!mxIsNumeric(prhs[imi])) { ++ mexPrintf("%s -- Architecture parameter vector must be numeric.\n",__FUNCT__); ++ mexErrMsgTxt(" "); ++ } ++ else { ++ napar =mxGetM(prhs[imi])*mxGetN(prhs[imi]); ++ if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { ++ apd=mxGetPr(prhs[imi]); ++ api = (int *) malloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])*sizeof(int)); ++ for (i=0; i=0; i--) ++ free(argvm[i]); ++ if (api) free(api); ++ if (archtyp) free(archtyp); ++ if (ewi) free(ewi); ++ if (vwi) free(vwi); ++ if (vli) free(vli); ++ if (adjjc) free(adjjc); ++ if (adjir) free(adjir);*/ ++ ++ return; ++#endif //#ifndef _HAVE_SCOTCH_ ++} ++ ++void GmapUsage( void ) ++{ ++ ++ mexPrintf("\n"); ++ mexPrintf("Usage: [maptab]=Scotch(adjmat,vertlb,vertwt,edgewt,archtyp,archpar,\n"); ++ mexPrintf(" Scotch-specific parameters);\n"); ++ mexPrintf("\n"); ++ ++ return; ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Scotch/Scotch.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Scotch/Scotch.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Scotch/Scotch.h (revision 12032) +@@ -0,0 +1,40 @@ ++/*!\file: Scotch.h ++ * \brief header file for Scotch module. ++ */ ++ ++#ifndef _SCOTCH_H ++#define _SCOTCH_H ++ ++/* local prototypes: */ ++void GmapUsage(void); ++ ++#include ++#include /* strcasecmp */ ++#include /* clock,time,difftime */ ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "Scotch" ++ ++/* Scotch structures and prototypes */ ++#ifdef MATLAB ++ #include "mat.h" ++ #include "mex.h" ++ #include "matrix.h" ++ ++ #define printf mexPrintf ++ #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) ++ #define malloc mxMalloc ++ #define calloc mxCalloc ++ #define realloc mxRealloc ++ #define free mxFree ++ #define exit(status) mexErrMsgTxt("exit=" #status) ++#endif ++ ++ ++#endif /* _SCOTCH_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp (revision 12032) +@@ -0,0 +1,44 @@ ++/*\file NodeConnectivity.c ++ *\brief: build node connectivity from elements. ++ */ ++ ++#include "./NodeConnectivity.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*inputs: */ ++ double* elements=NULL; ++ int nel,nods; ++ ++ /*outputs: */ ++ double* connectivity=NULL; ++ int width; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&NodeConnectivityUsage); ++ ++ /*Input datasets: */ ++ FetchData(&elements,&nel,NULL,ELEMENTS); ++ FetchData(&nods,NUMNODES); ++ ++ /*!Generate internal degree of freedom numbers: */ ++ NodeConnectivityx(&connectivity, &width,elements,nel, nods); ++ ++ /*write output datasets: */ ++ WriteData(CONNECTIVITY,connectivity,nods,width); ++ ++ /*Free ressources: */ ++ xfree((void**)&elements); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void NodeConnectivityUsage(void) { ++ _printf_(true,"\n"); ++ _printf_(true," usage: connectivity = %s(elements, numnodes);\n",__FUNCT__); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h (revision 12032) +@@ -0,0 +1,33 @@ ++/* ++ NodeConnectivity.h ++*/ ++ ++#ifndef _NODECONNECTIVITY_H ++#define _NODECONNECTIVITY_H ++ ++/* local prototypes: */ ++void NodeConnectivityUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "NodeConnectivity" ++ ++/* serial input macros: */ ++#define ELEMENTS (mxArray*)prhs[0] ++#define NUMNODES (mxArray*)prhs[1] ++ ++/* serial output macros: */ ++#define CONNECTIVITY (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 2 ++ ++#endif /* _NODECONNECTIVITY_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.cpp (revision 12032) +@@ -0,0 +1,86 @@ ++/*\file BamgConvertMesh.c ++ *\brief: bamg module. ++ */ ++#include "./BamgConvertMesh.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*input: */ ++ double* index=NULL; ++ int index_rows; ++ double* x=NULL; ++ int x_cols; ++ double* y=NULL; ++ int y_rows; ++ int y_cols; ++ ++ /*Output*/ ++ BamgMesh* bamgmesh=NULL; ++ BamgGeom* bamggeom=NULL; ++ mxArray* bamgmesh_mat=NULL; ++ mxArray* bamggeom_mat=NULL; ++ ++ /*Intermediary*/ ++ int nods; ++ int nels; ++ int verbose=0; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&BamgConvertMeshUsage); ++ ++ /*Initialize Bamg outputs*/ ++ bamggeom=new BamgGeom(); ++ bamgmesh=new BamgMesh(); ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs\n"); ++ FetchData(&index,&nels,&index_rows,INDEXHANDLE); ++ FetchData(&x,&nods,&x_cols,XHANDLE); ++ FetchData(&y,&y_rows,&y_cols,YHANDLE); ++ ++ /*Check inputs*/ ++ if (nels<0){ ++ _error_("Number of elements must be positive, check index number of lines"); ++ } ++ if (nods<0){ ++ _error_("Number of nods must be positive, check x and y sizes"); ++ } ++ if (index_rows!=3){ ++ _error_("index should have 3 columns"); ++ } ++ if (y_rows!=nods){ ++ _error_("x and y do not have the same length"); ++ } ++ if (x_cols>1 || y_cols>1){ ++ _error_("x and y should have only one column"); ++ } ++ ++ /* Run core computations: */ ++ if (verbose) printf("Call core\n"); ++ BamgConvertMeshx(bamgmesh,bamggeom,index,x,y,nods,nels); ++ ++ /*Generate output Matlab Structures*/ ++ bamggeom->SetStructureFields((void*)BAMGGEOMOUT); ++ bamgmesh->SetStructureFields((void*)BAMGMESHOUT); ++ ++ /*Clean up*/ ++ delete bamggeom; ++ delete bamgmesh; ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void BamgConvertMeshUsage(void) ++{ ++ _printf_(true,"BAMGCONVERTMESH - convert [x y index] to a bamg geom and mesh geom"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," [bamggeom bamgmesh]=BamgConvertMesh(index,x,y);\n"); ++ _printf_(true," index: index of the mesh\n"); ++ _printf_(true," x,y: coordinates of the nodes\n"); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.h (revision 12032) +@@ -0,0 +1,36 @@ ++/*!\file BamgConvertMesh.h ++ * \brief: prototype for Data Interpolation mex module. ++ */ ++ ++#ifndef _BAMGCONVERTMESH_H ++#define _BAMGCONVERTMESH_H ++ ++/* local prototypes: */ ++void BamgConvertMeshUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "BamgConvertMesh" ++ ++ ++/* serial input macros: */ ++#define INDEXHANDLE prhs[0] ++#define XHANDLE prhs[1] ++#define YHANDLE prhs[2] ++ ++/* serial output macros: */ ++#define BAMGMESHOUT (mxArray**)&plhs[0] ++#define BAMGGEOMOUT (mxArray**)&plhs[1] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 2 ++#undef NRHS ++#define NRHS 3 ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLOverlay/KMLOverlay.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLOverlay/KMLOverlay.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLOverlay/KMLOverlay.cpp (revision 12032) +@@ -0,0 +1,149 @@ ++/*\file KMLOverlay.c ++ *\brief: KML file overlay mex module. ++ */ ++#include "./KMLOverlay.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i,verbose=1; ++ ++ /*input: */ ++ char* filkml=NULL; ++ char* filkmz=NULL; ++ ++ FILE* fid=NULL; ++ ++ Options* options=NULL; ++ int nlat=0,nlong=0; ++ double* lataxis =NULL; ++ double* longaxis=NULL; ++ int nimages=0; ++ char** pimages=NULL; ++ double dzip=0; ++ char* czip=NULL; ++ ++ /* output: */ ++ int ierror=0; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ if (nlhs > NLHS) { ++ KMLOverlayUsage(); ++ _error_("KMLOverlay usage error"); ++ } ++ if (nrhs < NRHS) { ++ KMLOverlayUsage(); ++ _error_("KMLOverlay usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs:\n"); ++ FetchData(&filkml,FILENAME); ++ if (verbose) printf(" filkml=\"%s\"\n",filkml); ++ ++ if (verbose) printf("Parsing options:\n"); ++ options=new Options(NRHS,nrhs,prhs); ++// if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); ++ options->Get(&lataxis ,&nlat ,"lataxis" ); ++ if (verbose && lataxis) for (i=0; iGet(&longaxis,&nlong,"longaxis"); ++ if (verbose && longaxis) for (i=0; iGetOption("images"))->DeepEcho(); ++ options->Get(&pimages,&nimages,"images"); ++ if (verbose && pimages) for (i=0; iGet(&dzip,"zip",0.); ++ if (verbose) printf(" dzip=%g\n",dzip); ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs:\n"); ++ ++ if (nlat != 2) _error_("Latitudinal axes \"lataxis\" require two double values, not %d.",nlat); ++ if (nlong != 2) _error_("Longitudinal axes \"longaxis\" require two double values, not %d.",nlong); ++ if (!nimages) _error_("No image files provided."); ++ ++ if ((int)dzip) { ++ filkmz=filkml; ++ filkml=(char *) xmalloc(8*sizeof(char)); ++ strcpy(filkml,"doc.kml"); ++ } ++ ++ if (!strlen(filkml)) ++ strcpy(filkml,"stdout"); ++ ++ if (verbose) printf("Opening kml overlay file \"%s\".\n",filkml); ++ fid=fopen(filkml,"w"); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Calling core:\n"); ++ KMLOverlayx(&ierror, ++ lataxis,longaxis, ++ nimages,pimages, ++ fid); ++ ++ if (verbose) printf("Closing file \"%s\".\n",filkml); ++ fclose(fid); ++ ++ /* Create kmz file, if specified: */ ++ if ((int)dzip) { ++ czip=(char *) xmalloc((5+strlen(filkmz)+1+strlen(filkml)+1)*sizeof(char)); ++ czip[0]='\0'; ++ strcat(czip,"!zip "); ++ strcat(czip,filkmz); ++ strcat(czip," "); ++ strcat(czip,filkml); ++ for (i=0; i0; i--) xfree((void**)&(pimages[i-1])); ++ xfree((void**)&pimages); ++ } ++ xfree((void**)&longaxis); ++ xfree((void**)&lataxis); ++ delete options; ++ xfree((void**)&filkml); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void KMLOverlayUsage(void) ++{ ++ _printf_(true,"KMLOverlay - KML file overlay module:\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This module reads a list of image files and writes a KML or KMZ overlay file.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," ierror=KMLOverlay(kmlfile,'param name',param,...);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," kmlfile KML or KMZ file name (string)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," lataxis latitude axis (double vector [south north], required)\n"); ++ _printf_(true," longaxis longitude axis (double vector [west east], required)\n"); ++ _printf_(true," images relative or http image file names (string or array of strings or cell array of strings, required)\n"); ++ _printf_(true," zip flag to zip the doc.kml and image files into kmzfile (double, non-zero for kmz)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," ierror error flag (double, non-zero for error)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Example:\n"); ++ _printf_(true," KMLOverlay(kmlfile,'lataxis',[south north],'longaxis',[west east],'images',{'file1.png','http://issm/file2.png'},'zip',1);\n"); ++ _printf_(true,"\n"); ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLOverlay/KMLOverlay.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLOverlay/KMLOverlay.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLOverlay/KMLOverlay.h (revision 12032) +@@ -0,0 +1,33 @@ ++/*!\file KMLOverlay.h ++ * \brief: prototype for KML file overlay mex module. ++ */ ++ ++#ifndef _KMLOVERLAY_H ++#define _KMLOVERLAY_H ++ ++/* local prototypes: */ ++void KMLOverlayUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "KMLOverlay" ++ ++ ++/* serial input macros: */ ++#define FILENAME prhs[0] ++ ++/* serial output macros: */ ++#define ERRORFLAG (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NRHS ++#define NRHS 1 ++#undef NLHS ++#define NLHS 1 ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/.dirstamp +=================================================================== +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.cpp (revision 12032) +@@ -0,0 +1,114 @@ ++/*! \file ContourtoNodes ++ \brief: takes a contour file, and figures out which nodes (x,y list) ++ are inside this contour. ++ ++ usage: ++ [flags]=ContourToNodes(x,y,contours,interptype,edgevalue); ++ ++ where: ++ ++ input: ++ ++ x,y: node cooredinates ++ ++ contours: structure holding sets of vertices making open contours. ++ ++ interptype: string definining type of interpolation ('element', or 'node', or 'element and node'); ++ ++ edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons ++ ++ output: ++ flags: vector of flags (0 or 1), of size nods ++*/ ++ ++#include "./ContourToNodes.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { ++ ++ int i,j; ++ ++ /* required input: */ ++ double* x=NULL; ++ double* y=NULL; ++ int edgevalue; ++ char* interptype=NULL; ++ ++ /* output: */ ++ Vector* flags=NULL; ++ int nods; ++ ++ //contours ++ mxArray* matlabstructure=NULL; ++ int numcontours; ++ Contour** contours=NULL; ++ Contour* contouri=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ContourToNodesUsage); ++ ++ ++ /*Fetch inputs: */ ++ FetchData(&x,&nods,NULL,XHANDLE); ++ FetchData(&y,NULL,NULL,YHANDLE); ++ FetchData(&edgevalue,EDGEVALUEHANDLE); ++ ++ //Fetch contours ++ ++ if(mxIsChar(FILENAME)){ ++ /*Call expread on filename to build a contour array in the matlab workspace: */ ++ mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); ++ } ++ else{ ++ /*FILENAME is actually a structure, coming directly from expread: */ ++ matlabstructure=(mxArray*)FILENAME; ++ } ++ ++ numcontours=mxGetNumberOfElements(matlabstructure); ++ contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); ++ for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); ++ //set pointers. ++ contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); ++ contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); ++ *(contours+i)=contouri; ++ } ++ ++ /* Debugging of contours :{{{1*/ ++ /*for(i=0;inods); ++ for (j=0;jnods;j++){ ++ printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); ++ } ++ }*/ ++ /*}}}*/ ++ ++ /*Run interpolation routine: */ ++ ContourToNodesx(&flags,x,y,nods,contours,numcontours,edgevalue); ++ ++ /* output: */ ++ WriteData(FLAGS,flags); ++ ++ /*end module: */ ++ MODULEEND(); ++ ++} ++ ++void ContourToNodesUsage(void){ ++ printf(" usage:\n"); ++ printf(" [flags]=ContourToNodes(x,y,contourname,edgevalue);\n\n"); ++ printf(" where:\n"); ++ printf(" x,y: list of nodes.\n"); ++ printf(" contourname: name of .exp file containing the contours, or resulting structure from call to expread.\n"); ++ printf(" interptype: string definining type of interpolation ('element', or 'node').\n"); ++ printf(" edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons.\n"); ++ printf(" flags: vector of flags (0 or 1), of size nods.\n"); ++ printf("\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.h (revision 12032) +@@ -0,0 +1,44 @@ ++ ++/* ++ ContourToNodes.h ++*/ ++ ++ ++#ifndef _CONTOURTONODES_H ++#define _CONTOURTONODES_H ++ ++/* local prototypes: */ ++void ContourToNodesUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "ContourToNodes" ++ ++ ++#ifndef ALL ++#define ALL 0 ++#endif ++ ++/* input macros: */ ++#define XHANDLE prhs[0] ++#define YHANDLE prhs[1] ++#define FILENAME prhs[2] ++#define EDGEVALUEHANDLE prhs[3] ++ ++/* serial output macros: */ ++#define FLAGS (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 4 ++ ++ ++#endif /* _CONTOURTONODES_H */ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/HoleFiller/HoleFiller.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/HoleFiller/HoleFiller.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/HoleFiller/HoleFiller.cpp (revision 12032) +@@ -0,0 +1,69 @@ ++/*!\file: HoleFiller.cpp ++ * \brief fill holes in matlab velocity array ++ this matlab module is an adaptation of a routine written by Robber ++ Crippen. The original routine was designed for the SRTM mission at JPL, ++ and can be found in the current directory, under the name ++ HoleFillerCrippen. It fills void holes in an image, using an interpolation ++ algorithm, and optionnally a smoothing algorithm. ++ This matlab module extends the Crippen routine to be used in Matlab, ++ using double arrays found in the workspace, and loaded directly into memory. ++*/ ++ ++ ++#include "./HoleFiller.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], ++ int nrhs, const mxArray* prhs[]) ++{ ++ ++ int i,j; ++ ++ /* required input: */ ++ double* imagein=NULL; ++ int imagein_rows,imagein_cols; ++ int smooth_flag; ++ int smooth; ++ ++ ++ /* output: */ ++ mxArray* pfield=NULL; ++ double* imageout=NULL; ++ int imageout_rows,imageout_cols; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&HoleFillerUsage); ++ ++ /*Fetch data: */ ++ FetchData(&imagein,&imagein_rows,&imagein_cols,IMAGEIN); ++ FetchData(&smooth_flag,SMOOTH); ++ ++ /*Get smooth flag setup: */ ++ if (smooth_flag==0) ++ smooth=1; ++ else ++ smooth=0; ++ ++ /*Run core hole filler routine: */ ++ HoleFillerx( &imageout,imagein,imagein_rows,imagein_cols,smooth); ++ ++ /* output: */ ++ WriteData(IMAGEOUT,imageout,imagein_rows,imagein_cols); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++ ++void HoleFillerUsage(void) ++{ ++ printf(" HoleFiller usage:\n"); ++ printf(" [image_out]=HoleFiller(image_in,smooth);\n\n"); ++ printf(" where:\n"); ++ printf(" image_in in double format\n"); ++ printf(" smooth: 1 to smooth with a box filer, 0 to leave data raw\n"); ++ printf(" image_out in double format\n"); ++ printf("\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/HoleFiller/HoleFiller.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/HoleFiller/HoleFiller.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/HoleFiller/HoleFiller.h (revision 12032) +@@ -0,0 +1,36 @@ ++ ++/* ++ HoleFiller.h ++*/ ++ ++ ++#ifndef _HOLEFILLER_H ++#define _HOLEFILLER_H ++ ++/* local prototypes: */ ++void HoleFillerUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "HoleFiller" ++ ++ ++/* serial input macros: */ ++#define IMAGEIN prhs[0] ++#define SMOOTH prhs[1] ++ ++/* serial output macros: */ ++#define IMAGEOUT &plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 2 ++ ++#endif /* _HOLEFILLER_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 12032) +@@ -0,0 +1,114 @@ ++/*! \file MeshProfileIntersection.cpp ++ \brief: takes a .exp file (made of several profiles), and figures out its intersection ++ with a mesh. ++ ++ usage: ++ [segments]=MeshProfileIntersection(index,x,y,filename); ++ ++ where: ++ input: ++ index,x,y is a triangulation ++ filename: name of Argus style .exp file containing the segments (can be groups of disconnected segments) ++ output: ++ segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremitis for a segment ++ belonging to the elemnt_id element. there are as many lines in segments as there are segments intersecting the ++ mesh. ++*/ ++ ++#include "./MeshProfileIntersection.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { ++ ++ int i,j; ++ ++ /* required input: */ ++ //mesh ++ double* double_index=NULL; ++ int* index=NULL; ++ int nel; ++ double* x=NULL; ++ double* y=NULL; ++ int nods; ++ int dummy; ++ ++ //contours ++ mxArray* matlabstructure=NULL; ++ Contour** contours=NULL; ++ int numcontours; ++ Contour* contouri=NULL; ++ ++ /* output: */ ++ double* segments=NULL; ++ int numsegs; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&MeshProfileIntersectionUsage); ++ ++ /*First, call expread on filename to build a contour array in the matlab workspace: */ ++ mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); ++ ++ /*Fetch inputs: */ ++ //index ++ FetchData(&double_index,&nel,&dummy,INDEX); ++ if(dummy!=3 && dummy!=6)_error_(" element triangulation should be of 3 or 6 column width!"); ++ index=(int*)xmalloc(nel*3*sizeof(int)); ++ for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); ++ //set pointers. ++ contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); ++ contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); ++ *(contours+i)=contouri; ++ } ++ ++ /* Debugging of contours :{{{1*/ ++ /*for(i=0;inods); ++ for (j=0;jnods;j++){ ++ printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); ++ } ++ }*/ ++ /*}}}*/ ++ ++ /*Run interpolation routine: */ ++ MeshProfileIntersectionx(&segments,&numsegs,index,x,y,nel,nods,contours,numcontours); ++ ++ /* output: */ ++ WriteData(SEGMENTS,segments,numsegs,5); ++ ++ /*end module: */ ++ MODULEEND(); ++ ++} ++ ++void MeshProfileIntersectionUsage(void){ ++ printf(" usage:\n"); ++ printf(" [segments]=MeshProfileIntersection(index,x,y,filename);\n"); ++ printf(" where:\n"); ++ printf(" input:\n"); ++ printf(" index,x,y is a triangulation\n"); ++ printf(" filename: name of Argus style .exp file containing the segments (can be groups of disconnected segments)\n"); ++ printf(" output:\n"); ++ printf(" segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremitis for a segment \n"); ++ printf(" belonging to the elemnt_id element. there are as many lines in segments as there are segments intersecting the \n"); ++ printf(" mesh.\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.h (revision 12032) +@@ -0,0 +1,38 @@ ++ ++/* ++ MeshProfileIntersection.h ++*/ ++ ++ ++#ifndef _MESHPROFILEINTERSECTION_H ++#define _MESHPROFILEINTERSECTION_H ++ ++/* local prototypes: */ ++void MeshProfileIntersectionUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "MeshProfileIntersection" ++ ++/* input macros: */ ++#define INDEX prhs[0] ++#define X prhs[1] ++#define Y prhs[2] ++#define FILENAME prhs[3] ++ ++/* serial output macros: */ ++#define SEGMENTS (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 4 ++ ++#endif /* _MESHPROFILEINTERSECTION_H */ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp (revision 12032) +@@ -0,0 +1,327 @@ ++/*!\file: TriMeshRefine ++ * \brief refine a mesh output by TriMesh: ++ */ ++ ++#include "./TriMeshRefine.h" ++ ++ ++void mexFunction( int nlhs, mxArray* plhs[], ++ int nrhs, const mxArray* prhs[] ) ++{ ++ ++ ++ /*Matlab arrays: */ ++ mxArray* pmxa_array=NULL; ++ mxArray* pmxa_array2=NULL; ++ mxArray* pmxa_array3=NULL; ++ int i,j,k,counter; ++ ++ /* returned quantities: */ ++ ++ double* index=NULL; ++ double* x=NULL; ++ double* y=NULL; ++ double* segments=NULL; ++ double* segmentmarkerlist=NULL; ++ ++ /* input: */ ++ double* area=NULL; ++ double* tindex_in=NULL; ++ double* index_in=NULL; ++ int nel; ++ double* x_inm=NULL; //matlab vector ++ double* x_in=NULL; //copy of matlab vector ++ int nods; ++ double* y_inm=NULL;//matlab vector ++ double* y_in=NULL;//copy of matlab vector ++ double* tsegments_in=NULL; ++ double* segments_in=NULL; ++ double* tsegmentmarkers_in=NULL; ++ double* segmentmarkers_in=NULL; ++ ++ int num_seg; ++ char* order=NULL; ++ ++ /* Triangle structures: */ ++ struct triangulateio in,out; ++ char options[256]; ++ ++ /* verify correct usage: */ ++ if (nlhs==0 && nrhs==0) { ++ /* special case: */ ++ TriMeshRefineUsage(); ++ return; ++ } ++ ++ if (!( (nlhs==5) || (nrhs==6) || (nrhs==7) )){ ++ mexPrintf(" %s format error.\n", __FUNCT__); ++ TriMeshRefineUsage(); ++ printf(" "); ++ mexErrMsgTxt(" "); ++ } ++ ++ /*Fetch index_in: */ ++ if(mxIsDouble(prhs[0])){ ++ nel=mxGetM(prhs[0]); ++ tindex_in=mxGetPr(prhs[0]); ++ index_in=(double*)xmalloc(nel*3*sizeof(double)); ++ for (i=0;i NLHS) { ++ Ll2xyUsage(); ++ _error_("Ll2xy usage error"); ++ } ++ if (nrhs < NRHS) { ++ Ll2xyUsage(); ++ _error_("Ll2xy usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs:\n"); ++ FetchData(&lat,&nlat,LAT_IN); ++ if (verbose) ++ if (nlat == 1) printf(" lat=%g\n",lat[0]); ++ else printf(" lat=[%d values]\n",nlat); ++// for (i=0; iSize()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); ++ /* defaults are in Ll2xydef, so don't duplicate them here, and only use user values if both have been specified */ ++ if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { ++ options->Get(&cm,"central_meridian"); ++ if (verbose) printf(" cm=%g\n",cm); ++ options->Get(&sp,"standard_parallel"); ++ if (verbose) printf(" sp=%g\n",sp); ++ } ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs:\n"); ++ ++ if (nlat != nlon) _error_("Must have same number of lat[%d] and lon[%d] coordinates.",nlat,nlon); ++ else ncoord=nlat; ++ if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); ++ if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); ++ if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); ++ ++ x=(double *)xmalloc(ncoord*sizeof(double)); ++ y=(double *)xmalloc(ncoord*sizeof(double)); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Calling core:\n"); ++ if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) ++ iret=Ll2xyx(x,y, ++ lat,lon,ncoord, ++ sgn,cm,sp); ++ else ++ iret=Ll2xyx(x,y, ++ lat,lon,ncoord, ++ sgn); ++ if (verbose) printf(" iret=%d\n",iret); ++ ++ /*Write data: */ ++ WriteData(X_OUT,x,ncoord); ++ WriteData(Y_OUT,y,ncoord); ++ ++ /*Clean-up*/ ++ delete options; ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void Ll2xyUsage(void) ++{ ++ _printf_(true,"Ll2xy - lat/long to x/y coordinate transformation module:\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This module transforms lat/long to x/y coordinates.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," [x,y]=Ll2xy(lat,lon,sgn,'param name',param,...);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," lat latitude coordinates (double vector)\n"); ++ _printf_(true," lon longitude coordinates (double vector)\n"); ++ _printf_(true," sgn sign for hemisphere (double, +1 (north) or -1 (south))\n"); ++ _printf_(true,"\n"); ++ _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); ++ _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," x x coordinates (double vector)\n"); ++ _printf_(true," y y coordinates (double vector)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Examples:\n"); ++ _printf_(true," [x,y]=Ll2xy(lat,lon, 1);\n"); ++ _printf_(true," [x,y]=Ll2xy(lat,lon, 1,'central_meridian',45,'standard_parallel',70);\n"); ++ _printf_(true," [x,y]=Ll2xy(lat,lon,-1,'central_meridian', 0,'standard_parallel',71);\n"); ++ _printf_(true,"\n"); ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.h (revision 12032) +@@ -0,0 +1,36 @@ ++/* ++ BamgMesherUsage.h ++*/ ++ ++#ifndef _BAMG_MESHER_H_ ++#define _BAMG_MESHER_H_ ++ ++/* local prototypes: */ ++void BamgMesherUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "BamgMesher" ++ ++/* serial input macros: */ ++#define BAMGMESHIN (mxArray*)prhs[0] ++#define BAMGGEOMIN (mxArray*)prhs[1] ++#define BAMGOPTIONS (mxArray*)prhs[2] ++ ++/* serial output macros: */ ++#define BAMGMESHOUT (mxArray**)&plhs[0] ++#define BAMGGEOMOUT (mxArray**)&plhs[1] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 2 ++#undef NRHS ++#define NRHS 3 ++ ++#endif /* _BAMG_MESHER_H_ */ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp (revision 12032) +@@ -0,0 +1,56 @@ ++/*\file BamgMesher.c ++ *\brief: mesher that uses the bamg library ++ */ ++#include "./BamgMesher.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*Outputs*/ ++ mxArray* bamgmesh_mat=NULL; ++ mxArray* bamggeom_mat=NULL; ++ ++ /*diverse: */ ++ BamgOpts *bamgopts=NULL; ++ BamgMesh *bamgmesh_in=NULL; ++ BamgGeom *bamggeom_in=NULL; ++ BamgMesh *bamgmesh_out=NULL; ++ BamgGeom *bamggeom_out=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&BamgMesherUsage); ++ ++ /*Initialize variables*/ ++ bamgopts = new BamgOpts(BAMGOPTIONS); ++ bamggeom_in= new BamgGeom(BAMGGEOMIN); ++ bamgmesh_in= new BamgMesh(BAMGMESHIN); ++ ++ /*Initialize outputs*/ ++ bamggeom_out=new BamgGeom(); ++ bamgmesh_out=new BamgMesh(); ++ ++ /*!Generate internal degree of freedom numbers: */ ++ Bamgx(bamgmesh_out,bamggeom_out,bamgmesh_in,bamggeom_in,bamgopts); ++ ++ /*Generate output Matlab Structures*/ ++ bamggeom_out->SetStructureFields((void*)BAMGGEOMOUT); ++ bamgmesh_out->SetStructureFields((void*)BAMGMESHOUT); ++ ++ /*Free ressources: */ ++ delete bamgopts; ++ delete bamggeom_in; ++ delete bamggeom_out; ++ delete bamgmesh_in; ++ delete bamgmesh_out; ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void BamgMesherUsage(void){ ++ _printf_(true,"\n"); ++ _printf_(true," usage: [bamgmesh,bamggeom]=%s(bamgmesh,bamggeom,bamgoptions);\n",__FUNCT__); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromGridToMesh/InterpFromGridToMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromGridToMesh/InterpFromGridToMesh.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromGridToMesh/InterpFromGridToMesh.h (revision 12032) +@@ -0,0 +1,42 @@ ++/*!\file InterpFromGridToMesh.h ++ * \brief: prototype for Data Interpolation mex module. ++ */ ++ ++#ifndef _InterpFromGridToMesh_H ++#define _InterpFromGridToMesh_H ++ ++/* local prototypes: */ ++void InterpFromGridToMeshUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "InterpFromGridToMesh" ++ ++#undef CLEANUP ++#define CLEANUP InterpFromGridToMeshLocalCleanup(); ++ ++ ++/* serial input macros: */ ++#define XHANDLE prhs[0] ++#define YHANDLE prhs[1] ++#define DATAHANDLE prhs[2] ++#define XMESHHANDLE prhs[3] ++#define YMESHHANDLE prhs[4] ++#define DEFAULTHANDLE prhs[5] ++#define INTERPENUM prhs[6] ++ ++/* serial output macros: */ ++#define DATAMESH (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 6 ++ ++#endif /* _INTERPFROMGRIDTOMESH_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromGridToMesh/InterpFromGridToMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromGridToMesh/InterpFromGridToMesh.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromGridToMesh/InterpFromGridToMesh.cpp (revision 12032) +@@ -0,0 +1,95 @@ ++/*!\file InterpFromGridToMesh.c ++ * \brief: data interpolation from a list of (x,y,values) into mesh vertices ++ ++ InterpFromGridToMesh.c ++ ++ usage: ++ data_mesh=InterpFromGridToMesh(x,y,data,x_mesh,y_mesh); ++ ++ where: ++ ++ input: ++ x,y: coordinates of matrix data ++ data - matrix holding the data to be interpolated onto the mesh. ++ x_mesh,y_mesh: coordinates of the mesh vertices onto which we interpolate. ++ ++ output: ++ data_mesh: vector of mesh interpolated data. ++*/ ++ ++#include "./InterpFromGridToMesh.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { ++ ++ int i,j; ++ ++ /*input: */ ++ double* x=NULL; ++ double* y=NULL; ++ int x_rows,y_rows; ++ double* data=NULL; ++ int data_rows,data_cols; ++ double* x_mesh=NULL; ++ double* y_mesh=NULL; ++ int x_mesh_rows,y_mesh_rows; ++ double default_value; ++ int interpolationenum; ++ ++ /* output: */ ++ Vector* data_mesh=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ //CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&InterpFromGridToMeshUsage); ++ if((nlhs!=NLHS) || (nrhs!=6 && nrhs!=7)){ ++ InterpFromGridToMeshUsage(); ++ _error_(" usage. See above"); ++ } ++ ++ /*Input datasets: */ ++ FetchData(&x,&x_rows,NULL,XHANDLE); ++ FetchData(&y,&y_rows,NULL,YHANDLE); ++ FetchData(&data,&data_rows,&data_cols,DATAHANDLE); ++ FetchData(&x_mesh,&x_mesh_rows,NULL,XMESHHANDLE); ++ FetchData(&y_mesh,&y_mesh_rows,NULL,YMESHHANDLE); ++ FetchData(&default_value,DEFAULTHANDLE); ++ ++ /* Run core computations: */ ++ if(nrhs==7){ ++ FetchData(&interpolationenum,INTERPENUM); ++ InterpFromGridToMeshx(&data_mesh, x, x_rows, y, y_rows, data, data_rows,data_cols, x_mesh, y_mesh, x_mesh_rows,default_value,interpolationenum); ++ } ++ else{ ++ InterpFromGridToMeshx(&data_mesh, x, x_rows, y, y_rows, data, data_rows,data_cols, x_mesh, y_mesh, x_mesh_rows,default_value); ++ } ++ ++ /*Write data: */ ++ WriteData(DATAMESH,data_mesh); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void InterpFromGridToMeshUsage(void) ++{ ++ _printf_(true,"INTERPFROMGRIDTOMESH - interpolation from a grid onto a list of points\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This function is a multi-threaded mex file that interpolates a field\n"); ++ _printf_(true," defined on a grid onto a list of points\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," data_mesh=InterpFromGridToMesh(x,y,data,x_mesh,y_mesh,default_value);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," data: matrix holding the data to be interpolated onto the mesh.\n"); ++ _printf_(true," x,y: coordinates of matrix data. (x and y must be in increasing order)\n"); ++ _printf_(true," x_mesh,y_mesh: coordinates of the points onto which we interpolate.\n"); ++ _printf_(true," default_value: default value if no data is found (holes).\n"); ++ _printf_(true," data_mesh: vector of mesh interpolated data.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Example:\n"); ++ _printf_(true," load('velocities.mat');\n"); ++ _printf_(true," md.inversion.vx_obs=InterpFromGridToMesh(x_n,y_m,vx,md.mesh.x,md.mesh.y,0);\n"); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 12032) +@@ -0,0 +1,46 @@ ++ ++/* ++ InterpFromMeshToGrid.h ++*/ ++ ++ ++#ifndef _INTERPFROMMESHTOGRID_H ++#define _INTERPFROMMESHTOGRID_H ++ ++/* local prototypes: */ ++void InterpFromMeshToGridUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "InterpFromMeshToGrid" ++ ++/* serial input macros: */ ++#define INDEX (mxArray*)prhs[0] ++#define X (mxArray*)prhs[1] ++#define Y (mxArray*)prhs[2] ++#define MESHDATA (mxArray*)prhs[3] ++#define XMIN (mxArray*)prhs[4] ++#define YMAX (mxArray*)prhs[5] ++#define XPOSTING (mxArray*)prhs[6] ++#define YPOSTING (mxArray*)prhs[7] ++#define NLINES (mxArray*)prhs[8] ++#define NCOLS (mxArray*)prhs[9] ++#define DEFAULTVALUE (mxArray*)prhs[10] ++ ++/* serial output macros: */ ++#define XM (mxArray**)&plhs[0] ++#define YM (mxArray**)&plhs[1] ++#define GRIDDATA (mxArray**)&plhs[2] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 3 ++#undef NRHS ++#define NRHS 11 ++ ++#endif /* _INTERPFROMMESHTOGRID_H*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToGrid/InterpFromMeshToGrid.cpp (revision 12032) +@@ -0,0 +1,79 @@ ++/*\file InterpFromMeshToGrid.c ++ *\brief: compute diff between observed and modeled velocity ++ */ ++ ++#include "./InterpFromMeshToGrid.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*input datasets: */ ++ double* index=NULL; ++ int nel; ++ double* x=NULL; ++ int nods; ++ double* y=NULL; ++ double* meshdata=NULL; ++ int meshdata_length; ++ double xmin; ++ double ymax; ++ double xposting; ++ double yposting; ++ int nlines,ncols; ++ double default_value; ++ ++ /* output datasets: */ ++ double* griddata=NULL; ++ double* x_m=NULL; ++ double* y_m=NULL; ++ ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&InterpFromMeshToGridUsage); ++ ++ /*Input datasets: */ ++ FetchData(&index,&nel,NULL,INDEX); ++ FetchData(&x,&nods,NULL,X); ++ FetchData(&y,NULL,NULL,Y); ++ FetchData(&meshdata,&meshdata_length,NULL,MESHDATA); ++ FetchData(&xmin,XMIN); ++ FetchData(&ymax,YMAX); ++ FetchData(&xposting,XPOSTING); ++ FetchData(&yposting,YPOSTING); ++ FetchData(&nlines,NLINES); ++ FetchData(&ncols,NCOLS); ++ FetchData(&default_value,DEFAULTVALUE); ++ ++ /*Call core of computation: */ ++ InterpFromMeshToGridx(&x_m,&y_m,&griddata,index,x,y,nods,nel,meshdata,meshdata_length,xmin,ymax,xposting,yposting,nlines,ncols,default_value); ++ ++ /*Write results: */ ++ WriteData(XM,x_m,ncols); ++ WriteData(YM,y_m,nlines); ++ WriteData(GRIDDATA,griddata,nlines,ncols); ++ ++ /*Free ressources: */ ++ //let matlab do this. ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void InterpFromMeshToGridUsage(void) ++{ ++ _printf_(true,"INTERPFROMMESHTOGRID - interpolation of a data defined on a mesh onto a grid\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This function is a multi-threaded mex file that interpolates a field\n"); ++ _printf_(true," defined on a triangular mesh onto a regular grid\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," [x_m,y_m,griddata]=InterpFromMeshToGrid(index,x,y,data,xmin,ymax,xposting,yposting,nlines,ncols,default_value)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," index,x,y: delaunay triangulation defining the mesh.\n"); ++ _printf_(true," meshdata: vertex values of data to be interpolated.\n"); ++ _printf_(true," xmin,ymax,posting,nlines,ncols: parameters that define the grid\n"); ++ _printf_(true," default_value: value of points located out of the mesh.\n"); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.cpp (revision 12032) +@@ -0,0 +1,151 @@ ++/*\file KMLFileRead.c ++ *\brief: KML file reader module. ++ */ ++#include "./KMLFileRead.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i,j,nnodes=0,verbose=1; ++ KML_Object* kobj; ++ ++ /*input: */ ++ char* name=NULL; ++ ++ char* notes=NULL; ++ const mxArray* notesi; ++ mwIndex nindex; ++ ++ int* elem=NULL; ++ int melem=0,nelem=0; ++ ++ int* nodecon=NULL; ++ int mncon=0,nncon=0; ++ ++ double* lat=NULL; ++ int mlat=0,nlat=0,llat=0; ++ ++ double* lng=NULL; ++ int mlng=0,nlng=0,llng=0; ++ ++ int nparts=0; ++ ++ int* part=NULL; ++ int mprt=0,nprt=0,lprt=0; ++ ++ double* data=NULL; ++ int mdata=0,ndata=0; ++ ++ double* cmap=NULL; ++ int mcmap=0,ncmap=0; ++ ++ char* filnam=NULL; ++ ++ FILE* fidi=NULL; ++ FILE* fido=NULL; ++ ++ Options* options=NULL; ++ char* echo =NULL; ++ char* deepecho=NULL; ++ char* write =NULL; ++ ++ /* output: */ ++ int ierror=0; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ if (nlhs > NLHS) { ++ KMLFileReadUsage(); ++ _error_("KMLFileRead usage error"); ++ } ++ if (nrhs < NRHS) { ++ KMLFileReadUsage(); ++ _error_("KMLFileRead usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs:\n"); ++ FetchData(&filnam,FILENAME); ++ if (verbose) printf(" filnam =\"%s\"\n",filnam); ++ ++ if (verbose) printf("Parsing options:\n"); ++ options=new Options(NRHS,nrhs,prhs); ++ if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); ++ options->Get(&echo ,"echo" ,"off"); ++ options->Get(&deepecho,"deepecho","off"); ++ options->Get(&write ,"write" ,"off"); ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs:\n"); ++ ++ if (!strlen(filnam)) ++ strcpy(filnam,"stdout"); ++ ++ if (verbose) printf("Opening file \"%s\".\n",filnam); ++ fidi=fopen(filnam,"r"); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Calling core:\n"); ++ kobj=KMLFileReadx(fidi); ++ ++ if (verbose) printf("Closing file \"%s\".\n",filnam); ++ fclose(fidi); ++ ++ if (kobj) { ++ if (!strncmp(echo ,"on",2) || !strncmp(echo ,"y",1)) ++ kobj->Echo(); ++ if (!strncmp(deepecho,"on",2) || !strncmp(deepecho,"y",1)) ++ kobj->DeepEcho(); ++ if (strncmp(write,"off",3) && strncmp(write,"no",2)) { ++ if (!strncmp(write,"on",2) || !strncmp(write,"yes",3) || !strncmp(write,"stdout",6)) { ++ kobj->Write(stdout,""); ++ } ++ else { ++ if (verbose) printf("Opening file \"%s\".\n",write); ++ fido=fopen(write,"w"); ++ kobj->Write(fido,""); ++ if (verbose) printf("Closing file \"%s\".\n",write); ++ ierror=fclose(fido); ++ } ++ } ++ ++ delete kobj; ++ } ++ ++ /*Write data: */ ++ WriteData(ERRORFLAG,ierror); ++ ++ /*Clean-up*/ ++ xfree((void**)&write); ++ xfree((void**)&deepecho); ++ xfree((void**)&echo); ++ delete options; ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void KMLFileReadUsage(void) ++{ ++ _printf_(true,"KMLFileRead - KML file reader module:\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This module reads a KML file.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," [ierror]=KMLFileRead(kmlfile,'param name',param,...);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," kmlfile file name of kml file to be read (char)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," echo echo command (char, optional, 'off'/'on')\n"); ++ _printf_(true," deepecho deep echo command (char, optional, 'off'/'on')\n"); ++ _printf_(true," write write command (char, optional, 'off'/'stdout'/kmlfile)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," ierror return code (non-zero for error)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Examples:\n"); ++ _printf_(true," [ierror]=KMLFileRead('file.kml','deepecho','on');\n"); ++ _printf_(true," [ierror]=KMLFileRead('filin.kml','echo','on','write','filout.kml');\n"); ++ _printf_(true,"\n"); ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.h (revision 12032) +@@ -0,0 +1,33 @@ ++/*!\file KMLFileRead.h ++ * \brief: prototype for KML file reader mex module. ++ */ ++ ++#ifndef _KMLFILEREAD_H ++#define _KMLFILEREAD_H ++ ++/* local prototypes: */ ++void KMLFileReadUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "KMLFileRead" ++ ++ ++/* serial input macros: */ ++#define FILENAME prhs[0] ++ ++/* serial output macros: */ ++#define ERRORFLAG (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NRHS ++#define NRHS 1 ++#undef NLHS ++#define NLHS 1 ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/AverageFilter/AverageFilter.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/AverageFilter/AverageFilter.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/AverageFilter/AverageFilter.cpp (revision 12032) +@@ -0,0 +1,62 @@ ++/*!\file: AverageFilter.cpp ++ * \brief fill holes in matlab velocity array ++ this matlab module is an adaptation of a routine written by Robber ++ Crippen. The original routine was designed for the SRTM mission at JPL, ++ and can be found in the current directory, under the name ++ AverageFilterCrippen. It fills void holes in an image, using an interpolation ++ algorithm, and optionnally a smoothing algorithm. ++ This matlab module extends the Crippen routine to be used in Matlab, ++ using double arrays found in the workspace, and loaded directly into memory. ++*/ ++ ++ ++#include "./AverageFilter.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], ++ int nrhs, const mxArray* prhs[]) ++{ ++ ++ int i,j; ++ ++ /* required input: */ ++ double* imagein=NULL; ++ int imagein_rows,imagein_cols; ++ int smooth; ++ ++ ++ /* output: */ ++ mxArray* pfield=NULL; ++ double* imageout=NULL; ++ int imageout_rows,imageout_cols; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&AverageFilterUsage); ++ ++ /*Fetch data: */ ++ FetchData(&imagein,&imagein_rows,&imagein_cols,IMAGEIN); ++ FetchData(&smooth,SMOOTH); ++ ++ /*Run core hole filler routine: */ ++ AverageFilterx( &imageout,imagein,imagein_rows,imagein_cols,smooth); ++ ++ /* output: */ ++ WriteData(IMAGEOUT,imageout,imagein_rows,imagein_cols); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++ ++void AverageFilterUsage(void) ++{ ++ printf(" AverageFilter usage:\n"); ++ printf(" [image_out]=AverageFilter(image_in,pixels);\n\n"); ++ printf(" where:\n"); ++ printf(" image_in in double format\n"); ++ printf(" pixels: characteristic size of smoothing\n"); ++ printf(" image_out in double format\n"); ++ printf("\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/AverageFilter/AverageFilter.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/AverageFilter/AverageFilter.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/AverageFilter/AverageFilter.h (revision 12032) +@@ -0,0 +1,36 @@ ++ ++/* ++ AverageFilter.h ++*/ ++ ++ ++#ifndef _AVERAGEFILTER_H ++#define _AVERAGEFILTER_H ++ ++/* local prototypes: */ ++void AverageFilterUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "AverageFilter" ++ ++ ++/* serial input macros: */ ++#define IMAGEIN prhs[0] ++#define SMOOTH prhs[1] ++ ++/* serial output macros: */ ++#define IMAGEOUT &plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 2 ++ ++#endif /* _AVERAGEFILTER_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.cpp (revision 12032) +@@ -0,0 +1,117 @@ ++/*\file Shp2Kml.c ++ *\brief: shp to kml file conversion mex module. ++ */ ++ ++#ifdef HAVE_CONFIG_H ++#include "config.h" ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "./Shp2Kml.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i,verbose=1; ++ ++ /*input: */ ++ char *filshp=NULL,*filkml=NULL; ++ int sgn; ++ ++ Options* options=NULL; ++ double cm=0.,sp=0.; ++ ++ /* output: */ ++ int iret=0; ++ ++ #ifndef _HAVE_SHAPELIB_ //only works if shapelib library has been compiled in. ++ _error_(" Shapelib not available! Cannot carry out shp file translation!"); ++ #endif ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ if (nlhs > NLHS) { ++ Shp2KmlUsage(); ++ _error_("Shp2Kml usage error"); ++ } ++ if (nrhs < NRHS) { ++ Shp2KmlUsage(); ++ _error_("Shp2Kml usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs:\n"); ++ FetchData(&filshp,SHP_IN); ++ if (verbose) printf(" filshp=\"%s\"\n",filshp); ++ FetchData(&filkml,KML_IN); ++ if (verbose) printf(" filkml=\"%s\"\n",filkml); ++ FetchData(&sgn,SGN_IN); ++ if (verbose) printf(" sgn=%d\n",sgn); ++ ++ if (verbose) printf("Parsing options:\n"); ++ options=new Options(NRHS,nrhs,prhs); ++ if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); ++ /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ ++ if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { ++ options->Get(&cm,"central_meridian"); ++ if (verbose) printf(" cm=%g\n",cm); ++ options->Get(&sp,"standard_parallel"); ++ if (verbose) printf(" sp=%g\n",sp); ++ } ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs:\n"); ++ ++ if (sgn < -1 || sgn > +1) _error_("Hemisphere sgn=%d must be +1 (north), -1 (south), or 0 (no translation).",sgn); ++ if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); ++ if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Calling core:\n"); ++ if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) ++ iret=Shp2Kmlx(filshp,filkml, ++ sgn,cm,sp); ++ else ++ iret=Shp2Kmlx(filshp,filkml, ++ sgn); ++ if (verbose) printf(" iret=%d\n",iret); ++ ++ /*Write data: */ ++ WriteData(RET_OUT,iret); ++ ++ /*Clean-up*/ ++ delete options; ++ xfree((void**)&filkml); ++ xfree((void**)&filshp); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void Shp2KmlUsage(void) ++{ ++ _printf_(true,"Shp2Kml - shp to kml file conversion module:\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This module converts a file from shp to kml format.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," [ret]=Shp2Kml(filshp,filkml,sgn,'param name',param,...);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," filshp file name of shp file to be read (char, extension optional)\n"); ++ _printf_(true," filkml file name of kml file to be written (char)\n"); ++ _printf_(true," sgn sign for hemisphere (double, +1 (north); -1 (south); or 0 (no translation))\n"); ++ _printf_(true,"\n"); ++ _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); ++ _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," ret return code (non-zero for warning)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Examples:\n"); ++ _printf_(true," [ret]=Shp2Kml('file.shp','file.kml', 0);\n"); ++ _printf_(true," [ret]=Shp2Kml('file.shp','file.kml', 1,'central_meridian',45,'standard_parallel',70);\n"); ++ _printf_(true," [ret]=Shp2Kml('file.shp','file.kml',-1,'central_meridian', 0,'standard_parallel',71);\n"); ++ _printf_(true,"\n"); ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.h (revision 12032) +@@ -0,0 +1,36 @@ ++/*!\file Shp2Kml.h ++ * \brief: prototype for shp to kml file conversion mex module. ++ */ ++ ++#ifndef _SHP2KML_H ++#define _SHP2KML_H ++ ++/* local prototypes: */ ++void Shp2KmlUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "Shp2Kml" ++ ++ ++/* serial input macros: */ ++#define SHP_IN prhs[0] ++#define KML_IN prhs[1] ++#define SGN_IN prhs[2] ++ ++/* serial output macros: */ ++#define RET_OUT (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NRHS ++#define NRHS 3 ++#undef NLHS ++#define NLHS 1 ++ ++#endif ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp (revision 12032) +@@ -0,0 +1,328 @@ ++/*!\file: TriMeshProcessRifts.cpp ++ * \brief split a mesh where a rift (or fault) is present ++ */ ++ ++#include "./TriMeshProcessRifts.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], ++ int nrhs, const mxArray* prhs[] ) { ++ ++ ++ /*Matlab arrays: */ ++ mxArray* pmxa_array=NULL; ++ mxArray* pmxa_array2=NULL; ++ mxArray* pmxa_array3=NULL; ++ int i,j,k,counter; ++ ++ /* returned quantities: */ ++ int out_numrifts; ++ int* out_riftsnumsegments=NULL; ++ double** out_riftssegments=NULL; ++ int* out_riftsnumpairs=NULL; ++ double** out_riftspairs=NULL; ++ double* out_riftstips=NULL; ++ double** out_riftspenaltypairs=NULL; ++ int* out_riftsnumpenaltypairs=NULL; ++ ++ /*empty rifts structure: */ ++ double* pNaN=NULL; ++ const char* fnames[10]; ++ mwSize ndim=2; ++ mwSize dimensions[2] = {1,1}; ++ double* pair=NULL; ++ ++ ++ /* input: */ ++ double* tindex_in=NULL; ++ double* index_in=NULL; ++ int nel; ++ double* x_inm=NULL; //matlab vector ++ double* x_in=NULL; //copy of matlab vector ++ int nods; ++ double* y_inm=NULL;//matlab vector ++ double* y_in=NULL;//copy of matlab vector ++ double* tsegments_in=NULL; ++ double* segments_in=NULL; ++ double* tsegmentmarkers_in=NULL; ++ double* segmentmarkers_in=NULL; ++ ++ /* state: */ ++ double* state=NULL; ++ ++ int num_seg; ++ ++ /*rifts: */ ++ int riftflag; ++ int numrifts; ++ ++ /* verify correct usage: */ ++ if (nlhs==0 && nrhs==0) { ++ /* special case: */ ++ TriMeshProcessRiftsUsage(); ++ return; ++ } ++ ++ if (!( (nlhs==6) || (nrhs==5))){ ++ mexPrintf(" %s format error.\n", __FUNCT__); ++ TriMeshProcessRiftsUsage(); ++ printf(" "); ++ mexErrMsgTxt(" "); ++ } ++ ++ /*Fetch index_in: */ ++ if(mxIsDouble(prhs[0])){ ++ nel=mxGetM(prhs[0]); ++ tindex_in=mxGetPr(prhs[0]); ++ index_in=(double*)xmalloc(nel*3*sizeof(double)); ++ for (i=0;i NLHS) { ++ Exp2KmlUsage(); ++ _error_("Exp2Kml usage error"); ++ } ++ if (nrhs < NRHS) { ++ Exp2KmlUsage(); ++ _error_("Exp2Kml usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs:\n"); ++ FetchData(&filexp,EXP_IN); ++ if (verbose) printf(" filexp=\"%s\"\n",filexp); ++ FetchData(&filkml,KML_IN); ++ if (verbose) printf(" filkml=\"%s\"\n",filkml); ++ FetchData(&sgn,SGN_IN); ++ if (verbose) printf(" sgn=%d\n",sgn); ++ ++ if (verbose) printf("Parsing options:\n"); ++ options=new Options(NRHS,nrhs,prhs); ++ if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); ++ options->Get(&choles,"holes","no"); ++ if (!strncmp(choles,"y",1) || !strncmp(choles,"on",2)) ++ holes=true; ++ /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ ++ if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { ++ options->Get(&cm,"central_meridian"); ++ if (verbose) printf(" cm=%g\n",cm); ++ options->Get(&sp,"standard_parallel"); ++ if (verbose) printf(" sp=%g\n",sp); ++ } ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs:\n"); ++ ++ if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); ++ if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); ++ if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Calling core:\n"); ++ if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) ++ iret=Exp2Kmlx(filexp,filkml, ++ sgn,cm,sp, ++ holes); ++ else ++ iret=Exp2Kmlx(filexp,filkml, ++ sgn, ++ holes); ++ if (verbose) printf(" iret=%d\n",iret); ++ ++ /*Write data: */ ++ WriteData(RET_OUT,iret); ++ ++ /*Clean-up*/ ++ xfree((void**)&choles); ++ delete options; ++ xfree((void**)&filkml); ++ xfree((void**)&filexp); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void Exp2KmlUsage(void) ++{ ++ _printf_(true,"Exp2Kml - exp to kml file conversion module:\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This module converts a file from exp to kml format.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," [ret]=Exp2Kml(filexp,filkml,sgn,'param name',param,...);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," filexp file name of exp file to be read (char)\n"); ++ _printf_(true," filkml file name of kml file to be written (char)\n"); ++ _printf_(true," sgn sign for hemisphere (double, +1 (north) or -1 (south))\n"); ++ _printf_(true,"\n"); ++ _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); ++ _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); ++ _printf_(true," holes flag for treatment of multiple profiles (char, optional, 'yes' for holes))\n"); ++ _printf_(true,"\n"); ++ _printf_(true," ret return code (non-zero for warning)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Examples:\n"); ++ _printf_(true," [ret]=Exp2Kml('file.exp','file.kml', 1);\n"); ++ _printf_(true," [ret]=Exp2Kml('file.exp','file.kml', 1,'central_meridian',45,'standard_parallel',70,'holes','yes');\n"); ++ _printf_(true," [ret]=Exp2Kml('file.exp','file.kml',-1,'central_meridian', 0,'standard_parallel',71,'holes','yes');\n"); ++ _printf_(true,"\n"); ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Exp2Kml/Exp2Kml.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Exp2Kml/Exp2Kml.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Exp2Kml/Exp2Kml.h (revision 12032) +@@ -0,0 +1,36 @@ ++/*!\file Exp2Kml.h ++ * \brief: prototype for exp to kml file conversion mex module. ++ */ ++ ++#ifndef _EXP2KML_H ++#define _EXP2KML_H ++ ++/* local prototypes: */ ++void Exp2KmlUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "Exp2Kml" ++ ++ ++/* serial input macros: */ ++#define EXP_IN prhs[0] ++#define KML_IN prhs[1] ++#define SGN_IN prhs[2] ++ ++/* serial output macros: */ ++#define RET_OUT (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NRHS ++#define NRHS 3 ++#undef NLHS ++#define NLHS 1 ++ ++#endif ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.cpp (revision 12032) +@@ -0,0 +1,106 @@ ++/*\file Kml2Exp.c ++ *\brief: kml to exp file conversion mex module. ++ */ ++#include "./Kml2Exp.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i,verbose=1; ++ ++ /*input: */ ++ char *filkml=NULL,*filexp=NULL; ++ int sgn; ++ ++ Options* options=NULL; ++ double cm=0.,sp=0.; ++ ++ /* output: */ ++ int iret=0; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ if (nlhs > NLHS) { ++ Kml2ExpUsage(); ++ _error_("Kml2Exp usage error"); ++ } ++ if (nrhs < NRHS) { ++ Kml2ExpUsage(); ++ _error_("Kml2Exp usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs:\n"); ++ FetchData(&filkml,KML_IN); ++ if (verbose) printf(" filkml=\"%s\"\n",filkml); ++ FetchData(&filexp,EXP_IN); ++ if (verbose) printf(" filexp=\"%s\"\n",filexp); ++ FetchData(&sgn,SGN_IN); ++ if (verbose) printf(" sgn=%d\n",sgn); ++ ++ if (verbose) printf("Parsing options:\n"); ++ options=new Options(NRHS,nrhs,prhs); ++ if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); ++ /* defaults are in Ll2xydef, so don't duplicate them here, and only use user values if both have been specified */ ++ if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { ++ options->Get(&cm,"central_meridian"); ++ if (verbose) printf(" cm=%g\n",cm); ++ options->Get(&sp,"standard_parallel"); ++ if (verbose) printf(" sp=%g\n",sp); ++ } ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs:\n"); ++ ++ if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); ++ if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); ++ if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Calling core:\n"); ++ if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) ++ iret=Kml2Expx(filkml,filexp, ++ sgn,cm,sp); ++ else ++ iret=Kml2Expx(filkml,filexp, ++ sgn); ++ if (verbose) printf(" iret=%d\n",iret); ++ ++ /*Write data: */ ++ WriteData(RET_OUT,iret); ++ ++ /*Clean-up*/ ++ delete options; ++ xfree((void**)&filexp); ++ xfree((void**)&filkml); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void Kml2ExpUsage(void) ++{ ++ _printf_(true,"Kml2Exp - kml to exp file conversion module:\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This module converts a file from kml to exp format.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," [ret]=Kml2Exp(filexp,filkml,sgn,'param name',param,...);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," filkml file name of kml file to be read (char)\n"); ++ _printf_(true," filexp file name of exp file to be written (char)\n"); ++ _printf_(true," sgn sign for hemisphere (double, +1 (north) or -1 (south))\n"); ++ _printf_(true,"\n"); ++ _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); ++ _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," ret return code (non-zero for warning)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Examples:\n"); ++ _printf_(true," [ret]=Kml2Exp('file.kml','file.exp', 1);\n"); ++ _printf_(true," [ret]=Kml2Exp('file.kml','file.exp', 1,'central_meridian',45,'standard_parallel',70);\n"); ++ _printf_(true," [ret]=Kml2Exp('file.kml','file.exp',-1,'central_meridian', 0,'standard_parallel',71);\n"); ++ _printf_(true,"\n"); ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.h (revision 12032) +@@ -0,0 +1,36 @@ ++/*!\file Kml2Exp.h ++ * \brief: prototype for kml to exp file conversion mex module. ++ */ ++ ++#ifndef _KML2EXP_H ++#define _KML2EXP_H ++ ++/* local prototypes: */ ++void Kml2ExpUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "Kml2Exp" ++ ++ ++/* serial input macros: */ ++#define KML_IN prhs[0] ++#define EXP_IN prhs[1] ++#define SGN_IN prhs[2] ++ ++/* serial output macros: */ ++#define RET_OUT (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NRHS ++#define NRHS 3 ++#undef NLHS ++#define NLHS 1 ++ ++#endif ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp (revision 12032) +@@ -0,0 +1,52 @@ ++/*! \file PointCloudFindNeighbors ++ \brief: flag points that are too near one another, within an array of point coordinates ++*/ ++ ++#include "./PointCloudFindNeighbors.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { ++ ++ int i,j; ++ ++ /* required input: */ ++ double* x=NULL; ++ double* y=NULL; ++ int nods; ++ double mindistance; ++ double multithread; ++ ++ /* output: */ ++ Vector* flags=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&PointCloudFindNeighborsUsage); ++ ++ /*Fetch inputs: */ ++ FetchData(&x,&nods,NULL,XHANDLE); ++ FetchData(&y,NULL,NULL,YHANDLE); ++ FetchData(&mindistance,MINDISTANCE); ++ FetchData(&multithread,MULTITHREAD); ++ ++ /*Run core routine: */ ++ PointCloudFindNeighborsx(&flags,x,y,nods,mindistance,multithread); ++ ++ /* output: */ ++ WriteData(FLAGS,flags); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void PointCloudFindNeighborsUsage(void){ ++ printf(" usage:\n"); ++ printf(" [flags]=PointCloudFindNeighbors(x,y,mindistance,multithread);\n\n"); ++ printf(" where:\n"); ++ printf(" x,y: list of points.\n"); ++ printf(" mindistance: minimum distance that should exist between points in the cloud.\n"); ++ printf(" multithread: run multithreaded or not. with multithreads, flags can get 1 and 2 values in duplicates.\n"); ++ printf(" flags: array of flags (flag==1 means point is within mindistance of another point)\n"); ++ printf("\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PointCloudFindNeighbors/PointCloudFindNeighbors.h (revision 12032) +@@ -0,0 +1,44 @@ ++ ++/* ++ PointCloudFindNeighbors.h ++*/ ++ ++ ++#ifndef _POINTCLOUDFINDNEIGHBORS_H ++#define _POINTCLOUDFINDNEIGHBORS_H ++ ++/* local prototypes: */ ++void PointCloudFindNeighborsUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "PointCloudFindNeighbors" ++ ++ ++#ifndef ALL ++#define ALL 0 ++#endif ++ ++/* input macros: */ ++#define XHANDLE prhs[0] ++#define YHANDLE prhs[1] ++#define MINDISTANCE prhs[2] ++#define MULTITHREAD prhs[3] ++ ++/* serial output macros: */ ++#define FLAGS (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 4 ++ ++ ++#endif /* _POINTCLOUDFINDNEIGHBORS_H */ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp (revision 12032) +@@ -0,0 +1,47 @@ ++/*\file PropagateFlagsFromConnectivity.c ++ *\brief: propagate flags onto mesh, element by element, using connectivity. ++ */ ++ ++#include "./PropagateFlagsFromConnectivity.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*input/output datasets: */ ++ double* connectivity=NULL; ++ int nel; ++ double* pool=NULL; ++ double* flags=NULL; ++ int index; ++ int dummy; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&PropagateFlagsFromConnectivityUsage); ++ ++ /*Input datasets: */ ++ FetchData(&connectivity,&nel,&dummy,CONNECTIVITY); ++ FetchData(&pool,&dummy,POOL); ++ FetchData(&index,INDEX); ++ FetchData(&flags,&dummy,FLAGS); ++ ++ /*!Generate internal degree of freedom numbers: */ ++ PropagateFlagsFromConnectivityx(pool,connectivity,index,flags); ++ ++ /*write output datasets: */ ++ WriteData(POOLOUT,pool,nel); ++ ++ /*Free ressources: */ ++ xfree((void**)&connectivity); ++ xfree((void**)&flags); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void PropagateFlagsFromConnectivityUsage(void) { ++ printf("\n"); ++ printf(" usage: [pool] = %s(connectivity,pool,index,flags);\n",__FUNCT__); ++ printf("\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h (revision 12032) +@@ -0,0 +1,40 @@ ++ ++/* ++ PropagateFlagsFromConnectivity.h ++*/ ++ ++ ++#ifndef _PROPAGATEFLAGSFROMCONNECTIVITY_H ++#define _PROPAGATEFLAGSFROMCONNECTIVITY_H ++ ++/* local prototypes: */ ++void PropagateFlagsFromConnectivityUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "PropagateFlagsFromConnectivity" ++ ++/* serial input macros: */ ++#define CONNECTIVITY (mxArray*)prhs[0] ++#define POOL (mxArray*)prhs[1] ++#define INDEX (mxArray*)prhs[2] ++#define FLAGS (mxArray*)prhs[3] ++ ++/* serial output macros: */ ++#define POOLOUT (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 4 ++ ++ ++#endif /* _PROPAGATEFLAGSFROMCONNECTIVITY_H */ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.cpp (revision 12032) +@@ -0,0 +1,322 @@ ++/* ++ * TriMeshRifts: out of a domain outline file ( Argus format ), ++ * use the Triangle package to create a triangular mesh ++ * ++ */ ++ ++#include "./TriMeshRifts.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], ++ int nrhs, const mxArray* prhs[] ) ++{ ++ ++ ++ /*Matlab arrays: */ ++ mxArray* pmxa_array=NULL; ++ int i,j; ++ int counter,counter2,backcounter; ++ int prhs_counter; ++ ++ /* returned quantities: */ ++ ++ double* index=NULL; ++ double* x=NULL; ++ double* y=NULL; ++ double* segments=NULL; ++ double* segmentmarkerlist=NULL; ++ ++ /* input: */ ++ char* domainname=NULL; ++ char* riftname=NULL; ++ double area; ++ char* order=NULL; ++ ++ /*Domain outline variables: */ ++ int nprof; ++ int* profnvertices=NULL; ++ double** pprofx=NULL; ++ double** pprofy=NULL; ++ double* xprof=NULL; ++ double* yprof=NULL; ++ int numberofpoints; ++ ++ /*Rift outline variables: */ ++ int numrifts; ++ int* riftsnumvertices=NULL; ++ double** riftsverticesx=NULL; ++ double** riftsverticesy=NULL; ++ ++ /* Triangle structures: */ ++ struct triangulateio in,out; ++ char options[256]; ++ ++ /* verify correct usage: */ ++ if (nlhs==0 && nrhs==0) { ++ /* special case: */ ++ TriMeshRiftsUsage(); ++ return; ++ } ++ ++ if (!( (nlhs==5) ||(nrhs==2) || (nrhs==3) || (nrhs==4) )){ ++ mexPrintf(" %s format error.\n", __FUNCT__); ++ TriMeshRiftsUsage(); ++ printf(" "); ++ mexErrMsgTxt(" "); ++ } ++ ++ /*Fetch data needed by Triangle: */ ++ ++ prhs_counter=0; ++ /*First recover the domain outline file name: */ ++ if (!mxIsChar(prhs[prhs_counter])){ ++ mexPrintf("%s%s\n",__FUNCT__," error message; first argument should be the domain outline file name!"); ++ mexErrMsgTxt(" "); ++ } ++ domainname = (char *) mxMalloc((mxGetN(prhs[prhs_counter])+1)*sizeof(char)); ++ mxGetString(prhs[prhs_counter],domainname,mxGetN(prhs[prhs_counter])+1); ++ ++ /*Look for optional rifts file name: */ ++ prhs_counter++; ++ if (mxIsChar(prhs[prhs_counter])){ ++ riftname = (char *) mxMalloc((mxGetN(prhs[prhs_counter])+1)*sizeof(char)); ++ mxGetString(prhs[prhs_counter],riftname,mxGetN(prhs[prhs_counter])+1); ++ prhs_counter++; ++ } ++ ++ /*Recover the mesh density desired:*/ ++ area=mxGetScalar(prhs[prhs_counter]); ++ ++ /*Optionaly, recover desired order: */ ++ prhs_counter++; ++ if (mxIsChar(prhs[prhs_counter])){ ++ order = (char *) mxMalloc((mxGetN(prhs[prhs_counter])+1)*sizeof(char)); ++ mxGetString(prhs[prhs_counter],order,mxGetN(prhs[prhs_counter])+1); ++ } ++ ++ /*Start reading the domain outline file: */ ++ if(!DomainOutlineRead(&nprof,&profnvertices,&pprofx,&pprofy,NULL,domainname,false)){ ++ printf("%s%s%s\n",__FUNCT__," error message reading domain outline ",domainname); ++ mexErrMsgTxt(" "); ++ } ++ ++ /*Read rifts file if present: */ ++ if(riftname){ ++ if(!DomainOutlineRead(&numrifts,&riftsnumvertices,&riftsverticesx,&riftsverticesy,NULL,riftname,false)){ ++ printf("%s%s%s\n",__FUNCT__," error message reading rifts outline ",riftname); ++ mexErrMsgTxt(" "); ++ } ++ } ++ ++ /*Create initial triangulation to call triangulate():*/ ++ numberofpoints=0; ++ for (i=0;i=2 flag them ), outlinefilename an Argus domain outline file.\n"); ++ printf(" riftsoutlinename is an Argus domain file, defining rifts (ie: open profiles), \n"); ++ printf(" area is the maximum area desired for any element of the resulting mesh. \n"); ++ printf(" and ordered is a string ('yes' or 'no') that determines whether segments are output in the \n"); ++ printf(" order they are made by Triangle (ie none), or ordered counter clockwise around the domain outline.\n"); ++ printf(" riftsoutlinename and ordered are optional arguments.\n"); ++ printf("\n"); ++} ++ ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.h (revision 12032) +@@ -0,0 +1,23 @@ ++/*!\file: TriMeshRifts.h ++ * \brief header prototype ++ */ ++ ++#ifndef _TRIMESHRIFTS_H_ ++#define _TRIMESHRIFTS_H_ ++ ++#include "mex.h" ++#include "triangle.h" ++#include "string.h" ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++void TriMeshRiftsUsage(void); ++ ++#undef __FUNCT__ ++#define __FUNCT__ "TriMeshRifts" ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriaSearch/TriaSearch.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriaSearch/TriaSearch.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriaSearch/TriaSearch.cpp (revision 12032) +@@ -0,0 +1,66 @@ ++/*\file TriaSearch.c ++ *\brief: TriaSearch module. See TriaSearchx for more details. ++ */ ++#include "./TriaSearch.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i; ++ ++ /*input: */ ++ double* index=NULL; ++ int nel; ++ int dummy; ++ ++ double* x=NULL; ++ double* y=NULL; ++ int nods; ++ ++ double* x0=NULL; ++ double* y0=NULL; ++ int numberofnodes; ++ ++ /* output: */ ++ double* tria=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&TriaSearchUsage); ++ ++ /*Input datasets: */ ++ FetchData(&index,&nel,&dummy,INDEXHANDLE); ++ FetchData(&x,&nods,XHANDLE); ++ FetchData(&y,&nods,YHANDLE); ++ FetchData(&x0,&numberofnodes,X0HANDLE); ++ FetchData(&y0,&numberofnodes,Y0HANDLE); ++ ++ /* Echo: {{{1*/ ++ //printf("(x0,y0)=(%g,%g)\n",x0,y0); ++ /*}}}*/ ++ ++ /* Run core computations: */ ++ TriaSearchx(&tria,index,nel,x,y,nods,x0,y0,numberofnodes); ++ ++ /* c to matlab: */ ++ for(i=0;i=7){ ++ /*default values: */ ++ FetchData(&default_values,&num_default_values,DEFAULTHANDLE); ++ } ++ else{ ++ default_values=NULL; ++ num_default_values=0; ++ } ++ ++ if(nrhs>=8){ ++ ++ /*Call expread on filename to build a contour array in the matlab workspace: */ ++ mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); ++ ++ /*contours: */ ++ numcontours=mxGetNumberOfElements(matlabstructure); ++ contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); ++ for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); ++ //set pointers. ++ contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); ++ contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); ++ *(contours+i)=contouri; ++ } ++ ++ /* Debugging of contours :{{{1*/ ++ /*for(i=0;inods); ++ for (j=0;jnods;j++){ ++ printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); ++ } ++ }*/ ++ /*}}}*/ ++ } ++ else{ ++ numcontours=0; ++ contours=NULL; ++ } ++ ++ ++ /*some checks*/ ++ if (x_data_rows!=y_data_rows){ ++ _error_("vectors x and y should have the same length!"); ++ } ++ if (x_prime_rows!=y_prime_rows){ ++ _error_("vectors x_prime and y_prime should have the same length!"); ++ } ++ ++ /*get number of elements and number of nodes in the data*/ ++ nels_data=index_data_rows; ++ nods_data=x_data_rows; ++ nods_prime=x_prime_rows; ++ ++ /* Run core computations: */ ++ InterpFromMesh2dx(&data_prime,index_data,x_data,y_data,nods_data,nels_data,data,data_rows,x_prime,y_prime,nods_prime,default_values,num_default_values,contours,numcontours); ++ ++ /*Write data: */ ++ WriteData(DATAPRIME,data_prime); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void InterpFromMesh2dUsage(void) ++{ ++ _printf_(true," usage:\n"); ++ _printf_(true," data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime);\n\n"); ++ _printf_(true," or data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime,default_value);\n\n"); ++ _printf_(true," or data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime,default_value,contourname);\n\n"); ++ _printf_(true," where:\n"); ++ _printf_(true," x,y: coordinates of the nodes where data is defined\n"); ++ _printf_(true," index: index of the mesh where data is defined\n"); ++ _printf_(true," data - vector holding the data to be interpolated onto the points.\n"); ++ _printf_(true," x_prime,y_prime: coordinates of the mesh vertices onto which we interpolate.\n"); ++ _printf_(true," default_value: a scalar or vector of size length(x_prime).\n"); ++ _printf_(true," contourname: linear interpolation will happen on all x_interp,y_interp inside the contour, default value will be adopted on the rest of the mesh.\n"); ++ _printf_(true," data_prime: vector of prime interpolated data.\n"); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMesh2d/InterpFromMesh2d.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMesh2d/InterpFromMesh2d.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMesh2d/InterpFromMesh2d.h (revision 12032) +@@ -0,0 +1,40 @@ ++/*!\file InterpFromMesh2d.h ++ * \brief: prototype for Data Interpolation mex module. ++ */ ++ ++#ifndef _INTERPFROMMESH2D_H ++#define _INTERPFROMMESH2D_H ++ ++/* local prototypes: */ ++void InterpFromMesh2dUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "InterpFromMesh2d" ++ ++#undef CLEANUP ++#define CLEANUP InterpFromMesh2dLocalCleanup(); ++ ++/* serial input macros: */ ++#define INDEXHANDLE prhs[0] ++#define XHANDLE prhs[1] ++#define YHANDLE prhs[2] ++#define DATAHANDLE prhs[3] ++#define XPRIMEHANDLE prhs[4] ++#define YPRIMEHANDLE prhs[5] ++#define DEFAULTHANDLE prhs[6] ++#define FILENAME prhs[7] ++ ++/* serial output macros: */ ++#define DATAPRIME (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++ ++#endif /* _INTERPFROMMESH2D_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp (revision 12032) +@@ -0,0 +1,46 @@ ++/*\file ElementConnectivity.c ++ *\brief: build element connectivity using node connectivity and elements. ++ */ ++ ++#include "./ElementConnectivity.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*inputs: */ ++ double* elements=NULL; ++ double* nodeconnectivity=NULL; ++ int nel,nods; ++ int width; ++ ++ /*outputs: */ ++ double* elementconnectivity=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ElementConnectivityUsage); ++ ++ /*Input datasets: */ ++ FetchData(&elements,&nel,NULL,ELEMENTS); ++ FetchData(&nodeconnectivity,&nods,&width,NODECONNECTIVITY); ++ ++ /*!Generate internal degree of freedom numbers: */ ++ ElementConnectivityx(&elementconnectivity, elements,nel, nodeconnectivity, nods, width); ++ ++ /*write output datasets: */ ++ WriteData(ELEMENTCONNECTIVITY,elementconnectivity,nel,3); ++ ++ /*Free ressources: */ ++ xfree((void**)&elements); ++ xfree((void**)&nodeconnectivity); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void ElementConnectivityUsage(void) { ++ _printf_(true,"\n"); ++ _printf_(true," usage: elementconnectivity = %s(elements, nodeconnectivity);\n",__FUNCT__); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h (revision 12032) +@@ -0,0 +1,33 @@ ++/* ++ ElementConnectivity.h ++*/ ++ ++#ifndef _ELEMENTCONNECTIVITY_H ++#define _ELEMENTCONNECTIVITY_H ++ ++/* local prototypes: */ ++void ElementConnectivityUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "ElementConnectivity" ++ ++/* serial input macros: */ ++#define ELEMENTS (mxArray*)prhs[0] ++#define NODECONNECTIVITY (mxArray*)prhs[1] ++ ++/* serial output macros: */ ++#define ELEMENTCONNECTIVITY (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 2 ++ ++#endif /* _ELEMENTCONNECTIVITY_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/EnumToString/EnumToString.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/EnumToString/EnumToString.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/EnumToString/EnumToString.cpp (revision 12032) +@@ -0,0 +1,32 @@ ++/*\file EnumToString.c ++ *\brief:convert enum (int) to string ++ */ ++ ++#include "./EnumToString.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ char *name = NULL; ++ int enum_in; ++ ++ /*checks on arguments on the matlab side: */ ++ if(nrhs!=NRHS){ ++ EnumToStringUsage(); _error_(" usage. See above"); ++ } ++ ++ /*Fetch inputs: */ ++ FetchData(&enum_in,ENUMIN); ++ ++ /*Run core function: */ ++ EnumToStringx(&name,enum_in); ++ ++ /* output: */ ++ WriteData(NAME,name); ++} ++ ++void EnumToStringUsage(void) ++{ ++ _printf_(true,"\n"); ++ _printf_(true," usage: %sstring = EnumToString(enum);\n",__FUNCT__); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/EnumToString/EnumToString.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/EnumToString/EnumToString.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/EnumToString/EnumToString.h (revision 12032) +@@ -0,0 +1,32 @@ ++/*!\file: EnumToString.h ++ * \brief header file for EnumToString module. ++ */ ++ ++#ifndef _ENUMTOSTRING_H ++#define _ENUMTOSTRING_H ++ ++/* local prototypes: */ ++void EnumToStringUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++/* serial input macros: */ ++#define ENUMIN (mxArray*)prhs[0] ++ ++/* serial output macros: */ ++#define NAME (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 1 ++ ++#undef __FUNCT__ ++#define __FUNCT__ "EnumToString" ++ ++#endif /* _TEST_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/StringToEnum/StringToEnum.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/StringToEnum/StringToEnum.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/StringToEnum/StringToEnum.cpp (revision 12032) +@@ -0,0 +1,32 @@ ++/*\file StringToEnum.c ++ *\brief:convert enum (int) to string ++ */ ++ ++#include "./StringToEnum.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ char *name = NULL; ++ int enum_out; ++ ++ /*checks on arguments on the matlab side: */ ++ if(nrhs!=NRHS){ ++ StringToEnumUsage(); _error_(" usage. See above"); ++ } ++ ++ /*Fetch inputs: */ ++ FetchData(&name,NAME); ++ ++ /*Run core function: */ ++ enum_out=StringToEnumx(name); ++ ++ /* output: */ ++ WriteData(ENUMOUT,enum_out); ++} ++ ++void StringToEnumUsage(void) ++{ ++ _printf_(true,"\n"); ++ _printf_(true," usage: %senum = StringToEnum(string);\n",__FUNCT__); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/StringToEnum/StringToEnum.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/StringToEnum/StringToEnum.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/StringToEnum/StringToEnum.h (revision 12032) +@@ -0,0 +1,32 @@ ++/*!\file: StringToEnum.h ++ * \brief header file for StringToEnum module. ++ */ ++ ++#ifndef _STRINGTOENUM_H ++#define _STRINGTOENUM_H ++ ++/* local prototypes: */ ++void StringToEnumUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++/* serial input macros: */ ++#define NAME (mxArray*)prhs[0] ++ ++/* serial output macros: */ ++#define ENUMOUT (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 1 ++ ++#undef __FUNCT__ ++#define __FUNCT__ "StringToEnum" ++ ++#endif /* _TEST_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am (revision 12032) +@@ -0,0 +1,171 @@ ++INCLUDES = @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ ++EXEEXT=$(MATLABWRAPPEREXT) ++#Bin programs {{{1 ++if MODULES ++bin_PROGRAMS = AverageFilter\ ++ BamgMesher\ ++ BamgConvertMesh\ ++ BamgTriangulate\ ++ Chaco\ ++ ContourToMesh \ ++ ContourToNodes \ ++ ElementConnectivity\ ++ EnumToString\ ++ Exp2Kml \ ++ HoleFiller \ ++ InternalFront\ ++ InterpFromGridToMesh \ ++ InterpFromMeshToMesh2d \ ++ InterpFromMeshToMesh3d \ ++ InterpFromMeshToGrid \ ++ InterpFromMesh2d \ ++ KMLFileRead \ ++ KMLMeshWrite \ ++ KMLOverlay \ ++ Kml2Exp \ ++ Ll2xy \ ++ NodeConnectivity \ ++ MeshPartition\ ++ MeshProfileIntersection\ ++ PointCloudFindNeighbors\ ++ PropagateFlagsFromConnectivity\ ++ Scotch\ ++ Shp2Kml\ ++ StringToEnum\ ++ TriaSearch\ ++ TriMesh\ ++ TriMeshRifts\ ++ TriMeshNoDensity\ ++ TriMeshProcessRifts\ ++ TriMeshRefine\ ++ Xy2ll ++endif ++#}}} ++#Flags and libraries {{{1 ++LDADD = ../../c/libISSMCore.a ../../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) ++ ++#Triangle library ++AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER ++ ++#Matlab part ++AM_LDFLAGS = $(MEXLINK) ++AM_CXXFLAGS += -D_HAVE_MATLAB_MODULES_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread ++LDADD += $(MEXLIB) ../../c/libISSMMatlab.a ++ ++LDADD += ../../c/libISSMCore.a ../../c/libISSMModules.a ++ ++#Optimization flags: ++AM_CXXFLAGS += $(CXXOPTFLAGS) ++#}}} ++#Bin sources {{{1 ++AverageFilter_SOURCES = ../AverageFilter/AverageFilter.cpp\ ++ ../AverageFilter/AverageFilter.h ++ ++BamgMesher_SOURCES = ../BamgMesher/BamgMesher.cpp\ ++ ../BamgMesher/BamgMesher.h ++ ++BamgConvertMesh_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\ ++ ../BamgConvertMesh/BamgConvertMesh.h ++ ++BamgTriangulate_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp\ ++ ../BamgTriangulate/BamgTriangulate.h ++ ++Chaco_SOURCES = ../Chaco/Chaco.cpp\ ++ ../Chaco/Chaco.h ++ ++ContourToMesh_SOURCES = ../ContourToMesh/ContourToMesh.cpp\ ++ ../ContourToMesh/ContourToMesh.h ++ ++ContourToNodes_SOURCES = ../ContourToNodes/ContourToNodes.cpp\ ++ ../ContourToNodes/ContourToNodes.h ++ ++ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\ ++ ../ElementConnectivity/ElementConnectivity.h ++ ++EnumToString_SOURCES = ../EnumToString/EnumToString.cpp\ ++ ../EnumToString/EnumToString.h ++ ++StringToEnum_SOURCES = ../StringToEnum/StringToEnum.cpp\ ++ ../StringToEnum/StringToEnum.h ++ ++HoleFiller_SOURCES = ../HoleFiller/HoleFiller.cpp\ ++ ../HoleFiller/HoleFiller.h ++ ++InternalFront_SOURCES = ../InternalFront/InternalFront.cpp\ ++ ../InternalFront/InternalFront.h ++ ++InterpFromGridToMesh_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\ ++ ../InterpFromGridToMesh/InterpFromGridToMesh.h ++ ++InterpFromMeshToMesh2d_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\ ++ ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h ++ ++InterpFromMeshToMesh3d_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\ ++ ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h ++ ++InterpFromMeshToGrid_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\ ++ ../InterpFromMeshToGrid/InterpFromMeshToGrid.h ++ ++InterpFromMesh2d_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp\ ++ ../InterpFromMesh2d/InterpFromMesh2d.h ++ ++KMLFileRead_SOURCES = ../KMLFileRead/KMLFileRead.cpp\ ++ ../KMLFileRead/KMLFileRead.h ++ ++KMLMeshWrite_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp\ ++ ../KMLMeshWrite/KMLMeshWrite.h ++ ++KMLOverlay_SOURCES = ../KMLOverlay/KMLOverlay.cpp\ ++ ../KMLOverlay/KMLOverlay.h ++ ++Xy2ll_SOURCES = ../Xy2ll/Xy2ll.cpp\ ++ ../Xy2ll/Xy2ll.h ++ ++Ll2xy_SOURCES = ../Ll2xy/Ll2xy.cpp\ ++ ../Ll2xy/Ll2xy.h ++ ++Exp2Kml_SOURCES = ../Exp2Kml/Exp2Kml.cpp\ ++ ../Exp2Kml/Exp2Kml.h ++ ++Kml2Exp_SOURCES = ../Kml2Exp/Kml2Exp.cpp\ ++ ../Kml2Exp/Kml2Exp.h ++ ++MeshPartition_SOURCES = ../MeshPartition/MeshPartition.cpp\ ++ ../MeshPartition/MeshPartition.h ++ ++MeshProfileIntersection_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\ ++ ../MeshProfileIntersection/MeshProfileIntersection.h ++ ++NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\ ++ ../NodeConnectivity/NodeConnectivity.h ++ ++PointCloudFindNeighbors_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\ ++ ../PointCloudFindNeighbors/PointCloudFindNeighbors.h ++ ++PropagateFlagsFromConnectivity_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\ ++ ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h ++ ++Scotch_SOURCES = ../Scotch/Scotch.cpp\ ++ ../Scotch/Scotch.h ++ ++Shp2Kml_SOURCES = ../Shp2Kml/Shp2Kml.cpp\ ++ ../Shp2Kml/Shp2Kml.h ++ ++TriaSearch_SOURCES = ../TriaSearch/TriaSearch.cpp\ ++ ../TriaSearch/TriaSearch.h ++ ++TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\ ++ ../TriMesh/TriMesh.h ++ ++TriMeshRifts_SOURCES = ../TriMeshRifts/TriMeshRifts.cpp\ ++ ../TriMeshRifts/TriMeshRifts.h ++ ++TriMeshNoDensity_SOURCES = ../TriMeshNoDensity/TriMeshNoDensity.cpp\ ++ ../TriMeshNoDensity/TriMeshNoDensity.h ++ ++TriMeshProcessRifts_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\ ++ ../TriMeshProcessRifts/TriMeshProcessRifts.h ++ ++TriMeshRefine_SOURCES = ../TriMeshRefine/TriMeshRefine.cpp\ ++ ../TriMeshRefine/TriMeshRefine.h ++#}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgTriangulate/BamgTriangulate.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgTriangulate/BamgTriangulate.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgTriangulate/BamgTriangulate.cpp (revision 12032) +@@ -0,0 +1,58 @@ ++/*\file BamgTriangulate.c ++ *\brief: bamg module. ++ */ ++#include "./BamgTriangulate.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*input: */ ++ double* x=NULL; ++ double* y=NULL; ++ int x_cols; ++ int y_rows,y_cols; ++ int nods; ++ ++ /*Output*/ ++ int* index=NULL; ++ int nels; ++ ++ /*Intermediary*/ ++ int verbose=0; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&BamgTriangulateUsage); ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs\n"); ++ FetchData(&x,&nods,&x_cols,XHANDLE); ++ FetchData(&y,&y_rows,&y_cols,YHANDLE); ++ ++ /*Check inputs*/ ++ if(y_rows!=nods) _error_("x and y do not have the same length"); ++ if(x_cols>1 || y_cols>1) _error_("x and y should have only one column"); ++ if(nods<3) _error_("At least 3 points are required"); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Call core\n"); ++ BamgTriangulatex(&index,&nels,x,y,nods); ++ ++ /*Write output*/ ++ WriteData(INDEX,index,nels,3); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void BamgTriangulateUsage(void) ++{ ++ _printf_(true,"BAMGTRIANGULATE - Delaunay Triangulation of a list of points"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," index=BamgTriangulate(x,y);\n"); ++ _printf_(true," index: index of the triangulation\n"); ++ _printf_(true," x,y: coordinates of the nodes\n"); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgTriangulate/BamgTriangulate.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgTriangulate/BamgTriangulate.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgTriangulate/BamgTriangulate.h (revision 12032) +@@ -0,0 +1,34 @@ ++/*!\file BamgTriangulate.h ++ * \brief: prototype for Data Interpolation mex module. ++ */ ++ ++#ifndef _BAMGTRIANGULATE_H ++#define _BAMGTRIANGULATE_H ++ ++/* local prototypes: */ ++void BamgTriangulateUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "BamgTriangulate" ++ ++ ++/* serial input macros: */ ++#define XHANDLE prhs[0] ++#define YHANDLE prhs[1] ++ ++/* serial output macros: */ ++#define INDEX (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 2 ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12032) +@@ -0,0 +1,162 @@ ++/*\file InterpFromMeshToMesh2d.c ++ *\brief: bamg module. ++ */ ++#include "./InterpFromMeshToMesh2d.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i; ++ ++ /*input: */ ++ double* index=NULL; ++ int index_cols; ++ ++ double* x_data=NULL; ++ int x_data_rows; ++ ++ double* y_data=NULL; ++ int y_data_rows; ++ ++ double* data=NULL; ++ int data_rows; ++ int data_cols; ++ ++ double* x_interp=NULL; ++ double* y_interp=NULL; ++ ++ int x_interp_rows; ++ int y_interp_rows; ++ ++ double* default_values=NULL; ++ int num_default_values=0; ++ ++ //contours ++ mxArray* matlabstructure=NULL; ++ Contour** contours=NULL; ++ int numcontours; ++ Contour* contouri=NULL; ++ ++ /*Intermediary*/ ++ int nods_data; ++ int nels_data; ++ int nods_interp; ++ int verbose=0; ++ ++ /* output: */ ++ double* data_interp=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ if(nlhs!=NLHS){ ++ InterpFromMeshToMesh2dUsage(); ++ _error_("InterpFromMeshToMesh2dUsage usage error"); ++ } ++ if((nrhs!=6) & (nrhs!=8)){ ++ InterpFromMeshToMesh2dUsage(); ++ _error_("InterpFromMeshToMesh2dUsage usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs\n"); ++ FetchData(&index,&nels_data,&index_cols,INDEXHANDLE); ++ FetchData(&x_data,&x_data_rows,NULL,XHANDLE); ++ FetchData(&y_data,&y_data_rows,NULL,YHANDLE); ++ FetchData(&data,&data_rows,&data_cols,DATAHANDLE); ++ FetchData(&x_interp,&x_interp_rows,NULL,XINTERPHANDLE); ++ FetchData(&y_interp,&y_interp_rows,NULL,YINTERPHANDLE); ++ ++ if(nrhs==8){ ++ ++ /*Call expread on filename to build a contour array in the matlab workspace: */ ++ mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); ++ ++ /*default values: */ ++ FetchData(&default_values,&num_default_values,DEFAULTHANDLE); ++ ++ /*contours: */ ++ numcontours=mxGetNumberOfElements(matlabstructure); ++ contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); ++ for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); ++ //set pointers. ++ contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); ++ contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); ++ *(contours+i)=contouri; ++ } ++ ++ /* Debugging of contours :{{{1*/ ++ /*for(i=0;inods); ++ for (j=0;jnods;j++){ ++ printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); ++ } ++ }*/ ++ /*}}}*/ ++ } ++ else{ ++ num_default_values=0; ++ default_values=NULL; ++ numcontours=0; ++ contours=NULL; ++ } ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs\n"); ++ if (x_data_rows!=y_data_rows){ ++ _error_("vectors x and y should have the same length!"); ++ } ++ if (x_interp_rows!=y_interp_rows){ ++ _error_("vectors x_interp and y_interp should have the same length!"); ++ } ++ if (index_cols!=3){ ++ _error_("index should have 3 columns (input provided has %i columns)",index_cols); ++ } ++ ++ /*get number of elements and number of nodes in the data*/ ++ nods_data=x_data_rows; ++ nods_interp=x_interp_rows; ++ ++ /* Run core computations: */ ++ if (verbose) printf("Call core\n"); ++ InterpFromMeshToMesh2dx(&data_interp,index,x_data,y_data,nods_data,nels_data,data,data_rows,data_cols,x_interp,y_interp,nods_interp,default_values,num_default_values,contours,numcontours); ++ ++ /*Write data: */ ++ WriteData(DATAINTERP,data_interp,nods_interp,data_cols); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void InterpFromMeshToMesh2dUsage(void) ++{ ++ _printf_(true,"INTERFROMMESHTOMESH2D - interpolation from a 2d triangular mesh onto a list of point\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This function is a multi-threaded mex file that interpolates a field\n"); ++ _printf_(true," defined on a triangular mesh onto a list of point\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," data_interp=InterpFromMeshToMesh2d(index,x,y,data,x_interp,y_interp);\n"); ++ _printf_(true," or data_interp=InterpFromMeshToMesh2d(index,x,y,data,x_interp,y_interp,default_value,contourname);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," index: index of the mesh where data is defined\n"); ++ _printf_(true," x,y: coordinates of the nodes where data is defined\n"); ++ _printf_(true," data: matrix holding the data to be interpolated onto the mesh. (one column per field)\n"); ++ _printf_(true," x_interp,y_interp: coordinates of the points onto which we interpolate.\n"); ++ _printf_(true," if default_value and contourname not specified: linear interpolation will happen on all x_interp,y_interp.\n"); ++ _printf_(true," if (default_value,contourname) specified: linear interpolation will happen on all x_interp,y_interp inside the contour, default value will be adopted on the rest of the mesh.\n"); ++ _printf_(true," note that default_value is either a scalar, or a vector of size length(x_interp)\n"); ++ _printf_(true," data_interp: vector of mesh interpolated data.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Example:\n"); ++ _printf_(true," load('temperature.mat');\n"); ++ _printf_(true," md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y);\n"); ++ _printf_(true," md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y,253,'Contour.exp');\n"); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 12032) +@@ -0,0 +1,38 @@ ++/*!\file InterpFromMeshToMesh2d.h ++ * \brief: prototype for Data Interpolation mex module. ++ */ ++ ++#ifndef _INTERPFROMMESHTOMESH2d_H ++#define _INTERPFROMMESHTOMESH2d_H ++ ++/* local prototypes: */ ++void InterpFromMeshToMesh2dUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "InterpFromMeshToMesh2d" ++ ++ ++/* serial input macros: */ ++#define INDEXHANDLE prhs[0] ++#define XHANDLE prhs[1] ++#define YHANDLE prhs[2] ++#define DATAHANDLE prhs[3] ++#define XINTERPHANDLE prhs[4] ++#define YINTERPHANDLE prhs[5] ++#define DEFAULTHANDLE prhs[6] ++#define FILENAME prhs[7] ++ ++/* serial output macros: */ ++#define DATAINTERP (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshNoDensity/TriMeshNoDensity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshNoDensity/TriMeshNoDensity.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshNoDensity/TriMeshNoDensity.cpp (revision 12032) +@@ -0,0 +1,305 @@ ++/* ++ * TriMeshNoDensity: out of a domain outline file ( Argus format ), ++ * use the Triangle package to create a triangular mesh ++ * ++ */ ++ ++#include "./TriMeshNoDensity.h" ++ ++ ++void mexFunction( int nlhs, mxArray* plhs[], ++ int nrhs, const mxArray* prhs[] ) ++{ ++ ++ ++ /*Matlab arrays: */ ++ mxArray* pmxa_array=NULL; ++ int i,j; ++ int counter,counter2,backcounter; ++ int prhs_counter; ++ ++ /* returned quantities: */ ++ ++ double* index=NULL; ++ double* x=NULL; ++ double* y=NULL; ++ double* segments=NULL; ++ double* segmentmarkerlist=NULL; ++ ++ /* input: */ ++ char* domainname=NULL; ++ char* riftname=NULL; ++ ++ /*Domain outline variables: */ ++ int nprof; ++ int* profnvertices=NULL; ++ double** pprofx=NULL; ++ double** pprofy=NULL; ++ double* xprof=NULL; ++ double* yprof=NULL; ++ int numberofpoints; ++ ++ /*Rift outline variables: */ ++ int numrifts; ++ int* riftsnumvertices=NULL; ++ double** riftsverticesx=NULL; ++ double** riftsverticesy=NULL; ++ ++ /* Triangle structures: */ ++ struct triangulateio in,out; ++ char options[256]; ++ ++ /* verify correct usage: */ ++ if (nlhs==0 && nrhs==0) { ++ /* special case: */ ++ TriMeshNoDensityUsage(); ++ return; ++ } ++ ++ if (!( (nlhs==5) ||(nrhs==2) || (nrhs==3) )){ ++ mexPrintf(" %s format error.\n", __FUNCT__); ++ TriMeshNoDensityUsage(); ++ printf(" "); ++ mexErrMsgTxt(" "); ++ } ++ ++ /*Fetch data needed by Triangle: */ ++ ++ prhs_counter=0; ++ /*First recover the domain outline file name: */ ++ if (!mxIsChar(prhs[prhs_counter])){ ++ mexPrintf("%s%s\n",__FUNCT__," error message; first argument should be the domain outline file name!"); ++ mexErrMsgTxt(" "); ++ } ++ domainname = (char *) mxMalloc((mxGetN(prhs[prhs_counter])+1)*sizeof(char)); ++ mxGetString(prhs[prhs_counter],domainname,mxGetN(prhs[prhs_counter])+1); ++ ++ /*Look for optional rifts file name: */ ++ if (nrhs==2){ ++ prhs_counter++; ++ if (mxIsChar(prhs[prhs_counter])){ ++ riftname = (char *) mxMalloc((mxGetN(prhs[prhs_counter])+1)*sizeof(char)); ++ mxGetString(prhs[prhs_counter],riftname,mxGetN(prhs[prhs_counter])+1); ++ prhs_counter++; ++ } ++ } ++ ++ /*Start reading the domain outline file: */ ++ if(!DomainOutlineRead(&nprof,&profnvertices,&pprofx,&pprofy,NULL,domainname,false)){ ++ printf("%s%s%s\n",__FUNCT__," error message reading domain outline ",domainname); ++ mexErrMsgTxt(" "); ++ } ++ ++ /*Read rifts file if present: */ ++ if(riftname){ ++ if(!DomainOutlineRead(&numrifts,&riftsnumvertices,&riftsverticesx,&riftsverticesy,NULL,riftname,false)){ ++ printf("%s%s%s\n",__FUNCT__," error message reading rifts outline ",riftname); ++ mexErrMsgTxt(" "); ++ } ++ } ++ ++ /*Create initial triangulation to call triangulate():*/ ++ numberofpoints=0; ++ for (i=0;i=2 flag them ), outlinefilename an Argus domain outline file.\n"); ++ printf(" riftsoutlinename is an Argus domain file, defining rifts (ie: open profiles), \n"); ++ printf(" riftsoutlinename is an optional arguments.\n"); ++ printf("\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshNoDensity/TriMeshNoDensity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshNoDensity/TriMeshNoDensity.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshNoDensity/TriMeshNoDensity.h (revision 12032) +@@ -0,0 +1,23 @@ ++/*!\file: TriMeshNoDensity.h ++ * \brief header prototype ++ */ ++ ++#ifndef _TRIMESH_H_ ++#define _TRIMESH_H_ ++ ++#include "mex.h" ++#include "triangle.h" ++#include "string.h" ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++void TriMeshNoDensityUsage(void); ++ ++#undef __FUNCT__ ++#define __FUNCT__ "TriMeshNoDensity" ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Makefile.am (revision 12032) +@@ -0,0 +1,8 @@ ++SUBDIRS = ++if MATLAB ++SUBDIRS += matlab ++endif ++ ++if PYTHON ++SUBDIRS += python ++endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.h (revision 12032) +@@ -0,0 +1,47 @@ ++ ++/* ++ ContourToMesh.h ++*/ ++ ++ ++#ifndef _CONTOURTOMESH_H ++#define _CONTOURTOMESH_H ++ ++/* local prototypes: */ ++void ContourToMeshUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "ContourToMesh" ++ ++ ++#ifndef ALL ++#define ALL 0 ++#endif ++ ++/* input macros: */ ++#define INDEXHANDLE prhs[0] ++#define XHANDLE prhs[1] ++#define YHANDLE prhs[2] ++#define FILENAME prhs[3] ++#define INTERPTYPEHANDLE prhs[4] ++#define EDGEVALUEHANDLE prhs[5] ++ ++/* serial output macros: */ ++#define PLHS0 (mxArray**)&plhs[0] ++#define PLHS1 (mxArray**)&plhs[1] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 2 ++#undef NRHS ++#define NRHS 6 ++ ++ ++#endif /* _CONTOURTOMESH_H */ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/.dirstamp +=================================================================== +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/.deps/.dirstamp +=================================================================== +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12032) +@@ -0,0 +1,135 @@ ++/*! \file ContourtoMesh ++ \brief: takes an contour file, and figures out which nodes or elements from the mesh ++ are inside this contour. ++ usage: ++ [in_nod,in_elem]=ContourToMesh(index,x,y,contours,interptype,edgevalue); ++ ++ input: ++ ++ index,x,y: delaunay triangulation. ++ contours: structure holding sets of vertices making open contours. ++ interptype: string definining type of interpolation ('element', or 'node', or 'element and node'); ++ edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons ++ ++ output: ++ in_nod: vector of flags (0 or 1), of size nods if interptype is set to 'node' or 'element and node', ++ or of size 0 otherwise. ++ in_elem: vector of flags (0 or 1), of size nel if interptype is set to 'element' or 'element and node', ++ or of size 0 otherwise. ++*/ ++ ++#include "./ContourToMesh.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { ++ ++ int i,j; ++ ++ /* required input: */ ++ double* index=NULL; ++ double* x=NULL; ++ double* y=NULL; ++ int edgevalue; ++ char* interptype=NULL; ++ ++ /* output: */ ++ Vector* in_nod=NULL; ++ int nods; ++ Vector* in_elem=NULL; ++ int nel; ++ ++ //contours ++ mxArray* matlabstructure=NULL; ++ int numcontours; ++ Contour** contours=NULL; ++ Contour* contouri=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ //CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ContourToMeshUsage); Cant' use it here, as we have variable outputs. ++ if((nlhs!=1 && nlhs!=2) || (nrhs!=NRHS)){ ++ ContourToMeshUsage(); ++ _error_(" usage. See above"); ++ } ++ ++ /*First, call expread on filename to build a contour array in the matlab workspace: */ ++ mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); ++ ++ /*Fetch inputs: */ ++ FetchData(&index,&nel,NULL,INDEXHANDLE); ++ FetchData(&x,&nods,NULL,XHANDLE); ++ FetchData(&y,NULL,NULL,YHANDLE); ++ FetchData(&edgevalue,EDGEVALUEHANDLE); ++ ++ //Fetch contours ++ numcontours=mxGetNumberOfElements(matlabstructure); ++ contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); ++ for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); ++ //set pointers. ++ contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); ++ contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); ++ *(contours+i)=contouri; ++ } ++ ++ /*Fetch interptype: */ ++ FetchData(&interptype,INTERPTYPEHANDLE); ++ ++ /* Debugging of contours :{{{1*/ ++ /*for(i=0;inods); ++ for (j=0;jnods;j++){ ++ printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); ++ } ++ }*/ ++ /*}}}*/ ++ ++ /*Run interpolation routine: */ ++ ContourToMeshx( &in_nod,&in_elem,index,x,y,contours,numcontours,interptype,nel,nods,edgevalue); ++ ++ /* output: */ ++ if (strcmp(interptype,"node")==0){ ++ WriteData(PLHS0,in_nod); ++ } ++ else if (strcmp(interptype,"element")==0){ ++ WriteData(PLHS0,in_elem); ++ } ++ else if (strcmp(interptype,"element and node")==0){ ++ WriteData(PLHS0,in_nod); ++ WriteData(PLHS1,in_elem); ++ } ++ else _error_(" wrong interpolation type"); ++ ++ /*end module: */ ++ MODULEEND(); ++ ++} ++ ++void ContourToMeshUsage(void) ++{ ++ printf("CONTOURTOMESH - Flag the elements or nodes inside a contour\n"); ++ printf("\n"); ++ printf(" Usage: \n"); ++ printf(" [in_nod,in_elem]=ContourToMesh(index,x,y,contourname,interptype,edgevalue)\n\n"); ++ printf("\n"); ++ printf(" index,x,y: mesh triangulation.\n"); ++ printf(" contourname: name of .exp file containing the contours.\n"); ++ printf(" interptype: string definining type of interpolation ('element', or 'node').\n"); ++ printf(" edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons.\n"); ++ printf(" in_nod: vector of flags (0 or 1), of size nods if interptype is set to 'node' or 'element and node', \n"); ++ printf(" or of size 0 otherwise.\n"); ++ printf(" in_elem: vector of flags (0 or 1), of size nel if interptype is set to 'element' or 'element and node', \n"); ++ printf(" or of size 0 otherwise.\n"); ++ printf("\n"); ++ printf(" Example: \n"); ++ printf(" in_nod=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','node',1)\n"); ++ printf(" in_elements=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element',0)\n"); ++ printf(" [in_nodes,in_elements]=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element and node',0)\n"); ++ printf("\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.h (revision 12032) +@@ -0,0 +1,37 @@ ++/*!\file Xy2ll.h ++ * \brief: prototype for x/y to lat/long coordinate mex module. ++ */ ++ ++#ifndef _XY2LL_H ++#define _XY2LL_H ++ ++/* local prototypes: */ ++void Xy2llUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "Xy2ll" ++ ++ ++/* serial input macros: */ ++#define X_IN prhs[0] ++#define Y_IN prhs[1] ++#define SGN_IN prhs[2] ++ ++/* serial output macros: */ ++#define LAT_OUT (mxArray**)&plhs[0] ++#define LON_OUT (mxArray**)&plhs[1] ++ ++/* serial arg counts: */ ++#undef NRHS ++#define NRHS 3 ++#undef NLHS ++#define NLHS 2 ++ ++#endif ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.cpp (revision 12032) +@@ -0,0 +1,121 @@ ++/*\file Xy2ll.c ++ *\brief: x/y to lat/long coordinate mex module. ++ */ ++#include "./Xy2ll.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i,verbose=1; ++ ++ /*input: */ ++ double *x=NULL,*y=NULL; ++ int nx,ny,ncoord; ++ int sgn; ++ ++ Options* options=NULL; ++ double cm=0.,sp=0.; ++ ++ /* output: */ ++ double *lat=NULL,*lon=NULL; ++ int iret=0; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ if (nlhs > NLHS) { ++ Xy2llUsage(); ++ _error_("Xy2ll usage error"); ++ } ++ if (nrhs < NRHS) { ++ Xy2llUsage(); ++ _error_("Xy2ll usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs:\n"); ++ FetchData(&x,&nx,X_IN); ++ if (verbose) ++ if (nx == 1) printf(" x=%g\n",x[0]); ++ else printf(" x=[%d values]\n",nx); ++// for (i=0; iSize()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); ++ /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ ++ if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { ++ options->Get(&cm,"central_meridian"); ++ if (verbose) printf(" cm=%g\n",cm); ++ options->Get(&sp,"standard_parallel"); ++ if (verbose) printf(" sp=%g\n",sp); ++ } ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs:\n"); ++ ++ if (nx != ny) _error_("Must have same number of x[%d] and y[%d] coordinates.",nx,ny); ++ else ncoord=nx; ++ if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); ++ if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); ++ if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); ++ ++ lat=(double *)xmalloc(ncoord*sizeof(double)); ++ lon=(double *)xmalloc(ncoord*sizeof(double)); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Calling core:\n"); ++ if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) ++ iret=Xy2llx(lat,lon, ++ x,y,ncoord, ++ sgn,cm,sp); ++ else ++ iret=Xy2llx(lat,lon, ++ x,y,ncoord, ++ sgn); ++ if (verbose) printf(" iret=%d\n",iret); ++ ++ /*Write data: */ ++ WriteData(LAT_OUT,lat,ncoord); ++ WriteData(LON_OUT,lon,ncoord); ++ ++ /*Clean-up*/ ++ delete options; ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void Xy2llUsage(void) ++{ ++ _printf_(true,"Xy2ll - x/y to lat/long coordinate transformation module:\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This module transforms x/y to lat/long coordinates.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," [lat,lon]=Xy2ll(x,y,sgn,'param name',param,...);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," x x coordinates (double vector)\n"); ++ _printf_(true," y y coordinates (double vector)\n"); ++ _printf_(true," sgn sign for hemisphere (double, +1 (north) or -1 (south))\n"); ++ _printf_(true,"\n"); ++ _printf_(true," central_meridian central meridian (double, optional, but must specify with sp)\n"); ++ _printf_(true," standard_parallel standard parallel (double, optional, but must specify with cm)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," lat latitude coordinates (double vector)\n"); ++ _printf_(true," lon longitude coordinates (double vector)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Examples:\n"); ++ _printf_(true," [lat,lon]=Xy2ll(x,y, 1);\n"); ++ _printf_(true," [lat,lon]=Xy2ll(x,y, 1,'central_meridian',45,'standard_parallel',70);\n"); ++ _printf_(true," [lat,lon]=Xy2ll(x,y,-1,'central_meridian', 0,'standard_parallel',71);\n"); ++ _printf_(true,"\n"); ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.h (revision 12032) +@@ -0,0 +1,68 @@ ++/* ++ TriMesh.h ++*/ ++ ++#ifndef _TRIMESH_H ++#define _TRIMESH_H ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ ++#ifdef _HAVE_PYTHON_ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#endif ++ ++/*Header files: */ ++#include "../../c/include/globals.h" ++#include "../../c/toolkits/toolkits.h" ++#include "../../c/include/include.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++#include "../../c/io/io.h" ++#include "../../c/EnumDefinitions/EnumDefinitions.h" ++ ++#ifdef _HAVE_MATLAB_MODULES_ ++/* serial input macros: */ ++#define DOMAINOUTLINE (mxArray *)prhs[0] ++#define AREA (mxArray *)prhs[1] ++#define ORDER (mxArray *)prhs[2] ++/* serial output macros: */ ++#define INDEX (mxArray**)&plhs[0] ++#define X (mxArray**)&plhs[1] ++#define Y (mxArray**)&plhs[2] ++#define SEGMENTS (mxArray**)&plhs[3] ++#define SEGMENTMARKERLIST (mxArray**)&plhs[4] ++#endif ++ ++#ifdef _HAVE_PYTHON_MODULES_ ++/* serial input macros: */ ++#define DOMAINOUTLINE PyTuple_GetItem(args,0) ++#define AREA PyTuple_GetItem(args,1) ++#define ORDER PyTuple_GetItem(args,2) ++/* serial output macros: */ ++#define INDEX output,0 ++#define X output,1 ++#define Y output,2 ++#define SEGMENTS output,3 ++#define SEGMENTMARKERLIST output,4 ++#endif ++ ++#undef __FUNCT__ ++#define __FUNCT__ "TriMesh" ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 5 ++#undef NRHS ++#define NRHS 3 ++ ++/* local prototypes: */ ++void TriMeshUsage(void); ++ ++#endif /* _TRIMESH_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp (revision 12032) +@@ -0,0 +1,72 @@ ++/* ++ * TriMesh: mesh a domain using an .exp file ++ */ ++ ++#include "./TriMesh.h" ++ ++WRAPPER(TriMesh){ ++ ++ /* input: */ ++ char* domainname=NULL; ++ double area; ++ bool order; ++ ++ /*intermediary: */ ++ DataSet* domain=NULL; ++ ++ /* output: */ ++ Matrix* index=NULL; ++ Vector* x=NULL; ++ Vector* y=NULL; ++ Matrix* segments=NULL; ++ Vector* segmentmarkerlist=NULL; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CHECKARGUMENTS(NLHS,NRHS,&TriMeshUsage); ++ ++ /*Fetch data needed for meshing: */ ++ FetchData(&domainname,DOMAINOUTLINE); ++ FetchData(&area,AREA); ++ FetchData(&order,ORDER); ++ ++ /*Read domain outline: */ ++ domain=DomainOutlineRead(domainname,false); ++ ++ /*call x core: */ ++ TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,area,order); ++ ++ /*write outputs: */ ++ WriteData(INDEX,index); ++ WriteData(X,x); ++ WriteData(Y,y); ++ WriteData(SEGMENTS,segments); ++ WriteData(SEGMENTMARKERLIST,segmentmarkerlist); ++ ++ /*free ressources: */ ++ delete domain; ++ xdelete_module(&index); ++ xdelete_module(&x); ++ xdelete_module(&y); ++ xdelete_module(&segments); ++ xdelete_module(&segmentmarkerlist); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void TriMeshUsage(void) //{{{1 ++{ ++ printf("\n"); ++ printf(" usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,area,ordered) \n"); ++ printf(" where: index,x,y defines a triangulation, segments is an array made \n"); ++ printf(" of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment, \n"); ++ printf(" outlinefilename an Argus domain outline file, \n"); ++ printf(" area is the maximum area desired for any element of the resulting mesh, \n"); ++ printf(" and ordered is a bool that determines whether segments are output in the \n"); ++ printf(" order they are made by Triangle (ie none), or ordered counter clockwise around the domain outline.\n"); ++ printf("\n"); ++} ++//}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.h (revision 12032) +@@ -0,0 +1,42 @@ ++/*!\file KMLMeshWrite.h ++ * \brief: prototype for KML mesh writer mex module. ++ */ ++ ++#ifndef _KMLMESHWRITE_H ++#define _KMLMESHWRITE_H ++ ++/* local prototypes: */ ++void KMLMeshWriteUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "KMLMeshWrite" ++ ++ ++/* serial input macros: */ ++#define NAME prhs[0] ++#define NOTES prhs[1] ++#define ELEMHANDLE prhs[2] ++#define NODECONHANDLE prhs[3] ++#define LATHANDLE prhs[4] ++#define LNGHANDLE prhs[5] ++#define PARTHANDLE prhs[6] ++#define DATAHANDLE prhs[7] ++#define CMAPHANDLE prhs[8] ++#define FILENAME prhs[9] ++ ++/* serial output macros: */ ++#define ERRORFLAG (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NRHS ++#define NRHS 10 ++#undef NLHS ++#define NLHS 1 ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12032) +@@ -0,0 +1,198 @@ ++/*\file KMLMeshWrite.c ++ *\brief: KML mesh writer module. ++ */ ++#include "./KMLMeshWrite.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i,j,nnodes=0,verbose=1; ++ ++ /*input: */ ++ char* name=NULL; ++ ++ char* notes=NULL; ++ const mxArray* notesi; ++ mwIndex nindex; ++ ++ int* elem=NULL; ++ int melem=0,nelem=0; ++ ++ int* nodecon=NULL; ++ int mncon=0,nncon=0; ++ ++ double* lat=NULL; ++ int mlat=0,nlat=0,llat=0; ++ ++ double* lng=NULL; ++ int mlng=0,nlng=0,llng=0; ++ ++ int nparts=0; ++ ++ int* part=NULL; ++ int mprt=0,nprt=0,lprt=0; ++ ++ double* data=NULL; ++ int mdata=0,ndata=0; ++ ++ double* cmap=NULL; ++ int mcmap=0,ncmap=0; ++ ++ char* filnam=NULL; ++ ++ FILE* fid=NULL; ++ ++ Options* options=NULL; ++ ++ /* output: */ ++ int ierror=0; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ if (nlhs > NLHS) { ++ KMLMeshWriteUsage(); ++ _error_("KMLMeshWrite usage error"); ++ } ++ if (nrhs < NRHS) { ++ KMLMeshWriteUsage(); ++ _error_("KMLMeshWrite usage error"); ++ } ++ ++ /*Input datasets: */ ++ if (verbose) printf("Fetching inputs:\n"); ++ FetchData(&name,NAME); ++ if (verbose) printf(" name =\"%s\"\n",name); ++ ++/* notes is typically a cell array of character strings */ ++ if (mxIsCell(NOTES)) { ++ for (nindex=0; nindexSize()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); ++ ++ /*some checks*/ ++ if (verbose) printf("Checking inputs:\n"); ++ ++ for (i=0; i nnodes) ++ nnodes=elem[i]; ++ if (verbose) printf(" nnodes =%d\n",nnodes); ++ if (part) ++ for (i=0; i nparts) ++ nparts=part[i]+1; ++ if (verbose) printf(" nparts =%d\n",nparts); ++ ++ if (nodecon && (mncon != nnodes)) ++ _error_("Nodal connectivity table, if supplied, must be supplied for all nodes."); ++ else if (!nodecon) ++ mncon=nnodes; ++ if ((llat != nnodes) || (llng != nnodes) || (llat != llng)) ++ _error_("Latitude and longitude vectors must be supplied for all nodes."); ++ if (part && (lprt != nnodes)) ++ _error_("Partitioning vector, if supplied, must be supplied for all nodes."); ++ if (data && !((mdata == nnodes) || (mdata == melem))) ++ _error_("Data matrix, if supplied, must be supplied for all nodes or all elements."); ++ if (cmap && (ncmap != 3)) ++ _error_("Colormap matrix, if supplied, must have three columns for rgb."); ++ ++ if (!strlen(filnam)) ++ strcpy(filnam,"stdout"); ++ ++ if (verbose) printf("Opening file \"%s\".\n",filnam); ++ fid=fopen(filnam,"w"); ++ ++ /* Run core computations: */ ++ if (verbose) printf("Calling core:\n"); ++ KMLMeshWritex(&ierror, ++ name, ++ notes, ++ elem,melem,nelem, ++ nodecon,mncon,nncon, ++ lat,lng, ++ part, ++ data,mdata,ndata, ++ cmap,mcmap,ncmap, ++ fid); ++ ++ if (verbose) printf("Closing file \"%s\".\n",filnam); ++ fclose(fid); ++ ++ /*Write data: */ ++ WriteData(ERRORFLAG,ierror); ++ ++ /*Clean-up*/ ++ delete options; ++ if (mxIsCell(NOTES) && notes) xfree((void**)¬es); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void KMLMeshWriteUsage(void) ++{ ++ _printf_(true,"KMLMeshWrite - KML mesh writer module:\n"); ++ _printf_(true,"\n"); ++ _printf_(true," This module writes the mesh of a model as KML polygons into the specified KML file.\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Usage:\n"); ++ _printf_(true," ierror=KMLMeshWrite(name,notes,elem,nodecon,lat,long,part,data,cmap,kmlfile);\n"); ++ _printf_(true,"\n"); ++ _printf_(true," name model name (string, may be empty)\n"); ++ _printf_(true," notes model notes (string or cell array of strings, may be empty)\n"); ++ _printf_(true," elem elements (double array)\n"); ++ _printf_(true," nodecon nodal connectivity array (double array, may be empty)\n"); ++ _printf_(true," lat nodal latititudes (double vector)\n"); ++ _printf_(true," long nodal longitudes (double vector)\n"); ++ _printf_(true," part nodal partitions (double vector, may be empty)\n"); ++ _printf_(true," data nodal or element data (double vector, may be empty)\n"); ++ _printf_(true," cmap color map (double nx3 array, may be empty)\n"); ++ _printf_(true," kmlfile KML file name (string)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," ierror error flag (double, non-zero for error)\n"); ++ _printf_(true,"\n"); ++ _printf_(true," Example:\n"); ++ _printf_(true," KMLMeshWrite(md.name,md.notes,md.elements,md.nodeconnectivity,md.lat,md.long,md.part,md.fm_criterion,options.cmap,filekml);\n"); ++ _printf_(true,"\n"); ++} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.h (revision 12032) +@@ -0,0 +1,44 @@ ++/*!\file: Chaco.h ++ * \brief header file for Chaco module. ++ */ ++ ++#ifndef _CHACO_H ++#define _CHACO_H ++ ++/* local prototypes: */ ++void ChacoUsage(void); ++ ++#include ++#include /* strcasecmp */ ++#include /* clock,time,difftime */ ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/Container/Container.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++/* serial input macros: */ ++#define A_IN (mxArray*)prhs[0] ++#define VWGTS_IN (mxArray*)prhs[1] ++#define EWGTS_IN (mxArray*)prhs[2] ++#define X_IN (mxArray*)prhs[3] ++#define Y_IN (mxArray*)prhs[4] ++#define Z_IN (mxArray*)prhs[5] ++#define OPTNS_IN (mxArray*)prhs[6] ++#define NPARTS_IN (mxArray*)prhs[7] ++#define GOAL_IN (mxArray*)prhs[8] ++ ++/* serial output macros: */ ++#define ASSGN_OUT (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 9 ++ ++#undef __FUNCT__ ++#define __FUNCT__ "Chaco" ++ ++#endif /* _CHACO_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp (revision 12032) +@@ -0,0 +1,146 @@ ++/*\file Chaco.c ++ *\brief: Chaco partitioner mex module ++ */ ++ ++#ifdef HAVE_CONFIG_H ++#include "config.h" ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#include "./Chaco.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ int i; ++ int nterms; ++ ++ /*Inputs: */ ++ int nvtxs; /* number of vertices in graph */ ++ int *start; /* start of edge list for each vertex */ ++ int *adjacency; /* edge list data */ ++ int *vwgts=NULL; /* weights for all vertices */ ++ int nedges; ++ float *ewgts=NULL; /* weights for all edges */ ++ float *x=NULL; ++ float *y=NULL; ++ float *z=NULL; /* coordinates for inertial method */ ++ double options[10]={1,1,0,0,1,1,50,0,.001,7654321}; /* architecture and partitioning options */ ++ double* in_options=NULL; ++ int *nparts=NULL; /* number of parts options */ ++ int npart; ++ double *goal=NULL; /* desired set sizes */ ++ ++ /*intermediary pointers: */ ++ mwIndex *mwstart, *mwadjacency; ++ double *doublepointer; ++ ++ /*output: */ ++ short *assignment=NULL; /* set number of each vtx (length nvtxs+1) */ ++ double *doubleassignment=NULL; /*holds assignment, in double format, to return to matlab*/ ++ ++ ++ #ifndef _HAVE_CHACO_ //only works if dakota library has been compiled in. ++ _error_(" Chaco not available! Cannot carry out Chaco partitioning!"); ++ #endif ++ ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ChacoUsage); ++ ++ ++ /*Fetch adjacency matrix: */ ++ nvtxs = mxGetN(A_IN); ++ ++ mwstart = mxGetJc(A_IN); ++ start=(int*)xmalloc(nvtxs*sizeof(int)); ++ for (i=0; imatrix->GetSize(&rows,cols); + #endif + +- /*Now transpose the matrix: */ ++ /*Now transpose the matrix and allocate with Matlab's memory manager: */ + tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double)); + for(i=0;ivector->GetSize(&rows); + #endif + +- /*now create the matlab vector: */ ++ /*now create the matlab vector with Matlab's memory manager */ ++ vector_ptr2=(double*)mxMalloc(rows*sizeof(double)); ++ for(int i=0;ino, 1->artificial_diffusivity, 2->SUPG')) ++ string="%s\n%s"%(string,fielddisplay(obj,'maxiter','maximum number of non linear iterations')) ++ string="%s\n%s"%(string,fielddisplay(obj,'penalty_lock','stabilize unstable thermal constraints that keep zigzagging after n iteration (default is 0, no stabilization)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'penalty_threshold','threshold to declare convergence of thermal solution (default is 0)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'isenthalpy','use an enthalpy formulation to include temperate ice (default is 0)')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/settings.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/settings.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/settings.py (revision 12038) +@@ -0,0 +1,24 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class settings: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.io_gather = 0; ++ self.lowmem = 0; ++ self.results_as_patches = 0; ++ self.output_frequency = 0; ++ self.waitonlock = 0; ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=" general settings parameters:" ++ ++ string="%s\n%s"%(string,fielddisplay(obj,"io_gather","I/O gathering strategy for result outputs (default 1)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"lowmem","is the memory limited ? (0 or 1)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"results_as_patches","provide results as patches for each element (0 or 1)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"output_frequency","frequency at which results are saved in all solutions with multiple time_steps")) ++ string="%s\n%s"%(string,fielddisplay(obj,"waitonlock","maximum number of minutes to wait for batch results, or return 0")) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/balancethickness.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/balancethickness.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/balancethickness.py (revision 12038) +@@ -0,0 +1,20 @@ ++#module imports ++from fielddisplay import fielddisplay ++class balancethickness: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.spcthickness = float('NaN') ++ self.thickening_rate = float('NaN') ++ self.stabilization = 0 ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ string=' balance thickness solution parameters:' ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'thickening_rate','ice thickening rate used in the mass conservation (dh/dt)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'stabilization','0: None, 1: SU, 2: MacAyeal''s artificial diffusivity, 3:DG')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.py (revision 12038) +@@ -0,0 +1,18 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class groundingline: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.migration='' ++ self.melting_rate=float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' grounding line solution parameters:' ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,'migration','type of grounding line migration: ''SoftMigration'',''AgressiveMigration'' or ''None''')) ++ string="%s\n%s"%(string,fielddisplay(obj,'melting_rate','melting rate applied when previously grounded parts start floating')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/transient.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/transient.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/transient.py (revision 12038) +@@ -0,0 +1,23 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class transient: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.isprognostic = 0 ++ self.isdiagnostic = 0 ++ self.isthermal = 0 ++ self.isgroundingline = 0 ++ self.requested_outputs = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' transient solution parameters:' ++ string="%s\n%s"%(string,fielddisplay(obj,'isprognostic','indicates if a prognostic solution is used in the transient')) ++ string="%s\n%s"%(string,fielddisplay(obj,'isthermal','indicates if a thermal solution is used in the transient')) ++ string="%s\n%s"%(string,fielddisplay(obj,'isdiagnostic','indicates if a diagnostic solution is used in the transient')) ++ string="%s\n%s"%(string,fielddisplay(obj,'isgroundingline','indicates if a groundingline migration is used in the transient')) ++ string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','list of additional outputs requested')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/hydrology.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/hydrology.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/hydrology.py (revision 12038) +@@ -0,0 +1,29 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class hydrology: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.spcwatercolumn = float('NaN') ++ self.n = 0 ++ self.CR = 0 ++ self.p = 0 ++ self.q = 0 ++ self.kn = 0 ++ self.stabilization = 0 ++ ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ string=' hydrology solution parameters:' ++ string="%s\n\n%s"%(string,fielddisplay(obj,'spcwatercolumn','water thickness constraints (NaN means no constraint)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'n','Manning roughness coefficient')) ++ string="%s\n%s"%(string,fielddisplay(obj,'CR','tortuosity parameter')) ++ string="%s\n%s"%(string,fielddisplay(obj,'p','dimensionless exponent in Manning velocity formula')) ++ string="%s\n%s"%(string,fielddisplay(obj,'q','dimensionless exponent in Manning velocity formula')) ++ string="%s\n%s"%(string,fielddisplay(obj,'kn','parameter in effective pressure formula')) ++ string="%s\n%s"%(string,fielddisplay(obj,'stabilization','artificial diffusivity (default is 1). can be more than 1 to increase diffusivity.')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/surfaceforcings.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/surfaceforcings.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/surfaceforcings.py (revision 12038) +@@ -0,0 +1,19 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class surfaceforcings: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.precipitation = float('NaN') ++ self.mass_balance = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=" surface forcings parameters:" ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,'precipitation','surface precipitation [m/yr water eq]')) ++ string="%s\n%s"%(string,fielddisplay(obj,'mass_balance','surface mass balance [m/yr ice eq]')) ++ ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/rifts.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/rifts.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/rifts.py (revision 12038) +@@ -0,0 +1,18 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class rifts: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.riftstruct = float('NaN') ++ self.riftproperties = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' rifts parameters:' ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,'riftstruct','structure containing all rift information (vertices coordinates, segments, type of melange, ...)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'riftproperties','')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.py (revision 12038) +@@ -0,0 +1,108 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class mesh: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.x = float('NaN'); ++ self.y = float('NaN'); ++ self.z = float('NaN'); ++ self.elements = float('NaN'); ++ self.dimension = 0; ++ self.numberoflayers = 0; ++ self.numberofelements = 0; ++ self.numberofvertices = 0; ++ self.numberofedges = 0; ++ ++ self.lat = float('NaN'); ++ self.long = float('NaN'); ++ self.hemisphere = float('NaN'); ++ ++ self.elementonbed = float('NaN'); ++ self.elementonsurface = float('NaN'); ++ self.vertexonbed = float('NaN'); ++ self.vertexonsurface = float('NaN'); ++ self.lowerelements = float('NaN'); ++ self.lowervertex = float('NaN'); ++ self.upperelements = float('NaN'); ++ self.uppervertex = float('NaN'); ++ self.vertexonboundary = float('NaN'); ++ ++ self.edges = float('NaN'); ++ self.segments = float('NaN'); ++ self.segmentmarkers = float('NaN'); ++ self.vertexconnectivity = float('NaN'); ++ self.elementconnectivity = float('NaN'); ++ self.average_vertex_connectivity = 0; ++ ++ self.x2d = float('NaN'); ++ self.y2d = float('NaN'); ++ self.elements2d = float('NaN'); ++ self.numberofvertices2d = 0; ++ self.numberofelements2d = 0; ++ ++ self.extractedvertices = float('NaN'); ++ self.extractedelements = float('NaN'); ++ ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ if obj.dimension==3: ++ string="\n%s"%(" Elements and vertices of the original 2d mesh:") ++ ++ string="%s\n%s"%(string,fielddisplay(obj,"numberofelements2d","number of elements")) ++ string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices2d","number of vertices")) ++ string="%s\n%s"%(string,fielddisplay(obj,"elements2d","index into (x,y,z), coordinates of the vertices")) ++ string="%s\n%s"%(string,fielddisplay(obj,"x2d","vertices x coordinate")) ++ string="%s\n%s"%(string,fielddisplay(obj,"y2d","vertices y coordinate")) ++ ++ string="%s\n%s" %(string,"Elements and vertices of the extruded 3d mesh:") ++ else: ++ string="\n%s"%(" Elements and vertices:") ++ ++ string="%s\n%s"%(string,fielddisplay(obj,"numberofelements","number of elements")) ++ ++ ++ ++ ++ string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices","number of vertices")) ++ string="%s\n%s"%(string,fielddisplay(obj,"elements","index into (x,y,z), coordinates of the vertices")) ++ string="%s\n%s"%(string,fielddisplay(obj,"x","vertices x coordinate")) ++ string="%s\n%s"%(string,fielddisplay(obj,"y","vertices y coordinate")) ++ string="%s\n%s"%(string,fielddisplay(obj,"z","vertices z coordinate")) ++ string="%s\n%s"%(string,fielddisplay(obj,"edges","edges of the 2d mesh (vertex1 vertex2 element1 element2)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"numberofedges","number of edges of the 2d mesh")) ++ ++ string="%s%s"%(string,"\n Properties:") ++ ++ string="%s\n%s"%(string,fielddisplay(obj,"dimension","mesh dimension (2d or 3d)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"numberoflayers","number of extrusion layers")) ++ string="%s\n%s"%(string,fielddisplay(obj,"vertexonbed","lower vertices flags list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"elementonbed","lower elements flags list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"vertexonsurface","upper vertices flags list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"elementonsurface","upper elements flags list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"uppervertex","upper vertex list (NaN for vertex on the upper surface)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"upperelements","upper element list (NaN for element on the upper layer)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"lowervertex","lower vertex list (NaN for vertex on the lower surface)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"lowerelements","lower element list (NaN for element on the lower layer")) ++ string="%s\n%s"%(string,fielddisplay(obj,"vertexonboundary","vertices on the boundary of the domain flag list")) ++ ++ string="%s\n%s"%(string,fielddisplay(obj,"segments","edges on domain boundary (vertex1 vertex2 element)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"segmentmarkers","number associated to each segment")) ++ string="%s\n%s"%(string,fielddisplay(obj,"vertexconnectivity","list of vertices connected to vertex_i")) ++ string="%s\n%s"%(string,fielddisplay(obj,"elementconnectivity","list of vertices connected to element_i")) ++ string="%s\n%s"%(string,fielddisplay(obj,"average_vertex_connectivity","average number of vertices connected to one vertex")) ++ ++ string="%s%s"%(string,"\n Extracted model:") ++ ++ string="%s\n%s"%(string,fielddisplay(obj,"extractedvertices","vertices extracted from the model")) ++ string="%s\n%s"%(string,fielddisplay(obj,"extractedelements","elements extracted from the model")) ++ ++ string="%s%s"%(string,"\n Projection:") ++ string="%s\n%s"%(string,fielddisplay(obj,"lat","vertices latitude")) ++ string="%s\n%s"%(string,fielddisplay(obj,"long","vertices longitude")) ++ string="%s\n%s"%(string,fielddisplay(obj,"hemisphere","Indicate hemisphere ""n"" or ""s"" ")) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/timestepping.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/timestepping.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/timestepping.py (revision 12038) +@@ -0,0 +1,21 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class timestepping: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.time_step = 0; ++ self.final_time = 0; ++ self.time_adapt = 0; ++ self.cfl_coefficient = 0; ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=" timestepping parameters:" ++ string="%s\n\n%s"%(string,fielddisplay(obj,"time_step","length of time steps [yrs]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"final_time","final time to stop the simulation [yrs]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"time_adapt","use cfl condition to define time step ? (0 or 1) ")) ++ string="%s\n%s"%(string,fielddisplay(obj,"cfl_coefficient","coefficient applied to cfl condition")) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/constants.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/constants.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/constants.py (revision 12038) +@@ -0,0 +1,21 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class constants: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.g = 0 ++ self.yts = 0 ++ self.referencetemperature = 0 ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=" constants parameters:" ++ string="%s\n\n%s"%(string,fielddisplay(obj,"g","gravitational acceleration")) ++ string="%s\n%s"%(string,fielddisplay(obj,"yts","number of seconds in a year")) ++ string="%s\n%s"%(string,fielddisplay(obj,"referencetemperature","reference temperature used in the enthalpy model")) ++ ++ ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.py (revision 12038) +@@ -0,0 +1,217 @@ ++#GENERIC cluster class definition ++# ++# Usage: ++# cluster=generic('name','astrid',); ++# cluster=generic('name','astrid','np',3); ++# cluster=generic('name',oshostname(),'np',3,'login','username'); ++ ++ ++class generic: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.name='' ++ self.login='' ++ self.np=1 ++ self.port=0 ++ self.interactive=1 ++ self.codepath=issmtier() + '/bin' ++ self.executionpath=issmtier() + '/execution' ++ self.valgrind=issmtier() + '/externalpackages/valgrind/install/bin/valgrind' ++ self.valgrindlib=issmtier() + '/externalpackages/valgrind/install/lib/libmpidebug.so' ++ self.valgrindsup=issmtier() + '/externalpackages/valgrind/issm.supp' ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ string="class 'generic' object:" ++ string="%s\n\n%s"%(string,"%s%s"%(' name: ',obj.name)) ++ string="%s\n%s"%(string,"%s%i"%(' np: ',obj.np)) ++ string="%s\n%s"%(string,"%s%i"%(' port: ',obj.port)) ++ string="%s\n%s"%(string,"%s%s"%(' codepath: ',obj.codepath)) ++ string="%s\n%s"%(string,"%s%s"%(' executionpath: ',obj.executionpath)) ++ string="%s\n%s"%(string,"%s%s"%(' valgrind: ',obj.valgrind)) ++ string="%s\n%s"%(string,"%s%s"%(' valgrindlib: ',obj.valgrindlib)) ++ string="%s\n%s"%(string,"%s%s"%(' valgrindsup: ',obj.valgrindsup)) ++ return string ++ #}}} ++ ++ ++#old matlab ++# function cluster=generic(varargin) % {{{1 ++# ++# %use provided options to change fields ++# options=pairoptions(varargin{:}); ++# ++# %get name ++# if ~exist(options,'name'), error('option ''name'' has not been provided'); end ++# cluster.name=getfieldvalue(options,'name'); ++# ++# %initialize cluster using user settings if provided ++# if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end ++# ++# %OK get other fields ++# for i=1:size(options.list,1), ++# fieldname=options.list{i,1}; ++# fieldvalue=options.list{i,2}; ++# if ismember(fieldname,properties('generic')), ++# cluster.(fieldname)=fieldvalue; ++# else ++# disp(['''' fieldname ''' is not a property of cluster generic']); ++# end ++# end ++# end ++# %}}} ++# function checkconsistency(cluster,md,solution,analyses) % {{{1 ++# if cluster.np<1 ++# checkmessage(['number of processors should be at least 1']); ++# end ++# if isnan(cluster.np), ++# checkessage('number of processors should not be NaN!'); ++# end ++# end ++# %}}} ++# function BuildQueueScript(cluster,md) % {{{1 ++# ++# %retrieve parameters ++# modelname=md.miscellaneous.name; ++# solution=md.private.solution; ++# isvalgrind=md.debug.valgrind; ++# isgprof=md.debug.gprof; ++# ++# %open file for writing: ++# if ~ispc, ++# fid=fopen([modelname '.queue'],'w'); ++# else ++# fid=fopen([modelname '.bat'],'w'); ++# end ++# ++# %write instructions for launching a job on the cluster ++# if ~ispc, ++# fprintf(fid,'#!/bin/sh\n'); ++# else ++# fprintf(fid,'@echo off\n'); ++# end ++# ++# if ~isvalgrind, ++# if cluster.interactive ++# if ~ispc, ++# fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s ',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname); ++# else ++# fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),cluster.executionpath,modelname); ++# end ++# else ++# if ~ispc, ++# fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname); ++# else ++# fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog ',cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname); ++# end ++# end ++# else ++# if ~ispc, ++# %Add --gen-suppressions=all to get suppression lines ++# fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib); ++# fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',... ++# cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname); ++# else ++# error('valgrind not supported on windows platforms'); ++# end ++# end ++# ++# if isgprof, ++# if ~ispc, ++# fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname); ++# else ++# error('gprof not supported on windows platforms'); ++# end ++# ++# end ++# ++# if ~md.settings.io_gather, ++# if ~ispc, ++# %concatenate the output files: ++# fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname); ++# else ++# error('iogather not supported on windows platforms'); ++# end ++# ++# end ++# ++# %close file: ++# fclose(fid); ++# ++# %in interactive mode, create a run file, and errlog and outlog file ++# if cluster.interactive, ++# fid=fopen([modelname '.errlog'],'w'); fclose(fid); ++# fid=fopen([modelname '.outlog'],'w'); fclose(fid); ++# end ++# ++# ++# end ++# %}}} ++# function LaunchQueueJob(cluster,md,options)% {{{1 ++# ++# if ~ispc, ++# %lauch command, to be executed via ssh ++# launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.private.runtimename ' && mkdir ' md.private.runtimename ... ++# ' && cd ' md.private.runtimename ' && mv ../' md.private.runtimename '.tar.gz ./ && tar -zxf ' md.private.runtimename '.tar.gz && source ' md.miscellaneous.name '.queue ']; ++# ++# if ~strcmpi(options.batch,'yes'), ++# ++# %compress the files into one zip. ++# compressstring=['tar -zcf ' md.private.runtimename '.tar.gz ' md.miscellaneous.name '.bin ' md.miscellaneous.name '.queue ' md.miscellaneous.name '.petsc ']; ++# if md.qmu.isdakota, ++# compressstring=[compressstring md.miscellaneous.name '.qmu.in']; ++# end ++# if cluster.interactive, ++# compressstring=[compressstring ' ' md.miscellaneous.name '.errlog ' md.miscellaneous.name '.outlog ']; ++# end ++# system(compressstring); ++# ++# disp('uploading input file and queueing script'); ++# issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[md.private.runtimename '.tar.gz']}); ++# ++# disp('launching solution sequence on remote cluster'); ++# issmssh(cluster.name,cluster.login,cluster.port,launchcommand); ++# else ++# disp('batch mode requested: not launching job interactively'); ++# disp('launch solution sequence on remote cluster by hand'); ++# end ++# else ++# %launch right here, do not compress or archive. ++# system([md.miscellaneous.name '.bat']); ++# end ++# ++# end %}}} ++# function Download(cluster,md)% {{{1 ++# ++# if ~ispc, ++# %some check ++# if isempty(md.private.runtimename), ++# error('supply runtime name for results to be loaded!'); ++# end ++# ++# %Figure out the directory where all the files are in: ++# directory=[cluster.executionpath '/' md.private.runtimename '/']; ++# ++# %What packages are we picking up from remote cluster ++# packages={[md.miscellaneous.name '.outlog'],[md.miscellaneous.name '.errlog']}; ++# if md.qmu.isdakota, ++# packages{end+1}=[md.miscellaneous.name '.qmu.err']; ++# packages{end+1}=[md.miscellaneous.name '.qmu.out']; ++# if isfield(md.qmu.params,'tabular_graphics_data'), ++# if md.qmu.params.tabular_graphics_data==true, ++# packages{end+1}='dakota_tabular.dat'; ++# end ++# end ++# else ++# packages{end+1}=[md.miscellaneous.name '.outbin']; ++# end ++# ++# %copy files from cluster to present directory ++# issmscpin(cluster.name, cluster.login, cluster.port, directory, packages); ++# else ++# %do nothing! ++# end ++# end %}}} ++# +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/none.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/none.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/none.py (revision 12038) +@@ -0,0 +1,24 @@ ++#NONE cluster class definition ++# ++# Usage: ++# cluster=none(); ++# cluster=none('np',3); ++# cluster=none('np',3,'login','username'); ++ ++class none: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.name='none' ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ string="class 'none' object:" ++ string="%s\n\n%s"%(string,"%s%s"%(' name: ',obj.name)) ++ return string ++ #}}} ++ def checkconsistency(cluster,md,solution,analyses): ++ pass ++ def BuildQueueScript(cluster,md): ++ raise RuntimeError('none.BuildQueueScript error message: serial cluster cannot build queue script') +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.py (revision 12038) +@@ -0,0 +1,19 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class friction: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.coefficient = float('NaN') ++ self.p = float('NaN') ++ self.q = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string="Sigma= drag^2 * Neff ^r * u ^s, with Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p" ++ string="%s\n\n%s"%(string,fielddisplay(obj,"coefficient","friction coefficient [SI]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"p","p exponent")) ++ string="%s\n%s"%(string,fielddisplay(obj,"q","q exponent")) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py (revision 12038) +@@ -0,0 +1,41 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class materials: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.rho_ice = 0; ++ self.rho_water = 0; ++ self.mu_water = 0; ++ self.heatcapacity = 0; ++ self.latentheat = 0; ++ self.thermalconductivity = 0; ++ self.meltingpoint = 0; ++ self.beta = 0; ++ self.mixed_layer_capacity = 0; ++ self.thermal_exchange_velocity = 0; ++ self.rheology_B = float('NaN') ++ self.rheology_n = float('NaN') ++ self.rheology_law = ""; ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=" Materials:" ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,"rho_ice","ice density [kg/m^3]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"rho_water","water density [kg/m^3]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"mu_water","water viscosity [N s/m^2]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"heatcapacity","heat capacity [J/kg/K]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"thermalconductivity","ice thermal conductivity [W/m/K]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"meltingpoint","melting point of ice at 1atm in K")) ++ string="%s\n%s"%(string,fielddisplay(obj,"latentheat","latent heat of fusion [J/m^3]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"beta","rate of change of melting point with pressure [K/Pa]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"mixed_layer_capacity","mixed layer capacity [W/kg/K]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"thermal_exchange_velocity","thermal exchange velocity [m/s]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"rheology_B","flow law parameter [Pa/s^(1/n)]")) ++ string="%s\n%s"%(string,fielddisplay(obj,"rheology_n","Glen""s flow law exponent")) ++ string="%s\n%s"%(string,fielddisplay(obj,"rheology_law","law for the temperature dependance of the rheology: ""None"", ""Paterson"" or ""Arrhenius""")) ++ ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.py (revision 12038) +@@ -0,0 +1,63 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class diagnostic: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.spcvx = float('NaN') ++ self.spcvy = float('NaN') ++ self.spcvz = float('NaN') ++ self.restol = 0 ++ self.reltol = 0 ++ self.abstol = 0 ++ self.isnewton = 0 ++ self.stokesreconditioning = 0 ++ self.viscosity_overshoot = 0 ++ self.icefront = float('NaN') ++ self.maxiter = 0 ++ self.shelf_dampening = 0 ++ self.vertex_pairing = float('NaN') ++ self.penalty_factor = float('NaN') ++ self.rift_penalty_lock = float('NaN') ++ self.rift_penalty_threshold = 0 ++ self.referential = float('NaN') ++ self.requested_outputs = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ ++ string='\n Diagnostic solution parameters:' ++ string="%s\n\n%s"%(string,' Convergence criteria:') ++ ++ string="%s\n%s"%(string,fielddisplay(obj,'restol','mechanical equilibrium residual convergence criterion')) ++ string="%s\n%s"%(string,fielddisplay(obj,'reltol','velocity relative convergence criterion, NaN -> not applied')) ++ string="%s\n%s"%(string,fielddisplay(obj,'abstol','velocity absolute convergence criterion, NaN -> not applied')) ++ string="%s\n%s"%(string,fielddisplay(obj,'isnewton','Apply Newton''s method instead of a Picard fixed point method')) ++ string="%s\n%s"%(string,fielddisplay(obj,'maxiter','maximum number of nonlinear iterations')) ++ string="%s\n%s"%(string,fielddisplay(obj,'viscosity_overshoot','over-shooting constant new=new+C*(new-old)')) ++ ++ string="%s\n%s"%(string,' boundary conditions:') ++ ++ string="%s\n%s"%(string,fielddisplay(obj,'spcvx','x-axis velocity constraint (NaN means no constraint)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'spcvy','y-axis velocity constraint (NaN means no constraint)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'spcvz','z-axis velocity constraint (NaN means no constraint)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice')) ++ ++ string="%s\n%s"%(string,' Rift options:') ++ string="%s\n%s"%(string,fielddisplay(obj,'rift_penalty_threshold','threshold for instability of mechanical constraints')) ++ string="%s\n%s"%(string,fielddisplay(obj,'rift_penalty_lock','number of iterations before rift penalties are locked')) ++ ++ string="%s\n%s"%(string,' Penalty options:') ++ string="%s\n%s"%(string,fielddisplay(obj,'penalty_factor','offset used by penalties: penalty = Kmax*10^offset')) ++ string="%s\n%s"%(string,fielddisplay(obj,'vertex_pairing','pairs of vertices that are penalized')) ++ ++ string="%s\n%s"%(string,' Other:') ++ string="%s\n%s"%(string,fielddisplay(obj,'shelf_dampening','use dampening for floating ice ? Only for Stokes model')) ++ string="%s\n%s"%(string,fielddisplay(obj,'stokesreconditioning','multiplier for incompressibility equation. Only for Stokes model')) ++ string="%s\n%s"%(string,fielddisplay(obj,'referential','local referential')) ++ string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','additional outputs requested')) ++ ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/debug.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/debug.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/debug.py (revision 12038) +@@ -0,0 +1,18 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class debug: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.valgrind=False ++ self.gprof = False ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=" debug parameters:" ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,"valgrind","use Valgrind to debug (0 or 1)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"gprof","use gnu-profiler to find out where the time is spent")) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/initialization.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/initialization.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/initialization.py (revision 12038) +@@ -0,0 +1,32 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class initialization: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ ++ self.vx = float('NaN') ++ self.vy = float('NaN') ++ self.vz = float('NaN') ++ self.vel = float('NaN') ++ self.pressure = float('NaN') ++ self.temperature = float('NaN') ++ self.watercolumn = float('NaN') ++ self.waterfraction = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' initial field values:' ++ ++ string="%s\n%s"%(string,fielddisplay(obj,'vx','x component of velocity')) ++ string="%s\n%s"%(string,fielddisplay(obj,'vy','y component of velocity')) ++ string="%s\n%s"%(string,fielddisplay(obj,'vz','z component of velocity')) ++ string="%s\n%s"%(string,fielddisplay(obj,'vel','velocity norm')) ++ string="%s\n%s"%(string,fielddisplay(obj,'pressure','pressure field')) ++ string="%s\n%s"%(string,fielddisplay(obj,'temperature','temperature in Kelvins')) ++ string="%s\n%s"%(string,fielddisplay(obj,'watercolumn','thickness of subglacial water')) ++ string="%s\n%s"%(string,fielddisplay(obj,'waterfraction','fraction of water in the ice')) ++ ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.py (revision 12038) +@@ -0,0 +1,24 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class prognostic: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.spcthickness = float('NaN') ++ self.min_thickness = 0 ++ self.hydrostatic_adjustment = 0 ++ self.stabilization = 0 ++ self.vertex_pairing = float('NaN') ++ self.penalty_factor = 0 ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' Prognostic solution parameters:' ++ string="%s\n\n%s"%(string,fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'min_thickness','minimum ice thickness allowed')) ++ string="%s\n%s"%(string,fielddisplay(obj,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' ')) ++ string="%s\n%s"%(string,fielddisplay(obj,'stabilization','0->no, 1->artificial_diffusivity, 2->streamline upwinding, 3->discontinuous Galerkin')) ++ ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mask.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mask.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mask.py (revision 12038) +@@ -0,0 +1,26 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class mask: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.elementonfloatingice = float('NaN') ++ self.elementongroundedice = float('NaN') ++ self.elementonwater = float('NaN') ++ self.vertexonfloatingice = float('NaN') ++ self.vertexongroundedice = float('NaN') ++ self.vertexonwater = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ string=""; ++ string="%s\n%s"%(string,fielddisplay(obj,"elementonfloatingice","element on floating ice flags list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"vertexonfloatingice","vertex on floating ice flags list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"elementongroundedice","element on grounded ice list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"vertexongroundedice","vertex on grounded ice flags list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"elementonwater","element on water flags list")) ++ string="%s\n%s"%(string,fielddisplay(obj,"vertexonwater","vertex on water flags list")) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/radaroverlay.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/radaroverlay.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/radaroverlay.py (revision 12038) +@@ -0,0 +1,19 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class radaroverlay: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.pwr = float('NaN') ++ self.x = float('NaN') ++ self.y = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' radaroverlay parameters:' ++ string="%s\n\n%s"%(string,fielddisplay(obj,'pwr','radar power image (matrix)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'x','corresponding x coordinates')) ++ string="%s\n%s"%(string,fielddisplay(obj,'y','corresponding y coordinates')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model.py (revision 12038) +@@ -0,0 +1,115 @@ ++#module imports {{{ ++from mesh import mesh ++from mask import mask ++from geometry import geometry ++from constants import constants ++from surfaceforcings import surfaceforcings ++from basalforcings import basalforcings ++from materials import materials ++from friction import friction ++from flowequation import flowequation ++from timestepping import timestepping ++from initialization import initialization ++from rifts import rifts ++from debug import debug ++from verbose import verbose ++from settings import settings ++from solver import solver ++from none import none ++from balancethickness import balancethickness ++from diagnostic import diagnostic ++from groundingline import groundingline ++from hydrology import hydrology ++from prognostic import prognostic ++from thermal import thermal ++from steadystate import steadystate ++from transient import transient ++from autodiff import autodiff ++from flaim import flaim ++from inversion import inversion ++from qmu import qmu ++from radaroverlay import radaroverlay ++from miscellaneous import miscellaneous ++from private import private ++#}}} ++class model: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.mesh = mesh() ++ self.mask = mask() ++ self.geometry = geometry() ++ self.constants = constants() ++ self.surfaceforcings = surfaceforcings() ++ self.basalforcings = basalforcings() ++ self.materials = materials() ++ self.friction = friction() ++ self.flowequation = flowequation() ++ self.timestepping = timestepping() ++ self.initialization = initialization() ++ self.rifts = rifts() ++ ++ self.debug = debug() ++ self.verbose = verbose() ++ self.settings = settings() ++ self.solver = solver() ++ self.cluster = none() ++ ++ self.balancethickness = balancethickness() ++ self.diagnostic = diagnostic() ++ self.groundingline = groundingline() ++ self.hydrology = hydrology() ++ self.prognostic = prognostic() ++ self.thermal = thermal() ++ self.steadystate = steadystate() ++ self.transient = transient() ++ ++ self.autodiff = autodiff() ++ self.flaim = flaim() ++ self.inversion = inversion() ++ self.qmu = qmu() ++ ++ self.results = []; ++ self.radaroverlay = radaroverlay() ++ self.miscellaneous = miscellaneous() ++ self.private = private() ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ #print "Here %s the number: %d" % ("is", 37) ++ string="%19s: %-22s -- %s" % ("mesh","[%s,%s]" % ("1x1",obj.mesh.__class__.__name__),"mesh properties") ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("mask","[%s,%s]" % ("1x1",obj.mask.__class__.__name__),"defines grounded and floating elements")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("geometry","[%s,%s]" % ("1x1",obj.geometry.__class__.__name__),"surface elevation, bedrock topography, ice thickness,...")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("constants","[%s,%s]" % ("1x1",obj.constants.__class__.__name__),"physical constants")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("surfaceforcings","[%s,%s]" % ("1x1",obj.surfaceforcings.__class__.__name__),"surface forcings")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("basalforcings","[%s,%s]" % ("1x1",obj.basalforcings.__class__.__name__),"bed forcings")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("materials","[%s,%s]" % ("1x1",obj.materials.__class__.__name__),"material properties")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("friction","[%s,%s]" % ("1x1",obj.friction.__class__.__name__),"basal friction/drag properties")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flowequation","[%s,%s]" % ("1x1",obj.flowequation.__class__.__name__),"flow equations")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("timestepping","[%s,%s]" % ("1x1",obj.timestepping.__class__.__name__),"time stepping for transient models")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("initialization","[%s,%s]" % ("1x1",obj.initialization.__class__.__name__),"initial guess/state")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("rifts","[%s,%s]" % ("1x1",obj.rifts.__class__.__name__),"rifts properties'")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("debug","[%s,%s]" % ("1x1",obj.debug.__class__.__name__),"debugging tools (valgrind, gprof")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("verbose","[%s,%s]" % ("1x1",obj.verbose.__class__.__name__),"verbosity level in solve")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("settings","[%s,%s]" % ("1x1",obj.settings.__class__.__name__),"settings properties")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("solver","[%s,%s]" % ("1x1",obj.solver.__class__.__name__),"PETSc options for each solution'")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("cluster","[%s,%s]" % ("1x1",obj.cluster.__class__.__name__),"cluster parameters (number of cpus...)")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("balancethickness","[%s,%s]" % ("1x1",obj.balancethickness.__class__.__name__),"parameters for balancethickness solution")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("diagnostic","[%s,%s]" % ("1x1",obj.diagnostic.__class__.__name__),"parameters for diagnostic solution")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("groundingline","[%s,%s]" % ("1x1",obj.groundingline.__class__.__name__),"parameters for groundingline solution")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("hydrology","[%s,%s]" % ("1x1",obj.hydrology.__class__.__name__),"parameters for hydrology solution")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("prognostic","[%s,%s]" % ("1x1",obj.prognostic.__class__.__name__),"parameters for prognostic solution")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("thermal","[%s,%s]" % ("1x1",obj.thermal.__class__.__name__),"parameters for thermal solution")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("steadystate","[%s,%s]" % ("1x1",obj.steadystate.__class__.__name__),"parameters for steadystate solution")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("transient","[%s,%s]" % ("1x1",obj.transient.__class__.__name__),"parameters for transient solution")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("autodiff","[%s,%s]" % ("1x1",obj.autodiff.__class__.__name__),"automatic differentiation parameters")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flaim","[%s,%s]" % ("1x1",obj.flaim.__class__.__name__),"flaim parameters")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("inversion","[%s,%s]" % ("1x1",obj.inversion.__class__.__name__),"parameters for inverse methods")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("qmu","[%s,%s]" % ("1x1",obj.qmu.__class__.__name__),"dakota properties")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("results","[%s,%s]" % ("1x1",obj.results.__class__.__name__),"model results'")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("radaroverlay","[%s,%s]" % ("1x1",obj.radaroverlay.__class__.__name__),"radar image for plot overlay")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("miscellaneous","[%s,%s]" % ("1x1",obj.miscellaneous.__class__.__name__),"miscellaneous fields")) ++ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("miscellaneous","[%s,%s]" % ("1x1",obj.miscellaneous.__class__.__name__),"miscellaneous fields")) ++ return string; ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/autodiff.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/autodiff.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/autodiff.py (revision 12038) +@@ -0,0 +1,19 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class autodiff: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.isautodiff = False ++ self.forward = True ++ self.reverse = False ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' automatic differentiation parameters:' ++ string="%s\n%s"%(string,fielddisplay(obj,'isautodiff','indicates if the automatic differentiation is activated')) ++ string="%s\n%s"%(string,fielddisplay(obj,'forward','forward differentiation')) ++ string="%s\n%s"%(string,fielddisplay(obj,'reverse','backward differentiation')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/verbose.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/verbose.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/verbose.py (revision 12038) +@@ -0,0 +1,27 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class verbose: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.mprocessor = False ++ self.module = False ++ self.solution = False ++ self.solver = False ++ self.convergence = False ++ self.control = False ++ self.qmu = False ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string="%s%s%s\n\n"%("class '",obj.__class__.__name__,"'=") ++ string="%s%s\n"%(string," %15s : %s"%("mprocessor",obj.mprocessor)) ++ string="%s%s\n"%(string," %15s : %s"%("module",obj.module)) ++ string="%s%s\n"%(string," %15s : %s"%("solution",obj.solution)) ++ string="%s%s\n"%(string," %15s : %s"%("solver",obj.solver)) ++ string="%s%s\n"%(string," %15s : %s"%("convergence",obj.convergence)) ++ string="%s%s\n"%(string," %15s : %s"%("control",obj.control)) ++ string="%s%s\n"%(string," %15s : %s"%("qmu",obj.qmu)) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/pairoptions.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/pairoptions.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/pairoptions.py (revision 12038) +@@ -0,0 +1,38 @@ ++class pairoptions: ++ #properties ++ def __init__(self,*args): ++ # {{{ Properties ++ if len(args)%2==1: ++ raise RuntimeError('pairoption error message: an even number of options is required') ++ ++ #create a pairoption object ++ if len(args)==0: ++ self.list=[] ++ else: ++ self.list=[] ++ for i in range(int(round(len(args)/2))): ++ if isinstance(args[2*i],str): ++ self.list.append([args[2*i],args[2*i+1]]) ++ else: ++ #option is not a string, ignore it ++ print("%s%i%s"%('buildlist info: option number ',i,' is not a string, it will be ignored')) ++ continue ++ ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ if not obj.list: ++ string=' list: empty' ++ else: ++ string=" list: (%i)"%(len(obj.list)) ++ for i in range(len(obj.list)): ++ if isinstance(obj.list[i][1],str): ++ string2=" field: %-10s value: '%s'"%(obj.list[i][0],obj.list[i][1]) ++ elif isinstance(obj.list[i][1],float): ++ string2=" field: %-10s value: %g"%(obj.list[i][0],obj.list[i][1]) ++ elif isinstance(obj.list[i][1],int): ++ string2=" field: %-10s value: %i"%(obj.list[i][0],obj.list[i][1]) ++ else: ++ string2=" field: %-10s value: (%i)"%(len(obj.list[i][1])) ++ string="%s\n%s"%(string,string2) ++ return string +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/solver.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/solver.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/solver.py (revision 12038) +@@ -0,0 +1,49 @@ ++#module imports {{{ ++import fielddisplay ++import ismumps ++from mumpsoptions import * ++from iluasmoptions import * ++#}}} ++class solver: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ if ismumps: ++ self.options=[["NoneAnalysis",mumpsoptions()]] ++ else: ++ self.options=[["NoneAnalysis",iluasmoptions()]] ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ string2=" solver parameters:" ++ for i in range(len(obj.options)): ++ option=obj.options[i] ++ analysis=option[0] ++ ioptions=option[1] ++ ++ string="" ++ for i in range(len(ioptions)): ++ option=ioptions[i] ++ if not option: ++ #do nothing ++ pass ++ elif len(option)==1: ++ #this option has only one argument ++ string="%s%s%s"%(string," -",option[0]) ++ elif len(option)==2: ++ #option with value. value can be string or scalar ++ if isinstance(option[1],float): ++ string="%s%s%s%s%s"%(string," -",option[0]," ","%g"%(option[1])) ++ elif isinstance(option[1],str): ++ string="%s%s%s%s%s"%(string," -",option[0]," ",option[1]) ++ elif isinstance(option[1],int): ++ string="%s%s%s%s%s"%(string," -",option[0]," ","%i"%(option[1])) ++ else: ++ raise RuntimeError("%s%s%s"%("PetscString error: option #","%i"%(i)," is not well formatted")) ++ else: ++ raise RuntimeError("%s%s%s"%("PetscString error: option #","%i"%(i)," is not well formatted")) ++ ++ string2="%s\n%s"%(string2," %s -> '%s'"%(analysis,string)) ++ return string2 ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flaim.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flaim.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flaim.py (revision 12038) +@@ -0,0 +1,50 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class flaim: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.targets = '' ++ self.tracks = '' ++ self.flightreqs = {} ++ self.criterion = float('NaN') ++ self.gridsatequator = 200000 ++ self.usevalueordering = True ++ self.split_antimeridian = True ++ self.solution = '' ++ self.quality = 0 ++ self.path_optimize = False ++ self.opt_ndir = 1 ++ self.opt_dist = 25 ++ self.opt_niter = 30000 ++ #}}} ++ def __repr__(obj): ++ # {{{ Displa ++ string=' FLAIM - Flight Line Adaptation using Ice sheet Modeling:' ++ ++ string="%s\n\n%s"%(string,' Input:') ++ string="%s\n%s"%(string,fielddisplay(obj,'targets' ,'name of kml output targets file ')) ++ string="%s\n%s"%(string,fielddisplay(obj,'tracks' ,'name of kml input tracks file ')) ++ string="%s\n%s"%(string,fielddisplay(obj,'flightreqs' ,'structure of kml flight requirements (not used yet)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'criterion' ,'element or nodal criterion for flight path evaluation (metric)')) ++ ++ string="%s\n\n%s"%(string,' Arguments:') ++ string="%s\n%s"%(string,fielddisplay(obj,'gridsatequator' ,'number of grids at equator (determines resolution)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'usevalueordering' ,'flag to consider target values for flight path evaluation')) ++ string="%s\n%s"%(string,fielddisplay(obj,'split_antimeridian' ,'flag to split polygons on the antimeridian')) ++ ++ string="%s\n\n%s"%(string,' Optimization:') ++ string="%s\n%s"%(string,fielddisplay(obj,'path_optimize' ,'optimize? (default false)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'opt_ndir' ,['number of directions to test when moving a point. If this value = 1, a random direction is tested.',\ ++ 'A value > 1 results in directions equally spaced from [0, 2*PI] being tested.',\ ++ 'For example, 4 would result in directions [0, PI/2, PI, 3PI/2].'])) ++ string="%s\n%s"%(string,fielddisplay(obj,'opt_dist' ,'specifies the distance in km (default 25) to move a randomly selected path point on each iteration')) ++ string="%s\n%s"%(string,fielddisplay(obj,'opt_niter' ,['number of iterations (default 30,000) to run for flightplan optimization',\ ++ 'i.e. the number of times to randomly select a point and move it.'])) ++ ++ string="%s\n\n%s"%(string,' Output:') ++ string="%s\n%s"%(string,fielddisplay(obj,'solution' ,'name of kml solution file')) ++ string="%s\n%s"%(string,fielddisplay(obj,'quality' ,'quality of kml solution')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/steadystate.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/steadystate.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/steadystate.py (revision 12038) +@@ -0,0 +1,19 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class steadystate: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.reltol = 0 ++ self.maxiter = 0 ++ self.requested_outputs = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' steadystate solution parameters:' ++ string="%s\n%s"%(string,fielddisplay(obj,'reltol','relative tolerance criterion')) ++ string="%s\n%s"%(string,fielddisplay(obj,'maxiter','maximum number of iterations')) ++ string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','additional requested outputs')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/geometry.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/geometry.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/geometry.py (revision 12038) +@@ -0,0 +1,25 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class geometry: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.surface = float('NaN') ++ self.thickness = float('NaN') ++ self.bed = float('NaN') ++ self.bathymetry = float('NaN') ++ self.hydrostatic_ratio = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ ++ string=" geometry parameters:" ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,'surface','surface elevation')) ++ string="%s\n%s"%(string,fielddisplay(obj,'thickness','ice thickness')) ++ string="%s\n%s"%(string,fielddisplay(obj,'bed','bed elevation')) ++ string="%s\n%s"%(string,fielddisplay(obj,'bathymetry','bathymetry elevation')) ++ string="%s\n%s"%(string,fielddisplay(obj,'hydrostatic_ratio','coefficient for ice shelves'' thickness correction: hydrostatic_ratio H_obs+ (1-hydrostatic_ratio) H_hydro')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/qmu.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/qmu.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/qmu.py (revision 12038) +@@ -0,0 +1,29 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class qmu: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.isdakota = 0 ++ self.variables = {} ++ self.responses = {} ++ self.method = {} ++ self.params = {} ++ self.results = {} ++ self.partition = float('NaN') ++ self.numberofpartitions = 0 ++ self.numberofresponses = 0 ++ self.variabledescriptors = [] ++ self.responsedescriptors = [] ++ self.mass_flux_profile_directory = float('NaN') ++ self.mass_flux_profiles = float('NaN') ++ self.mass_flux_segments = [] ++ self.adjacency = float('NaN') ++ self.vertex_weight = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=" qmu parameters: not implemented yet!" ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/miscellaneous.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/miscellaneous.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/miscellaneous.py (revision 12038) +@@ -0,0 +1,20 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class miscellaneous: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.notes = '' ++ self.name = '' ++ self.dummy = {} ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' miscellaneous parameters:' ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,'notes','notes in a cell of strings')) ++ string="%s\n%s"%(string,fielddisplay(obj,'name','model name')) ++ string="%s\n%s"%(string,fielddisplay(obj,'dummy','empty field to store some data')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/private.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/private.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/private.py (revision 12038) +@@ -0,0 +1,19 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class private: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.runtimename = '' ++ self.bamg = {} ++ self.solution = ''; ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' private parameters: do not change' ++ string="%s\n%s"%(string,fielddisplay(obj,'runtimename','name of the run launched')) ++ string="%s\n%s"%(string,fielddisplay(obj,'bamg','structure with mesh properties construced if bamg is used to mesh the domain')) ++ string="%s\n%s"%(string,fielddisplay(obj,'solution','type of solution launched')) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/inversion.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/inversion.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/inversion.py (revision 12038) +@@ -0,0 +1,59 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class inversion: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.iscontrol = 0 ++ self.tao = 0 ++ self.incomplete_adjoint = 0 ++ self.control_parameters = float('NaN') ++ self.nsteps = 0 ++ self.maxiter_per_step = float('NaN') ++ self.cost_functions = float('NaN') ++ self.cost_functions_coefficients = float('NaN') ++ self.gradient_scaling = float('NaN') ++ self.cost_function_threshold = 0 ++ self.min_parameters = float('NaN') ++ self.max_parameters = float('NaN') ++ self.step_threshold = float('NaN') ++ self.gradient_only = 0 ++ self.vx_obs = float('NaN') ++ self.vy_obs = float('NaN') ++ self.vz_obs = float('NaN') ++ self.vel_obs = float('NaN') ++ self.thickness_obs = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string='\n Inversion parameters:' ++ string="%s\n%s"%(string,fielddisplay(obj,'iscontrol','is inversion activated?')) ++ string="%s\n%s"%(string,fielddisplay(obj,'incomplete_adjoint','do we assume linear viscosity?')) ++ string="%s\n%s"%(string,fielddisplay(obj,'control_parameters','parameter where inverse control is carried out; ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}')) ++ string="%s\n%s"%(string,fielddisplay(obj,'nsteps','number of optimization searches')) ++ string="%s\n%s"%(string,fielddisplay(obj,'cost_functions','indicate the type of response for each optimization step')) ++ string="%s\n%s"%(string,fielddisplay(obj,'cost_functions_coefficients','cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter')) ++ string="%s\n%s"%(string,fielddisplay(obj,'cost_function_threshold','misfit convergence criterion. Default is 1%, NaN if not applied')) ++ string="%s\n%s"%(string,fielddisplay(obj,'maxiter_per_step','maximum iterations during each optimization step')) ++ string="%s\n%s"%(string,fielddisplay(obj,'gradient_scaling','scaling factor on gradient direction during optimization, for each optimization step')) ++ string="%s\n%s"%(string,fielddisplay(obj,'step_threshold','decrease threshold for misfit, default is 30%')) ++ string="%s\n%s"%(string,fielddisplay(obj,'min_parameters','absolute minimum acceptable value of the inversed parameter on each vertex')) ++ string="%s\n%s"%(string,fielddisplay(obj,'max_parameters','absolute maximum acceptable value of the inversed parameter on each vertex')) ++ string="%s\n%s"%(string,fielddisplay(obj,'gradient_only','stop control method solution at gradient')) ++ string="%s\n%s"%(string,fielddisplay(obj,'vx_obs','observed velocity x component [m/a]')) ++ string="%s\n%s"%(string,fielddisplay(obj,'vy_obs','observed velocity y component [m/a]')) ++ string="%s\n%s"%(string,fielddisplay(obj,'vel_obs','observed velocity magnitude [m/a]')) ++ string="%s\n%s"%(string,fielddisplay(obj,'thickness_obs','observed thickness [m]')) ++ string="%s\n%s"%(string,'Available cost functions:') ++ string="%s\n%s"%(string,' 101: SurfaceAbsVelMisfit') ++ string="%s\n%s"%(string,' 102: SurfaceRelVelMisfit') ++ string="%s\n%s"%(string,' 103: SurfaceLogVelMisfit') ++ string="%s\n%s"%(string,' 104: SurfaceLogVxVyMisfit') ++ string="%s\n%s"%(string,' 105: SurfaceAverageVelMisfit') ++ string="%s\n%s"%(string,' 201: ThicknessAbsMisfit') ++ string="%s\n%s"%(string,' 501: DragCoefficientAbsGradient') ++ string="%s\n%s"%(string,' 502: RheologyBbarAbsGradient') ++ string="%s\n%s"%(string,' 503: ThicknessAbsGradient') ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/basalforcings.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/basalforcings.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/basalforcings.py (revision 12038) +@@ -0,0 +1,20 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class basalforcings: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ self.melting_rate = float('NaN') ++ self.melting_rate_correction = float('NaN') ++ self.geothermalflux = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=" basal forcings parameters:" ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,"melting_rate","basal melting rate (positive if melting)")) ++ string="%s\n%s"%(string,fielddisplay(obj,"melting_rate_correction","additional melting applied when the grounding line retreats")) ++ string="%s\n%s"%(string,fielddisplay(obj,"geothermalflux","geothermal heat flux [W/m^2]")) ++ return string ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flowequation.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flowequation.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flowequation.py (revision 12038) +@@ -0,0 +1,31 @@ ++#module imports ++from fielddisplay import fielddisplay ++ ++class flowequation: ++ #properties ++ def __init__(self): ++ # {{{ Properties ++ ++ self.ismacayealpattyn = 0; ++ self.ishutter = 0; ++ self.isstokes = 0; ++ self.vertex_equation = float('NaN') ++ self.element_equation = float('NaN') ++ self.bordermacayeal = float('NaN') ++ self.borderpattyn = float('NaN') ++ self.borderstokes = float('NaN') ++ #}}} ++ def __repr__(obj): ++ # {{{ Display ++ string=' flow equation parameters:' ++ ++ string="%s\n\n%s"%(string,fielddisplay(obj,'ismacayealpattyn','is the macayeal or pattyn approximation used ?')) ++ string="%s\n%s"%(string,fielddisplay(obj,'ishutter','is the shallow ice approximation used ?')) ++ string="%s\n%s"%(string,fielddisplay(obj,'isstokes','are the Full-Stokes equations used ?')) ++ string="%s\n%s"%(string,fielddisplay(obj,'vertex_equation','flow equation for each vertex')) ++ string="%s\n%s"%(string,fielddisplay(obj,'element_equation','flow equation for each element')) ++ string="%s\n%s"%(string,fielddisplay(obj,'bordermacayeal','vertices on MacAyeal''s border (for tiling)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'borderpattyn','vertices on Pattyn''s border (for tiling)')) ++ string="%s\n%s"%(string,fielddisplay(obj,'borderstokes','vertices on Stokes'' border (for tiling)')) ++ return string ++ #}}} Index: /issm/oecreview/Archive/12010-12040/ISSM-12038-12039.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12038-12039.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12038-12039.diff (revision 12325) @@ -0,0 +1,44 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in +Makefile + + + __pycache__ +Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in +Makefile + + + __pycache__ +Makefile.in +Makefile + + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12038) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12039) +@@ -34,6 +34,15 @@ + sys.path.append(root) + file=os.path.splitext(file)[0] + #__import__(file) ++ ++for root,dirs,files in os.walk(ISSM_TIER+ '/src/m'): ++ for file in files: ++ if file.find(".py") != -1: ++ if file.find(".pyc") == -1: ++ #add to path ++ sys.path.append(root) ++ file=os.path.splitext(file)[0] ++ #__import__(file) + + sys.path.append(ISSM_TIER + '/src/modules/python') + Index: /issm/oecreview/Archive/12010-12040/ISSM-12039-12040.diff =================================================================== --- /issm/oecreview/Archive/12010-12040/ISSM-12039-12040.diff (revision 12325) +++ /issm/oecreview/Archive/12010-12040/ISSM-12039-12040.diff (revision 12325) @@ -0,0 +1,124 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 12039) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 12040) +@@ -62,7 +62,7 @@ + + mxArray* dataref=NULL; + double* vector_ptr=NULL; +- double* vector_ptr2=NULL; ++ double* vector_matlab=NULL; + int rows; + + if(vector){ +@@ -75,13 +75,13 @@ + #endif + + /*now create the matlab vector with Matlab's memory manager */ +- vector_ptr2=(double*)mxMalloc(rows*sizeof(double)); +- for(int i=0;i30; +- displayunit(offset,name,'not displayed',comment), +- else +- displayunit(offset,name,['''' field ''''],comment), +- end +- +- %numeric +- elseif isnumeric(field) +- +- %get size +- fieldsize=size(field); +- +- %double +- if max(fieldsize)==1, +- displayunit(offset,name,num2str(field),comment), +- %matrix +- else +- displayunit(offset,name,['(' num2str(fieldsize(1)) 'x' num2str(fieldsize(2)) ')'],comment), +- end +- +- %logical +- elseif islogical(field) +- +- %get size +- fieldsize=size(field); +- +- %single value +- if max(fieldsize)==1, +- if (field) +- displayunit(offset,name,'true',comment), +- else +- displayunit(offset,name,'false',comment), +- end +- %matrix +- else +- displayunit(offset,name,['(' num2str(fieldsize(1)) 'x' num2str(fieldsize(2)) ')'],comment), +- end +- +- %structure +- elseif isstruct(field), +- if ~isempty(fields(field)) +- displayunit(offset,name,'(structure)',comment), +- struct_display(field,[offset ' ']), +- else +- displayunit(offset,name,'N/A',comment), +- end +- +- %cell +- elseif iscell(field), +- cell_display(offset,name,field,comment), +- +- else +- displayunit(offset,name,'not displayed',comment), +- +- end +-end%}}} +- +-function struct_display(structure,offset) % {{{ +- +- structure_fields=fields(structure); +- +- for i=1:length(structure_fields), +- +- %get current field +- field=structure.(structure_fields{i}); +- +- %recursive call if necessary +- if isstruct(field), +- displayunit(offset,structure_fields{i},'(structure)',''), +- struct_display(field,[offset ' ']); +- +- %display value +- else +- parsedisplay(offset,structure_fields{i},field,''); +- end +- end +-end% }}} +-function cell_display(offset,name,field,comment) % {{{ +- +- %initialization +- string='{'; +- +- %go through the cell and fill string +- if length(field)<5; +- for i=1:length(field), +- if ischar(field{i}), +- string=[string '''' field{i} ''',']; +- elseif (isnumeric(field{i}) & length(field{i})==1) +- string=[string num2str(field{i}) ',' ]; +- else +- string='{'; +- break +- end +- end +- end +- if strcmp(string,'{'), +- string=['(' num2str(size(field,1)) 'x' num2str(size(field,2)) ')']; +- else +- string=[string(1:end-1) '}']; +- end +- +- %call displayunit +- displayunit(offset,name,string,comment); +-end% }}} +-function displayunit(offset,name,characterization,comment),% {{{ +- +- %take care of name +- if length(name)>23, +- name=[name(1:20) '...']; +- end +- +- %take care of characterization +- if (strcmp(characterization,['''' '''']) | strcmp(characterization,'NaN')), +- characterization='N/A'; +- end +- if length(characterization)>15, +- characterization=[characterization(1:12) '...']; +- end +- +- %print +- if isempty(comment) +- disp(sprintf('%s%-23s: %-15s',offset,name,characterization)); +- else +- if ischar(comment), +- disp(sprintf('%s%-23s: %-15s -- %s',offset,name,characterization,comment)); +- elseif iscell(comment), +- disp(sprintf('%s%-23s: %-15s -- %s',offset,name,characterization,comment{1})); +- for i=2:length(comment), +- disp(sprintf('%s%-23s %-15s %s',offset,'','',comment{i})); +- end +- else +- error('fielddisplay error message: format for comment not supportet yet'); +- end +- end +-end% }}} Index: /issm/oecreview/Archive/12041-12060/ISSM-12042-12043.diff =================================================================== --- /issm/oecreview/Archive/12041-12060/ISSM-12042-12043.diff (revision 12325) +++ /issm/oecreview/Archive/12041-12060/ISSM-12042-12043.diff (revision 12325) @@ -0,0 +1,642 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12042) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12043) +@@ -13,6 +13,7 @@ + #include "../../include/include.h" + #include "./matlabio.h" + ++/*Primitive data types*/ + /*FUNCTION FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/ + void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){ + +@@ -241,27 +242,6 @@ + + } + /*}}}*/ +-/*FUNCTION FetchData(Matrix** pmatrix,const mxArray* dataref){{{1*/ +-void FetchData(Matrix** pmatrix,const mxArray* dataref){ +- +- Matrix* outmatrix=NULL; +- int dummy=0; +- +- if (mxIsClass(dataref,"double") ){ +- +- /*Convert matlab matrix to matrix: */ +- outmatrix=MatlabMatrixToMatrix(dataref); +- +- } +- else{ +- /*This is an error: we don't have the correct input!: */ +- _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); +- } +- +- /*Assign output pointers:*/ +- *pmatrix=outmatrix; +-} +-/*}}}*/ + /*FUNCTION FetchData(double** pvector,int* pM,const mxArray* dataref){{{1*/ + void FetchData(double** pvector,int* pM,const mxArray* dataref){ + +@@ -385,30 +365,6 @@ + if (pM)*pM=outvector_rows; + } + /*}}}*/ +-/*FUNCTION FetchData(Vector** pvector,const mxArray* dataref){{{1*/ +-void FetchData(Vector** pvector,const mxArray* dataref){ +- +- Vector* vector=NULL; +- int dummy; +- +- if(mxIsEmpty(dataref)){ +- /*Nothing to pick up. Just initialize matrix pointer to NULL: */ +- vector=new Vector(0); +- } +- else if (mxIsClass(dataref,"double") ){ +- +- /*Convert matlab vector to petsc vector: */ +- vector=MatlabVectorToVector(dataref); +- } +- else{ +- /*This is an error: we don't have the correct input!: */ +- _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); +- } +- +- /*Assign output pointers:*/ +- *pvector=vector; +-} +-/*}}}*/ + /*FUNCTION FetchData(char** pstring,const mxArray* dataref){{{1*/ + void FetchData(char** pstring,const mxArray* dataref){ + +@@ -525,3 +481,133 @@ + *pboolean=*mxbool_ptr; + } + /*}}}*/ ++ ++/*ISSM objects*/ ++/*FUNCTION FetchData(Matrix** pmatrix,const mxArray* dataref){{{1*/ ++void FetchData(Matrix** pmatrix,const mxArray* dataref){ ++ ++ Matrix* outmatrix=NULL; ++ int dummy=0; ++ ++ if (mxIsClass(dataref,"double") ){ ++ ++ /*Convert matlab matrix to matrix: */ ++ outmatrix=MatlabMatrixToMatrix(dataref); ++ ++ } ++ else{ ++ /*This is an error: we don't have the correct input!: */ ++ _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); ++ } ++ ++ /*Assign output pointers:*/ ++ *pmatrix=outmatrix; ++} ++/*}}}*/ ++/*FUNCTION FetchData(Vector** pvector,const mxArray* dataref){{{1*/ ++void FetchData(Vector** pvector,const mxArray* dataref){ ++ ++ Vector* vector=NULL; ++ int dummy; ++ ++ if(mxIsEmpty(dataref)){ ++ /*Nothing to pick up. Just initialize matrix pointer to NULL: */ ++ vector=new Vector(0); ++ } ++ else if (mxIsClass(dataref,"double") ){ ++ ++ /*Convert matlab vector to petsc vector: */ ++ vector=MatlabVectorToVector(dataref); ++ } ++ else{ ++ /*This is an error: we don't have the correct input!: */ ++ _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); ++ } ++ ++ /*Assign output pointers:*/ ++ *pvector=vector; ++} ++/*}}}*/ ++/*FUNCTION FetchData(BamgGeom** pbamggeom,const mxArray* dataref){{{1*/ ++void FetchData(BamgGeom** pbamggeom,const mxArray* dataref){ ++ ++ /*Initialize output*/ ++ BamgGeom* bamggeom=new BamgGeom(); ++ ++ /*Fetch all fields*/ ++ FetchData(&bamggeom->Vertices,&bamggeom->VerticesSize[0],&bamggeom->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices")); ++ FetchData(&bamggeom->Edges, &bamggeom->EdgesSize[0], &bamggeom->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges")); ++ FetchData(&bamggeom->Corners, &bamggeom->CornersSize[0], &bamggeom->CornersSize[1], mxGetAssignedField(dataref,0,"Corners")); ++ FetchData(&bamggeom->RequiredVertices,&bamggeom->RequiredVerticesSize[0],&bamggeom->RequiredVerticesSize[1],mxGetAssignedField(dataref,0,"RequiredVertices")); ++ FetchData(&bamggeom->RequiredEdges, &bamggeom->RequiredEdgesSize[0], &bamggeom->RequiredEdgesSize[1], mxGetAssignedField(dataref,0,"RequiredEdges")); ++ FetchData(&bamggeom->CrackedEdges,&bamggeom->CrackedEdgesSize[0],&bamggeom->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges")); ++ FetchData(&bamggeom->SubDomains,&bamggeom->SubDomainsSize[0],&bamggeom->SubDomainsSize[1],mxGetAssignedField(dataref,0,"SubDomains")); ++ ++ /*Assign output pointers:*/ ++ *pbamggeom=bamggeom; ++} ++/*}}}*/ ++/*FUNCTION FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){{{1*/ ++void FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){ ++ ++ /*Initialize output*/ ++ BamgMesh* bamgmesh=new BamgMesh(); ++ ++ /*Fetch all fields*/ ++ FetchData(&bamgmesh->Vertices,&bamgmesh->VerticesSize[0],&bamgmesh->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices")); ++ FetchData(&bamgmesh->Edges, &bamgmesh->EdgesSize[0], &bamgmesh->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges")); ++ FetchData(&bamgmesh->Triangles, &bamgmesh->TrianglesSize[0], &bamgmesh->TrianglesSize[1], mxGetAssignedField(dataref,0,"Triangles")); ++ FetchData(&bamgmesh->CrackedEdges,&bamgmesh->CrackedEdgesSize[0],&bamgmesh->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges")); ++ FetchData(&bamgmesh->VerticesOnGeomEdge,&bamgmesh->VerticesOnGeomEdgeSize[0],&bamgmesh->VerticesOnGeomEdgeSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomEdge")); ++ FetchData(&bamgmesh->VerticesOnGeomVertex,&bamgmesh->VerticesOnGeomVertexSize[0],&bamgmesh->VerticesOnGeomVertexSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomVertex")); ++ FetchData(&bamgmesh->EdgesOnGeomEdge, &bamgmesh->EdgesOnGeomEdgeSize[0], &bamgmesh->EdgesOnGeomEdgeSize[1], mxGetAssignedField(dataref,0,"EdgesOnGeomEdge")); ++ FetchData(&bamgmesh->IssmSegments,&bamgmesh->IssmSegmentsSize[0],&bamgmesh->IssmSegmentsSize[1],mxGetAssignedField(dataref,0,"IssmSegments")); ++ ++ /*Assign output pointers:*/ ++ *pbamgmesh=bamgmesh; ++} ++/*}}}*/ ++/*FUNCTION FetchData(BamgOpts** pbamgopts,const mxArray* dataref){{{1*/ ++void FetchData(BamgOpts** pbamgopts,const mxArray* dataref){ ++ ++ /*Initialize output*/ ++ BamgOpts* bamgopts=new BamgOpts(); ++ ++ /*Fetch all fields*/ ++ FetchData(&bamgopts->anisomax,mxGetField(dataref,0,"anisomax")); ++ FetchData(&bamgopts->cutoff,mxGetField(dataref,0,"cutoff")); ++ FetchData(&bamgopts->coeff,mxGetField(dataref,0,"coeff")); ++ FetchData(&bamgopts->errg,mxGetField(dataref,0,"errg")); ++ FetchData(&bamgopts->gradation,mxGetField(dataref,0,"gradation")); ++ FetchData(&bamgopts->Hessiantype,mxGetField(dataref,0,"Hessiantype")); ++ FetchData(&bamgopts->MaxCornerAngle,mxGetField(dataref,0,"MaxCornerAngle")); ++ FetchData(&bamgopts->maxnbv,mxGetField(dataref,0,"maxnbv")); ++ FetchData(&bamgopts->maxsubdiv,mxGetField(dataref,0,"maxsubdiv")); ++ FetchData(&bamgopts->Metrictype,mxGetField(dataref,0,"Metrictype")); ++ FetchData(&bamgopts->nbjacobi,mxGetField(dataref,0,"nbjacobi")); ++ FetchData(&bamgopts->nbsmooth,mxGetField(dataref,0,"nbsmooth")); ++ FetchData(&bamgopts->omega,mxGetField(dataref,0,"omega")); ++ FetchData(&bamgopts->power,mxGetField(dataref,0,"power")); ++ FetchData(&bamgopts->verbose,mxGetField(dataref,0,"verbose")); ++ ++ FetchData(&bamgopts->Crack,mxGetField(dataref,0,"Crack")); ++ FetchData(&bamgopts->geometricalmetric,mxGetField(dataref,0,"geometricalmetric")); ++ FetchData(&bamgopts->KeepVertices,mxGetField(dataref,0,"KeepVertices")); ++ FetchData(&bamgopts->splitcorners,mxGetField(dataref,0,"splitcorners")); ++ ++ FetchData(&bamgopts->hmin,mxGetField(dataref,0,"hmin")); ++ FetchData(&bamgopts->hmax,mxGetField(dataref,0,"hmax")); ++ FetchData(&bamgopts->hminVertices,&bamgopts->hminVerticesSize[0],&bamgopts->hminVerticesSize[1],mxGetField(dataref,0,"hminVertices")); ++ FetchData(&bamgopts->hmaxVertices,&bamgopts->hmaxVerticesSize[0],&bamgopts->hmaxVerticesSize[1],mxGetField(dataref,0,"hmaxVertices")); ++ FetchData(&bamgopts->hVertices,&bamgopts->hVerticesSize[0],&bamgopts->hVerticesSize[1],mxGetField(dataref,0,"hVertices")); ++ FetchData(&bamgopts->metric,&bamgopts->metricSize[0],&bamgopts->metricSize[1],mxGetField(dataref,0,"metric")); ++ FetchData(&bamgopts->field,&bamgopts->fieldSize[0],&bamgopts->fieldSize[1],mxGetField(dataref,0,"field")); ++ FetchData(&bamgopts->err,&bamgopts->errSize[0],&bamgopts->errSize[1],mxGetField(dataref,0,"err")); ++ ++ /*Additional checks*/ ++ bamgopts->Check(); ++ ++ /*Assign output pointers:*/ ++ *pbamgopts=bamgopts; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 12042) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 12043) +@@ -14,84 +14,8 @@ + + #include + +-/*FUNCTION WriteData(mxArray** pdataref,Matrix* matrix){{{1*/ +-void WriteData(mxArray** pdataref,Matrix* matrix){ +- +- int i,j; +- mxArray* dataref=NULL; +- double* matrix_ptr=NULL; +- int rows,cols; +- double* tmatrix_ptr=NULL; +- +- if(matrix){ +- +- #ifdef _HAVE_PETSC_ +- PetscMatrixToDoubleMatrix(&matrix_ptr,&rows,&cols,matrix->matrix); +- #else +- matrix_ptr=matrix->matrix->ToSerial(); +- matrix->matrix->GetSize(&rows,cols); +- #endif + +- /*Now transpose the matrix and allocate with Matlab's memory manager: */ +- tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double)); +- for(i=0;ivector); +- #else +- vector_ptr=vector->vector->ToMPISerial(); +- vector->vector->GetSize(&rows); +- #endif +- +- /*now create the matlab vector with Matlab's memory manager */ +- vector_matlab=(double*)mxMalloc(rows*sizeof(double)); +- for(int i=0;iVerticesSize[0], bamggeom->VerticesSize[1], bamggeom->Vertices); ++ i++; SetStructureField(dataref,"Edges", bamggeom->EdgesSize[0], bamggeom->EdgesSize[1], bamggeom->Edges); ++ i++; SetStructureField(dataref,"TangentAtEdges", bamggeom->TangentAtEdgesSize[0], bamggeom->TangentAtEdgesSize[1], bamggeom->TangentAtEdges); ++ i++; SetStructureField(dataref,"RequiredVertices",bamggeom->RequiredVerticesSize[0],bamggeom->RequiredVerticesSize[1],bamggeom->RequiredVertices); ++ i++; SetStructureField(dataref,"RequiredEdges", bamggeom->RequiredEdgesSize[0], bamggeom->RequiredEdgesSize[1], bamggeom->RequiredEdges); ++ i++; SetStructureField(dataref,"CrackedEdges", bamggeom->CrackedEdgesSize[0], bamggeom->CrackedEdgesSize[1], bamggeom->CrackedEdges); ++ i++; SetStructureField(dataref,"SubDomains", bamggeom->SubDomainsSize[0], bamggeom->SubDomainsSize[1], bamggeom->SubDomains); ++ _assert_(i==numfields); ++ ++ /*Assign output*/ ++ *pdataref=dataref; ++} ++/*}}}*/ ++/*FUNCTION WriteData(mxArray** pdataref,BamgMesh* bamgmesh){{{1*/ ++void WriteData(mxArray** pdataref,BamgMesh* bamgmesh){ ++ ++ /*Intermediary*/ ++ int i; ++ mxArray *dataref = NULL; ++ const int numfields = 16; ++ const char *fnames[numfields]; ++ mwSize ndim = 2; ++ mwSize dimensions[2] = {1,1}; ++ ++ /*Initialize field names*/ ++ i=0; ++ fnames[i++] = "Triangles"; ++ fnames[i++] = "Vertices"; ++ fnames[i++] = "Edges"; ++ fnames[i++] = "IssmSegments"; ++ fnames[i++] = "IssmEdges"; ++ fnames[i++] = "Quadrilaterals"; ++ fnames[i++] = "VerticesOnGeomVertex"; ++ fnames[i++] = "VerticesOnGeomEdge"; ++ fnames[i++] = "EdgesOnGeomEdge"; ++ fnames[i++] = "SubDomains"; ++ fnames[i++] = "SubDomainsFromGeom"; ++ fnames[i++] = "ElementConnectivity"; ++ fnames[i++] = "NodalConnectivity"; ++ fnames[i++] = "NodalElementConnectivity"; ++ fnames[i++] = "CrackedVertices"; ++ fnames[i++] = "CrackedEdges"; ++ _assert_(i==numfields); ++ ++ /*Initialize Matlab structure*/ ++ dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames); ++ ++ /*set each matlab each field*/ ++ i=0; ++ i++; SetStructureField(dataref,"Triangles", bamgmesh->TrianglesSize[0],bamgmesh->TrianglesSize[1], bamgmesh->Triangles); ++ i++; SetStructureField(dataref,"Vertices",bamgmesh->VerticesSize[0], bamgmesh->VerticesSize[1],bamgmesh->Vertices); ++ i++; SetStructureField(dataref,"Edges", bamgmesh->EdgesSize[0],bamgmesh->EdgesSize[1], bamgmesh->Edges); ++ i++; SetStructureField(dataref,"IssmSegments",bamgmesh->IssmSegmentsSize[0], bamgmesh->IssmSegmentsSize[1],bamgmesh->IssmSegments); ++ i++; SetStructureField(dataref,"IssmEdges", bamgmesh->IssmEdgesSize[0],bamgmesh->IssmEdgesSize[1], bamgmesh->IssmEdges); ++ i++; SetStructureField(dataref,"Quadrilaterals",bamgmesh->QuadrilateralsSize[0], bamgmesh->QuadrilateralsSize[1],bamgmesh->Quadrilaterals); ++ i++; SetStructureField(dataref,"VerticesOnGeomVertex",bamgmesh->VerticesOnGeomVertexSize[0],bamgmesh->VerticesOnGeomVertexSize[1], bamgmesh->VerticesOnGeomVertex); ++ i++; SetStructureField(dataref,"VerticesOnGeomEdge",bamgmesh->VerticesOnGeomEdgeSize[0],bamgmesh->VerticesOnGeomEdgeSize[1], bamgmesh->VerticesOnGeomEdge); ++ i++; SetStructureField(dataref,"EdgesOnGeomEdge", bamgmesh->EdgesOnGeomEdgeSize[0], bamgmesh->EdgesOnGeomEdgeSize[1],bamgmesh->EdgesOnGeomEdge); ++ i++; SetStructureField(dataref,"SubDomains",bamgmesh->SubDomainsSize[0], bamgmesh->SubDomainsSize[1],bamgmesh->SubDomains); ++ i++; SetStructureField(dataref,"SubDomainsFromGeom", bamgmesh->SubDomainsFromGeomSize[0], bamgmesh->SubDomainsFromGeomSize[1],bamgmesh->SubDomainsFromGeom); ++ i++; SetStructureField(dataref,"ElementConnectivity",bamgmesh->ElementConnectivitySize[0],bamgmesh->ElementConnectivitySize[1], bamgmesh->ElementConnectivity); ++ i++; SetStructureField(dataref,"NodalConnectivity",bamgmesh->NodalConnectivitySize[0],bamgmesh->NodalConnectivitySize[1], bamgmesh->NodalConnectivity); ++ i++; SetStructureField(dataref,"NodalElementConnectivity", bamgmesh->NodalElementConnectivitySize[0], bamgmesh->NodalElementConnectivitySize[1],bamgmesh->NodalElementConnectivity); ++ i++; SetStructureField(dataref,"CrackedVertices", bamgmesh->CrackedVerticesSize[0],bamgmesh->CrackedVerticesSize[1], bamgmesh->CrackedVertices); ++ i++; SetStructureField(dataref,"CrackedEdges",bamgmesh->CrackedEdgesSize[0], bamgmesh->CrackedEdgesSize[1],bamgmesh->CrackedEdges); ++ _assert_(i==numfields); ++ ++ /*Assign output*/ ++ *pdataref=dataref; ++} ++/*}}}*/ ++/*FUNCTION WriteData(mxArray** pdataref,Matrix* matrix){{{1*/ ++void WriteData(mxArray** pdataref,Matrix* matrix){ ++ ++ int i,j; ++ int rows,cols; ++ mxArray *dataref = NULL; ++ double *matrix_ptr = NULL; ++ double *tmatrix_ptr = NULL; ++ ++ if(matrix){ ++ ++ #ifdef _HAVE_PETSC_ ++ PetscMatrixToDoubleMatrix(&matrix_ptr,&rows,&cols,matrix->matrix); ++ #else ++ matrix_ptr=matrix->matrix->ToSerial(); ++ matrix->matrix->GetSize(&rows,cols); ++ #endif ++ ++ /*Now transpose the matrix and allocate with Matlab's memory manager: */ ++ tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double)); ++ for(i=0;ivector); ++ #else ++ vector_ptr=vector->vector->ToMPISerial(); ++ vector->vector->GetSize(&rows); ++ #endif ++ ++ /*now create the matlab vector with Matlab's memory manager */ ++ vector_matlab=(double*)mxMalloc(rows*sizeof(double)); ++ for(int i=0;iCrackedVerticesSize[0]=0, this->CrackedVerticesSize[1]=0; this->CrackedVertices=NULL; + this->CrackedEdgesSize[0]=0, this->CrackedEdgesSize[1]=0; this->CrackedEdges=NULL; + +- this->VerticesOnGeomVertexSize[0]=0, this->VerticesOnGeomVertexSize[1]=0;this->VerticesOnGeomVertex=NULL; +- this->VerticesOnGeomEdgeSize[0]=0, this->VerticesOnGeomEdgeSize[1]=0; this->VerticesOnGeomEdge=NULL; +- this->EdgesOnGeomEdgeSize[0]=0, this->EdgesOnGeomEdgeSize[1]=0; this->EdgesOnGeomEdge=NULL; ++ this->VerticesOnGeomVertexSize[0]=0, this->VerticesOnGeomVertexSize[1]=0; this->VerticesOnGeomVertex=NULL; ++ this->VerticesOnGeomEdgeSize[0]=0, this->VerticesOnGeomEdgeSize[1]=0; this->VerticesOnGeomEdge=NULL; ++ this->EdgesOnGeomEdgeSize[0]=0, this->EdgesOnGeomEdgeSize[1]=0; this->EdgesOnGeomEdge=NULL; + + this->IssmEdgesSize[0]=0, this->IssmEdgesSize[1]=0; this->IssmEdges=NULL; + this->IssmSegmentsSize[0]=0, this->IssmSegmentsSize[1]=0; this->IssmSegments=NULL; +@@ -27,8 +27,6 @@ + this->ElementConnectivitySize[0]=0, this->ElementConnectivitySize[1]=0; this->ElementConnectivity=NULL; + this->NodalConnectivitySize[0]=0, this->NodalConnectivitySize[1]=0; this->NodalConnectivity=NULL; + this->NodalElementConnectivitySize[0]=0, this->NodalElementConnectivitySize[1]=0; this->NodalElementConnectivity=NULL; +- +- + } + /*}}}*/ + /*FUNCTION BamgMesh::~BamgMesh(){{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgOpts.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgOpts.h (revision 12042) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgOpts.h (revision 12043) +@@ -49,7 +49,6 @@ + double* err; + + BamgOpts(); +- BamgOpts(void* module_struct); + ~BamgOpts(); + + void Check(void); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.h (revision 12042) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgGeom.h (revision 12043) +@@ -25,11 +25,7 @@ + double* SubDomains; + + BamgGeom(); +- BamgGeom(void* module_struct); + ~BamgGeom(); +- +- void SetStructureFields(void* matlab_struct); +- void SetStructureField(void* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); + }; + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgMesh.h (revision 12042) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgMesh.h (revision 12043) +@@ -46,12 +46,7 @@ + double* NodalElementConnectivity; + + BamgMesh(); +- BamgMesh(void* module_struct); + ~BamgMesh(); +- +- void SetStructureFields(void* module_struct); +- void SetStructureField(void* module_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); +- + }; + + #endif Index: /issm/oecreview/Archive/12041-12060/ISSM-12043-12044.diff =================================================================== --- /issm/oecreview/Archive/12041-12060/ISSM-12043-12044.diff (revision 12325) +++ /issm/oecreview/Archive/12041-12060/ISSM-12043-12044.diff (revision 12325) @@ -0,0 +1,48 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.cpp (revision 12043) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgConvertMesh/BamgConvertMesh.cpp (revision 12044) +@@ -63,8 +63,8 @@ + BamgConvertMeshx(bamgmesh,bamggeom,index,x,y,nods,nels); + + /*Generate output Matlab Structures*/ +- bamggeom->SetStructureFields((void*)BAMGGEOMOUT); +- bamgmesh->SetStructureFields((void*)BAMGMESHOUT); ++ WriteData(BAMGGEOMOUT,bamggeom); ++ WriteData(BAMGMESHOUT,bamgmesh); + + /*Clean up*/ + delete bamggeom; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp (revision 12043) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp (revision 12044) +@@ -22,21 +22,21 @@ + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&BamgMesherUsage); + +- /*Initialize variables*/ +- bamgopts = new BamgOpts(BAMGOPTIONS); +- bamggeom_in= new BamgGeom(BAMGGEOMIN); +- bamgmesh_in= new BamgMesh(BAMGMESHIN); +- + /*Initialize outputs*/ + bamggeom_out=new BamgGeom(); + bamgmesh_out=new BamgMesh(); + ++ /*Fetch inputs: */ ++ FetchData(&bamgopts,BAMGOPTIONS); ++ FetchData(&bamggeom_in,BAMGMESHIN); ++ FetchData(&bamgmesh_in,BAMGGEOMIN); ++ + /*!Generate internal degree of freedom numbers: */ + Bamgx(bamgmesh_out,bamggeom_out,bamgmesh_in,bamggeom_in,bamgopts); + + /*Generate output Matlab Structures*/ +- bamggeom_out->SetStructureFields((void*)BAMGGEOMOUT); +- bamgmesh_out->SetStructureFields((void*)BAMGMESHOUT); ++ WriteData(BAMGGEOMOUT,bamggeom); ++ WriteData(BAMGMESHOUT,bamgmesh); + + /*Free ressources: */ + delete bamgopts; Index: /issm/oecreview/Archive/12041-12060/ISSM-12044-12045.diff =================================================================== --- /issm/oecreview/Archive/12041-12060/ISSM-12044-12045.diff (revision 12325) +++ /issm/oecreview/Archive/12041-12060/ISSM-12044-12045.diff (revision 12325) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp (revision 12044) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp (revision 12045) +@@ -35,8 +35,8 @@ + Bamgx(bamgmesh_out,bamggeom_out,bamgmesh_in,bamggeom_in,bamgopts); + + /*Generate output Matlab Structures*/ +- WriteData(BAMGGEOMOUT,bamggeom); +- WriteData(BAMGMESHOUT,bamgmesh); ++ WriteData(BAMGGEOMOUT,bamggeom_out); ++ WriteData(BAMGMESHOUT,bamgmesh_out); + + /*Free ressources: */ + delete bamgopts; Index: /issm/oecreview/Archive/12041-12060/ISSM-12045-12046.diff =================================================================== --- /issm/oecreview/Archive/12041-12060/ISSM-12045-12046.diff (revision 12325) +++ /issm/oecreview/Archive/12041-12060/ISSM-12045-12046.diff (revision 12325) @@ -0,0 +1,83 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 12045) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 12046) +@@ -27,7 +27,7 @@ + tmatrix=(double*)mxMalloc(M*N*sizeof(double)); + for(int i=0;i NLHS) { +- KMLOverlayUsage(); +- _error_("KMLOverlay usage error"); ++ if(nlhs>NLHS){ ++ KMLOverlayUsage(); _error_("KMLOverlay usage error"); + } +- if (nrhs < NRHS) { +- KMLOverlayUsage(); +- _error_("KMLOverlay usage error"); ++ if(nrhsSize()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); + options->Get(&lataxis ,&nlat ,"lataxis" ); + if (verbose && lataxis) for (i=0; iGet(&longaxis,&nlong,"longaxis"); + if (verbose && longaxis) for (i=0; iGetOption("images"))->DeepEcho(); + options->Get(&pimages,&nimages,"images"); + if (verbose && pimages) for (i=0; iGet(&dzip,"zip",0.); + if (verbose) printf(" dzip=%g\n",dzip); + + /*some checks*/ +- if (verbose) printf("Checking inputs:\n"); +- +- if (nlat != 2) _error_("Latitudinal axes \"lataxis\" require two double values, not %d.",nlat); +- if (nlong != 2) _error_("Longitudinal axes \"longaxis\" require two double values, not %d.",nlong); ++ if (nlat !=2) _error_("Latitudinal axes \"lataxis\" require two double values, not %d.",nlat); ++ if (nlong!=2) _error_("Longitudinal axes \"longaxis\" require two double values, not %d.",nlong); + if (!nimages) _error_("No image files provided."); + +- if ((int)dzip) { ++ if ((int)dzip){ + filkmz=filkml; +- filkml=(char *) xmalloc(8*sizeof(char)); ++ filkml=(char*)mxMalloc(8*sizeof(char)); + strcpy(filkml,"doc.kml"); + } + +- if (!strlen(filkml)) +- strcpy(filkml,"stdout"); ++ if(!strlen(filkml)) strcpy(filkml,"stdout"); + +- if (verbose) printf("Opening kml overlay file \"%s\".\n",filkml); ++ if(verbose) printf("Opening kml overlay file \"%s\".\n",filkml); + fid=fopen(filkml,"w"); + + /* Run core computations: */ + if (verbose) printf("Calling core:\n"); +- KMLOverlayx(&ierror, +- lataxis,longaxis, +- nimages,pimages, +- fid); ++ KMLOverlayx(&ierror,lataxis,longaxis,nimages,pimages,fid); + + if (verbose) printf("Closing file \"%s\".\n",filkml); + fclose(fid); + + /* Create kmz file, if specified: */ + if ((int)dzip) { +- czip=(char *) xmalloc((5+strlen(filkmz)+1+strlen(filkml)+1)*sizeof(char)); ++ czip=(char*)mxMalloc((5+strlen(filkmz)+1+strlen(filkml)+1)*sizeof(char)); + czip[0]='\0'; + strcat(czip,"!zip "); + strcat(czip,filkmz); +@@ -95,7 +82,7 @@ + strcat(czip,filkml); + for (i=0; i NLHS) { +- Ll2xyUsage(); +- _error_("Ll2xy usage error"); ++ Ll2xyUsage(); _error_("Ll2xy usage error"); + } + if (nrhs < NRHS) { +- Ll2xyUsage(); +- _error_("Ll2xy usage error"); ++ Ll2xyUsage(); _error_("Ll2xy usage error"); + } + + /*Input datasets: */ +- if (verbose) printf("Fetching inputs:\n"); + FetchData(&lat,&nlat,LAT_IN); +- if (verbose) +- if (nlat == 1) printf(" lat=%g\n",lat[0]); +- else printf(" lat=[%d values]\n",nlat); +-// for (i=0; iSize()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); + /* defaults are in Ll2xydef, so don't duplicate them here, and only use user values if both have been specified */ +- if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { ++ if(options->GetOption("central_meridian") || options->GetOption("standard_parallel")){ + options->Get(&cm,"central_meridian"); + if (verbose) printf(" cm=%g\n",cm); + options->Get(&sp,"standard_parallel"); +@@ -60,27 +46,20 @@ + + /*some checks*/ + if (verbose) printf("Checking inputs:\n"); +- +- if (nlat != nlon) _error_("Must have same number of lat[%d] and lon[%d] coordinates.",nlat,nlon); ++ if (nlat != nlon) _error_("Must have same number of lat[%d] and lon[%d] coordinates.",nlat,nlon); + else ncoord=nlat; + if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + +- x=(double *)xmalloc(ncoord*sizeof(double)); +- y=(double *)xmalloc(ncoord*sizeof(double)); ++ x=(double*)mxMalloc(ncoord*sizeof(double)); ++ y=(double*)mxMalloc(ncoord*sizeof(double)); + + /* Run core computations: */ +- if (verbose) printf("Calling core:\n"); + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) +- iret=Ll2xyx(x,y, +- lat,lon,ncoord, +- sgn,cm,sp); ++ iret=Ll2xyx(x,y,lat,lon,ncoord,sgn,cm,sp); + else +- iret=Ll2xyx(x,y, +- lat,lon,ncoord, +- sgn); +- if (verbose) printf(" iret=%d\n",iret); ++ iret=Ll2xyx(x,y,lat,lon,ncoord,sgn); + + /*Write data: */ + WriteData(X_OUT,x,ncoord); +@@ -93,8 +72,7 @@ + MODULEEND(); + } + +-void Ll2xyUsage(void) +-{ ++void Ll2xyUsage(void){ + _printf_(true,"Ll2xy - lat/long to x/y coordinate transformation module:\n"); + _printf_(true,"\n"); + _printf_(true," This module transforms lat/long to x/y coordinates.\n"); +@@ -118,4 +96,3 @@ + _printf_(true," [x,y]=Ll2xy(lat,lon,-1,'central_meridian', 0,'standard_parallel',71);\n"); + _printf_(true,"\n"); + } +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp (revision 12048) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/BamgMesher/BamgMesher.cpp (revision 12049) +@@ -31,7 +31,7 @@ + FetchData(&bamggeom_in,BAMGMESHIN); + FetchData(&bamgmesh_in,BAMGGEOMIN); + +- /*!Generate internal degree of freedom numbers: */ ++ /*Call x layer*/ + Bamgx(bamgmesh_out,bamggeom_out,bamgmesh_in,bamggeom_in,bamgopts); + + /*Generate output Matlab Structures*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.cpp (revision 12048) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLFileRead/KMLFileRead.cpp (revision 12049) +@@ -10,39 +10,27 @@ + + /*input: */ + char* name=NULL; +- + char* notes=NULL; + const mxArray* notesi; + mwIndex nindex; +- + int* elem=NULL; + int melem=0,nelem=0; +- + int* nodecon=NULL; + int mncon=0,nncon=0; +- + double* lat=NULL; + int mlat=0,nlat=0,llat=0; +- + double* lng=NULL; + int mlng=0,nlng=0,llng=0; +- + int nparts=0; +- + int* part=NULL; + int mprt=0,nprt=0,lprt=0; +- + double* data=NULL; + int mdata=0,ndata=0; +- + double* cmap=NULL; + int mcmap=0,ncmap=0; +- + char* filnam=NULL; +- + FILE* fidi=NULL; + FILE* fido=NULL; +- + Options* options=NULL; + char* echo =NULL; + char* deepecho=NULL; +@@ -56,32 +44,24 @@ + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { +- KMLFileReadUsage(); +- _error_("KMLFileRead usage error"); ++ KMLFileReadUsage(); _error_("KMLFileRead usage error"); + } + if (nrhs < NRHS) { +- KMLFileReadUsage(); +- _error_("KMLFileRead usage error"); ++ KMLFileReadUsage(); _error_("KMLFileRead usage error"); + } + + /*Input datasets: */ +- if (verbose) printf("Fetching inputs:\n"); + FetchData(&filnam,FILENAME); +- if (verbose) printf(" filnam =\"%s\"\n",filnam); ++ FetchData(&options,NRHS,nrhs,prhs); ++ FetchData(&options,NRHS,nrhs,prhs); + +- if (verbose) printf("Parsing options:\n"); +- options=new Options(NRHS,nrhs,prhs); +- if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); + options->Get(&echo ,"echo" ,"off"); + options->Get(&deepecho,"deepecho","off"); + options->Get(&write ,"write" ,"off"); + + /*some checks*/ +- if (verbose) printf("Checking inputs:\n"); ++ if (!strlen(filnam)) strcpy(filnam,"stdout"); + +- if (!strlen(filnam)) +- strcpy(filnam,"stdout"); +- + if (verbose) printf("Opening file \"%s\".\n",filnam); + fidi=fopen(filnam,"r"); + +@@ -92,7 +72,7 @@ + if (verbose) printf("Closing file \"%s\".\n",filnam); + fclose(fidi); + +- if (kobj) { ++ if (kobj){ + if (!strncmp(echo ,"on",2) || !strncmp(echo ,"y",1)) + kobj->Echo(); + if (!strncmp(deepecho,"on",2) || !strncmp(deepecho,"y",1)) +@@ -109,7 +89,6 @@ + ierror=fclose(fido); + } + } +- + delete kobj; + } + +@@ -126,8 +105,7 @@ + MODULEEND(); + } + +-void KMLFileReadUsage(void) +-{ ++void KMLFileReadUsage(void){ + _printf_(true,"KMLFileRead - KML file reader module:\n"); + _printf_(true,"\n"); + _printf_(true," This module reads a KML file.\n"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.cpp (revision 12048) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Shp2Kml/Shp2Kml.cpp (revision 12049) +@@ -17,7 +17,6 @@ + /*input: */ + char *filshp=NULL,*filkml=NULL; + int sgn; +- + Options* options=NULL; + double cm=0.,sp=0.; + +@@ -33,26 +32,18 @@ + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { +- Shp2KmlUsage(); +- _error_("Shp2Kml usage error"); ++ Shp2KmlUsage(); _error_("Shp2Kml usage error"); + } + if (nrhs < NRHS) { +- Shp2KmlUsage(); +- _error_("Shp2Kml usage error"); ++ Shp2KmlUsage(); _error_("Shp2Kml usage error"); + } + + /*Input datasets: */ +- if (verbose) printf("Fetching inputs:\n"); + FetchData(&filshp,SHP_IN); +- if (verbose) printf(" filshp=\"%s\"\n",filshp); + FetchData(&filkml,KML_IN); +- if (verbose) printf(" filkml=\"%s\"\n",filkml); + FetchData(&sgn,SGN_IN); +- if (verbose) printf(" sgn=%d\n",sgn); ++ FetchData(&options,NRHS,nrhs,prhs); + +- if (verbose) printf("Parsing options:\n"); +- options=new Options(NRHS,nrhs,prhs); +- if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); + /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ + if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { + options->Get(&cm,"central_meridian"); +@@ -62,21 +53,15 @@ + } + + /*some checks*/ +- if (verbose) printf("Checking inputs:\n"); +- + if (sgn < -1 || sgn > +1) _error_("Hemisphere sgn=%d must be +1 (north), -1 (south), or 0 (no translation).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + + /* Run core computations: */ +- if (verbose) printf("Calling core:\n"); + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) +- iret=Shp2Kmlx(filshp,filkml, +- sgn,cm,sp); ++ iret=Shp2Kmlx(filshp,filkml,sgn,cm,sp); + else +- iret=Shp2Kmlx(filshp,filkml, +- sgn); +- if (verbose) printf(" iret=%d\n",iret); ++ iret=Shp2Kmlx(filshp,filkml,sgn); + + /*Write data: */ + WriteData(RET_OUT,iret); +@@ -90,8 +75,7 @@ + MODULEEND(); + } + +-void Shp2KmlUsage(void) +-{ ++void Shp2KmlUsage(void){ + _printf_(true,"Shp2Kml - shp to kml file conversion module:\n"); + _printf_(true,"\n"); + _printf_(true," This module converts a file from shp to kml format.\n"); +@@ -114,4 +98,3 @@ + _printf_(true," [ret]=Shp2Kml('file.shp','file.kml',-1,'central_meridian', 0,'standard_parallel',71);\n"); + _printf_(true,"\n"); + } +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Exp2Kml/Exp2Kml.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Exp2Kml/Exp2Kml.cpp (revision 12048) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Exp2Kml/Exp2Kml.cpp (revision 12049) +@@ -24,29 +24,21 @@ + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { +- Exp2KmlUsage(); +- _error_("Exp2Kml usage error"); ++ Exp2KmlUsage(); _error_("Exp2Kml usage error"); + } + if (nrhs < NRHS) { +- Exp2KmlUsage(); +- _error_("Exp2Kml usage error"); ++ Exp2KmlUsage(); _error_("Exp2Kml usage error"); + } + + /*Input datasets: */ +- if (verbose) printf("Fetching inputs:\n"); + FetchData(&filexp,EXP_IN); +- if (verbose) printf(" filexp=\"%s\"\n",filexp); + FetchData(&filkml,KML_IN); +- if (verbose) printf(" filkml=\"%s\"\n",filkml); + FetchData(&sgn,SGN_IN); +- if (verbose) printf(" sgn=%d\n",sgn); ++ FetchData(&options,NRHS,nrhs,prhs); + +- if (verbose) printf("Parsing options:\n"); +- options=new Options(NRHS,nrhs,prhs); +- if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); + options->Get(&choles,"holes","no"); +- if (!strncmp(choles,"y",1) || !strncmp(choles,"on",2)) +- holes=true; ++ if (!strncmp(choles,"y",1) || !strncmp(choles,"on",2)) holes=true; ++ + /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ + if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { + options->Get(&cm,"central_meridian"); +@@ -56,23 +48,15 @@ + } + + /*some checks*/ +- if (verbose) printf("Checking inputs:\n"); +- +- if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); ++ if (sgn !=+1 && sgn !=-1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + + /* Run core computations: */ +- if (verbose) printf("Calling core:\n"); + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) +- iret=Exp2Kmlx(filexp,filkml, +- sgn,cm,sp, +- holes); ++ iret=Exp2Kmlx(filexp,filkml,sgn,cm,sp,holes); + else +- iret=Exp2Kmlx(filexp,filkml, +- sgn, +- holes); +- if (verbose) printf(" iret=%d\n",iret); ++ iret=Exp2Kmlx(filexp,filkml,sgn,holes); + + /*Write data: */ + WriteData(RET_OUT,iret); +@@ -87,8 +71,7 @@ + MODULEEND(); + } + +-void Exp2KmlUsage(void) +-{ ++void Exp2KmlUsage(void){ + _printf_(true,"Exp2Kml - exp to kml file conversion module:\n"); + _printf_(true,"\n"); + _printf_(true," This module converts a file from exp to kml format.\n"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.cpp (revision 12048) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kml2Exp/Kml2Exp.cpp (revision 12049) +@@ -10,7 +10,6 @@ + /*input: */ + char *filkml=NULL,*filexp=NULL; + int sgn; +- + Options* options=NULL; + double cm=0.,sp=0.; + +@@ -22,26 +21,18 @@ + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { +- Kml2ExpUsage(); +- _error_("Kml2Exp usage error"); ++ Kml2ExpUsage(); _error_("Kml2Exp usage error"); + } + if (nrhs < NRHS) { +- Kml2ExpUsage(); +- _error_("Kml2Exp usage error"); ++ Kml2ExpUsage(); _error_("Kml2Exp usage error"); + } + + /*Input datasets: */ +- if (verbose) printf("Fetching inputs:\n"); + FetchData(&filkml,KML_IN); +- if (verbose) printf(" filkml=\"%s\"\n",filkml); + FetchData(&filexp,EXP_IN); +- if (verbose) printf(" filexp=\"%s\"\n",filexp); + FetchData(&sgn,SGN_IN); +- if (verbose) printf(" sgn=%d\n",sgn); ++ FetchData(&options,NRHS,nrhs,prhs); + +- if (verbose) printf("Parsing options:\n"); +- options=new Options(NRHS,nrhs,prhs); +- if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); + /* defaults are in Ll2xydef, so don't duplicate them here, and only use user values if both have been specified */ + if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { + options->Get(&cm,"central_meridian"); +@@ -51,21 +42,15 @@ + } + + /*some checks*/ +- if (verbose) printf("Checking inputs:\n"); +- +- if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); ++ if (sgn !=+1 && sgn!= -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + + /* Run core computations: */ +- if (verbose) printf("Calling core:\n"); + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) +- iret=Kml2Expx(filkml,filexp, +- sgn,cm,sp); ++ iret=Kml2Expx(filkml,filexp,sgn,cm,sp); + else +- iret=Kml2Expx(filkml,filexp, +- sgn); +- if (verbose) printf(" iret=%d\n",iret); ++ iret=Kml2Expx(filkml,filexp,sgn); + + /*Write data: */ + WriteData(RET_OUT,iret); +@@ -79,8 +64,7 @@ + MODULEEND(); + } + +-void Kml2ExpUsage(void) +-{ ++void Kml2ExpUsage(void){ + _printf_(true,"Kml2Exp - kml to exp file conversion module:\n"); + _printf_(true,"\n"); + _printf_(true," This module converts a file from kml to exp format.\n"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.cpp (revision 12048) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Xy2ll/Xy2ll.cpp (revision 12049) +@@ -11,7 +11,6 @@ + double *x=NULL,*y=NULL; + int nx,ny,ncoord; + int sgn; +- + Options* options=NULL; + double cm=0.,sp=0.; + +@@ -24,32 +23,18 @@ + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { +- Xy2llUsage(); +- _error_("Xy2ll usage error"); ++ Xy2llUsage(); _error_("Xy2ll usage error"); + } + if (nrhs < NRHS) { +- Xy2llUsage(); +- _error_("Xy2ll usage error"); ++ Xy2llUsage(); _error_("Xy2ll usage error"); + } + + /*Input datasets: */ +- if (verbose) printf("Fetching inputs:\n"); + FetchData(&x,&nx,X_IN); +- if (verbose) +- if (nx == 1) printf(" x=%g\n",x[0]); +- else printf(" x=[%d values]\n",nx); +-// for (i=0; iSize()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); + /* defaults are in Xy2lldef, so don't duplicate them here, and only use user values if both have been specified */ + if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) { + options->Get(&cm,"central_meridian"); +@@ -59,28 +44,21 @@ + } + + /*some checks*/ +- if (verbose) printf("Checking inputs:\n"); +- + if (nx != ny) _error_("Must have same number of x[%d] and y[%d] coordinates.",nx,ny); + else ncoord=nx; + if (sgn != +1 && sgn != -1) _error_("Hemisphere sgn=%d must be +1 (north) or -1 (south).",sgn); + if (fabs(cm) > 180.) _error_("Central meridian cm=%g must be between -180 (west) and +180 (east) degrees.",cm); + if (sp < 0. || sp > 90.) _error_("Standard parallel sp=%g must be between 0 and 90 degrees (in specified hemisphere).",sp); + +- lat=(double *)xmalloc(ncoord*sizeof(double)); +- lon=(double *)xmalloc(ncoord*sizeof(double)); ++ lat=(double*)mxMalloc(ncoord*sizeof(double)); ++ lon=(double*)mxMalloc(ncoord*sizeof(double)); + + /* Run core computations: */ + if (verbose) printf("Calling core:\n"); + if (options->GetOption("central_meridian") && options->GetOption("standard_parallel")) +- iret=Xy2llx(lat,lon, +- x,y,ncoord, +- sgn,cm,sp); ++ iret=Xy2llx(lat,lon,x,y,ncoord,sgn,cm,sp); + else +- iret=Xy2llx(lat,lon, +- x,y,ncoord, +- sgn); +- if (verbose) printf(" iret=%d\n",iret); ++ iret=Xy2llx(lat,lon,x,y,ncoord,sgn); + + /*Write data: */ + WriteData(LAT_OUT,lat,ncoord); +@@ -93,8 +71,7 @@ + MODULEEND(); + } + +-void Xy2llUsage(void) +-{ ++void Xy2llUsage(void){ + _printf_(true,"Xy2ll - x/y to lat/long coordinate transformation module:\n"); + _printf_(true,"\n"); + _printf_(true," This module transforms x/y to lat/long coordinates.\n"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12048) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12049) +@@ -9,38 +9,26 @@ + + /*input: */ + char* name=NULL; +- + char* notes=NULL; + const mxArray* notesi; + mwIndex nindex; +- + int* elem=NULL; + int melem=0,nelem=0; +- + int* nodecon=NULL; + int mncon=0,nncon=0; +- + double* lat=NULL; + int mlat=0,nlat=0,llat=0; +- + double* lng=NULL; + int mlng=0,nlng=0,llng=0; +- + int nparts=0; +- + int* part=NULL; + int mprt=0,nprt=0,lprt=0; +- + double* data=NULL; + int mdata=0,ndata=0; +- + double* cmap=NULL; + int mcmap=0,ncmap=0; +- + char* filnam=NULL; +- + FILE* fid=NULL; +- + Options* options=NULL; + + /* output: */ +@@ -51,18 +39,14 @@ + + /*checks on arguments on the matlab side: */ + if (nlhs > NLHS) { +- KMLMeshWriteUsage(); +- _error_("KMLMeshWrite usage error"); ++ KMLMeshWriteUsage(); _error_("KMLMeshWrite usage error"); + } + if (nrhs < NRHS) { +- KMLMeshWriteUsage(); +- _error_("KMLMeshWrite usage error"); ++ KMLMeshWriteUsage(); _error_("KMLMeshWrite usage error"); + } + + /*Input datasets: */ +- if (verbose) printf("Fetching inputs:\n"); + FetchData(&name,NAME); +- if (verbose) printf(" name =\"%s\"\n",name); + + /* notes is typically a cell array of character strings */ + if (mxIsCell(NOTES)) { +@@ -84,46 +68,24 @@ + } + else + FetchData(¬es,NOTES); +- if (verbose) printf(" notes =\"%s\"\n",notes); +- + FetchData(&elem,&melem,&nelem,ELEMHANDLE); +- if (verbose) printf(" elem =size [%d x %d]\n",melem,nelem); + FetchData(&nodecon,&mncon,&nncon,NODECONHANDLE); +- if (verbose) printf(" nodecon=size [%d x %d]\n",mncon,nncon); + FetchData(&lat,&mlat,&nlat,LATHANDLE); + llat=mlat*nlat; +- if (verbose) printf(" lat =length [%d]\n",llat); + FetchData(&lng,&mlng,&nlng,LNGHANDLE); + llng=mlng*nlng; +- if (verbose) printf(" lng =length [%d]\n",llng); + FetchData(&part,&mprt,&nprt,PARTHANDLE); + lprt=mprt*nprt; +- if (verbose) printf(" part =length [%d]\n",lprt); + FetchData(&data,&mdata,&ndata,DATAHANDLE); +- if (verbose) printf(" data =size [%d x %d]\n",mdata,ndata); + FetchData(&cmap,&mcmap,&ncmap,CMAPHANDLE); +- if (verbose) printf(" cmap =size [%d x %d]\n",mcmap,ncmap); + FetchData(&filnam,FILENAME); +- if (verbose) printf(" filnam =\"%s\"\n",filnam); ++ FetchData(&options,NRHS,nrhs,prhs); + +- if (verbose) printf("Parsing options:\n"); +- options=new Options(NRHS,nrhs,prhs); +-// if (options->Size()) for(i=0;iSize();i++) ((Option*)options->GetObjectByOffset(i))->DeepEcho(); +- + /*some checks*/ +- if (verbose) printf("Checking inputs:\n"); ++ for (i=0; innodes) nnodes=elem[i]; ++ if(part) for (i=0; i nparts) nparts=part[i]+1; + +- for (i=0; i nnodes) +- nnodes=elem[i]; +- if (verbose) printf(" nnodes =%d\n",nnodes); +- if (part) +- for (i=0; i nparts) +- nparts=part[i]+1; +- if (verbose) printf(" nparts =%d\n",nparts); +- +- if (nodecon && (mncon != nnodes)) ++ if (nodecon && (mncon != nnodes)) + _error_("Nodal connectivity table, if supplied, must be supplied for all nodes."); + else if (!nodecon) + mncon=nnodes; +@@ -135,27 +97,12 @@ + _error_("Data matrix, if supplied, must be supplied for all nodes or all elements."); + if (cmap && (ncmap != 3)) + _error_("Colormap matrix, if supplied, must have three columns for rgb."); +- + if (!strlen(filnam)) + strcpy(filnam,"stdout"); + +- if (verbose) printf("Opening file \"%s\".\n",filnam); +- fid=fopen(filnam,"w"); +- + /* Run core computations: */ +- if (verbose) printf("Calling core:\n"); +- KMLMeshWritex(&ierror, +- name, +- notes, +- elem,melem,nelem, +- nodecon,mncon,nncon, +- lat,lng, +- part, +- data,mdata,ndata, +- cmap,mcmap,ncmap, +- fid); +- +- if (verbose) printf("Closing file \"%s\".\n",filnam); ++ fid=fopen(filnam,"w"); ++ KMLMeshWritex(&ierror,name,notes,elem,melem,nelem,nodecon,mncon,nncon,lat,lng,part,data,mdata,ndata,cmap,mcmap,ncmap,fid); + fclose(fid); + + /*Write data: */ +@@ -169,8 +116,7 @@ + MODULEEND(); + } + +-void KMLMeshWriteUsage(void) +-{ ++void KMLMeshWriteUsage(void){ + _printf_(true,"KMLMeshWrite - KML mesh writer module:\n"); + _printf_(true,"\n"); + _printf_(true," This module writes the mesh of a model as KML polygons into the specified KML file.\n"); +@@ -195,4 +141,3 @@ + _printf_(true," KMLMeshWrite(md.name,md.notes,md.elements,md.nodeconnectivity,md.lat,md.long,md.part,md.fm_criterion,options.cmap,filekml);\n"); + _printf_(true,"\n"); + } +- Index: /issm/oecreview/Archive/12041-12060/ISSM-12049-12050.diff =================================================================== --- /issm/oecreview/Archive/12041-12060/ISSM-12049-12050.diff (revision 12325) +++ /issm/oecreview/Archive/12041-12060/ISSM-12049-12050.diff (revision 12325) @@ -0,0 +1,396 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.cpp (revision 12049) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToNodes/ContourToNodes.cpp (revision 12050) +@@ -67,10 +67,10 @@ + } + + numcontours=mxGetNumberOfElements(matlabstructure); +- contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); ++ contours=(Contour**)mxMalloc(numcontours*sizeof(Contour*)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 12049) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 12050) +@@ -54,7 +54,7 @@ + //index + FetchData(&double_index,&nel,&dummy,INDEX); + if(dummy!=3 && dummy!=6)_error_(" element triangulation should be of 3 or 6 column width!"); +- index=(int*)xmalloc(nel*3*sizeof(int)); ++ index=(int*)mxMalloc(nel*3*sizeof(int)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp (revision 12049) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp (revision 12050) +@@ -64,7 +64,7 @@ + if(mxIsDouble(prhs[0])){ + nel=mxGetM(prhs[0]); + tindex_in=mxGetPr(prhs[0]); +- index_in=(double*)xmalloc(nel*3*sizeof(double)); ++ index_in=(double*)mxMalloc(nel*3*sizeof(double)); + for (i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12049) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12050) +@@ -77,10 +77,10 @@ + + /*contours: */ + numcontours=mxGetNumberOfElements(matlabstructure); +- contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); ++ contours=(Contour**)mxMalloc(numcontours*sizeof(Contour*)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12049) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12050) +@@ -64,10 +64,10 @@ + + //Fetch contours + numcontours=mxGetNumberOfElements(matlabstructure); +- contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); ++ contours=(Contour**)mxMalloc(numcontours*sizeof(Contour*)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12049) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12050) +@@ -54,12 +54,12 @@ + notesi=mxGetCell(NOTES,nindex); + if (notesi && mxIsChar(notesi) && mxGetNumberOfElements(notesi)) { + if (!notes) { +- notes=(char *) xmalloc((mxGetNumberOfElements(notesi)+1)*sizeof(char)); ++ notes=(char *) mxMalloc((mxGetNumberOfElements(notesi)+1)*sizeof(char)); + mxGetString(notesi,notes,mxGetNumberOfElements(notesi)+1); + } + else { + /* note that strlen does not include trailing null */ +- notes=(char *) xrealloc(notes,(strlen(notes)+1+mxGetNumberOfElements(notesi)+1)*sizeof(char)); ++ notes=(char *) mxRealloc(notes,(strlen(notes)+1+mxGetNumberOfElements(notesi)+1)*sizeof(char)); + strcat(notes,"\n"); + mxGetString(notesi,¬es[strlen(notes)],mxGetNumberOfElements(notesi)+1); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp (revision 12049) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp (revision 12050) +@@ -57,16 +57,16 @@ + nvtxs = mxGetN(A_IN); + + mwstart = mxGetJc(A_IN); +- start=(int*)xmalloc(nvtxs*sizeof(int)); ++ start=(int*)mxMalloc(nvtxs*sizeof(int)); + for (i=0; iAddOption(option); ++ option=NULL; ++ } ++ ++ /*Assign output pointers:*/ ++ *poptions=options; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h (revision 12050) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h (revision 12051) +@@ -48,6 +48,7 @@ + void FetchData(BamgGeom** bamggeom,const mxArray* dataref); + void FetchData(BamgMesh** bamgmesh,const mxArray* dataref); + void FetchData(BamgOpts** bamgopts,const mxArray* dataref); ++void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref); + + Option* OptionParse(char* name, const mxArray* prhs[]); + OptionDouble* OptionDoubleParse( char* name, const mxArray* prhs[]); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h (revision 12050) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h (revision 12051) +@@ -14,7 +14,6 @@ + + /*constructors, destructors*/ + Options(); +- Options(int istart, int nrhs, void* module_references); + ~Options(); + + /*numerics*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12050) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12051) +@@ -749,7 +749,6 @@ + ./matlab/io/MatlabVectorToVector.cpp\ + ./matlab/io/MatlabVectorToDoubleVector.cpp\ + ./matlab/io/MatlabMatrixToDoubleMatrix.cpp\ +- ./matlab/Container/Options.cpp\ + ./matlab/io/MatlabMatrixToPetscMatrix.cpp\ + ./matlab/io/MatlabVectorToPetscVector.cpp\ + ./matlab/io/PetscMatrixToDoubleMatrix.cpp\ Index: /issm/oecreview/Archive/12041-12060/ISSM-12051-12052.diff =================================================================== --- /issm/oecreview/Archive/12041-12060/ISSM-12051-12052.diff (revision 12325) +++ /issm/oecreview/Archive/12041-12060/ISSM-12051-12052.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12051) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12052) +@@ -621,7 +621,7 @@ + Options* options=new Options(); + + /*Fetch all options*/ +- for (i=istart; inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 12059) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 12060) +@@ -54,7 +54,7 @@ + //index + FetchData(&double_index,&nel,&dummy,INDEX); + if(dummy!=3 && dummy!=6)_error_(" element triangulation should be of 3 or 6 column width!"); +- index=(int*)mxMalloc(nel*3*sizeof(int)); ++ index=(int*)xmalloc(nel*3*sizeof(int)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp (revision 12059) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRefine/TriMeshRefine.cpp (revision 12060) +@@ -64,7 +64,7 @@ + if(mxIsDouble(prhs[0])){ + nel=mxGetM(prhs[0]); + tindex_in=mxGetPr(prhs[0]); +- index_in=(double*)mxMalloc(nel*3*sizeof(double)); ++ index_in=(double*)xmalloc(nel*3*sizeof(double)); + for (i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12059) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12060) +@@ -77,10 +77,10 @@ + + /*contours: */ + numcontours=mxGetNumberOfElements(matlabstructure); +- contours=(Contour**)mxMalloc(numcontours*sizeof(Contour*)); ++ contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12059) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12060) +@@ -25,23 +25,23 @@ + int i,j; + + /* required input: */ +- double* index=NULL; +- double* x=NULL; +- double* y=NULL; + int edgevalue; +- char* interptype=NULL; ++ double *index = NULL; ++ double *x = NULL; ++ double *y = NULL; ++ char *interptype = NULL; + + /* output: */ +- Vector* in_nod=NULL; +- int nods; +- Vector* in_elem=NULL; +- int nel; ++ Vector *in_nod = NULL; ++ int nods; ++ Vector *in_elem = NULL; ++ int nel; + + //contours +- mxArray* matlabstructure=NULL; +- int numcontours; +- Contour** contours=NULL; +- Contour* contouri=NULL; ++ mxArray *matlabstructure = NULL; ++ int numcontours; ++ Contour **contours = NULL; ++ Contour *contouri = NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -64,10 +64,10 @@ + + //Fetch contours + numcontours=mxGetNumberOfElements(matlabstructure); +- contours=(Contour**)mxMalloc(numcontours*sizeof(Contour*)); ++ contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); + for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); + //set pointers. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12059) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/KMLMeshWrite/KMLMeshWrite.cpp (revision 12060) +@@ -54,12 +54,12 @@ + notesi=mxGetCell(NOTES,nindex); + if (notesi && mxIsChar(notesi) && mxGetNumberOfElements(notesi)) { + if (!notes) { +- notes=(char *) mxMalloc((mxGetNumberOfElements(notesi)+1)*sizeof(char)); ++ notes=(char *) xmalloc((mxGetNumberOfElements(notesi)+1)*sizeof(char)); + mxGetString(notesi,notes,mxGetNumberOfElements(notesi)+1); + } + else { + /* note that strlen does not include trailing null */ +- notes=(char *) mxRealloc(notes,(strlen(notes)+1+mxGetNumberOfElements(notesi)+1)*sizeof(char)); ++ notes=(char*)xrealloc(notes,(strlen(notes)+1+mxGetNumberOfElements(notesi)+1)*sizeof(char)); + strcat(notes,"\n"); + mxGetString(notesi,¬es[strlen(notes)],mxGetNumberOfElements(notesi)+1); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp (revision 12059) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp (revision 12060) +@@ -17,56 +17,52 @@ + int nterms; + + /*Inputs: */ +- int nvtxs; /* number of vertices in graph */ +- int *start; /* start of edge list for each vertex */ +- int *adjacency; /* edge list data */ +- int *vwgts=NULL; /* weights for all vertices */ +- int nedges; +- float *ewgts=NULL; /* weights for all edges */ +- float *x=NULL; +- float *y=NULL; +- float *z=NULL; /* coordinates for inertial method */ +- double options[10]={1,1,0,0,1,1,50,0,.001,7654321}; /* architecture and partitioning options */ +- double* in_options=NULL; +- int *nparts=NULL; /* number of parts options */ +- int npart; +- double *goal=NULL; /* desired set sizes */ ++ int nvtxs; /* number of vertices in graph */ ++ int *start; /* start of edge list for each vertex */ ++ int *adjacency; /* edge list data */ ++ int *vwgts = NULL; /* weights for all vertices */ ++ int nedges; ++ float *ewgts = NULL; /* weights for all edges */ ++ float *x = NULL; ++ float *y = NULL; ++ float *z = NULL; /* coordinates for inertial method */ ++ double options[10] = {1,1,0,0,1,1,50,0,.001,7654321}; /* architecture and partitioning options */ ++ double *in_options = NULL; ++ int *nparts = NULL; /* number of parts options */ ++ int npart; ++ double *goal = NULL; /* desired set sizes */ + + /*intermediary pointers: */ + mwIndex *mwstart, *mwadjacency; + double *doublepointer; + + /*output: */ +- short *assignment=NULL; /* set number of each vtx (length nvtxs+1) */ +- double *doubleassignment=NULL; /*holds assignment, in double format, to return to matlab*/ ++ short *assignment = NULL; /* set number of each vtx (length nvtxs+1) */ ++ double *doubleassignment = NULL; /*holds assignment, in double format, to return to matlab */ + +- + #ifndef _HAVE_CHACO_ //only works if dakota library has been compiled in. + _error_(" Chaco not available! Cannot carry out Chaco partitioning!"); + #endif + +- + /*Boot module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ + CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ChacoUsage); + +- + /*Fetch adjacency matrix: */ + nvtxs = mxGetN(A_IN); +- + mwstart = mxGetJc(A_IN); +- start=(int*)mxMalloc(nvtxs*sizeof(int)); ++ start=(int*)xmalloc(nvtxs*sizeof(int)); + for (i=0; iGetObjectByOffset(i); + in.numberofpoints+=contour->nods; + } ++ if (rifts){ ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ in.numberofpoints+=contour->nods; ++ } ++ } + /*number of point attributes: */ + in.numberofpointattributes=1; + +@@ -62,9 +68,19 @@ + counter++; + } + } ++ if(rifts){ ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ for (j=0;jnods;j++){ ++ in.pointlist[2*counter+0]=contour->x[j]; ++ in.pointlist[2*counter+1]=contour->y[j]; ++ counter++; ++ } ++ } ++ } + + /*fill in the point attribute list: */ +- in.pointattributelist = (REAL *) xmalloc(in.numberofpoints * in.numberofpointattributes * sizeof(REAL)); ++ in.pointattributelist = (REAL*)xmalloc(in.numberofpoints*in.numberofpointattributes*sizeof(REAL)); + for (i=0;iGetObjectByOffset(i); + in.numberofsegments+=contour->nods; + } ++ if(rifts){ ++ for(i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ /*for rifts, we have one less segment as we have vertices*/ ++ in.numberofsegments+=contour->nods-1; ++ } ++ } + + in.segmentlist = (int *) xmalloc(in.numberofsegments * 2 * sizeof(int)); + in.segmentmarkerlist = (int *) xcalloc(in.numberofsegments,sizeof(int)); +@@ -97,6 +120,20 @@ + counter++; + backcounter=counter; + } ++ counter2=counter; ++ if(rifts){ ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ for (j=0;j<(contour->nods-1);j++){ ++ in.segmentlist[2*counter2+0]=counter; ++ in.segmentlist[2*counter2+1]=counter+1; ++ in.segmentmarkerlist[counter2]=2+i; ++ counter2++; ++ counter++; ++ } ++ counter++; ++ } ++ } + + /*Build regions: */ + in.numberofregions = 0; Index: /issm/oecreview/Archive/12061-12080/ISSM-12063-12064.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12063-12064.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12063-12064.diff (revision 12325) @@ -0,0 +1,427 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12063) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12064) +@@ -75,10 +75,10 @@ + + dnl 1. See if matlab has been provided + AC_ARG_WITH([matlab-dir], +- AS_HELP_STRING([--with-matlab-dir = DIR], [matlab root directory. necessary for serial build.]), ++ AS_HELP_STRING([--with-matlab-dir=DIR], [matlab root directory. necessary for serial build.]), + [MATLAB_ROOT=$withval],[MATLAB_ROOT=""]) + +- AC_MSG_CHECKING([wether Matlab is enabled]) ++ AC_MSG_CHECKING([whether matlab is enabled]) + if test -d "$MATLAB_ROOT"; then + HAVE_MATLAB=yes + else +@@ -92,7 +92,7 @@ + + dnl 2. if matlab is provided, get version number + if test x$HAVE_MATLAB = xyes; then +- AC_MSG_CHECKING([for Matlab version]) ++ AC_MSG_CHECKING([for matlab version]) + MATLAB_VERSION="" + + dnl For Matlab R2008a and more, the version number is stored in .VERSION +@@ -155,7 +155,7 @@ + AC_MSG_RESULT($MATLAB_VERSION ($MATLAB_MAJOR.$MATLAB_MINOR)) + + dnl 3. Get Matlab libraries +- AC_MSG_CHECKING(for Matlab headers and libraries in $MATLAB_ROOT) ++ AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT) + MATLABINCL=-I"$MATLAB_ROOT/extern/include"; + + dnl OS-dependent variables and checks +@@ -208,9 +208,9 @@ + dnl }}} + dnl triangle {{{ + AC_ARG_WITH([triangle-dir], +- AS_HELP_STRING([--with-triangle-dir = DIR], [triangle root directory. necessary for serial build]), ++ AS_HELP_STRING([--with-triangle-dir=DIR], [triangle root directory. necessary for serial build]), + [TRIANGLE_ROOT=$withval],[TRIANGLE_ROOT=""]) +- AC_MSG_CHECKING(for Triangle headers and libraries) ++ AC_MSG_CHECKING(for triangle headers and libraries) + + if test -d "$TRIANGLE_ROOT"; then + +@@ -249,9 +249,9 @@ + dnl }}} + dnl dakota{{{ + AC_ARG_WITH([dakota-dir], +- AS_HELP_STRING([--with-dakota-dir = DIR], [dakota root directory. necessary for serial build]), ++ AS_HELP_STRING([--with-dakota-dir=DIR], [dakota root directory. necessary for serial build]), + [DAKOTA_ROOT=$withval],[DAKOTA_ROOT=""]) +- AC_MSG_CHECKING(for Dakota) ++ AC_MSG_CHECKING(for dakota) + + if test -d "$DAKOTA_ROOT"; then + +@@ -282,9 +282,9 @@ + dnl }}} + dnl boost{{{ + AC_ARG_WITH([boost-dir], +- AS_HELP_STRING([--with-boost-dir = DIR], [boost root directory.]), ++ AS_HELP_STRING([--with-boost-dir=DIR], [boost root directory.]), + [BOOST_ROOT=$withval],[BOOST_ROOT=""]) +- AC_MSG_CHECKING(for Boost) ++ AC_MSG_CHECKING(for boost) + + if test -d "$BOOST_ROOT"; then + dnl defaults +@@ -303,9 +303,9 @@ + dnl }}} + dnl python{{{ + AC_ARG_WITH([python-dir], +- AS_HELP_STRING([--with-python-dir = DIR], [python root directory.]), ++ AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]), + [PYTHON_ROOT=$withval],[PYTHON_ROOT=""]) +- AC_MSG_CHECKING(for Python) ++ AC_MSG_CHECKING(for python) + + if test -d "$PYTHON_ROOT"; then + dnl defaults +@@ -327,11 +327,30 @@ + AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes]) + AC_MSG_RESULT($HAVE_PYTHON) + dnl }}} ++ dnl python-version{{{ ++ AC_ARG_WITH([python-version], ++ AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]), ++ [PYTHONVERSION=$withval],[PYTHONVERSION=""]) ++ AC_MSG_CHECKING(for python version) ++ ++ HAVE_PYTHON3="no" ++ ++ dnl recover major: ++ PYTHON_MAJOR=${PYTHONVERSION%.*} ++ ++ if test x$PYTHON_MAJOR = x3; then ++ dnl are we running python 3? ++ HAVE_PYTHON3="yes" ++ fi ++ ++ AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes]) ++ AC_MSG_RESULT($PYTHON_MAJOR) ++ dnl }}} + dnl python-numpy{{{ + AC_ARG_WITH([python-numpy-dir], +- AS_HELP_STRING([--with-python-numpy-dir = DIR], [python-numpy root directory.]), ++ AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]), + [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT=""]) +- AC_MSG_CHECKING(for Python-Numpy) ++ AC_MSG_CHECKING(for python-numpy) + + if test -d "$PYTHON_NUMPY_ROOT"; then + dnl defaults +@@ -347,9 +366,9 @@ + dnl }}} + dnl chaco{{{ + AC_ARG_WITH([chaco-dir], +- AS_HELP_STRING([--with-chaco-dir = DIR], [chaco root directory.]), ++ AS_HELP_STRING([--with-chaco-dir=DIR], [chaco root directory.]), + [CHACO_ROOT=$withval],[CHACO_ROOT=""]) +- AC_MSG_CHECKING(for Chaco) ++ AC_MSG_CHECKING(for chaco) + + if test -d "$CHACO_ROOT"; then + +@@ -369,9 +388,9 @@ + dnl }}} + dnl scotch{{{ + AC_ARG_WITH([scotch-dir], +- AS_HELP_STRING([--with-scotch-dir = DIR], [scotch root directory.]), ++ AS_HELP_STRING([--with-scotch-dir=DIR], [scotch root directory.]), + [SCOTCH_ROOT=$withval],[SCOTCH_ROOT=""]) +- AC_MSG_CHECKING(for Scotch) ++ AC_MSG_CHECKING(for scotch) + + if test -d "$SCOTCH_ROOT"; then + +@@ -391,9 +410,9 @@ + dnl }}} + dnl adolc{{{ + AC_ARG_WITH([adolc-dir], +- AS_HELP_STRING([--with-adolc-dir = DIR], [adolc root directory.]), ++ AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]), + [ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) +- AC_MSG_CHECKING(for ADOLC) ++ AC_MSG_CHECKING(for adolc) + + if test "x$ADOLC_ROOT" = "xno"; then + HAVE_ADOLC=no +@@ -419,9 +438,9 @@ + dnl }}} + dnl adic2{{{ + AC_ARG_WITH([adic2-dir], +- AS_HELP_STRING([--with-adic2-dir = DIR], [adic2 root directory.]), ++ AS_HELP_STRING([--with-adic2-dir=DIR], [adic2 root directory.]), + [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) +- AC_MSG_CHECKING(for ADIC2) ++ AC_MSG_CHECKING(for adic2) + + if test "x$ADIC2_ROOT" = "xno"; then + HAVE_ADIC2=no +@@ -447,9 +466,9 @@ + dnl }}} + dnl gsl{{{ + AC_ARG_WITH([gsl-dir], +- AS_HELP_STRING([--with-gsl-dir = DIR], [gsl root directory.]), ++ AS_HELP_STRING([--with-gsl-dir=DIR], [gsl root directory.]), + [GSL_ROOT=$withval],[GSL_ROOT=""]) +- AC_MSG_CHECKING(for Gsl) ++ AC_MSG_CHECKING(for gsl) + + if test -d "$GSL_ROOT"; then + +@@ -470,9 +489,9 @@ + dnl }}} + dnl rose{{{ + AC_ARG_WITH([rose-dir], +- AS_HELP_STRING([--with-rose-dir = DIR], [rose root directory.]), ++ AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]), + [ROSE_ROOT=$withval],[ROSE_ROOT=""]) +- AC_MSG_CHECKING(for Rose) ++ AC_MSG_CHECKING(for rose) + + if test -d "$ROSE_ROOT"; then + +@@ -493,12 +512,12 @@ + dnl }}} + dnl metis{{{ + AC_ARG_WITH([metis-dir], +- AS_HELP_STRING([--with-metis-dir = DIR],[metis root directory. necessary for serial build]), ++ AS_HELP_STRING([--with-metis-dir=DIR],[metis root directory. necessary for serial build]), + [METIS_ROOT=$withval],[METIS_ROOT=""]) + + if test -d "$METIS_ROOT"; then + +- AC_MSG_CHECKING(for Metis headers and libraries in $METIS_ROOT) ++ AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT) + + dnl first figure out version of metis: does the VERSION file exist? + if test -e "$METIS_ROOT/VERSION"; then +@@ -565,7 +584,7 @@ + [MPILIB=$withval],[MPILIB=""]) + + AC_ARG_WITH([mpi-include], +- AS_HELP_STRING([--with-mpi-include = DIR],[mpi include directory, necessary for parallel build]), ++ AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]), + [MPI_INCLUDE=$withval],[MPI_INCLUDE=""]) + + if test -z "$MPILIB" ; then +@@ -574,6 +593,7 @@ + if test -z "$MPI_INCLUDE" ; then + HAVE_MPI=no + else ++ HAVE_MPI=yes + MPIINCL=-I"$MPI_INCLUDE/" + AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src]) + AC_DEFINE([HAVE_MPI],[1],[Mpi Flag for Dakota (DO NOT REMOVE)]) +@@ -581,15 +601,15 @@ + AC_SUBST([MPILIB]) + fi + fi +- AC_MSG_RESULT(done) ++ AC_MSG_RESULT($HAVE_MPI) + dnl }}} + dnl petsc{{{ + AC_ARG_WITH([petsc-dir], +- AS_HELP_STRING([--with-petsc-dir = DIR],[PETSc root directory, necessary for parallel build]), ++ AS_HELP_STRING([--with-petsc-dir=DIR],[PETSc root directory, necessary for parallel build]), + [PETSC_ROOT=$withval],[PETSC_ROOT=""]) + + if test -d "$PETSC_ROOT"; then +- AC_MSG_CHECKING(for PETSc version) ++ AC_MSG_CHECKING(for petsc version) + PETSC_MAJOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MAJOR" | sed 's/#define PETSC_VERSION_MAJOR//' | sed 's/ //g'` + PETSC_MINOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MINOR" | sed 's/#define PETSC_VERSION_MINOR//' | sed 's/ //g'` + AC_DEFINE_UNQUOTED([_PETSC_MAJOR_],$PETSC_MAJOR,[PETSc version major]) +@@ -597,7 +617,7 @@ + AC_MSG_RESULT($PETSC_MAJOR.$PETSC_MINOR) + + PETSC_VERSION_DATE_HG=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_DATE_HG" | sed 's/#define PETSC_VERSION_DATE_HG//' | sed 's/ //g' | sed -e 's/\"//g' ` +- AC_MSG_CHECKING(wether PETSc is the development version) ++ AC_MSG_CHECKING(whether petsc is the development version) + if test x$PETSC_VERSION_DATE_HG = xunknown; then + AC_DEFINE([_HAVE_PETSCDEV_],[1],[with PETSc-dev]) + AC_MSG_RESULT(yes) +@@ -607,10 +627,10 @@ + fi + + AC_ARG_WITH([petsc-arch], +- AS_HELP_STRING([--with-petsc-arch = DIR],[PETSc arch , necessary for parallel build]), ++ AS_HELP_STRING([--with-petsc-arch=DIR],[PETSc arch , necessary for parallel build]), + [PETSC_ARCH=$withval],[PETSC_ARCH=""]) + +- AC_MSG_CHECKING(for PETSc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH) ++ AC_MSG_CHECKING(for petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH) + + if test -d "$PETSC_ROOT"; then + +@@ -654,9 +674,9 @@ + dnl }}} + dnl tao{{{ + AC_ARG_WITH([tao-dir], +- AS_HELP_STRING([--with-tao-dir = DIR], [tao root directory.]), ++ AS_HELP_STRING([--with-tao-dir=DIR], [tao root directory.]), + [TAO_ROOT=$withval],[TAO_ROOT=""]) +- AC_MSG_CHECKING(for Tao) ++ AC_MSG_CHECKING(for tao) + + if test -d "$TAO_ROOT"; then + +@@ -674,10 +694,10 @@ + dnl }}} + dnl slepc{{{ + AC_ARG_WITH([slepc-dir], +- AS_HELP_STRING([--with-slepc-dir = DIR],[slepc root directory]), ++ AS_HELP_STRING([--with-slepc-dir=DIR],[slepc root directory]), + [SLEPC_ROOT=$withval],[SLEPC_ROOT=""]) + +- AC_MSG_CHECKING(for Slepc headers and libraries in $SLEPC_ROOT) ++ AC_MSG_CHECKING(for slepc headers and libraries in $SLEPC_ROOT) + if test -d "$SLEPC_ROOT"; then + HAVE_SLEPC=yes + SLEPCINCL=-I"$SLEPC_ROOT/include" +@@ -693,10 +713,10 @@ + dnl }}} + dnl shapelib{{{ + AC_ARG_WITH([shapelib-dir], +- AS_HELP_STRING([--with-shapelib-dir = DIR], [shapelib root directory]), ++ AS_HELP_STRING([--with-shapelib-dir=DIR], [shapelib root directory]), + [SHAPELIB_ROOT=$withval],[SHAPELIB_ROOT=""]) + +- AC_MSG_CHECKING(for Shapelib headers and libraries in $SHAPELIB_ROOT) ++ AC_MSG_CHECKING(for shapelib headers and libraries in $SHAPELIB_ROOT) + if test -d "$SHAPELIB_ROOT"; then + + dnl defaults +@@ -714,10 +734,10 @@ + dnl }}} + dnl scalapack{{{ + AC_ARG_WITH([scalapack-dir], +- AS_HELP_STRING([--with-scalapack-dir = DIR],[scalapack root directory]), ++ AS_HELP_STRING([--with-scalapack-dir=DIR],[scalapack root directory]), + [SCALAPACK_ROOT=$withval],[SCALAPACK_ROOT=""]) + +- AC_MSG_CHECKING(for Scalapack headers and libraries in $SCALAPACK_ROOT) ++ AC_MSG_CHECKING(for scalapack headers and libraries in $SCALAPACK_ROOT) + if test -d "$SCALAPACK_ROOT"; then + + dnl defaults +@@ -733,10 +753,10 @@ + dnl }}} + dnl blas{{{ + AC_ARG_WITH([blas-lapack-dir], +- AS_HELP_STRING([--with-blas-lapack-dir = DIR],[blas-lapack root directory]), ++ AS_HELP_STRING([--with-blas-lapack-dir=DIR],[blas-lapack root directory]), + [BLASLAPACK_ROOT=$withval],[BLASLAPACK_ROOT=""]) + +- AC_MSG_CHECKING(for Blas and Lapack headers and libraries in $BLASLAPACK_ROOT) ++ AC_MSG_CHECKING(for blas and lapack headers and libraries in $BLASLAPACK_ROOT) + if test -d "$BLASLAPACK_ROOT"; then + + dnl defaults +@@ -766,7 +786,7 @@ + dnl }}} + dnl mkl{{{ + AC_ARG_WITH([mkl-dir], +- AS_HELP_STRING([--with-mkl-dir = DIR],[mkl root directory]), ++ AS_HELP_STRING([--with-mkl-dir=DIR],[mkl root directory]), + [MKL_ROOT=$withval],[MKL_ROOT=""]) + + AC_MSG_CHECKING(for mkl headers and libraries in $MKL_ROOT) +@@ -785,16 +805,16 @@ + AC_MSG_RESULT($HAVE_MKL) + dnl }}} + dnl plapack{{{ ++ AC_MSG_CHECKING(for plapack) ++ + AC_ARG_WITH([plapack-lib], + AS_HELP_STRING([--with-plapack-lib = lib],[plapack library]), + [PLAPACK_LIB=$withval],[PLAPACK_LIB=""]) +- AC_MSG_CHECKING(for Plapack libraries) + + AC_ARG_WITH([plapack-include], + AS_HELP_STRING([--with-plapack-include = include], + [plapack include ]), + [PLAPACK_INCLUDE=$withval],[PLAPACK_INCLUDE=""]) +- AC_MSG_CHECKING(for Plapack headers) + + if test -n "$PLAPACK_LIB"; then + if test -n "$PLAPACK_INCLUDE"; then +@@ -817,10 +837,10 @@ + dnl }}} + dnl mumps{{{ + AC_ARG_WITH([mumps-dir], +- AS_HELP_STRING([--with-mumps-dir = DIR],[mumps root directory]), ++ AS_HELP_STRING([--with-mumps-dir=DIR],[mumps root directory]), + [MUMPS_ROOT=$withval],[MUMPS_ROOT=""]) + +- AC_MSG_CHECKING(for Mumps headers and libraries in $MUMPS_ROOT) ++ AC_MSG_CHECKING(for mumps headers and libraries in $MUMPS_ROOT) + if test -d "$MUMPS_ROOT"; then + + dnl defaults +@@ -842,10 +862,10 @@ + dnl }}} + dnl blacs{{{ + AC_ARG_WITH([blacs-dir], +- AS_HELP_STRING([--with-blacs-dir = DIR],[blacs root directory]), ++ AS_HELP_STRING([--with-blacs-dir=DIR],[blacs root directory]), + [BLACS_ROOT=$withval],[BLACS_ROOT=""]) + +- AC_MSG_CHECKING(for Blacs headers and libraries in $BLACS_ROOT) ++ AC_MSG_CHECKING(for blacs headers and libraries in $BLACS_ROOT) + if test -d "$BLACS_ROOT"; then + + dnl defaults +@@ -863,10 +883,10 @@ + dnl }}} + dnl hypre{{{ + AC_ARG_WITH([hypre-dir], +- AS_HELP_STRING([--with-hypre-dir = DIR],[hypre root directory]), ++ AS_HELP_STRING([--with-hypre-dir=DIR],[hypre root directory]), + [HYPRE_ROOT=$withval],[HYPRE_ROOT=""]) + +- AC_MSG_CHECKING(for Hypre headers and libraries in $HYPRE_ROOT) ++ AC_MSG_CHECKING(for hypre headers and libraries in $HYPRE_ROOT) + if test -d "$HYPRE_ROOT"; then + + dnl defaults +@@ -884,10 +904,10 @@ + dnl }}} + dnl ml{{{ + AC_ARG_WITH([ml-dir], +- AS_HELP_STRING([--with-ml-dir = DIR],[ml root directory]), ++ AS_HELP_STRING([--with-ml-dir=DIR],[ml root directory]), + [ML_ROOT=$withval],[ML_ROOT=""]) + +- AC_MSG_CHECKING(for Ml headers and libraries in $ML_ROOT) ++ AC_MSG_CHECKING(for ml headers and libraries in $ML_ROOT) + if test -d "$ML_ROOT"; then + + dnl defaults +@@ -1201,6 +1221,12 @@ + AC_MSG_ERROR([need at least python or matlab support to compile modules (or use --with-modules=no)]); + fi + ++ dnl check that we python version if python compile is specified ++ dnl if test "$HAVE_PYTHON" = "yes" && test "$HAVE_PYTHONVERSION" = "no" ; then ++ dnl AC_MSG_ERROR([need python-version if python compile is required!]); ++ dnl fi ++ ++ + AC_MSG_RESULT(done) + dnl }}} + +@@ -1210,7 +1236,7 @@ + AC_ARG_WITH([cxxoptflags], + AS_HELP_STRING([--with-cxxoptflags = CXXOPTFLAGS], [optimization using CXX flags, ex: --with-cxxoptflags=-march=opteron -O3]), + [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2"]) +- AC_MSG_CHECKING(for C++ optimization flags) ++ AC_MSG_CHECKING(for c++ optimization flags) + AC_SUBST([CXXOPTFLAGS]) + AC_MSG_RESULT(done) + Index: /issm/oecreview/Archive/12061-12080/ISSM-12064-12065.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12064-12065.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12064-12065.diff (revision 12325) @@ -0,0 +1,32 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/bin +___________________________________________________________________ +Modified: svn:ignore + - *.mexa64 +*.mexw64 +*.mexw32 +Makefile +Makefile.in +issm.exe +*.m +*.h +@pairoptions +@modellist +*.bat +*.rtf + + + *.mexa64 +*.mexw64 +*.mexw32 +Makefile +Makefile.in +issm.exe +*.m +*.h +@pairoptions +@modellist +*.bat +*.rtf +*.py + + Index: /issm/oecreview/Archive/12061-12080/ISSM-12065-12066.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12065-12066.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12065-12066.diff (revision 12325) @@ -0,0 +1,17 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12065) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12066) +@@ -9,12 +9,6 @@ + + import os,sys + +- +-#First check we are running python 3 at least +-if sys.version_info[0] < 3: +- print("ISSM can only work in Python 3. Exiting python") +- sys.exit(1) +- + #Recover ISSM_TIER, ISSM_DIR and USERNAME + ISSM_TIER=os.getenv('ISSM_TIER') + USERNAME =os.getenv('USER') Index: /issm/oecreview/Archive/12061-12080/ISSM-12066-12067.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12066-12067.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12066-12067.diff (revision 12325) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh (revision 12066) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh (revision 12067) +@@ -3,12 +3,15 @@ + #petsc 3.2 + #mpich 1.4 + ++pythonversion=2.7 ++ + ./configure \ + --prefix=$ISSM_TIER \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_TIER/externalpackages/python/install\ +- --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ ++ --with-python-version=$pythonversion \ ++ --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ Index: /issm/oecreview/Archive/12061-12080/ISSM-12067-12068.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12067-12068.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12067-12068.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp (revision 12067) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Chaco/Chaco.cpp (revision 12068) +@@ -53,7 +53,7 @@ + /*Fetch adjacency matrix: */ + nvtxs = mxGetN(A_IN); + mwstart = mxGetJc(A_IN); +- start=(int*)xmalloc(nvtxs*sizeof(int)); ++ start=(int*)xmalloc((nvtxs+1)*sizeof(int)); + for (i=0; i=2 flag them ), outlinefilename an Argus domain outline file.\n"); +- printf(" riftsoutlinename is an Argus domain file, defining rifts (ie: open profiles), \n"); +- printf(" area is the maximum area desired for any element of the resulting mesh. \n"); +- printf(" and ordered is a string ('yes' or 'no') that determines whether segments are output in the \n"); ++ printf(" of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment, \n"); ++ printf(" outlinefilename an Argus domain outline file, \n"); ++ printf(" area is the maximum area desired for any element of the resulting mesh, \n"); ++ printf(" and ordered is a bool that determines whether segments are output in the \n"); + printf(" order they are made by Triangle (ie none), or ordered counter clockwise around the domain outline.\n"); +- printf(" riftsoutlinename and ordered are optional arguments.\n"); + printf("\n"); + } +- +- +- +- ++//}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.h (revision 12070) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMeshRifts/TriMeshRifts.h (revision 12071) +@@ -5,19 +5,66 @@ + #ifndef _TRIMESHRIFTS_H_ + #define _TRIMESHRIFTS_H_ + +-#include "mex.h" +-#include "triangle.h" +-#include "string.h" ++#ifdef HAVE_CONFIG_H ++#include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif + ++/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ ++#ifdef _HAVE_PYTHON_ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#endif ++ ++/*Header files: */ + #include "../../c/include/globals.h" ++#include "../../c/toolkits/toolkits.h" ++#include "../../c/include/include.h" + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" + #include "../../c/issm-binding.h" ++#include "../../c/io/io.h" ++#include "../../c/EnumDefinitions/EnumDefinitions.h" + +-void TriMeshRiftsUsage(void); ++#ifdef _HAVE_MATLAB_MODULES_ ++/* serial input macros: */ ++#define DOMAINOUTLINE (mxArray *)prhs[0] ++#define RIFTSOUTLINE (mxArray *)prhs[1] ++#define AREA (mxArray *)prhs[2] ++#define ORDER (mxArray *)prhs[3] ++/* serial output macros: */ ++#define INDEX (mxArray**)&plhs[0] ++#define X (mxArray**)&plhs[1] ++#define Y (mxArray**)&plhs[2] ++#define SEGMENTS (mxArray**)&plhs[3] ++#define SEGMENTMARKERLIST (mxArray**)&plhs[4] ++#endif + ++#ifdef _HAVE_PYTHON_MODULES_ ++/* serial input macros: */ ++#define DOMAINOUTLINE PyTuple_GetItem(args,0) ++#define RIFTSOUTLINE PyTuple_GetItem(args,1) ++#define AREA PyTuple_GetItem(args,2) ++#define ORDER PyTuple_GetItem(args,3) ++/* serial output macros: */ ++#define INDEX output,0 ++#define X output,1 ++#define Y output,2 ++#define SEGMENTS output,3 ++#define SEGMENTMARKERLIST output,4 ++#endif ++ + #undef __FUNCT__ + #define __FUNCT__ "TriMeshRifts" + +-#endif ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 5 ++#undef NRHS ++#define NRHS 4 ++ ++/* local prototypes: */ ++void TriMeshRiftsUsage(void); ++ ++#endif /* _TRIMESHRIFTS_H_*/ Index: /issm/oecreview/Archive/12061-12080/ISSM-12071-12072.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12071-12072.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12071-12072.diff (revision 12325) @@ -0,0 +1,83 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12071) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12072) +@@ -301,6 +301,26 @@ + AM_CONDITIONAL([BOOST], [test x$HAVE_BOOST = xyes]) + AC_MSG_RESULT($HAVE_BOOST) + dnl }}} ++ dnl python-version{{{ ++ AC_ARG_WITH([python-version], ++ AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]), ++ [PYTHONVERSION=$withval],[PYTHONVERSION=""]) ++ AC_MSG_CHECKING(for python version) ++ ++ HAVE_PYTHON3="no" ++ ++ dnl recover major: ++ PYTHON_MAJOR=${PYTHONVERSION%.*} ++ ++ if test x$PYTHON_MAJOR = x3; then ++ dnl are we running python 3? ++ HAVE_PYTHON3="yes" ++ fi ++ AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major]) ++ ++ AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes]) ++ AC_MSG_RESULT($PYTHON_MAJOR) ++ dnl }}} + dnl python{{{ + AC_ARG_WITH([python-dir], + AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]), +@@ -311,7 +331,7 @@ + dnl defaults + HAVE_PYTHON=yes + PYTHONINCL=-I$PYTHON_ROOT/include +- PYTHONLIB="-L$PYTHON_ROOT/lib -lpython3.2" ++ PYTHONLIB="-L$PYTHON_ROOT/lib -lpython$PYTHONVERSION" + PYTHONEXT=.so + PYTHONLINK="-dynamiclib" + +@@ -327,25 +347,6 @@ + AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes]) + AC_MSG_RESULT($HAVE_PYTHON) + dnl }}} +- dnl python-version{{{ +- AC_ARG_WITH([python-version], +- AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]), +- [PYTHONVERSION=$withval],[PYTHONVERSION=""]) +- AC_MSG_CHECKING(for python version) +- +- HAVE_PYTHON3="no" +- +- dnl recover major: +- PYTHON_MAJOR=${PYTHONVERSION%.*} +- +- if test x$PYTHON_MAJOR = x3; then +- dnl are we running python 3? +- HAVE_PYTHON3="yes" +- fi +- +- AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes]) +- AC_MSG_RESULT($PYTHON_MAJOR) +- dnl }}} + dnl python-numpy{{{ + AC_ARG_WITH([python-numpy-dir], + AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]), +@@ -1221,12 +1222,11 @@ + AC_MSG_ERROR([need at least python or matlab support to compile modules (or use --with-modules=no)]); + fi + +- dnl check that we python version if python compile is specified +- dnl if test "$HAVE_PYTHON" = "yes" && test "$HAVE_PYTHONVERSION" = "no" ; then +- dnl AC_MSG_ERROR([need python-version if python compile is required!]); +- dnl fi ++ check that we python version if python compile is specified ++ if test "$HAVE_PYTHON" = "yes" && test "$PYTHONVERSION" = "" ; then ++ AC_MSG_ERROR([need python-version if python compile is required!]); ++ fi + +- + AC_MSG_RESULT(done) + dnl }}} + Index: /issm/oecreview/Archive/12061-12080/ISSM-12072-12073.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12072-12073.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12072-12073.diff (revision 12325) @@ -0,0 +1,103 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h (revision 12072) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h (revision 12073) +@@ -27,7 +27,8 @@ + #define MODULEEND(); ModuleEnd(); \ + return output; + //}}} +-/* WRAPPER {{{1*/ ++#if _PYTHON_MAJOR_ >=3 ++/* WRAPPER 3.2 {{{1*/ + #define WRAPPER(modulename,...) \ + \ + static PyObject* modulename(PyObject* self,PyObject* args);\ +@@ -53,6 +54,25 @@ + \ + static PyObject* modulename(PyObject* self,PyObject* args) + /*}}}*/ ++#else ++/* WRAPPER 2.7 {{{1*/ ++#define WRAPPER(modulename,...) \ ++\ ++static PyObject* modulename(PyObject* self,PyObject* args);\ ++static PyMethodDef modulename##_funcs[] = {\ ++ {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ ++ {NULL,NULL,0,NULL}\ ++};\ ++\ ++PyMODINIT_FUNC init##modulename(void){\ ++\ ++ import_array();\ ++ (void) Py_InitModule(#modulename, modulename##_funcs);\ ++}\ ++\ ++static PyObject* modulename(PyObject* self,PyObject* args) ++/*}}}*/ ++#endif + /* CHECKARGUMENTS {{{1*/ + #define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12072) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12073) +@@ -15,21 +15,7 @@ + #include "../../include/include.h" + #include "../../shared/shared.h" + +-/*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{1*/ +-void FetchData(char** pstring,PyObject* py_unicode){ +- +- PyObject* py_bytes; +- char* string=NULL; +- +- +- /*convert to bytes format: */ +- PyUnicode_FSConverter(py_unicode,&py_bytes); +- +- /*convert from bytes to string: */ +- string=PyBytes_AS_STRING(py_bytes); +- +- *pstring=string; +-} ++/*Primitive data types*/ + /*FUNCTION FetchData(double* pscalar,PyObject* py_float){{{1*/ + void FetchData(double* pscalar,PyObject* py_float){ + +@@ -70,3 +56,35 @@ + + } + /*}}}*/ ++ ++/*Python version dependent: */ ++#if _PYTHON_MAJOR_ >= 3 ++/*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{1*/ ++void FetchData(char** pstring,PyObject* py_unicode){ ++ ++ PyObject* py_bytes; ++ char* string=NULL; ++ ++ ++ /*convert to bytes format: */ ++ PyUnicode_FSConverter(py_unicode,&py_bytes); ++ ++ /*convert from bytes to string: */ ++ string=PyBytes_AS_STRING(py_bytes); ++ ++ *pstring=string; ++} ++/*}}}*/ ++#else ++/*FUNCTION FetchData(char** pstring,PyObject* py_string){{{1*/ ++void FetchData(char** pstring,PyObject* py_string){ ++ ++ char* string=NULL; ++ ++ /*extract internal string: */ ++ string=PyString_AsString(py_string); ++ ++ *pstring=string; ++} ++/*}}}*/ ++#endif Index: /issm/oecreview/Archive/12061-12080/ISSM-12073-12074.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12073-12074.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12073-12074.diff (revision 12325) @@ -0,0 +1,30 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12073) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12074) +@@ -726,13 +726,7 @@ + ./python/python-binding.h\ + ./python/io/WritePythonData.cpp\ + ./python/io/CheckNumPythonArguments.cpp\ +- ./python/io/FetchPythonData.cpp\ +- ./python/objects/Bamg/BamgGeom.h\ +- ./python/objects/Bamg/BamgGeom.cpp\ +- ./python/objects/Bamg/BamgMesh.h\ +- ./python/objects/Bamg/BamgMesh.cpp\ +- ./python/objects/Bamg/BamgOpts.h\ +- ./python/objects/Bamg/BamgOpts.cpp ++ ./python/io/FetchPythonData.cpp + + #}}} + #Matlab sources {{{1 +@@ -934,8 +928,10 @@ + if PYTHON + libISSMPython_a_SOURCES = $(python_sources) + libISSMPython_a_CXXFLAGS= $(ALLCXXFLAGS) ++if PYTHON3 + libISSMPython_a_CXXFLAGS+= -DNPY_NO_DEPRECATED_API + endif ++endif + + if MATLAB + libISSMMatlab_a_SOURCES = $(matlab_sources) Index: /issm/oecreview/Archive/12061-12080/ISSM-12074-12075.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12074-12075.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12074-12075.diff (revision 12325) @@ -0,0 +1,108 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am (revision 12074) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am (revision 12075) +@@ -13,7 +13,10 @@ + + #Python part + AM_LDFLAGS = $(PYTHONLINK) +-AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_ -DNPY_NO_DEPRECATED_API ++AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_ ++if PYTHON3 ++AM_CXXFLAGS += -DNPY_NO_DEPRECATED_API ++endif + LDADD += $(BOOSTLIB) $(PYTHONLIB) ../../c/libISSMPython.a + + LDADD += ../../c/libISSMCore.a ../../c/libISSMModules.a +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/Makefile.am (revision 12075) +@@ -0,0 +1,11 @@ ++bin_SCRIPTS = petscversion.py ++CLEANFILES = $(bin_SCRIPTS) ++ ++if PYTHON3 ++%.py : %.2.py ++ cp -f $< $@ ++ 2to3 -n -w $@ ++else ++%.py : %.2.py ++ ln -s -f $< $@ ++endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.2.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.2.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.2.py (revision 12075) +@@ -0,0 +1,39 @@ ++#PETSCVERSION - recover petsc version number, inside config.h file ++# ++# Usage: ++# PETSC_VERSION=petscversion(); ++ ++#Module imports {{{ ++import os ++import sys ++from issmtier import * ++#}}} ++ ++def petscversion(): ++ ++ #default ++ PETSC_VERSION=3; ++ ++ configfile=issmtier() + "/bin/config.h" #should find it in the install target ++ ++ if not os.path.isfile(configfile): ++ raise RuntimeError("%s%s%s"%("File ",configfile," not found. ISSM has not been configured yet!")) ++ ++ #go through the file, and recover the line we want ++ fid=open(configfile,'r'); ++ ++ tline=fid.readline() ++ while tline: ++ ++ if tline=='': ++ break ++ ++ if tline[0:21]=="#define _PETSC_MAJOR_": ++ PETSC_VERSION=int(tline[22]) ++ break ++ ++ tline=fid.readline() ++ ++ fid.close(); ++ ++ return PETSC_VERSION + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model +___________________________________________________________________ +Modified: svn:ignore + - __pycache__ + + + Makefile +__pycache__ + + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/Makefile.am (revision 12075) +@@ -0,0 +1 @@ ++SUBDIRS = model + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py +___________________________________________________________________ +Added: svn:ignore + + Makefile + + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am (revision 12074) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am (revision 12075) +@@ -1,2 +1,2 @@ +-EXTRA_DIST = perl pro +-SUBDIRS = c modules m ++EXTRA_DIST = perl pro py ++SUBDIRS = c modules m Index: /issm/oecreview/Archive/12061-12080/ISSM-12075-12076.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12075-12076.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12075-12076.diff (revision 12325) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 12075) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 12076) +@@ -35,7 +35,9 @@ + #List all Makefiles + AC_CONFIG_FILES([Makefile + src/Makefile +- src/c/Makefile ++ src/c/Makefile ++ src/py/Makefile ++ src/py/model/Makefile + src/modules/Makefile + src/modules/python/Makefile + src/modules/matlab/Makefile Index: /issm/oecreview/Archive/12061-12080/ISSM-12076-12077.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12076-12077.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12076-12077.diff (revision 12325) @@ -0,0 +1,44 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.py (revision 12076) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.py (revision 12077) +@@ -1,39 +0,0 @@ +-#PETSCVERSION - recover petsc version number, inside config.h file +-# +-# Usage: +-# PETSC_VERSION=petscversion(); +- +-#Module imports {{{ +-import os +-import sys +-from issmtier import * +-#}}} +- +-def petscversion(): +- +- #default +- PETSC_VERSION=3; +- +- configfile=issmtier() + "/bin/config.h" #should find it in the install target +- +- if not os.path.isfile(configfile): +- raise RuntimeError("%s%s%s"%("File ",configfile," not found. ISSM has not been configured yet!")) +- +- #go through the file, and recover the line we want +- fid=open(configfile,'r'); +- +- tline=fid.readline() +- while tline: +- +- if tline=='': +- break +- +- if tline[0:21]=="#define _PETSC_MAJOR_": +- PETSC_VERSION=int(tline[22]) +- break +- +- tline=fid.readline() +- +- fid.close(); +- +- return PETSC_VERSION Index: /issm/oecreview/Archive/12061-12080/ISSM-12077-12078.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12077-12078.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12077-12078.diff (revision 12325) @@ -0,0 +1,108 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12077) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 12078) +@@ -19,18 +19,20 @@ + /*The following macros hide the error exception handling in a matlab module. Just put + * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ ++//exception.Report(); + + #define MODULEBOOT(); ModuleBoot(); \ + try{ + + #define MODULEEND(); ModuleEnd(); }\ + catch(ErrorException &exception){\ +- exception.Report(); \ +- mexErrMsgTxt(""); \ ++ mexErrMsgTxt("ISSM Error"); \ + }\ +- catch (exception& e) {\ +- _printf_(true,"Standard exception: %s\n",e.what());\ +- mexErrMsgTxt(" ");\ ++ catch (exception &e){\ ++ mexErrMsgTxt(exprintf("Standard exception: %s\n",e.what()));\ ++ }\ ++ catch(...){\ ++ mexErrMsgTxt("An unexpected error occurred");\ + } + //}}} + /* WRAPPER {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h (revision 12077) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/include/macros.h (revision 12078) +@@ -56,6 +56,9 @@ + catch (exception& e) {\ + _printf_(true,"Standard exception: %s\n",e.what());\ + return 1;\ ++ }\ ++ catch(...){\ ++ _printf_(true,"An unexpected error occurred");\ + } + /*}}}*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp (revision 12077) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp (revision 12078) +@@ -28,6 +28,10 @@ + } + + ErrorException::~ErrorException() throw(){ ++ extern int num_procs; ++ /*We want the report only for matlab modules, otherwise we get twice the report ++ * We assume that if num_procs==1, it is a module (FIXME)*/ ++ if(num_procs==1) this->Report(); + } + + const char* ErrorException::what() const throw(){ +@@ -36,13 +40,20 @@ + + void ErrorException::Report(){ + extern int my_rank; ++ extern int num_procs; + + if (function_name=="" || file_line==0){ //WINDOWS + printf("%s%s","Error message: ",what()); + } + else{ +- printf("\n[%i] ??? Error using ==> %s:%i\n",my_rank,file_name.c_str(),file_line); +- printf("[%i] %s error message: %s\n\n",my_rank,function_name.c_str(),what()); ++ if(num_procs==1){ ++ printf("\n??? Error using ==> %s:%i\n",file_name.c_str(),file_line); ++ printf("%s error message: %s\n\n",function_name.c_str(),what()); ++ } ++ else{ ++ printf("\n[%i] ??? Error using ==> %s:%i\n",my_rank,file_name.c_str(),file_line); ++ printf("[%i] %s error message: %s\n\n",my_rank,function_name.c_str(),what()); ++ } + } + return; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/exceptions.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/exceptions.h (revision 12077) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/exceptions.h (revision 12078) +@@ -16,19 +16,18 @@ + /*We derive our classes from the c++ exception class: */ + class ErrorException: public exception { + ++ public: ++ + string what_str; + string function_name; + string file_name; + int file_line; + +- public: + + ErrorException(const string &what_arg); //for windows + ErrorException(string what_file,string what_function,int what_line,string what_arg);//UNIX + ~ErrorException() throw(); +- + virtual const char *what() const throw(); +- + void Report(); + + }; Index: /issm/oecreview/Archive/12061-12080/ISSM-12078-12079.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12078-12079.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12078-12079.diff (revision 12325) @@ -0,0 +1,20 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/exceptions.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/exceptions.h (revision 12078) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exceptions/exceptions.h (revision 12079) +@@ -16,14 +16,12 @@ + /*We derive our classes from the c++ exception class: */ + class ErrorException: public exception { + +- public: +- + string what_str; + string function_name; + string file_name; + int file_line; + +- ++ public: + ErrorException(const string &what_arg); //for windows + ErrorException(string what_file,string what_function,int what_line,string what_arg);//UNIX + ~ErrorException() throw(); Index: /issm/oecreview/Archive/12061-12080/ISSM-12079-12080.diff =================================================================== --- /issm/oecreview/Archive/12061-12080/ISSM-12079-12080.diff (revision 12325) +++ /issm/oecreview/Archive/12061-12080/ISSM-12079-12080.diff (revision 12325) @@ -0,0 +1,428 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/TriMesh/trimesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/TriMesh/trimesh.h (revision 12079) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/TriMesh/trimesh.h (revision 12080) +@@ -5,40 +5,31 @@ + #ifndef _SHARED_TRIMESH_H + #define _SHARED_TRIMESH_H + +- + #include + #include + +- +- + //#define REAL double //took it out because it may conflict with stdlib.h defines. put back if necessary +- + int AssociateSegmentToElement(double** psegments,int nseg, double* index,int nel); + int OrderSegments(double** psegments,int nseg, double* index,int nel); +- + int GridInsideHole(double* px0,double* py0,int n,double* x,double* y); + int FindElement(double A,double B,double* index,int nel); +- + int SplitMeshForRifts(int* pnel,double** pindex,int* pnods,double** px,double** py,int* pnsegs,double** psegments,double** psegmentmarkerlist); +- + int IsGridOnRift(int* riftsegments, int nriftsegs, int node); + int GridElementsList(int** pGridElements, int* pNumGridElements,int node,double * index,int nel); + int IsNeighbor(int el1,int el2,double* index); + int IsOnRift(int el,int nriftsegs,int* riftsegments); + void RiftSegmentsFromSegments(int* pnriftsegs, int** priftsegments, int nel, double* index, int nsegs,double* segments); + int DetermineGridElementListOnOneSideOfRift(int* pNumGridElementListOnOneSideOfRift, int** pGridElementListOnOneSideOfRift, int segmentnumber, int nriftsegs, int* riftsegments, int node,double* index,int nel); +-int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs); ++int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs,int nods,int nel); + int pnpoly(int npol, double *xp, double *yp, double x, double y); + int FindElement(double A,double B,double* index,int nel); + int RemoveRifts(double** pindex,double** px,double** py,int* pnods,double** psegments,int* pnumsegs,int numrifts1,int* rifts1numsegs,double** rifts1segments,double** rifts1pairs,int nel); + int IsRiftPresent(int* priftflag,int* pnumrifts, double* segmentmarkerlist,int nsegs); +-int SplitRiftSegments(double** psegments,double** psegmentmarkerlist, int* pnumsegs, int* pnumrifts,int** priftsnumsegs,double*** priftssegments,int numrifts); ++int SplitRiftSegments(double** psegments,double** psegmentmarkerlist, int* pnumsegs, int* pnumrifts,int** priftsnumsegs,double*** priftssegments,int numrifts,int nods,int nels); + int OrderRifts(double** priftstips, double** riftssegments,double** riftspairs,int numrifts,int* riftsnumsegments,double* x,double* y,int nods,int nels); + int PenaltyPairs(double*** priftspenaltypairs,int** priftsnumpenaltypairs,int numrifts,double** riftssegments, + int* riftsnumsegments,double** riftspairs,double* riftstips,double* x,double* y); +- + int RemoveCornersFromRifts(double** pindex,int* pnel,double** px,double** py,int* pnods, double* segments,double* segmentmarkers,int num_seg); + int PairRiftElements(int** priftsnumpairs, double*** priftspairs,int numrifts,int* riftsnumsegments, double** riftssegments,double* x,double* y); + +- + #endif /* _SHARED_TRIMESH_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/TriMesh/SplitMeshForRifts.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/TriMesh/SplitMeshForRifts.cpp (revision 12079) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/TriMesh/SplitMeshForRifts.cpp (revision 12080) +@@ -56,7 +56,7 @@ + for (i=0;i0 && node4>0); ++ if ((x[node1-1]==x[node4-1]) && (y[node1-1]==y[node4-1])){ + /*Swap node3 and node4:*/ + temp_node=node3; + node3=node4; Index: /issm/oecreview/Archive/12081-12100/ISSM-12086-12087.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12086-12087.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12086-12087.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_overlay.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_overlay.m (revision 12086) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_overlay.m (revision 12087) +@@ -95,7 +95,7 @@ + %h_data=0.7*ones(size(data_grid)); + %h_data(find(data_grid>data_mean))=1; + h_data=1*ones(size(data_grid)); +- h_data(find(data_grid>data_mean))=0.7; ++ h_data(find(data_grid1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end; ++if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end; + if ~isnan(md.surfaceforcings.mass_balance), + md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers); + end; +@@ -100,8 +100,8 @@ + md.mask.vertexonwater=project2d(md,md.mask.vertexonwater,1); + + %lat long +-md.mesh.lat=project2d(md,md.mesh.lat,1); +-md.mesh.long=project2d(md,md.mesh.long,1); ++if numel(md.mesh.lat)>1, md.mesh.lat=project2d(md,md.mesh.lat,1); end ++if numel(md.mesh.long)>1, md.mesh.long=project2d(md,md.mesh.long,1); end + + %Initialize with the 2d mesh + md.mesh.x=md.mesh.x2d; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m (revision 12087) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m (revision 12088) +@@ -39,6 +39,7 @@ + data_min=min(data_grid(:)); + data_max=max(data_grid(:)); + end ++options=changefieldvalue(options,'cbYLim',[data_min data_max]); + if whitepos==1, + white =data_max + (data_max-data_min)/55; + options=changefieldvalue(options,'caxis',[data_min white]); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m (revision 12087) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m (revision 12088) +@@ -219,6 +219,9 @@ + warning on MATLAB:log:logOfZero; + set(c,'YTickLabel',labels); + end ++ if exist(options,'cbYLim'); ++ set(c,'YLim',getfieldvalue(options,'cbYLim')); ++ end + if exist(options,'colorbartitle'), + set(get(c,'title'),'FontSize',getfieldvalue(options,'colorbarfontsize',fontsize),'String',getfieldvalue(options,'colorbartitle'),... + 'Color',getfieldvalue(options,'FontColor','k')); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/meshrefine.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/meshrefine.m (revision 12087) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/meshrefine.m (revision 12088) +@@ -1,40 +0,0 @@ +-function md=meshrefine(md,areas) +-%MESHREFINE: refined the mesh from a model, according to an area metric. +-% +-% Usage: +-% md=meshrefine(md,metric) +- +-%some checks on list of arguments +-if ((nargin~=2) | (nargout~=1)), +- meshrefineusage(); +- error('meshrefine error message'); +-end +-if ( (isempty(areas)) | (length(areas)~=md.mesh.numberofelements) | (length(find(isnan(areas))))), +- meshrefineusage(); +- error('meshrefine error message'); +-end +- +-%Refine using TriMeshRefine +-[md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshRefine(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers,areas,'yes'); +- +-%Fill in rest of fields: +-md.mesh.numberofelements=length(md.mesh.elements); +-md.mesh.numberofvertices=length(md.mesh.x); +-md.mesh.z=zeros(md.mesh.numberofvertices,1); +-md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; +-md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); +-md.mesh.vertexonsurface=ones(md.mesh.numberofvertices,1); +-md.mesh.elementonbed=ones(md.mesh.numberofelements,1); +-md.mesh.elementonsurface=ones(md.mesh.numberofelements,1); +- +-%Now, build the connectivity tables for this mesh. +-md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +-md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); +- +-%type of model +-md.mesh.dimension=2; +-end +- +-function meshrefineusage(), +-disp('usage: md=meshrefine(md,areas)'); +-end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/meshnodensity.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/meshnodensity.m (revision 12087) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/meshnodensity.m (revision 12088) +@@ -1,71 +0,0 @@ +-function md=meshnodensity(md,domainname,varargin) +-%MESH - create model mesh +-% +-% This routine creates a model mesh using TriMeshNoDensity and a domain outline +-% where md is a @model object, domainname is the name of an Argus domain outline file, +-% Riftname is an optional argument (Argus domain outline) describing rifts. +-% The difference with mesh.m is that the resolution of the mesh follows that of the domain +-% outline and the riftoutline +-% +-% Usage: +-% md=meshnodensity(md,domainname) +-% or md=meshnodensity(md,domainname,riftname); +-% +-% Examples: +-% md=meshnodensity(md,'DomainOutline.exp'); +-% md=meshnodensity(md,'DomainOutline.exp','Rifts.exp'); +- +-if (nargin==2), +- riftname=''; +-end +-if (nargin==3), +- riftname=varargin{1}; +-end +- +-%Mesh using TriMeshNoDensity +-if strcmp(riftname,''), +- [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshNoDensity(domainname); +-else +- [elements,x,y,segments,segmentmarkers]=TriMeshNoDensity(domainname,riftname); +- +- %check that all the created nodes belong to at least one element +- orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); +- for i=1:length(orphan), +- %get rid of the orphan node i +- %update x and y +- x=[x(1:orphan(i)-(i-1)-1); x(orphan(i)-(i-1)+1:end)]; +- y=[y(1:orphan(i)-(i-1)-1); y(orphan(i)-(i-1)+1:end)]; +- %update elements +- pos=find(elements>orphan(i)-(i-1)); +- elements(pos)=elements(pos)-1; +- %update segments +- pos1=find(segments(:,1)>orphan(i)-(i-1)); +- pos2=find(segments(:,2)>orphan(i)-(i-1)); +- segments(pos1,1)=segments(pos1,1)-1; +- segments(pos2,2)=segments(pos2,2)-1; +- end +- +- %plug into md +- md.mesh.x=x; +- md.mesh.y=y; +- md.mesh.elements=elements; +- md.mesh.segments=segments; +- md.mesh.segmentmarkers=segmentmarkers; +-end +- +-%Fill in rest of fields: +-md.mesh.numberofelements=length(md.mesh.elements); +-md.mesh.numberofvertices=length(md.mesh.x); +-md.mesh.z=zeros(md.mesh.numberofvertices,1); +-md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; +-md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); +-md.mesh.vertexonsurface=ones(md.mesh.numberofvertices,1); +-md.mesh.elementonbed=ones(md.mesh.numberofelements,1); +-md.mesh.elementonsurface=ones(md.mesh.numberofelements,1); +- +-%Now, build the connectivity tables for this mesh. +-md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +-md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); +- +-%type of model +-md.mesh.dimension=2; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/exptool.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/exptool.m (revision 12087) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/exptool.m (revision 12088) +@@ -70,7 +70,7 @@ + error(['exptool error message:, ' filename ' does not exist. Exiting...']); + else + %read file +- B=expread(filename,1); ++ B=expread(filename); + %go through all profiles of B + for i=1:size(B,2) + %plug profile in A Index: /issm/oecreview/Archive/12081-12100/ISSM-12088-12089.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12088-12089.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12088-12089.diff (revision 12325) @@ -0,0 +1,26 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m (revision 12088) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m (revision 12089) +@@ -39,7 +39,6 @@ + data_min=min(data_grid(:)); + data_max=max(data_grid(:)); + end +-options=changefieldvalue(options,'cbYLim',[data_min data_max]); + if whitepos==1, + white =data_max + (data_max-data_min)/55; + options=changefieldvalue(options,'caxis',[data_min white]); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m (revision 12088) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m (revision 12089) +@@ -219,9 +219,6 @@ + warning on MATLAB:log:logOfZero; + set(c,'YTickLabel',labels); + end +- if exist(options,'cbYLim'); +- set(c,'YLim',getfieldvalue(options,'cbYLim')); +- end + if exist(options,'colorbartitle'), + set(get(c,'title'),'FontSize',getfieldvalue(options,'colorbarfontsize',fontsize),'String',getfieldvalue(options,'colorbartitle'),... + 'Color',getfieldvalue(options,'FontColor','k')); Index: /issm/oecreview/Archive/12081-12100/ISSM-12089-12090.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12089-12090.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12089-12090.diff (revision 12325) @@ -0,0 +1,27 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am (revision 12089) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am (revision 12090) +@@ -35,9 +35,7 @@ + TriaSearch\ + TriMesh\ + TriMeshRifts\ +- TriMeshNoDensity\ + TriMeshProcessRifts\ +- TriMeshRefine\ + Xy2ll + endif + #}}} +@@ -160,12 +158,6 @@ + TriMeshRifts_SOURCES = ../TriMeshRifts/TriMeshRifts.cpp\ + ../TriMeshRifts/TriMeshRifts.h + +-TriMeshNoDensity_SOURCES = ../TriMeshNoDensity/TriMeshNoDensity.cpp\ +- ../TriMeshNoDensity/TriMeshNoDensity.h +- + TriMeshProcessRifts_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\ + ../TriMeshProcessRifts/TriMeshProcessRifts.h +- +-TriMeshRefine_SOURCES = ../TriMeshRefine/TriMeshRefine.cpp\ +- ../TriMeshRefine/TriMeshRefine.h + #}}} Index: /issm/oecreview/Archive/12081-12100/ISSM-12090-12091.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12090-12091.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12090-12091.diff (revision 12325) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh (revision 12091) +@@ -0,0 +1,10 @@ ++#!/bin/sh ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --without-mpi \ ++ --without-matlab \ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --without-metis \ ++ --with-vendor=arm ++ --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12081-12100/ISSM-12091-12092.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12091-12092.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12091-12092.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12091) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12092) +@@ -1222,7 +1222,7 @@ + AC_MSG_ERROR([need at least python or matlab support to compile modules (or use --with-modules=no)]); + fi + +- check that we python version if python compile is specified ++ dnl check that we have python version if python compile is specified + if test "$HAVE_PYTHON" = "yes" && test "$PYTHONVERSION" = "" ; then + AC_MSG_ERROR([need python-version if python compile is required!]); + fi Index: /issm/oecreview/Archive/12081-12100/ISSM-12092-12093.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12092-12093.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12092-12093.diff (revision 12325) @@ -0,0 +1,424 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp (revision 12093) +@@ -13,7 +13,6 @@ + #include "../../Container/DataSet.h" + + int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname,bool whole=true){ +- + + /*indexing: */ + int i,counter; +@@ -127,29 +126,29 @@ + + DataSet* DomainOutlineRead(char* domainname,bool whole=true){ + +- /*indexing: */ +- int i; +- + /*intermediary: */ +- int nprof; +- int* profnvertices=NULL; +- double** pprofx=NULL; +- double** pprofy=NULL; ++ int nprof; ++ int *profnvertices = NULL; ++ double **pprofx = NULL; ++ double **pprofy = NULL; ++ Contour *contour = NULL; + +- Contour* contour=NULL; +- + /*output: */ + DataSet* domain=NULL; + +- /*get domain outline from intermediary function:*/ +- DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname,whole); ++ /*If domainname is an empty string, return empty dataset*/ ++ if (strcmp(domainname,"")==0){ ++ nprof=0; ++ } ++ else{ ++ DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname,whole); ++ } + + /*now create dataset of contours: */ + domain=new DataSet(0); + +- for(i=0;iAddObject(new Contour(i,profnvertices[i],pprofx[i],pprofy[i],1)); + } +- + return domain; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.h (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.h (revision 12093) +@@ -10,6 +10,6 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void TriMeshRiftsx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area,bool order); ++void TriMeshRiftsx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area); + + #endif /* _TRIMESHX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.cpp (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.cpp (revision 12093) +@@ -19,7 +19,7 @@ + #endif + /*}}}*/ + +-void TriMeshRiftsx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area,bool order){ ++void TriMeshRiftsx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area){ + + /*indexing: */ + int i,j; +@@ -47,12 +47,11 @@ + contour=(Contour*)domain->GetObjectByOffset(i); + in.numberofpoints+=contour->nods; + } +- if (rifts){ +- for (i=0;iSize();i++){ +- contour=(Contour*)rifts->GetObjectByOffset(i); +- in.numberofpoints+=contour->nods; +- } ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ in.numberofpoints+=contour->nods; + } ++ + /*number of point attributes: */ + in.numberofpointattributes=1; + +@@ -68,14 +67,12 @@ + counter++; + } + } +- if(rifts){ +- for (i=0;iSize();i++){ +- contour=(Contour*)rifts->GetObjectByOffset(i); +- for (j=0;jnods;j++){ +- in.pointlist[2*counter+0]=contour->x[j]; +- in.pointlist[2*counter+1]=contour->y[j]; +- counter++; +- } ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ for (j=0;jnods;j++){ ++ in.pointlist[2*counter+0]=contour->x[j]; ++ in.pointlist[2*counter+1]=contour->y[j]; ++ counter++; + } + } + +@@ -93,12 +90,10 @@ + contour=(Contour*)domain->GetObjectByOffset(i); + in.numberofsegments+=contour->nods; + } +- if(rifts){ +- for(i=0;iSize();i++){ +- contour=(Contour*)rifts->GetObjectByOffset(i); +- /*for rifts, we have one less segment as we have vertices*/ +- in.numberofsegments+=contour->nods-1; +- } ++ for(i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ /*for rifts, we have one less segment as we have vertices*/ ++ in.numberofsegments+=contour->nods-1; + } + + in.segmentlist = (int *) xmalloc(in.numberofsegments * 2 * sizeof(int)); +@@ -121,18 +116,16 @@ + backcounter=counter; + } + counter2=counter; +- if(rifts){ +- for (i=0;iSize();i++){ +- contour=(Contour*)rifts->GetObjectByOffset(i); +- for (j=0;j<(contour->nods-1);j++){ +- in.segmentlist[2*counter2+0]=counter; +- in.segmentlist[2*counter2+1]=counter+1; +- in.segmentmarkerlist[counter2]=2+i; +- counter2++; +- counter++; +- } ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ for (j=0;j<(contour->nods-1);j++){ ++ in.segmentlist[2*counter2+0]=counter; ++ in.segmentlist[2*counter2+1]=counter+1; ++ in.segmentmarkerlist[counter2]=2+i; ++ counter2++; + counter++; + } ++ counter++; + } + + /*Build regions: */ +@@ -195,9 +188,7 @@ + AssociateSegmentToElement(&segments,out.numberofsegments,index,out.numberoftriangles); + + /*Order segments so that their normals point outside the domain: */ +- if(order){ +- OrderSegments(&segments,out.numberofsegments, index,out.numberoftriangles); +- } ++ OrderSegments(&segments,out.numberofsegments, index,out.numberoftriangles); + + /*Output : */ + index_matrix=new Matrix(index,out.numberoftriangles,3,1); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp (revision 12093) +@@ -19,7 +19,7 @@ + #endif + /*}}}*/ + +-void TriMeshx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,double area,bool order){ ++void TriMeshx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area){ + + /*indexing: */ + int i,j; +@@ -34,7 +34,7 @@ + double* segmentmarkerlist=NULL; + + /*intermediary: */ +- int counter,backcounter; ++ int counter,counter2,backcounter; + Contour* contour=NULL; + + /* Triangle structures needed to call Triangle library routines: */ +@@ -47,6 +47,11 @@ + contour=(Contour*)domain->GetObjectByOffset(i); + in.numberofpoints+=contour->nods; + } ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ in.numberofpoints+=contour->nods; ++ } ++ + /*number of point attributes: */ + in.numberofpointattributes=1; + +@@ -62,9 +67,17 @@ + counter++; + } + } ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ for (j=0;jnods;j++){ ++ in.pointlist[2*counter+0]=contour->x[j]; ++ in.pointlist[2*counter+1]=contour->y[j]; ++ counter++; ++ } ++ } + + /*fill in the point attribute list: */ +- in.pointattributelist = (REAL *) xmalloc(in.numberofpoints * in.numberofpointattributes * sizeof(REAL)); ++ in.pointattributelist = (REAL*)xmalloc(in.numberofpoints*in.numberofpointattributes*sizeof(REAL)); + for (i=0;iGetObjectByOffset(i); + in.numberofsegments+=contour->nods; + } ++ for(i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ /*for rifts, we have one less segment as we have vertices*/ ++ in.numberofsegments+=contour->nods-1; ++ } + + in.segmentlist = (int *) xmalloc(in.numberofsegments * 2 * sizeof(int)); + in.segmentmarkerlist = (int *) xcalloc(in.numberofsegments,sizeof(int)); +@@ -97,6 +115,18 @@ + counter++; + backcounter=counter; + } ++ counter2=counter; ++ for (i=0;iSize();i++){ ++ contour=(Contour*)rifts->GetObjectByOffset(i); ++ for (j=0;j<(contour->nods-1);j++){ ++ in.segmentlist[2*counter2+0]=counter; ++ in.segmentlist[2*counter2+1]=counter+1; ++ in.segmentmarkerlist[counter2]=2+i; ++ counter2++; ++ counter++; ++ } ++ counter++; ++ } + + /*Build regions: */ + in.numberofregions = 0; +@@ -158,9 +188,7 @@ + AssociateSegmentToElement(&segments,out.numberofsegments,index,out.numberoftriangles); + + /*Order segments so that their normals point outside the domain: */ +- if(order){ +- OrderSegments(&segments,out.numberofsegments, index,out.numberoftriangles); +- } ++ OrderSegments(&segments,out.numberofsegments, index,out.numberoftriangles); + + /*Output : */ + index_matrix=new Matrix(index,out.numberoftriangles,3,1); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.h (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.h (revision 12093) +@@ -6,11 +6,10 @@ + #define _TRIMESHX_H_ + + #include "string.h" +- + #include "../../Container/Container.h" + #include "../../objects/objects.h" + + /* local prototypes: */ +-void TriMeshx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,double area,bool order); ++void TriMeshx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area); + + #endif /* _TRIMESHX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12093) +@@ -792,8 +792,6 @@ + ./modules/TriaSearchx/TriaSearchx.cpp\ + ./modules/TriMeshx/TriMeshx.h\ + ./modules/TriMeshx/TriMeshx.cpp\ +- ./modules/TriMeshRiftsx/TriMeshRiftsx.h\ +- ./modules/TriMeshRiftsx/TriMeshRiftsx.cpp\ + ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h\ + ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp\ + ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am (revision 12093) +@@ -34,7 +34,6 @@ + StringToEnum\ + TriaSearch\ + TriMesh\ +- TriMeshRifts\ + TriMeshProcessRifts\ + Xy2ll + endif +@@ -155,9 +154,6 @@ + TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\ + ../TriMesh/TriMesh.h + +-TriMeshRifts_SOURCES = ../TriMeshRifts/TriMeshRifts.cpp\ +- ../TriMeshRifts/TriMeshRifts.h +- + TriMeshProcessRifts_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\ + ../TriMeshProcessRifts/TriMeshProcessRifts.h + #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.h (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.h (revision 12093) +@@ -30,8 +30,8 @@ + #ifdef _HAVE_MATLAB_MODULES_ + /* serial input macros: */ + #define DOMAINOUTLINE (mxArray *)prhs[0] +-#define AREA (mxArray *)prhs[1] +-#define ORDER (mxArray *)prhs[2] ++#define RIFTSOUTLINE (mxArray *)prhs[1] ++#define AREA (mxArray *)prhs[2] + /* serial output macros: */ + #define INDEX (mxArray**)&plhs[0] + #define X (mxArray**)&plhs[1] +@@ -43,8 +43,8 @@ + #ifdef _HAVE_PYTHON_MODULES_ + /* serial input macros: */ + #define DOMAINOUTLINE PyTuple_GetItem(args,0) +-#define AREA PyTuple_GetItem(args,1) +-#define ORDER PyTuple_GetItem(args,2) ++#define RIFTSOUTLINE PyTuple_GetItem(args,1) ++#define AREA PyTuple_GetItem(args,2) + /* serial output macros: */ + #define INDEX output,0 + #define X output,1 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp (revision 12092) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp (revision 12093) +@@ -7,19 +7,20 @@ + WRAPPER(TriMesh){ + + /* input: */ +- char* domainname=NULL; +- double area; +- bool order; ++ char *domainname = NULL; ++ char *riftsname = NULL; ++ double area; + + /*intermediary: */ +- DataSet* domain=NULL; ++ DataSet *domain = NULL; ++ DataSet *rifts = NULL; + + /* output: */ +- Matrix* index=NULL; +- Vector* x=NULL; +- Vector* y=NULL; +- Matrix* segments=NULL; +- Vector* segmentmarkerlist=NULL; ++ Matrix *index = NULL; ++ Vector *x = NULL; ++ Vector *y = NULL; ++ Matrix *segments = NULL; ++ Vector *segmentmarkerlist = NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -29,15 +30,16 @@ + + /*Fetch data needed for meshing: */ + FetchData(&domainname,DOMAINOUTLINE); ++ FetchData(&riftsname,RIFTSOUTLINE); + FetchData(&area,AREA); +- FetchData(&order,ORDER); + + /*Read domain outline: */ +- domain=DomainOutlineRead(domainname,false); ++ domain = DomainOutlineRead(domainname,false); ++ rifts = DomainOutlineRead(riftsname,false); + + /*call x core: */ +- TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,area,order); +- ++ TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,rifts,area); ++ + /*write outputs: */ + WriteData(INDEX,index); + WriteData(X,x); +@@ -47,6 +49,7 @@ + + /*free ressources: */ + delete domain; ++ delete rifts; + xdelete_module(&index); + xdelete_module(&x); + xdelete_module(&y); +@@ -60,13 +63,11 @@ + void TriMeshUsage(void) //{{{1 + { + printf("\n"); +- printf(" usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,area,ordered) \n"); ++ printf(" usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,rifts,area) \n"); + printf(" where: index,x,y defines a triangulation, segments is an array made \n"); + printf(" of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment, \n"); + printf(" outlinefilename an Argus domain outline file, \n"); + printf(" area is the maximum area desired for any element of the resulting mesh, \n"); +- printf(" and ordered is a bool that determines whether segments are output in the \n"); +- printf(" order they are made by Triangle (ie none), or ordered counter clockwise around the domain outline.\n"); + printf("\n"); + } + //}}} Index: /issm/oecreview/Archive/12081-12100/ISSM-12093-12094.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12093-12094.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12093-12094.diff (revision 12325) @@ -0,0 +1,65 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.m (revision 12093) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.m (revision 12094) +@@ -37,36 +37,33 @@ + area=resolution^2; + + %Mesh using TriMesh +-if strcmp(riftname,''), +- [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,area,true); +-else +- [elements,x,y,segments,segmentmarkers]=TriMeshRifts(domainname,riftname,area,true); ++[elements,x,y,segments,segmentmarkers]=TriMesh(domainname,riftname,area); + +- %check that all the created nodes belong to at least one element +- orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); +- for i=1:length(orphan), +- %get rid of the orphan node i +- %update x and y +- x=[x(1:orphan(i)-(i-1)-1); x(orphan(i)-(i-1)+1:end)]; +- y=[y(1:orphan(i)-(i-1)-1); y(orphan(i)-(i-1)+1:end)]; +- %update elements +- pos=find(elements>orphan(i)-(i-1)); +- elements(pos)=elements(pos)-1; +- %update segments +- pos1=find(segments(:,1)>orphan(i)-(i-1)); +- pos2=find(segments(:,2)>orphan(i)-(i-1)); +- segments(pos1,1)=segments(pos1,1)-1; +- segments(pos2,2)=segments(pos2,2)-1; +- end +- +- %plug into md +- md.mesh.x=x; +- md.mesh.y=y; +- md.mesh.elements=elements; +- md.mesh.segments=segments; +- md.mesh.segmentmarkers=segmentmarkers; ++%check that all the created nodes belong to at least one element ++orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); ++for i=1:length(orphan), ++ disp('WARNING: removing orphans'); ++ %get rid of the orphan node i ++ %update x and y ++ x=[x(1:orphan(i)-(i-1)-1); x(orphan(i)-(i-1)+1:end)]; ++ y=[y(1:orphan(i)-(i-1)-1); y(orphan(i)-(i-1)+1:end)]; ++ %update elements ++ pos=find(elements>orphan(i)-(i-1)); ++ elements(pos)=elements(pos)-1; ++ %update segments ++ pos1=find(segments(:,1)>orphan(i)-(i-1)); ++ pos2=find(segments(:,2)>orphan(i)-(i-1)); ++ segments(pos1,1)=segments(pos1,1)-1; ++ segments(pos2,2)=segments(pos2,2)-1; + end + ++%plug into md ++md.mesh.x=x; ++md.mesh.y=y; ++md.mesh.elements=elements; ++md.mesh.segments=segments; ++md.mesh.segmentmarkers=segmentmarkers; ++ + %Fill in rest of fields: + md.mesh.numberofelements=length(md.mesh.elements); + md.mesh.numberofvertices=length(md.mesh.x); Index: /issm/oecreview/Archive/12081-12100/ISSM-12095-12096.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12095-12096.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12095-12096.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h (revision 12095) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h (revision 12096) +@@ -111,7 +111,6 @@ + #include "./TimeAdaptx/TimeAdaptx.h" + #include "./TriaSearchx/TriaSearchx.h" + #include "./TriMeshx/TriMeshx.h" +-#include "./TriMeshRiftsx/TriMeshRiftsx.h" + #include "./ThicknessAbsMisfitx/ThicknessAbsMisfitx.h" + #include "./ThicknessAbsGradientx/ThicknessAbsGradientx.h" + #include "./UpdateVertexPositionsx/UpdateVertexPositionsx.h" Index: /issm/oecreview/Archive/12081-12100/ISSM-12096-12097.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12096-12097.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12096-12097.diff (revision 12325) @@ -0,0 +1,203 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh (revision 12097) +@@ -0,0 +1,78 @@ ++#This installs the Android SDK (Software Development Kit) ++#which is needed for the compilation of the Java project. ++ ++step=3; ++ ++#Different steps here. ++#1: install sdk, ant and sdk tools ++#2: install an emulator. ++#3: test the emulator ++#4: cleanup ++ ++present_dir=`pwd`; ++default_droid="Android-4.0" ++ ++if [[ $step == "1" ]]; then ++ ++ #Cleanup the install ++ rm -rf install-sdk install-ant ++ ++ # Install Android SDK and NDK. ++ unzip -o android-sdk-r16-macosx.zip ++ unzip -o apache-ant-1.8.2-bin.zip ++ ++ #Move to install ++ mv android-sdk-macosx install-sdk ++ mv apache-ant-1.8.2 install-ant ++ ++ #Post_install configuration: ++ #We need specific settings for specific platforms, for the SDK to ++ #function properly ++ ++ #For now, we need to install: ++ #android sdk platform tools ++ #and a specific android api: API 15 ++ #Note: API 15 corresponds to Android 4.0.3 ++ ++ cd install-sdk/tools/ && source ./android update sdk -t platform-tools,android-15,android-14,system-image --no-ui ++ ++fi ++ ++if [[ $step == "2" ]]; then ++ ++ #Once this is done, we need to install an emulator. Location will default to ~/.android/avd, ++ #which we will move to $ISSM_TIER/externalpackages/android-emulators. ++ #For now, it's called: Android-4.0.3 ++ ++ ++ #Here we delete the Android-4.0.3 device if it already exists. ++ cd $present_dir/install-sdk/tools ++ ++ if [ -e $ANDROID_DIR/android-emulators/$default_droid ] ++ then ++ echo "Deleting previously created device: $default_droid" ++ ./android delete avd -n $default_droid ++ fi ++ ++ #Android will prompt the user to specify hardware emulation options. For now, default ++ #default settings will suffice. Press 'enter' to take default settings or enter 'no'. ++ ++ ./android create avd -f -n $default_droid -t 1 -p $ANDROID_DIR/android-emulators/$default_droid --abi armeabi-v7a ++fi ++ ++if [[ $step == "3" ]]; then ++ #Here we will start up our default emulator to test that it is working properly. ++ #Once the device has booted we will use the Android Debug Bridge tool to gain ++ #a terminal in our device. ++ ++ cd $present_dir/install-sdk/tools ++ ./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/test & ++ ++ cd ../platform-tools ++ ./adb wait-for-device shell ++ ++fi ++ ++if [[ $step == "4" ]]; then ++ rm -rf install-sdk install-ant ++fi + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/apache-ant-1.8.2-bin.zip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/apache-ant-1.8.2-bin.zip +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/android-sdk-r16-macosx.zip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/android-sdk-r16-macosx.zip +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk +___________________________________________________________________ +Added: svn:ignore + + install-sdk +install-ant + + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-ndk/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-ndk/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-ndk/install.sh (revision 12097) +@@ -0,0 +1,22 @@ ++#This installs the Android NDK (Native Development Kit) ++#which is needed for the compilation of C/C++ code into the ++#native architecture of the Android device. ++ ++#The android-ndk-r7b-darwin-x86.tar.bz2 dummy.tar.bz2 file was downloaded ++#from the android developer website: ++ ++#Cleanup the install ++rm -rf install ++rm -rf $ANDROID_DIR/arm-linux-android-4.0 ++ ++# Install Android SDK and NDK. ++cp android-ndk-r7b-darwin-x86.tar.bz2 dummy.tar.bz2 ++bunzip2 dummy.tar.bz2 ++tar -xvf dummy.tar ++rm -rf dummy.tar dummy.tar.bz2 ++ ++#Move to install ++mv android-ndk-r7b install ++ ++#Create Standalone Development Directory ++$ANDROID_NDK_DIR/build/tools/make-standalone-toolchain.sh --platform=android-5 --install-dir=$ANDROID_DIR/arm-linux-android-4.0 + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-ndk/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-ndk/android-ndk-r7b-darwin-x86.tar.bz2 +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-ndk/android-ndk-r7b-darwin-x86.tar.bz2 +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 12096) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 12097) +@@ -172,17 +172,17 @@ + #packagemaker + PACKAGEMAKER_DIR="$ISSM_TIER/externalpackages/packagemaker/install" + ++#android-dev-dir ++ANDROID_DIR="$ISSM_TIER/externalpackages/android" ++ + #android-ndk +-ANDROID_NDK_DIR="$ISSM_TIER/externalpackages/android-ndk/install" ++ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install" + +-#android-dev-dir +-ANDROID_DEV_DIR="$ISSM_TIER/externalpackages/android-dev-dir" +- + #android-sdk +-ANDROID_SDK_DIR="$ISSM_TIER/externalpackages/android-sdk/install-sdk" ++ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk" + + #android-ant +-ANDROID_ANT_DIR="$ISSM_TIER/externalpackages/android-sdk/install-ant" ++ANDROID_ANT_DIR="$ANDROID_DIR/android-sdk/install-ant" + + #gsl + GSL_DIR="$ISSM_TIER/externalpackages/gsl/install" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 12096) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 12097) +@@ -241,8 +241,8 @@ + export ANDROID_NDK_DIR + export PATH="$PATH:$ANDROID_NDK_DIR/" + +-#ANDROID_DEV_DIR +-export ANDROID_DEV_DIR ++#ANDROID_DIR ++export ANDROID_DIR + + #ANDROID_SDK + export PATH="$PATH:$ANDROID_SDK_DIR/" Index: /issm/oecreview/Archive/12081-12100/ISSM-12097-12098.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12097-12098.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12097-12098.diff (revision 12325) @@ -0,0 +1,187 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/exp.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/exp.h (revision 12097) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/exp.h (revision 12098) +@@ -12,11 +12,11 @@ + int IsInPoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue); + int IsOutsidePoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue); + int IsInPolySerial(double* in,double* xc,double* yc,int numvertices,double* x,double* y,int nods, int edgevalue); +-int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname,bool whole); ++int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname); + int pnpoly(int npol, double *xp, double *yp, double x, double y, int edgevalue); + +-int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname,bool whole); +-DataSet* DomainOutlineRead(char* domainname,bool whole); ++int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname); ++DataSet* DomainOutlineRead(char* domainname); + + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineWrite.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineWrite.cpp (revision 12097) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineWrite.cpp (revision 12098) +@@ -10,7 +10,7 @@ + #include "../../include/include.h" + #include "../Exceptions/exceptions.h" + +-int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname,bool whole=true){ ++int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname){ + + + /*Error management: */ +@@ -20,13 +20,6 @@ + /*I/O: */ + FILE* fid=NULL; + +- /*input: */ +-// int nprof; //number of profiles in the domainname file +-// int* profnvertices=NULL; //array holding the number of vertices for the nprof profiles +-// double** pprofx=NULL; //array of profiles x coordinates +-// double** pprofy=NULL; //array of profiles y coordinates +-// bool* closed=NULL; //array holding closed flags for the nprof profiles +- + /*open domain outline file for writing: */ + if ((fid=fopen(domainname,"w"))==NULL){ + _error_("%s%s","could not open domain file ",domainname); +@@ -42,10 +35,7 @@ + fprintf(fid,"%s %s %s %s\n","#","Points","Count","Value"); + + /*Write number of profile vertices: */ +- if(closed[counter] && !whole) +- fprintf(fid,"%u %s\n",profnvertices[counter]+1,"1."); +- else +- fprintf(fid,"%u %s\n",profnvertices[counter] ,"1."); ++ fprintf(fid,"%u %s\n",profnvertices[counter] ,"1."); + + /*Write next line: */ + fprintf(fid,"%s %s %s %s %s\n","#","X","pos","Y","pos"); +@@ -55,10 +45,6 @@ + fprintf(fid,"%lf\t%lf\n",pprofx[counter][i],pprofy[counter][i]); + } + +- /*Now check that we are dealing with open contours: */ +- if(closed[counter] && !whole) +- fprintf(fid,"%lf\t%lf\n",pprofx[counter][0],pprofy[counter][0]); +- + /*Write blank line: */ + if(counter < nprof-1) fprintf(fid,"\n"); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp (revision 12097) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp (revision 12098) +@@ -12,7 +12,7 @@ + #include "../Exceptions/exceptions.h" + #include "../../Container/DataSet.h" + +-int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname,bool whole=true){ ++int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname){ + + /*indexing: */ + int i,counter; +@@ -100,9 +100,6 @@ + cl=false; + if((x[0]==x[n-1]) && (y[0]==y[n-1])){ + cl=true; +- if (!whole) { +- n=n-1; +- } + } + + /*Assign pointers: */ +@@ -124,7 +121,7 @@ + else xfree((void**)&closed); + } + +-DataSet* DomainOutlineRead(char* domainname,bool whole=true){ ++DataSet* DomainOutlineRead(char* domainname){ + + /*intermediary: */ + int nprof; +@@ -141,7 +138,7 @@ + nprof=0; + } + else{ +- DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname,whole); ++ DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname); + } + + /*now create dataset of contours: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp (revision 12097) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp (revision 12098) +@@ -60,7 +60,7 @@ + + /* read exp file */ + +- if (!DomainOutlineRead(&nprof,&pnvert,&pprofx,&pprofy,&closed,filexp,true)) ++ if (!DomainOutlineRead(&nprof,&pnvert,&pprofx,&pprofy,&closed,filexp)) + _error_("Error reading exp file."); + _printf_(true,"Exp2Kmlx -- Reading %d exp profiles from file \"%s\".\n",nprof,filexp); + // for (i=0; iSize();i++){ + contour=(Contour*)domain->GetObjectByOffset(i); +- in.numberofpoints+=contour->nods; ++ in.numberofpoints+=contour->nods-1; + } + for (i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); +@@ -61,7 +61,7 @@ + counter=0; + for (i=0;iSize();i++){ + contour=(Contour*)domain->GetObjectByOffset(i); +- for (j=0;jnods;j++){ ++ for (j=0;jnods-1;j++){ + in.pointlist[2*counter+0]=contour->x[j]; + in.pointlist[2*counter+1]=contour->y[j]; + counter++; +@@ -88,7 +88,7 @@ + in.numberofsegments=0; + for (i=0;iSize();i++){ + contour=(Contour*)domain->GetObjectByOffset(i); +- in.numberofsegments+=contour->nods; ++ in.numberofsegments+=contour->nods-1; + } + for(i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); +@@ -102,7 +102,7 @@ + backcounter=0; + for (i=0;iSize();i++){ + contour=(Contour*)domain->GetObjectByOffset(i); +- for (j=0;jnods-1;j++){ ++ for (j=0;jnods-2;j++){ + in.segmentlist[2*counter+0]=counter; + in.segmentlist[2*counter+1]=counter+1; + in.segmentmarkerlist[counter]=0; +@@ -137,7 +137,7 @@ + in.holelist = (REAL *) xmalloc(in.numberofholes * 2 * sizeof(REAL)); + for (i=0;iSize()-1;i++){ + contour=(Contour*)domain->GetObjectByOffset(i+1); +- GridInsideHole(&in.holelist[2*i+0],&in.holelist[2*i+1],contour->nods,contour->x,contour->y); ++ GridInsideHole(&in.holelist[2*i+0],&in.holelist[2*i+1],contour->nods-1,contour->x,contour->y); + } + } + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp (revision 12097) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp (revision 12098) +@@ -34,8 +34,8 @@ + FetchData(&area,AREA); + + /*Read domain outline: */ +- domain = DomainOutlineRead(domainname,false); +- rifts = DomainOutlineRead(riftsname,false); ++ domain = DomainOutlineRead(domainname); ++ rifts = DomainOutlineRead(riftsname); + + /*call x core: */ + TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,rifts,area); Index: /issm/oecreview/Archive/12081-12100/ISSM-12098-12099.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12098-12099.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12098-12099.diff (revision 12325) @@ -0,0 +1,52 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/dox/issm.dox +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/dox/issm.dox (revision 12098) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/dox/issm.dox (revision 12099) +@@ -45,37 +45,37 @@ + LanguagefilesblankcommentcodeTotal + + +- C++ 53315491172755800590771 ++ C++ 49914338163405465185329 + + +- MATLAB 9777199137023169052591 ++ MATLAB 9196875131843035050409 + + +- C/C++ Header 399306927271035816154 ++ C/C++ Header 36626652529940014594 + + +- m4 71061242894110244 ++ m4 79938082379310 + + +- Objective C 9980370468 ++ Python 4718351810991800 + + +- Bourne Shell 86198271430 ++ Objective C 9980370468 + + + Perl 32123240284 + + +- IDL 1184124146 ++ Bourne Shell 54671226343 + + +- C 2332430 ++ IDL 1184124146 + + +- Python 2141318 ++ C 2332430 + + +- SUM: 19412702234078110036171136 ++ SUM: 18582524032752104721162713 + + + Index: /issm/oecreview/Archive/12081-12100/ISSM-12099-12100.diff =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-12099-12100.diff (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-12099-12100.diff (revision 12325) @@ -0,0 +1,36 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test452.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test452.m (revision 12099) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test452.m (revision 12100) +@@ -1,7 +1,6 @@ + md=triangle(model,'../Exp/Square.exp',350000); + md=setmask(md,'../Exp/SquareShelf.exp',''); + md=parameterize(md,'../Par/SquareSheetShelf.par'); +-md.cluster=none; + md.initialization.vx(:)=0; + md.initialization.vy(:)=0; + md.initialization.vel(:)=0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test448.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test448.m (revision 12099) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test448.m (revision 12100) +@@ -2,7 +2,6 @@ + md=setmask(md,'../Exp/SquareShelf.exp',''); + md=parameterize(md,'../Par/SquareSheetShelf.par'); + md=setflowequation(md,'macayeal','all'); +-md.cluster=none; + md.initialization.vx(:)=0; + md.initialization.vy(:)=0; + md.initialization.vel(:)=0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test450.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test450.m (revision 12099) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test450.m (revision 12100) +@@ -2,7 +2,6 @@ + md=setmask(md,'../Exp/SquareShelf.exp',''); + md=parameterize(md,'../Par/SquareSheetShelf.par'); + md=setflowequation(md,'macayeal','all'); +-md.cluster=none; + md.initialization.vx(:)=0; + md.initialization.vy(:)=0; + md.initialization.vel(:)=0; Index: /issm/oecreview/Archive/12081-12100/ISSM-DocReview-12081-12100.tex =================================================================== --- /issm/oecreview/Archive/12081-12100/ISSM-DocReview-12081-12100.tex (revision 12325) +++ /issm/oecreview/Archive/12081-12100/ISSM-DocReview-12081-12100.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12081-12100/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12081-12100/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12081-12100/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12081-12100 Index: /issm/oecreview/Archive/12081-12100/Makefile =================================================================== --- /issm/oecreview/Archive/12081-12100/Makefile (revision 12325) +++ /issm/oecreview/Archive/12081-12100/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12081-12100 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12081-12100/log.tex =================================================================== --- /issm/oecreview/Archive/12081-12100/log.tex (revision 12325) +++ /issm/oecreview/Archive/12081-12100/log.tex (revision 12325) @@ -0,0 +1,38 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12081-12082.diff: \\ Function name: \\M /issm/trunk-jpl/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp \\ Export determination: 6. \\Rationale: Reorganizing and adding assertion for safety +M /issm/trunk-jpl/src/m/model/mesh/triangle.m converting to 'order' to bollean \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12082-12083.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/mesh/triangle.m \\ Export determination: 6. \\Rationale: converting to 'order' to bollean +M /issm/trunk-jpl/externalpackages/android-sdk/install.sh Minor bug \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12083-12084.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/android-sdk/install.sh \\ Export determination: 6. \\Rationale: Minor bug +M /issm/trunk-jpl/externalpackages/android-ndk/install.sh Minor bug \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12084-12085.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/android-ndk/install.sh \\ Export determination: 6. \\Rationale: Minor bug +M /issm/trunk-jpl/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp Fixed WriteData \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12085-12086.diff: \\ Function name: \\M /issm/trunk-jpl/src/modules/TriMeshProcessRifts/TriMeshProcessRifts.cpp \\ Export determination: 6. \\Rationale: Fixed WriteData +M /issm/trunk-jpl/src/c/shared/TriMesh/SplitMeshForRifts.cpp M /issm/trunk-jpl/src/c/shared/TriMesh/TriMeshUtils.cpp Fixed checks \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12086-12087.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/shared/TriMesh/SplitMeshForRifts.cpp M /issm/trunk-jpl/src/c/shared/TriMesh/TriMeshUtils.cpp \\ Export determination: 6. \\Rationale: Fixed checks +M /issm/trunk-jpl/src/m/model/plot/plot\_overlay.m redblue is flipped in overlay \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12087-12088.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/plot/plot\_overlay.m \\ Export determination: 6. \\Rationale: redblue is flipped in overlay +M /issm/trunk-jpl/src/m/model/collapse.m D /issm/trunk-jpl/src/m/model/mesh/meshnodensity.m D /issm/trunk-jpl/src/m/model/mesh/meshrefine.m M /issm/trunk-jpl/src/m/model/plot/applyoptions.m M /issm/trunk-jpl/src/m/model/plot/plot\_gridded.m M /issm/trunk-jpl/src/m/utils/Exp/exptool.m never used (that's 2 modules less) \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12088-12089.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/collapse.m D /issm/trunk-jpl/src/m/model/mesh/meshnodensity.m D /issm/trunk-jpl/src/m/model/mesh/meshrefine.m M /issm/trunk-jpl/src/m/model/plot/applyoptions.m M /issm/trunk-jpl/src/m/model/plot/plot\_gridded.m M /issm/trunk-jpl/src/m/utils/Exp/exptool.m \\ Export determination: 6. \\Rationale: never used (that's 2 modules less) +M /issm/trunk-jpl/src/m/model/plot/applyoptions.m M /issm/trunk-jpl/src/m/model/plot/plot\_gridded.m reverted: to be implemented by Chris \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12089-12090.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/plot/applyoptions.m M /issm/trunk-jpl/src/m/model/plot/plot\_gridded.m \\ Export determination: 6. \\Rationale: reverted: to be implemented by Chris +D /issm/trunk-jpl/src/modules/TriMeshNoDensity D /issm/trunk-jpl/src/modules/TriMeshRefine M /issm/trunk-jpl/src/modules/matlab/Makefile.am Removed 2 modules never used \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12090-12091.diff: \\ Function name: \\D /issm/trunk-jpl/src/modules/TriMeshNoDensity D /issm/trunk-jpl/src/modules/TriMeshRefine M /issm/trunk-jpl/src/modules/matlab/Makefile.am \\ Export determination: 6. \\Rationale: Removed 2 modules never used +A /issm/trunk-jpl/configs/config-arm.sh ARM processors configuration file \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12091-12092.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-arm.sh \\ Export determination: 6. \\Rationale: ARM processors configuration file +M /issm/trunk-jpl/m4/issm\_options.m4 commenting comments \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-12092-12093.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: commenting comments +M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.cpp M /issm/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.h M /issm/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp M /issm/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.h M /issm/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp M /issm/trunk-jpl/src/modules/TriMesh/TriMesh.cpp M /issm/trunk-jpl/src/modules/TriMesh/TriMesh.h D /issm/trunk-jpl/src/modules/TriMeshRifts M /issm/trunk-jpl/src/modules/matlab/Makefile.am Merging TriMesh and TriMeshRifts \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-12093-12094.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.cpp M /issm/trunk-jpl/src/c/modules/TriMeshRiftsx/TriMeshRiftsx.h M /issm/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp M /issm/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.h M /issm/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp M /issm/trunk-jpl/src/modules/TriMesh/TriMesh.cpp M /issm/trunk-jpl/src/modules/TriMesh/TriMesh.h D /issm/trunk-jpl/src/modules/TriMeshRifts M /issm/trunk-jpl/src/modules/matlab/Makefile.am \\ Export determination: 6. \\Rationale: Merging TriMesh and TriMeshRifts +M /issm/trunk-jpl/src/m/model/mesh/triangle.m Merging TriMesh and TriMeshRifts \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-12094-12095.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/mesh/triangle.m \\ Export determination: 6. \\Rationale: Merging TriMesh and TriMeshRifts +D /issm/trunk-jpl/src/c/modules/TriMeshRiftsx not needed anymore \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-12095-12096.diff: \\ Function name: \\D /issm/trunk-jpl/src/c/modules/TriMeshRiftsx \\ Export determination: 6. \\Rationale: not needed anymore +M /issm/trunk-jpl/src/c/modules/modules.h minor \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-12096-12097.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/modules.h \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh A /issm/trunk-jpl/externalpackages/android A /issm/trunk-jpl/externalpackages/android/android-emulators (from /issm/trunk-jpl/externalpackages/android-dev-dir/android-emulators:12095) A /issm/trunk-jpl/externalpackages/android/android-ndk (from /issm/trunk-jpl/externalpackages/android-ndk:12095) M /issm/trunk-jpl/externalpackages/android/android-ndk/install.sh A /issm/trunk-jpl/externalpackages/android/android-sdk (from /issm/trunk-jpl/externalpackages/android-sdk:12095) M /issm/trunk-jpl/externalpackages/android/android-sdk/install.sh D /issm/trunk-jpl/externalpackages/android-dev-dir D /issm/trunk-jpl/externalpackages/android-ndk D /issm/trunk-jpl/externalpackages/android-sdk Modification to environment variables and file strucutre of Android. \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-12097-12098.diff: \\ Function name: \\M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh A /issm/trunk-jpl/externalpackages/android A /issm/trunk-jpl/externalpackages/android/android-emulators (from /issm/trunk-jpl/externalpackages/android-dev-dir/android-emulators:12095) A /issm/trunk-jpl/externalpackages/android/android-ndk (from /issm/trunk-jpl/externalpackages/android-ndk:12095) M /issm/trunk-jpl/externalpackages/android/android-ndk/install.sh A /issm/trunk-jpl/externalpackages/android/android-sdk (from /issm/trunk-jpl/externalpackages/android-sdk:12095) M /issm/trunk-jpl/externalpackages/android/android-sdk/install.sh D /issm/trunk-jpl/externalpackages/android-dev-dir D /issm/trunk-jpl/externalpackages/android-ndk D /issm/trunk-jpl/externalpackages/android-sdk \\ Export determination: 6. \\Rationale: Modification to environment variables and file strucutre of Android. +M /issm/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp M /issm/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp M /issm/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp M /issm/trunk-jpl/src/c/shared/Exp/DomainOutlineWrite.cpp M /issm/trunk-jpl/src/c/shared/Exp/exp.h M /issm/trunk-jpl/src/modules/TriMesh/TriMesh.cpp Removed 'whole' option of DomainOutlineRead (missleading) \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-12098-12099.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp M /issm/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp M /issm/trunk-jpl/src/c/shared/Exp/DomainOutlineRead.cpp M /issm/trunk-jpl/src/c/shared/Exp/DomainOutlineWrite.cpp M /issm/trunk-jpl/src/c/shared/Exp/exp.h M /issm/trunk-jpl/src/modules/TriMesh/TriMesh.cpp \\ Export determination: 6. \\Rationale: Removed 'whole' option of DomainOutlineRead (missleading) +M /issm/trunk-jpl/src/dox/issm.dox updated code stats \\\\ +\noindent \textbf{Change \#19} with diff file ISSM-12099-12100.diff: \\ Function name: \\M /issm/trunk-jpl/src/dox/issm.dox \\ Export determination: 6. \\Rationale: updated code stats +M /issm/trunk-jpl/test/NightlyRun/test448.m M /issm/trunk-jpl/test/NightlyRun/test450.m M /issm/trunk-jpl/test/NightlyRun/test452.m no more serial solution \\\\ Index: /issm/oecreview/Archive/12081-12100/r1.tex =================================================================== --- /issm/oecreview/Archive/12081-12100/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12081-12100/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12081 Index: /issm/oecreview/Archive/12081-12100/r2.tex =================================================================== --- /issm/oecreview/Archive/12081-12100/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12081-12100/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12100 Index: /issm/oecreview/Archive/12101-12120/Date.tex =================================================================== --- /issm/oecreview/Archive/12101-12120/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12101-12120/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12101-12120/ISSM-12101-12102.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12101-12102.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12101-12102.diff (revision 12325) @@ -0,0 +1,1917 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12102) +@@ -1,8 +1,9 @@ + from model import * + from TriMesh import * ++from triangle import * + +-#md=model() +-#md=triangle(md,'../Exp/Square.exp',150000); ++md=model() ++md=triangle(md,'../Exp/Square.exp',150000); + +-[index,x,y,segments,segmentmarkers]=TriMesh('../Exp/Square.exp',15000.0**2.0,True) +-print(index,x,y,segments,segmentmarkers) ++#[index,x,y,segments,segmentmarkers]=TriMesh('../Exp/Square.exp',15000.0**2.0,True) ++#print(index,x,y,segments,segmentmarkers) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12102) +@@ -571,12 +571,7 @@ + else + HAVE_METIS=no + fi +- +- if test $HAVE_METIS = no; then +- AC_MSG_ERROR([--with-metis-dir missing. Metis is needed to run ISSM]); +- else +- AC_MSG_RESULT($HAVE_METIS) +- fi ++ AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes]) + dnl }}} + dnl mpi{{{ + AC_MSG_CHECKING(for mpi) +@@ -602,6 +597,7 @@ + AC_SUBST([MPILIB]) + fi + fi ++ AM_CONDITIONAL([MPI], [test x$HAVE_MPI = xyes]) + AC_MSG_RESULT($HAVE_MPI) + dnl }}} + dnl petsc{{{ +@@ -1227,6 +1223,15 @@ + AC_MSG_ERROR([need python-version if python compile is required!]); + fi + ++ dnl check that if we have MPI, we have metis ++ if test "$HAVE_METIS" = "yes" && test "$HAVE_MPI" = "no" ; then ++ AC_MSG_ERROR([need mpi if using the metis partitioner!]); ++ fi ++ ++ ++ ++ ++ + AC_MSG_RESULT(done) + dnl }}} + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/scipy/install-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/scipy/install-macosx64.sh (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/scipy/install-macosx64.sh (revision 12102) +@@ -18,8 +18,8 @@ + + #install numpy + cd numpy +- python3.2 setup.py build +- python3.2 setup.py install ++ python setup.py build ++ python setup.py install + + + elif [[ $install == "2" ]];then +@@ -29,8 +29,8 @@ + + #install scipy + cd scipy +- python3.2 setup.py build +- python3.2 setup.py install ++ python setup.py build ++ python setup.py install + + elif [[ $install == "3" ]];then + rm -rf numpy scipy +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/nose/install-macosx64sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/nose/install-macosx64sh (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/nose/install-macosx64sh (revision 12102) +@@ -1,10 +1,27 @@ + #/bin/bash +-#Install Python3 nose module ++#Install Python nose module + +-rm -rf py3k ++pythonversion=2 ++ ++rm -rf src + +-svn checkout http://python-nose.googlecode.com/svn/branches/py3k +-cd py3k ++if [[ $pythonversion == "3" ]];then + +-python3.2 ./setup.py build +-python3.2 ./setup.py install ++ svn checkout http://python-nose.googlecode.com/svn/branches/py3k ++ mv py3k src ++ ++ cd src ++ python ./setup.py build ++ python ./setup.py install ++fi ++ ++if [[ $pythonversion == "2" ]];then ++ ++ tar -zxvf nose-1.1.2.tar.gz ++ mv nose-1.1.2 src ++ rm -rf nose-1.1.2 ++ ++ cd src ++ python ./setup.py build ++ python ./setup.py install ++fi +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 12102) +@@ -41,14 +41,22 @@ + ierr=PetscInitialize(&argc,&argv,(char*)0,""); + if(ierr) _error_("Could not initialize Petsc"); + #else ++ #ifdef _HAVE_MPI_ + MPI_Init(&argc,&argv); + #endif ++ #endif + ++ #ifdef _HAVE_MPI_ + MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); ++ #else ++ start=(double)clock(); ++ #endif + + /*Size and rank: */ ++ #ifdef _HAVE_MPI_ + MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); + MPI_Comm_size(MPI_COMM_WORLD,&num_procs); ++ #endif + + /*First process inputs*/ + _printf_(true,"\n"); +@@ -61,7 +69,11 @@ + AnalysisConfiguration(&analyses,&numanalyses,solution_type); + + /*Create femmodel, using input file: */ ++ #ifdef _HAVE_MPI_ + MPI_Barrier(MPI_COMM_WORLD); start_init=MPI_Wtime(); ++ #else ++ start_init=(double)clock(); ++ #endif + femmodel=new FemModel(binfilename,outbinfilename,solution_type,analyses,numanalyses); + + /*get type of solution we are going to run: */ +@@ -81,10 +93,19 @@ + femmodel->parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); + femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum); + femmodel->parameters->FindParam(&tao_analysis,InversionTaoEnum); ++ #ifdef _HAVE_MPI_ + MPI_Barrier(MPI_COMM_WORLD); finish_init=MPI_Wtime(); ++ #else ++ finish_init=(double)clock(); ++ #endif + + _printf_(true,"call computational core:\n"); ++ #ifdef _HAVE_MPI_ + MPI_Barrier(MPI_COMM_WORLD); start_core=MPI_Wtime( ); ++ #else ++ start_core=(double)clock(); ++ #endif ++ + if(dakota_analysis){ + #ifdef _HAVE_DAKOTA_ + Dakotax(femmodel); +@@ -105,8 +126,12 @@ + else{ + solutioncore(femmodel); + } ++ #ifdef _HAVE_MPI_ + MPI_Barrier(MPI_COMM_WORLD); finish_core=MPI_Wtime( ); +- ++ #else ++ finish_core=(double)clock(); ++ #endif ++ + _printf_(true,"write results to disk:\n"); + OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); + +@@ -126,18 +151,29 @@ + delete femmodel; + + /*Get finish time and close*/ ++ #ifdef _HAVE_MPI_ + MPI_Barrier(MPI_COMM_WORLD); finish = MPI_Wtime( ); + _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",finish_init-start_init); + _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",finish_core-start_core); + _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600),int(int(finish-start)%3600/60),int(finish-start)%60); ++ #else ++ finish=(double)clock(); ++ _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",(finish_init-start_init)/CLOCKS_PER_SEC); ++ _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",(finish_core-start_core)/CLOCKS_PER_SEC); ++ _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600/CLOCKS_PER_SEC),int(int((finish-start)/CLOCKS_PER_SEC)%3600/60),(int(finish-start)/CLOCKS_PER_SEC)%60); ++ #endif + ++ + ++ #ifdef _HAVE_PETSC_ + _printf_(true,"closing MPI and Petsc\n"); +- #ifdef _HAVE_PETSC_ + PetscFinalize(); + #else ++ #ifdef _HAVE_MPI_ ++ _printf_(true,"closing MPI and Petsc\n"); + MPI_Finalize(); + #endif ++ #endif + + /*end module: */ + ISSMEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp (revision 12102) +@@ -1,47 +0,0 @@ +-/* \file PetscVectorToDoubleVector.cpp +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-/*Petsc includes: */ +-#include "petscmat.h" +-#include "petscvec.h" +-#include "petscksp.h" +- +-#include "mex.h" +-#include "../../shared/shared.h" +-#include +- +-void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){ +- +- int i; +- int rows; +- int *idxm = NULL; +- double *vector = NULL; +- +- /*output: */ +- mxArray* dataref=NULL; +- +- /*Get size of vector: */ +- if(petsc_vector){ +- VecGetSize(petsc_vector,&rows); +- if(rows){ +- idxm=(int*)xmalloc(rows*sizeof(int)); +- vector=(double*)xmalloc(rows*sizeof(double)); +- for(i=0;i +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +- +-/*Petsc includes: */ +-#include "petscmat.h" +-#include "petscvec.h" +-#include "petscksp.h" +- +-/*Petsc includes: */ +-#include "mex.h" +- +-#include "../../shared/shared.h" +-#include +- +- +-void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat petsc_matrix){ +- +- int i,j,k; +- +- /*output: */ +- double* matrix=NULL; +- int rows,cols; +- +- /*intermediary: */ +- int* idxm=NULL; +- int* idxn=NULL; +- +- /*Some needed information: */ +- MatGetSize(petsc_matrix,&rows,&cols); +- +- idxm=(int*)xmalloc(rows*sizeof(int)); +- idxn=(int*)xmalloc(cols*sizeof(int)); +- +- for(i=0;imatrix); + #else + matrix_ptr=matrix->matrix->ToSerial(); +- matrix->matrix->GetSize(&rows,cols); ++ matrix->matrix->GetSize(&rows,&cols); + #endif + + /*Now transpose the matrix and allocate with Matlab's memory manager: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/matlabio.h (revision 12102) +@@ -71,15 +71,16 @@ + int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); + int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); + int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); +-int MatlabMatrixToPetscMatrix(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix); + +-/*Matlab to Petsc routines: */ +-int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector); +-void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat matrix); +-void PetscVectorToDoubleVector(double** pvector, int* prows, Vec vector); +- + /*Matlab to SeqMat routines: */ + SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref); + SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); + ++/*Matlab to Petsc routines: */ ++#ifdef _HAVE_PETSC_ ++int MatlabMatrixToPetscMatrix(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix); ++int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector); ++#endif ++ ++ + #endif /* _IO_H_ */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Loads.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Loads.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Loads.cpp (revision 12102) +@@ -62,9 +62,14 @@ + localloads=this->Size(); + + /*figure out total number of loads combining all the cpus (no clones here)*/ ++ #ifdef _HAVE_MPI_ + MPI_Reduce(&localloads,&numberofloads,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&numberofloads,1,MPI_INT,0,MPI_COMM_WORLD); ++ #else ++ numberofloads=localloads; ++ #endif + ++ + return numberofloads; + } + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Constraints.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Constraints.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Constraints.cpp (revision 12102) +@@ -47,8 +47,13 @@ + localconstraints=this->Size(); + + /*figure out total number of constraints combining all the cpus (no clones here)*/ +- MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); +- MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); ++ #ifdef _HAVE_MPI_ ++ MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); ++ MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); ++ #else ++ numberofconstraints=localconstraints; ++ #endif ++ + + return numberofconstraints; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp (revision 12102) +@@ -82,10 +82,14 @@ + /* Now every object has distributed dofs, but locally, and with a dof count starting from + * 0. This means the dofs between all the cpus are not unique. We now offset the dofs of eache + * cpus by the total last dofs of the previus cpu, starting from 0. +- * First: bet number of dofs for each cpu*/ ++ * First: get number of dofs for each cpu*/ + alldofcount=(int*)xmalloc(num_procs*sizeof(int)); ++ #ifdef _HAVE_MPI_ + MPI_Gather(&dofcount,1,MPI_INT,alldofcount,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(alldofcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); ++ #else ++ alldofcount[0]=dofcount; ++ #endif + + /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/ + dofcount=0; +@@ -118,7 +122,11 @@ + node->ShowTrueDofs(truedofs,maxdofspernode,setenum);//give maxdofspernode, column size, so that nodes can index into truedofs + } + } ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); ++ #else ++ alltruedofs[0]=truedofs[0]; ++ #endif + + /* Now every cpu knows the true dofs of everyone else that is not a clone*/ + for (i=0;iSize();i++){ +@@ -161,7 +169,11 @@ + * when we start building the dof list for all vertexs, a cpu can check whether its vertex already has been + * dealt with by another cpu. We take the minimum because we are going to manage dof assignment in increasing + * order of cpu rank. This is also why we initialized this array to num_procs.*/ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)ranks,(void*)minranks,numnodes,MPI_INT,MPI_MIN,MPI_COMM_WORLD); ++ #else ++ for(i=0;iSize();i++){ +@@ -204,8 +216,9 @@ + } + + /*Grab max of all cpus: */ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)&max,(void*)&allmax,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); +- max=allmax; ++ #endif + + return max; + } +@@ -236,7 +249,11 @@ + } + + /*Gather from all cpus: */ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)&numdofs,(void*)&allnumdofs,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); ++ #else ++ allnumdofs=numdofs; ++ #endif + return allnumdofs; + } + /*}}}*/ +@@ -259,7 +276,11 @@ + } + + /*Gather from all cpus: */ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)&numnodes,(void*)&allnumnodes,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); ++ #else ++ allnumnodes=numnodes; ++ #endif + + return allnumnodes; + } +@@ -285,9 +306,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&max_sid,&node_max_sid,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_max_sid,1,MPI_INT,0,MPI_COMM_WORLD); + max_sid=node_max_sid; ++ #endif + + if(max_sid==1){ + return 0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp (revision 12102) +@@ -124,6 +124,7 @@ + } + + /*Synchronize across cluster, so as to not end up with different sizes for each patch on each cpu: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&numvertices,&max_numvertices,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&max_numvertices,1,MPI_INT,0,MPI_COMM_WORLD); + numvertices=max_numvertices; +@@ -131,6 +132,7 @@ + MPI_Reduce (&numnodes,&max_numnodes,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&max_numnodes,1,MPI_INT,0,MPI_COMM_WORLD); + numnodes=max_numnodes; ++ #endif + + /*Ok, initialize Patch object: */ + patch=new Patch(numrows,numvertices,numnodes); +@@ -190,9 +192,13 @@ + /*No patch here, we prepare vectors*/ + + /*Get rank of first cpu that has results*/ ++ #ifdef _HAVE_MPI_ + if(this->Size()) rank=my_rank; + else rank=num_procs; + MPI_Allreduce (&rank,&minrank,1,MPI_INT,MPI_MIN,MPI_COMM_WORLD); ++ #else ++ minrank=my_rank; ++ #endif + + /*see what the first element of this partition has in stock (this is common to all partitions)*/ + if(my_rank==minrank){ +@@ -200,10 +206,13 @@ + Element* element=(Element*)this->GetObjectByOffset(0); + element->ListResultsInfo(&resultsenums,&resultssizes,&resultstimes,&resultssteps,&numberofresults); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&numberofresults,1,MPI_DOUBLE,minrank,MPI_COMM_WORLD); ++ #endif + + /*Get out if there is no results. Otherwise broadcast info*/ + if(!numberofresults) return; ++ #ifdef _HAVE_MPI_ + if(my_rank!=minrank){ + resultsenums=(int*)xmalloc(numberofresults*sizeof(int)); + resultssizes=(int*)xmalloc(numberofresults*sizeof(int)); +@@ -214,6 +223,7 @@ + MPI_Bcast(resultssizes,numberofresults,MPI_INT,minrank,MPI_COMM_WORLD); + MPI_Bcast(resultstimes,numberofresults,MPI_DOUBLE,minrank,MPI_COMM_WORLD); + MPI_Bcast(resultssteps,numberofresults,MPI_INT,minrank,MPI_COMM_WORLD); ++ #endif + + /*Loop over all results and get nodal vector*/ + for(int i=0;iSize(); ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)&local_nelem,(void*)&numberofelements,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); ++ #else ++ numberofelements=local_nelem; ++ #endif + + return numberofelements; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.cpp (revision 12102) +@@ -60,8 +60,12 @@ + * cpus by the total last dofs of the previus cpu, starting from 0. + * First: bet number of dofs for each cpu*/ + alldofcount=(int*)xmalloc(num_procs*sizeof(int)); ++ #ifdef _HAVE_MPI_ + MPI_Gather(&dofcount,1,MPI_INT,alldofcount,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(alldofcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); ++ #else ++ alldofcount[0]=dofcount; ++ #endif + + /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/ + dofcount=0; +@@ -84,7 +88,11 @@ + Vertex* vertex=(Vertex*)this->GetObjectByOffset(i); + vertex->ShowTrueDofs(truedofs); + } ++ #ifdef _HAVE_MPI_ + MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numberofobjects*numberofdofsperobject,MPI_INT,MPI_MAX,MPI_COMM_WORLD); ++ #else ++ for(i=0;iSize();i++){ +@@ -120,7 +128,11 @@ + * when we start building the dof list for all vertexs, a cpu can check whether its vertex already has been + * dealt with by another cpu. We take the minimum because we are going to manage dof assignment in increasing + * order of cpu rank. This is also why we initialized this array to num_procs.*/ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)ranks,(void*)minranks,numberofobjects,MPI_INT,MPI_MIN,MPI_COMM_WORLD); ++ #else ++ for(i=0;iSize();i++){ +@@ -148,9 +160,11 @@ + if (sid>max_sid)max_sid=sid; + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&max_sid,&vertex_max_sid,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&vertex_max_sid,1,MPI_INT,0,MPI_COMM_WORLD); + max_sid=vertex_max_sid; ++ #endif + + /*sid starts at 0*/ + max_sid++; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp (revision 12102) +@@ -26,9 +26,11 @@ + } + + /*Sum all J from all cpus of the cluster:*/ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + J=J_sum; ++ #endif + + /*Assign output pointers: */ + *pJ=J; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp (revision 12102) +@@ -31,9 +31,11 @@ + } + + /*Figure out minimum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&minvz,&node_minvz,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_minvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + minvz=node_minvz; ++ #endif + + /*Assign output pointers:*/ + *pminvz=minvz; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12102) +@@ -31,9 +31,11 @@ + } + + /*Figure out minimum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&maxvx,&node_maxvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxvx=node_maxvx; ++ #endif + + /*Assign output pointers:*/ + *pmaxvx=maxvx; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TimeAdaptx/TimeAdaptx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TimeAdaptx/TimeAdaptx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TimeAdaptx/TimeAdaptx.cpp (revision 12102) +@@ -31,9 +31,11 @@ + } + + /*Figure out minimum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&min_dt,&node_min_dt,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_min_dt,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + min_dt=node_min_dt; ++ #endif + + /*Assign output pointers:*/ + *pdt=min_dt; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 12102) +@@ -155,8 +155,12 @@ + } + vec_nodes_on_floatingice->Assemble(); + ++ #ifdef _HAVE_MPI_ + MPI_Allreduce(&local_nflipped,&nflipped,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); + _printf_(VerboseConvergence()," Additional number of vertices allowed to unground: %i\n",nflipped); ++ #else ++ nflipped=local_nflipped; ++ #endif + + /*Avoid leaks: */ + xfree((void**)&elements_neighboring_floatingce); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/IceVolumex/IceVolumex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/IceVolumex/IceVolumex.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/IceVolumex/IceVolumex.cpp (revision 12102) +@@ -18,8 +18,12 @@ + Element* element=(Element*)elements->GetObjectByOffset(i); + local_ice_volume+=element->IceVolume(); + } ++ #ifdef _HAVE_MPI_ + MPI_Reduce(&local_ice_volume,&total_ice_volume,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&total_ice_volume,1,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #else ++ total_ice_volume=local_ice_volume; ++ #endif + + /*Assign output pointers: */ + *pV=total_ice_volume; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp (revision 12102) +@@ -31,9 +31,11 @@ + } + + /*Figure out maximum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&maxabsvx,&node_maxabsvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxabsvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxabsvx=node_maxabsvx; ++ #endif + + /*Assign output pointers:*/ + *pmaxabsvx=maxabsvx; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp (revision 12102) +@@ -32,9 +32,11 @@ + } + + /*Figure out minimum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&minvel,&node_minvel,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_minvel,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + minvel=node_minvel; ++ #endif + + /*Assign output pointers:*/ + *pminvel=minvel; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVelx/MaxVelx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVelx/MaxVelx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVelx/MaxVelx.cpp (revision 12102) +@@ -32,9 +32,11 @@ + } + + /*Figure out maximum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&maxvel,&node_maxvel,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxvel,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxvel=node_maxvel; ++ #endif + + /*Assign output pointers:*/ + *pmaxvel=maxvel; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12102) +@@ -31,9 +31,11 @@ + } + + /*Figure out minimum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&maxvy,&node_maxvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxvy=node_maxvy; ++ #endif + + /*Assign output pointers:*/ + *pmaxvy=maxvy; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp (revision 12102) +@@ -30,9 +30,11 @@ + } + + /*Sum all J from all cpus of the cluster:*/ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + J=J_sum; ++ #endif + + /*Assign output pointers: */ + *pJ=J; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp (revision 12102) +@@ -36,8 +36,10 @@ + } + + /*Broadcast whether we found the element: */ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( &found,&sumfound,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); + if(!sumfound)_error_("%s%i%s","could not find material with id",index," to compute ElementResponse"); ++ #endif + + /*Ok, we found the element, compute responseocity: */ + if(my_rank==cpu_found){ +@@ -45,8 +47,10 @@ + } + + /*Broadcast and plug into response: */ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( &cpu_found,&cpu_found,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + MPI_Bcast(&response,1,MPI_DOUBLE,cpu_found,MPI_COMM_WORLD); ++ #endif + + *presponse=response; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceAreax/SurfaceAreax.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceAreax/SurfaceAreax.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceAreax/SurfaceAreax.cpp (revision 12102) +@@ -27,9 +27,11 @@ + } + + /*Sum all J from all cpus of the cluster:*/ +- MPI_Reduce (&S,&S_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); ++ #ifdef _HAVE_MPI_ ++ MPI_Reduce (&S,&S_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&S_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + S=S_sum; ++ #endif + + /*add surface area to element inputs:*/ + InputUpdateFromConstantx(elements,nodes,vertices,loads,materials,parameters,S,SurfaceAreaEnum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MeshPartitionx/MeshPartitionx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MeshPartitionx/MeshPartitionx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MeshPartitionx/MeshPartitionx.cpp (revision 12102) +@@ -41,7 +41,9 @@ + + /*Partition using Metis:*/ + if (num_procs>1){ ++ #ifdef _HAVE_METIS_ + METIS_PartMeshNodalPatch(&numberofelements,&numberofnodes, index, &etype, &numflag, &num_procs, &edgecut, epart, npart); ++ #endif + } + else if (num_procs==1){ + /*METIS does not know how to deal with one cpu only!*/ +@@ -66,7 +68,9 @@ + + /*Partition using Metis:*/ + if (num_procs>1){ ++ #ifdef _HAVE_METIS_ + METIS_PartMeshNodalPatch(&numberofelements2d,&numberofnodes2d, index2d, &etype2d, &numflag, &num_procs, &edgecut, epart2d, npart2d); ++ #endif + } + else if (num_procs==1){ + /*METIS does not know how to deal with one cpu only!*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/NodalValuex/NodalValuex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/NodalValuex/NodalValuex.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/NodalValuex/NodalValuex.cpp (revision 12102) +@@ -35,12 +35,18 @@ + } + + /*Broadcast whether we found the element: */ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( &found,&sumfound,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); + if(!sumfound)_error_("%s%i%s%s","could not find element with vertex with id",index," to compute nodal value ",EnumToStringx(natureofdataenum)); ++ #endif + + /*Broadcast and plug into response: */ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( &cpu_found,&cpu_found,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + MPI_Bcast(&value,1,MPI_DOUBLE,cpu_found,MPI_COMM_WORLD); ++ #else ++ value=cpu_found; ++ #endif + + *pnodalvalue=value; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12102) +@@ -32,9 +32,11 @@ + } + + /*Figure out maximum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&maxabsvy,&node_maxabsvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxabsvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxabsvy=node_maxabsvy; ++ #endif + + /*Assign output pointers:*/ + *pmaxabsvy=maxabsvy; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp (revision 12102) +@@ -26,9 +26,11 @@ + } + + /*Sum all J from all cpus of the cluster:*/ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + J=J_sum; ++ #endif + + /*Assign output pointers: */ + *pJ=J; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp (revision 12102) +@@ -31,9 +31,11 @@ + } + + /*Figure out minimum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&minvx,&node_minvx,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_minvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + minvx=node_minvx; ++ #endif + + /*Assign output pointers:*/ + *pminvx=minvx; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp (revision 12102) +@@ -26,9 +26,11 @@ + } + + /*Sum all J from all cpus of the cluster:*/ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + J=J_sum; ++ #endif + + /*Assign output pointers: */ + *pJ=J; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12102) +@@ -32,9 +32,11 @@ + } + + /*Figure out minimum across the cluster: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&maxvz,&node_maxvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&node_maxvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + maxvz=node_maxvz; ++ #endif + + /*Assign output pointers:*/ + *pmaxvz=maxvz; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12102) +@@ -35,9 +35,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); + num_unstable_constraints=sum_num_unstable_constraints; ++ #endif + + /*Have we converged? : */ + if (num_unstable_constraints==0) converged=1; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12102) +@@ -27,9 +27,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; ++ #endif + + return found; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12102) +@@ -31,9 +31,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; ++ #endif + + return found; + } +@@ -92,9 +94,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); + num_unstable_constraints=sum_num_unstable_constraints; ++ #endif + + /*Assign output pointers: */ + *pnum_unstable_constraints=num_unstable_constraints; +@@ -130,9 +134,11 @@ + } + + /*Is there just one found? that would mean we have frozen! : */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; ++ #endif + + return found; + } +@@ -188,9 +194,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; ++ #endif + + return found; + } +@@ -219,9 +227,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); + found=mpi_found; ++ #endif + + if (found){ + /*We found an unstable constraint. : */ +@@ -278,9 +288,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); + num_unstable_constraints=sum_num_unstable_constraints; ++ #endif + + /*Assign output pointers: */ + *pnum_unstable_constraints=num_unstable_constraints; +@@ -316,9 +328,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&max_penetration,&mpi_max_penetration,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); + MPI_Bcast(&mpi_max_penetration,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + max_penetration=mpi_max_penetration; ++ #endif + + /*feed max_penetration to inputs: */ + for(i=0;iSize();i++){ +@@ -353,9 +367,11 @@ + } + } + ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); + num_unstable_constraints=sum_num_unstable_constraints; ++ #endif + + return num_unstable_constraints; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp (revision 12102) +@@ -26,9 +26,11 @@ + } + + /*Sum all J from all cpus of the cluster:*/ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + J=J_sum; ++ #endif + + /*Assign output pointers: */ + *pJ=J; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12102) +@@ -29,8 +29,10 @@ + } + + /*In parallel, we need to gather the converged status: */ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)&num_notconverged,(void*)&total_notconverged,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); + num_notconverged=total_notconverged; ++ #endif + _printf_(VerboseConvergence()," #elements above convergence criterion = %i\n",num_notconverged); + + /*Free ressources:*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp (revision 12102) +@@ -26,9 +26,11 @@ + } + + /*Sum all J from all cpus of the cluster:*/ ++ #ifdef _HAVE_MPI_ + MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + J=J_sum; ++ #endif + + /*Assign output pointers: */ + *pJ=J; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12102) +@@ -92,22 +92,26 @@ + } + + /*Ok, broadcast to other cpus: */ ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&numanalyses,1,MPI_INT,0,MPI_COMM_WORLD); + if(my_rank!=0){ + analyses=(double*)xmalloc(numanalyses*sizeof(double)); + strings=(char**)xmalloc(numanalyses*sizeof(char*)); + } + MPI_Bcast(analyses,numanalyses,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #endif + for(i=0;i ++ + /*Petsc includes: */ + #include "petscmat.h" + #include "petscvec.h" + #include "petscksp.h" + +-#include "mex.h" +-#include "../../shared/shared.h" +-#include ++#include "../../../shared/shared.h" + + void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){ + +@@ -23,9 +23,6 @@ + int *idxm = NULL; + double *vector = NULL; + +- /*output: */ +- mxArray* dataref=NULL; +- + /*Get size of vector: */ + if(petsc_vector){ + VecGetSize(petsc_vector,&rows); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp (revision 12102) +@@ -9,6 +9,7 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + ++#include + + /*Petsc includes: */ + #include "petscmat.h" +@@ -16,12 +17,9 @@ + #include "petscksp.h" + + /*Petsc includes: */ +-#include "mex.h" ++#include "../../../shared/shared.h" + +-#include "../../shared/shared.h" +-#include + +- + void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat petsc_matrix){ + + int i,j,k; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 12102) +@@ -19,8 +19,14 @@ + #include "./petsc/petscincludes.h" + #endif + ++#ifdef _HAVE_MPI_ + #include "./mpi/mpiincludes.h" ++#endif ++ ++#ifdef _HAVE_METIS_ + #include "./metis/metisincludes.h" ++#endif ++ + #include "./triangle/triangleincludes.h" + #include "./toolkitsenums.h" + #include "./issm/issmtoolkit.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12102) +@@ -205,20 +205,12 @@ + ./shared/Wrapper/wrappershared.h\ + ./shared/Wrapper/ModuleBoot.cpp\ + ./shared/Wrapper/ModuleEnd.cpp\ +- ./toolkits/mpi/mpiincludes.h\ +- ./toolkits/mpi/patches/mpipatches.h\ +- ./toolkits/mpi/patches/DetermineLocalSize.cpp\ +- ./toolkits/mpi/patches/MPI_Upperrow.cpp\ +- ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ +- ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp\ + ./toolkits/metis/metisincludes.h\ + ./toolkits/issm/issmtoolkit.h\ + ./toolkits/issm/SeqVec.h\ + ./toolkits/issm/SeqVec.cpp\ + ./toolkits/issm/SeqMat.h\ + ./toolkits/issm/SeqMat.cpp\ +- ./toolkits/metis/patches/metispatches.h\ +- ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp\ + ./toolkits/triangle/triangleincludes.h\ + ./toolkitsenums.h\ + ./toolkits.h\ +@@ -699,6 +691,8 @@ + ./toolkits/petsc/patches/NewMat.cpp\ + ./toolkits/petsc/patches/SerialToVec.cpp\ + ./toolkits/petsc/patches/VecFree.cpp\ ++ ./toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp\ ++ ./toolkits/petsc/patches/PetscVectorToDoubleVector.cpp\ + ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ + ./toolkits/petsc/patches/KSPFree.cpp\ + ./toolkits/petsc/patches/ISFree.cpp\ +@@ -721,6 +715,18 @@ + gsl_sources= ./modules/Solverx/SolverxGsl.cpp + + #}}} ++#Mpi sources {{{1 ++mpi_sources= ./toolkits/mpi/mpiincludes.h\ ++ ./toolkits/mpi/patches/mpipatches.h\ ++ ./toolkits/mpi/patches/DetermineLocalSize.cpp\ ++ ./toolkits/mpi/patches/MPI_Upperrow.cpp\ ++ ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ ++ ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp ++#}}} ++#Metis sources {{{1 ++metis_sources= ./toolkits/metis/patches/metispatches.h\ ++ ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp ++#}}} + #Python sources {{{1 + python_sources= ./python/io/pythonio.h\ + ./python/python-binding.h\ +@@ -743,13 +749,14 @@ + ./matlab/io/MatlabVectorToVector.cpp\ + ./matlab/io/MatlabVectorToDoubleVector.cpp\ + ./matlab/io/MatlabMatrixToDoubleMatrix.cpp\ +- ./matlab/io/MatlabMatrixToPetscMatrix.cpp\ +- ./matlab/io/MatlabVectorToPetscVector.cpp\ +- ./matlab/io/PetscMatrixToDoubleMatrix.cpp\ +- ./matlab/io/PetscVectorToDoubleVector.cpp\ + ./matlab/io/MatlabMatrixToSeqMat.cpp\ + ./matlab/io/MatlabVectorToSeqVec.cpp + #}}} ++#Matlab and Petsc sources {{{1 ++matlabpetsc_sources= ./matlab/io/MatlabMatrixToPetscMatrix.cpp\ ++ ./matlab/io/MatlabVectorToPetscVector.cpp ++ ++#}}} + #Modules sources{{{1 + module_sources= ./objects/Options/Option.cpp\ + ./objects/Options/Option.h\ +@@ -910,6 +917,22 @@ + if THREED + issm_sources += $(threed_sources) + endif ++ ++if MPI ++issm_sources += $(mpi_sources) ++endif ++ ++if METIS ++issm_sources += $(metis_sources) ++endif ++ ++if PETSC ++if MATLAB ++issm_sources += $(matlabpetsc_sources) ++endif ++endif ++ ++ + #}}} + #Library flags and sources {{{1 + ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Metric.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Metric.h (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Metric.h (revision 12102) +@@ -4,6 +4,7 @@ + #include "./include.h" + #include "../../shared/Bamg/shared.h" + #include "R2.h" ++#include + + namespace bamg { + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Patch.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Patch.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Patch.cpp (revision 12102) +@@ -119,11 +119,17 @@ + int total_numrows; + int node_numrows; + double *total_values = NULL; ++ #ifdef _HAVE_MPI_ + MPI_Status status; ++ #endif + + /*First, figure out total number of rows combining all the cpus: */ ++ #ifdef _HAVE_MPI_ + MPI_Reduce(&this->numrows,&total_numrows,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&total_numrows,1,MPI_INT,0,MPI_COMM_WORLD); ++ #else ++ total_numrows=this->numrows; ++ #endif + + /*return if patch empty*/ + if(total_numrows==0) return; +@@ -139,6 +145,7 @@ + } + + /*Now, ask other nodes to send their values: */ ++ #ifdef _HAVE_MPI_ + for (i=1;inumrows,1,MPI_INT,0,1,MPI_COMM_WORLD); +@@ -150,6 +157,7 @@ + count+=node_numrows*this->numcols; + } + } ++ #endif + + /*Now, node 0 has total_values, of size total_numrows*this->numcols. Update the fields in the patch, to reflect this new + * reality. For other cpus, no point in keeping their data anymore: */ +@@ -158,8 +166,10 @@ + xfree((void**)&this->values); + this->values=total_values; + } ++ #ifdef _HAVE_MPI_ + else{ + this->numrows=0; + xfree((void**)&this->values); + } ++ #endif + }/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp (revision 12102) +@@ -197,7 +197,9 @@ + + /*Ok, we have reached the end of the file. break: */ + record_code=0; //0 means bailout ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*tell others cpus we are bailing: */ ++ #endif + break; + } + else{ +@@ -206,19 +208,22 @@ + fread(&record_length,sizeof(int),1,this->fid); + fread(&record_code,sizeof(int),1,this->fid); + ++ #ifdef _HAVE_MPI_ + /*Tell other cpus what we are doing: */ + MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*tell other cpus what we are going to do: */ + + /*Tell other cpus the name of the data, then branch according to the data type: */ + MPI_Bcast(&record_enum,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&record_length,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + +- + switch(record_code){ + case 1: + /*Read the boolean and broadcast it to other cpus:*/ + if(fread(&booleanint,sizeof(int),1,this->fid)!=1) _error_(" could not read boolean "); ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*create BoolParam: */ + this->constants->AddObject(new BoolParam(record_enum,(bool)booleanint)); //cast to boolean +@@ -227,7 +232,9 @@ + case 2: + /*Read the integer and broadcast it to other cpus:*/ + if(fread(&integer,sizeof(int),1,this->fid)!=1) _error_(" could not read integer "); ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*create IntParam: */ + this->constants->AddObject(new IntParam(record_enum,integer)); +@@ -236,7 +243,9 @@ + case 3: + /*Read the scalar and broadcast it to other cpus:*/ + if(fread(&scalar,sizeof(double),1,this->fid)!=1) _error_(" could not read scalar "); ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #endif + + /*create DoubleParam: */ + this->constants->AddObject(new DoubleParam(record_enum,scalar)); +@@ -245,7 +254,9 @@ + case 4: + /*We have to read a string from disk. First read the dimensions of the string, then the string: */ + if(fread(&string_size,sizeof(int),1,this->fid)!=1) _error_(" could not read length of string "); ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + if(string_size){ + string=(char*)xmalloc((string_size+1)*sizeof(char)); +@@ -253,7 +264,9 @@ + + /*Read string, then broadcast: */ + if(fread(string,string_size*sizeof(char),1,this->fid)!=1)_error_(" could not read string "); ++ #ifdef _HAVE_MPI_ + MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); ++ #endif + } + else{ + string=(char*)xmalloc(sizeof(char)); +@@ -307,6 +320,7 @@ + } + } + } //}}} ++ #ifdef _HAVE_MPI_ + else{ //cpu ~0 {{{2 + for(;;){ //wait on cpu 0 + MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*get from cpu 0 what we are going to do: */ +@@ -376,6 +390,7 @@ + } + } + } //}}} ++ #endif + } + /*}}}*/ + /*FUNCTION IoModel::FetchData(bool* pbool,int data_enum){{{1*/ +@@ -398,7 +413,9 @@ + if(my_rank==0){ + if(fread(&booleanint,sizeof(int),1,fid)!=1) _error_(" could not read boolean "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*cast to bool: */ + /*Assign output pointers: */ +@@ -427,7 +444,9 @@ + if(fread(&integer,sizeof(int),1,fid)!=1) _error_(" could not read integer "); + } + ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*Assign output pointers: */ + *pinteger=integer; +@@ -455,7 +474,9 @@ + if(my_rank==0){ + if(fread(&scalar,sizeof(double),1,fid)!=1)_error_(" could not read scalar "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #endif + + /*Assign output pointers: */ + *pscalar=scalar; +@@ -486,7 +507,9 @@ + if(fread(&string_size,sizeof(int),1,fid)!=1) _error_(" could not read length of string "); + } + ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*Now allocate string: */ + if(string_size){ +@@ -497,7 +520,9 @@ + if(my_rank==0){ + if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); ++ #endif + } + else{ + string=(char*)xmalloc(sizeof(char)); +@@ -537,12 +562,16 @@ + if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix "); + } + ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + if(my_rank==0){ + if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); + } +- MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); ++ #ifdef _HAVE_MPI_ ++ MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*Now allocate matrix: */ + if(M*N){ +@@ -553,7 +582,9 @@ + if(fread(matrix,M*N*sizeof(double),1,fid)!=1) _error_("could not read matrix "); + } + ++ #ifdef _HAVE_MPI_ + MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #endif + } + + /*Now cast to integer: */ +@@ -601,12 +632,16 @@ + if(my_rank==0){ + if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + if(my_rank==0){ + if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*Now allocate matrix: */ + if(M*N){ +@@ -616,7 +651,9 @@ + if(my_rank==0){ + if(fread(matrix,M*N*sizeof(double),1,fid)!=1) _error_("could not read matrix "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #endif + } + + /*Assign output pointers: */ +@@ -651,7 +688,9 @@ + if(my_rank==0){ + if(fread(&numstrings,sizeof(int),1,fid)!=1) _error_(" could not read length of string array"); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&numstrings,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*Now allocate string array: */ + if(numstrings){ +@@ -664,7 +703,9 @@ + if(my_rank==0){ + if(fread(&string_size,sizeof(int),1,fid)!=1) _error_(" could not read length of string "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + if(string_size){ + string=(char*)xmalloc((string_size+1)*sizeof(char)); + string[string_size]='\0'; +@@ -673,7 +714,9 @@ + if(my_rank==0){ + if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); ++ #endif + } + else{ + string=(char*)xmalloc(sizeof(char)); +@@ -716,7 +759,9 @@ + if(my_rank==0){ + if(fread(&numrecords,sizeof(int),1,fid)!=1) _error_("could not read number of records in matrix array "); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&numrecords,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + if(numrecords){ + +@@ -737,12 +782,16 @@ + if(my_rank==0){ + if(fread(&M,sizeof(int),1,fid)!=1) _error_("%s%i%s","could not read number of rows in ",i,"th matrix of matrix array"); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + if(my_rank==0){ + if(fread(&N,sizeof(int),1,fid)!=1) _error_("%s%i%s","could not read number of columns in ",i,"th matrix of matrix array"); + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*Now allocate matrix: */ + if(M*N){ +@@ -753,7 +802,9 @@ + if(fread(matrix,M*N*sizeof(double),1,fid)!=1) _error_("could not read matrix "); + } + ++ #ifdef _HAVE_MPI_ + MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #endif + } + + /*Assign: */ +@@ -1046,13 +1097,17 @@ + } + } + } ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&found,1,MPI_INT,0,MPI_COMM_WORLD); + if(!found)_error_("%s %s ","could not find data with name",EnumToStringx(data_enum)); ++ #endif + + /*Broadcast code and vector type: */ ++ #ifdef _HAVE_MPI_ + MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); + if(record_code==5) MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif + + /*Assign output pointers:*/ + *pcode=record_code; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am (revision 12102) +@@ -1,2 +1,2 @@ +-EXTRA_DIST = perl pro py +-SUBDIRS = c modules m ++EXTRA_DIST = perl pro ++SUBDIRS = c modules m py +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py (revision 12102) +@@ -0,0 +1,55 @@ ++from TriMesh import * ++from numpy import * ++ ++def triangle(md, domainname, resolution,riftname=''): ++ #TRIANGLE - create model mesh using the triangle package ++ # ++ # This routine creates a model mesh using TriMesh and a domain outline, to within a certain resolution ++ # where md is a @model object, domainname is the name of an Argus domain outline file, ++ # and resolution is a characteristic length for the mesh (same unit as the domain outline ++ # unit). Riftname is an optional argument (Argus domain outline) describing rifts. ++ # ++ # Usage: ++ # md=triangle(md,domainname,resolution) ++ # or md=triangle(md,domainname, resolution, riftname) ++ # ++ # Examples: ++ # md=triangle(md,'DomainOutline.exp',1000); ++ # md=triangle(md,'DomainOutline.exp',1000,'Rifts.exp'); ++ ++ ++ #Figure out a characteristic area. Resolution is a node oriented concept (ex a 1000m resolution node would ++ #be made of 1000*1000 area squares). ++ ++ #Check that mesh was not already run, and warn user: ++ if md.mesh.numberofelements != 0.: ++ choice = input('This model already has a mesh. Are you sure you want to go ahead? (y/n)') ++ if choice != 'y': ++ print 'no meshing done ... exiting' ++ return [] ++ ++ area = resolution**2. ++ ++ #Mesh using TriMesh ++ [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,riftname,area) ++ ++ #Fill in rest of fields: ++ md.mesh.numberofelements = size(md.mesh.elements) ++ md.mesh.numberofvertices = size(md.mesh.x) ++ md.mesh.z = zeros(md.mesh.numberofvertices) ++ md.mesh.vertexonboundary = zeros(md.mesh.numberofvertices) ++ md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)] = 1. ++ md.mesh.vertexonbed = ones(md.mesh.numberofvertices) ++ md.mesh.vertexonsurface = ones(md.mesh.numberofvertices) ++ md.mesh.elementonbed = ones(md.mesh.numberofelements) ++ md.mesh.elementonsurface = ones(md.mesh.numberofelements) ++ ++ #Now, build the connectivity tables for this mesh. ++ print "Node: NodeConnectivity not implemented yet!" ++ #md.mesh.vertexconnectivity = NodeConnectivity((md.mesh.elements), (md.mesh.numberofvertices)) ++ print "Node: ElementConnectivity not implemented yet!" ++ #md.mesh.elementconnectivity = ElementConnectivity((md.mesh.elements), (md.mesh.vertexconnectivity)) ++ ++ #type of model ++ md.mesh.dimension = 2. ++ return md +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 12102) +@@ -1,28 +1,15 @@ + #!/bin/sh + +-#petsc 3.2 +-#mpich 1.4 ++pythonversion=2.7 + + ./configure \ + --prefix=$ISSM_TIER \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-matlab-dir=$MATLAB_DIR \ ++ --with-python-dir=$ISSM_TIER/externalpackages/python/install\ ++ --with-python-version=$pythonversion \ ++ --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ +- --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ +- --with-numthreads=8 \ + --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install +-# --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +-# --with-petsc-arch=$ISSM_ARCH \ +-# --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +-# --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +-# --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +-# --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +-# --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ +-# --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12101) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12102) +@@ -81,6 +81,7 @@ + from hydrology import * + from miscellaneous import * + from private import * ++from triangle import * + + #}}} + Index: /issm/oecreview/Archive/12101-12120/ISSM-12102-12103.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12102-12103.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12102-12103.diff (revision 12325) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh (revision 12102) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh (revision 12103) +@@ -1,10 +1,12 @@ + #!/bin/sh + ++pythonversion=2.7 ++ + ./configure \ + --prefix=$ISSM_TIER \ +- --without-mpi \ +- --without-matlab \ ++ --with-python-dir=$ISSM_TIER/externalpackages/python/install\ ++ --with-python-version=$pythonversion \ ++ --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-vendor=arm \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --without-metis \ +- --with-vendor=arm + --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install Index: /issm/oecreview/Archive/12101-12120/ISSM-12103-12104.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12103-12104.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12103-12104.diff (revision 12325) @@ -0,0 +1,19 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 12103) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 12104) +@@ -73,10 +73,14 @@ + for(i=0;imatrix=NewMat(M,N,sparsity); ++ printf("-------------- file: Matrix.cpp line: %i\n",__LINE__); + MatSetValues(this->matrix,M,idxm,N,idxn,serial_mat,INSERT_VALUES); ++ printf("-------------- file: Matrix.cpp line: %i\n",__LINE__); + MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); ++ printf("-------------- file: Matrix.cpp line: %i\n",__LINE__); + + xfree((void**)&idxm); + xfree((void**)&idxn); Index: /issm/oecreview/Archive/12101-12120/ISSM-12104-12105.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12104-12105.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12104-12105.diff (revision 12325) @@ -0,0 +1,19 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 12104) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 12105) +@@ -73,14 +73,10 @@ + for(i=0;imatrix=NewMat(M,N,sparsity); +- printf("-------------- file: Matrix.cpp line: %i\n",__LINE__); + MatSetValues(this->matrix,M,idxm,N,idxn,serial_mat,INSERT_VALUES); +- printf("-------------- file: Matrix.cpp line: %i\n",__LINE__); + MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); +- printf("-------------- file: Matrix.cpp line: %i\n",__LINE__); + + xfree((void**)&idxm); + xfree((void**)&idxn); Index: /issm/oecreview/Archive/12101-12120/ISSM-12105-12106.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12105-12106.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12105-12106.diff (revision 12325) @@ -0,0 +1,18 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp (revision 12105) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp (revision 12106) +@@ -67,7 +67,12 @@ + o_nz=(int)((double)nnz/(double)M/2.0); //number of non zeros per row/2 + + #ifdef _HAVE_PETSCDEV_ +- MatCreateAIJ(MPI_COMM_WORLD,m,n,M,N,d_nz,NULL,o_nz,NULL,&outmatrix); ++ if(sparsity==1){ ++ MatCreateDense(MPI_COMM_WORLD,m,n,M,N,NULL,&outmatrix); ++ } ++ else{ ++ MatCreateAIJ(MPI_COMM_WORLD,m,n,M,N,d_nz,NULL,o_nz,NULL,&outmatrix); ++ } + #else + MatCreateMPIAIJ(MPI_COMM_WORLD,m,n,M,N,d_nz,NULL,o_nz,NULL,&outmatrix); + #endif Index: /issm/oecreview/Archive/12101-12120/ISSM-12106-12107.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12106-12107.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12106-12107.diff (revision 12325) @@ -0,0 +1,28 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh (revision 12106) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh (revision 12107) +@@ -5,6 +5,7 @@ + if [ $STEP -eq 1 ]; then + # Adapted from petsc 3.2. + # Used Mercurial to get code ++ rm -rf src + hg clone http://petsc.cs.iit.edu/petsc/petsc-dev src + cd src + hg clone http://petsc.cs.iit.edu/petsc/BuildSystem config/BuildSystem +@@ -24,6 +25,7 @@ + + + if [ $STEP -eq 2 ]; then ++ rm -rf install + cd src + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +@@ -41,6 +43,7 @@ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ ++ --download-spai=yes \ + --with-pic=1 + + #Compile petsc and install it Index: /issm/oecreview/Archive/12101-12120/ISSM-12107-12108.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12107-12108.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12107-12108.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp (revision 12107) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Nodes.cpp (revision 12108) +@@ -125,7 +125,7 @@ + #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else +- alltruedofs[0]=truedofs[0]; ++ for(i=0;iShowTrueDofs(truedofs,maxdofspernode,setenum);//give maxdofspernode, column size, so that nodes can index into truedofs + } + } ++ + #ifdef _HAVE_MPI_ +- MPI_Allreduce ( (void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); ++ MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else + for(i=0;iNumberOfNodes(analysis_type); + +@@ -218,6 +218,7 @@ + /*Grab max of all cpus: */ + #ifdef _HAVE_MPI_ + MPI_Allreduce ( (void*)&max,(void*)&allmax,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); ++ max=allmax; + #endif + + return max; Index: /issm/oecreview/Archive/12101-12120/ISSM-12109-12110.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12109-12110.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12109-12110.diff (revision 12325) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12109) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12110) +@@ -1,9 +1,5 @@ + from model import * +-from TriMesh import * + from triangle import * + +-md=model() ++md=model(); + md=triangle(md,'../Exp/Square.exp',150000); +- +-#[index,x,y,segments,segmentmarkers]=TriMesh('../Exp/Square.exp',15000.0**2.0,True) +-#print(index,x,y,segments,segmentmarkers) Index: /issm/oecreview/Archive/12101-12120/ISSM-12110-12111.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12110-12111.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12110-12111.diff (revision 12325) @@ -0,0 +1,20 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12110) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test101.py (revision 12111) +@@ -1,5 +0,0 @@ +-from model import * +-from triangle import * +- +-md=model(); +-md=triangle(md,'../Exp/Square.exp',150000); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py (revision 12111) +@@ -0,0 +1,5 @@ ++from model import * ++from triangle import * ++ ++md=model(); ++md=triangle(md,'../Exp/Square.exp',150000); Index: /issm/oecreview/Archive/12101-12120/ISSM-12111-12112.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12111-12112.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12111-12112.diff (revision 12325) @@ -0,0 +1,541 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py (revision 12112) +@@ -1,5 +1,7 @@ + from model import * + from triangle import * ++from setmask import * + + md=model(); + md=triangle(md,'../Exp/Square.exp',150000); ++md=setmask(md,'all',''); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h (revision 12112) +@@ -20,20 +20,19 @@ + class Parameters; + + //void WriteData(PyObject* py_tuple,DataSet* dataset); +-//void WriteData(PyObject* py_tuple,double* matrix, int M,int N); + //void WriteData(PyObject* py_tuple,int* matrix, int M,int N); + //void WriteData(PyObject* py_tuple,double* vector, int M); + //void WriteData(PyObject* py_tuple,int integer); + //void WriteData(PyObject* py_tuple,bool boolean); + //void WriteData(PyObject* py_tuple,double scalar); + //void WriteData(DataHandle* py_tuple,Parameters* parameters); ++void WriteData(PyObject* py_tuple, int index, double* matrix, int M,int N); + void WriteData(PyObject* py_tuple, int index, char* string); + void WriteData(PyObject* py_tuple, int index, Matrix* matrix); + void WriteData(PyObject* py_tuple, int index, Vector* vector); + + + //void FetchData(DataSet** pdataset,PyObject* py_ref); +-//void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_ref); + //void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); + //void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_ref); + //void FetchData(bool** pmatrix,int* pM,int *pN,PyObject* py_ref); +@@ -46,6 +45,7 @@ + //void FetchData(Vector** pvector,PyObject* py_ref); + //void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); + //void FetchData(Parameters** pparameters, DataHandle py_ref); ++void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_array); + void FetchData(char** pstring,PyObject* py_unicode); + void FetchData(double* pscalar,PyObject* py_float); + void FetchData(int* pinteger,PyObject* py_long); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12112) +@@ -56,7 +56,31 @@ + + } + /*}}}*/ ++/*FUNCTION FetchData(double** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{1*/ ++void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_matrix){ + ++ /*output: */ ++ double* matrix=NULL; ++ int M,N; ++ int ndim; ++ npy_intp* dims=NULL; ++ ++ /*retrive dimensions: */ ++ ndim=PyArray_NDIM((const PyArrayObject*)py_matrix); ++ if(ndim!=2)_error_("expecting an MxN matrix in input!"); ++ dims=PyArray_DIMS((PyArrayObject*)py_matrix); ++ M=dims[0]; N=dims[1]; ++ ++ /*retrieve internal value: */ ++ matrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); ++ ++ /*output: */ ++ if(pM)*pM=M; ++ if(pN)*pN=N; ++ if(pmatrix)*pmatrix=matrix; ++} ++/*}}}*/ ++ + /*Python version dependent: */ + #if _PYTHON_MAJOR_ >= 3 + /*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 12112) +@@ -63,3 +63,16 @@ + + } + /*}}}*/ ++/*FUNCTION WriteData(PyObject* py_tuple,int index, double* matrix, int M, int N){{{1*/ ++void WriteData(PyObject* tuple, int index, double* matrix, int M,int N){ ++ ++ npy_intp dims[2]={0,0}; ++ PyObject* array=NULL; ++ ++ dims[0]=(npy_intp)M; ++ dims[1]=(npy_intp)N; ++ array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,matrix); ++ ++ PyTuple_SetItem(tuple, index, array); ++ ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am (revision 12112) +@@ -2,7 +2,9 @@ + EXEEXT=$(PYTHONWRAPPEREXT) + #Bin programs {{{1 + if MODULES +-bin_PROGRAMS = TriMesh ++bin_PROGRAMS = TriMesh \ ++ NodeConnectivity \ ++ ElementConnectivity + endif + #}}} + #Flags and libraries {{{1 +@@ -25,6 +27,12 @@ + AM_CXXFLAGS += $(CXXOPTFLAGS) + #}}} + #Bin sources {{{1 ++ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\ ++ ../ElementConnectivity/ElementConnectivity.h ++ ++NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\ ++ ../NodeConnectivity/NodeConnectivity.h ++ + TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\ + ../TriMesh/TriMesh.h + #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp (revision 12112) +@@ -4,11 +4,12 @@ + + #include "./NodeConnectivity.h" + +-void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++WRAPPER(NodeConnectivity){ + + /*inputs: */ + double* elements=NULL; +- int nel,nods; ++ int nel; ++ int nods; + + /*outputs: */ + double* connectivity=NULL; +@@ -17,8 +18,8 @@ + /*Boot module: */ + MODULEBOOT(); + +- /*checks on arguments on the matlab side: */ +- CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&NodeConnectivityUsage); ++ /*checks on arguments: */ ++ CHECKARGUMENTS(NLHS,NRHS,&NodeConnectivityUsage); + + /*Input datasets: */ + FetchData(&elements,&nel,NULL,ELEMENTS); +@@ -30,9 +31,6 @@ + /*write output datasets: */ + WriteData(CONNECTIVITY,connectivity,nods,width); + +- /*Free ressources: */ +- xfree((void**)&elements); +- + /*end module: */ + MODULEEND(); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h (revision 12112) +@@ -5,29 +5,54 @@ + #ifndef _NODECONNECTIVITY_H + #define _NODECONNECTIVITY_H + +-/* local prototypes: */ +-void NodeConnectivityUsage(void); ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif + ++/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ ++#ifdef _HAVE_PYTHON_ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#endif ++ ++/*Header files: */ + #include "../../c/include/globals.h" ++#include "../../c/toolkits/toolkits.h" ++#include "../../c/include/include.h" + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" + #include "../../c/issm-binding.h" ++#include "../../c/io/io.h" ++#include "../../c/EnumDefinitions/EnumDefinitions.h" + +-#undef __FUNCT__ +-#define __FUNCT__ "NodeConnectivity" +- ++#ifdef _HAVE_MATLAB_MODULES_ + /* serial input macros: */ + #define ELEMENTS (mxArray*)prhs[0] + #define NUMNODES (mxArray*)prhs[1] +- + /* serial output macros: */ + #define CONNECTIVITY (mxArray**)&plhs[0] ++#endif + ++#ifdef _HAVE_PYTHON_MODULES_ ++/* serial input macros: */ ++#define ELEMENTS PyTuple_GetItem(args,0) ++#define NUMNODES PyTuple_GetItem(args,1) ++/* serial output macros: */ ++#define CONNECTIVITY output,0 ++#endif ++ ++#undef __FUNCT__ ++#define __FUNCT__ "NodeConnectivity" ++ + /* serial arg counts: */ + #undef NLHS + #define NLHS 1 + #undef NRHS + #define NRHS 2 + ++/* local prototypes: */ ++void NodeConnectivityUsage(void); ++ + #endif /* _NODECONNECTIVITY_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp (revision 12112) +@@ -4,7 +4,7 @@ + + #include "./ElementConnectivity.h" + +-void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++WRAPPER(ElementConnectivity){ + + /*inputs: */ + double* elements=NULL; +@@ -18,8 +18,8 @@ + /*Boot module: */ + MODULEBOOT(); + +- /*checks on arguments on the matlab side: */ +- CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ElementConnectivityUsage); ++ /*checks on arguments: */ ++ CHECKARGUMENTS(NLHS,NRHS,&ElementConnectivityUsage); + + /*Input datasets: */ + FetchData(&elements,&nel,NULL,ELEMENTS); +@@ -31,10 +31,6 @@ + /*write output datasets: */ + WriteData(ELEMENTCONNECTIVITY,elementconnectivity,nel,3); + +- /*Free ressources: */ +- xfree((void**)&elements); +- xfree((void**)&nodeconnectivity); +- + /*end module: */ + MODULEEND(); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h (revision 12112) +@@ -5,29 +5,56 @@ + #ifndef _ELEMENTCONNECTIVITY_H + #define _ELEMENTCONNECTIVITY_H + +-/* local prototypes: */ +-void ElementConnectivityUsage(void); ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif + ++/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ ++#ifdef _HAVE_PYTHON_ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#endif ++ ++/*Header files: */ + #include "../../c/include/globals.h" ++#include "../../c/toolkits/toolkits.h" ++#include "../../c/include/include.h" + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" + #include "../../c/issm-binding.h" ++#include "../../c/io/io.h" ++#include "../../c/EnumDefinitions/EnumDefinitions.h" + +-#undef __FUNCT__ +-#define __FUNCT__ "ElementConnectivity" +- ++#ifdef _HAVE_MATLAB_MODULES_ + /* serial input macros: */ ++/* serial input macros: */ + #define ELEMENTS (mxArray*)prhs[0] + #define NODECONNECTIVITY (mxArray*)prhs[1] +- + /* serial output macros: */ + #define ELEMENTCONNECTIVITY (mxArray**)&plhs[0] ++#endif + ++#ifdef _HAVE_PYTHON_MODULES_ ++/* serial input macros: */ ++/* serial input macros: */ ++#define ELEMENTS PyTuple_GetItem(args,0) ++#define NODECONNECTIVITY PyTuple_GetItem(args,1) ++/* serial output macros: */ ++#define ELEMENTCONNECTIVITY output,0 ++#endif ++ ++#undef __FUNCT__ ++#define __FUNCT__ "ElementConnectivity" ++ + /* serial arg counts: */ + #undef NLHS + #define NLHS 1 + #undef NRHS + #define NRHS 2 + ++/* local prototypes: */ ++void ElementConnectivityUsage(void); ++ + #endif /* _ELEMENTCONNECTIVITY_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/TriMesh/TriMesh.cpp (revision 12112) +@@ -25,7 +25,7 @@ + /*Boot module: */ + MODULEBOOT(); + +- /*checks on arguments on the matlab side: */ ++ /*checks on arguments: */ + CHECKARGUMENTS(NLHS,NRHS,&TriMeshUsage); + + /*Fetch data needed for meshing: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py (revision 12112) +@@ -1,5 +1,7 @@ +-from TriMesh import * + from numpy import * ++import TriMesh as tm ++import NodeConnectivity as nc ++import ElementConnectivity as ec + + def triangle(md, domainname, resolution,riftname=''): + #TRIANGLE - create model mesh using the triangle package +@@ -31,7 +33,7 @@ + area = resolution**2. + + #Mesh using TriMesh +- [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,riftname,area) ++ [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=tm.TriMesh(domainname,riftname,area) + + #Fill in rest of fields: + md.mesh.numberofelements = size(md.mesh.elements) +@@ -45,10 +47,8 @@ + md.mesh.elementonsurface = ones(md.mesh.numberofelements) + + #Now, build the connectivity tables for this mesh. +- print "Node: NodeConnectivity not implemented yet!" +- #md.mesh.vertexconnectivity = NodeConnectivity((md.mesh.elements), (md.mesh.numberofvertices)) +- print "Node: ElementConnectivity not implemented yet!" +- #md.mesh.elementconnectivity = ElementConnectivity((md.mesh.elements), (md.mesh.vertexconnectivity)) ++ [md.mesh.vertexconnectivity]= nc.NodeConnectivity(md.mesh.elements, md.mesh.numberofvertices) ++ [md.mesh.elementconnectivity] = ec.ElementConnectivity(md.mesh.elements, md.mesh.vertexconnectivity) + + #type of model + md.mesh.dimension = 2. + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in +Makefile + + + __pycache__ +Makefile.in +Makefile + + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/setmask.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/setmask.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/setmask.py (revision 12112) +@@ -0,0 +1,55 @@ ++from numpy import * ++import FlagElements as fe ++ ++def setmask(md, floatingicename, groundedicename): ++ #SETMASK - establish boundaries between grounded and floating ice. ++ # ++ # By default, ice is considered grounded. The contour floatingicename defines nodes ++ # for which ice is floating. The contour groundedicename defines nodes inside an floatingice, ++ # that are grounded (ie: ice rises, islands, etc ...) ++ # All input files are in the Argus format (extension .exp). ++ # ++ # Usage: ++ # md=setmask(md,floatingicename,groundedicename) ++ # ++ # Examples: ++ # md=setmask(md,'all',''); ++ # md=setmask(md,'Iceshelves.exp','Islands.exp'); ++ ++ #%Get assigned fields ++ x = md.mesh.x ++ y = md.mesh.y ++ elements = md.mesh.elements ++ ++ #Assign elementonfloatingice, elementongroundedice, vertexongroundedice and vertexonfloatingice. Only change at your own peril! This is synchronized heavily with the GroundingLineMigration module. {{{1 ++ elementonfloatingice = fe.FlagElements(md, floatingicename) ++ elementongroundedice = fe.FlagElements(md, groundedicename) ++ ++ #Because groundedice nodes and elements can be included into an floatingice, we need to update. Remember, all the previous ++ #arrays come from domain outlines that can intersect one another: ++ ++ elementonfloatingice = logical_and(elementonfloatingice,~elementongroundedice) ++ elementongroundedice = ~elementonfloatingice ++ ++ #the order here is important. we choose vertexongroundedice as default on the grounding line. ++ vertexonfloatingice = zeros(md.mesh.numberofvertices,'bool') ++ vertexongroundedice = zeros(md.mesh.numberofvertices,'bool') ++ ++ pos=argwhere(elementongroundedice==1) ++ pos=md.mesh.elements[pos,:]-1 ++ if pos.size: ++ vertexongroundedice[pos]=True ++ ++ pos=argwhere(~vertexongroundedice) ++ if pos.size: ++ vertexonfloatingice[pos]=True; ++ #%}}} ++ ++ #Return: ++ md.mask.elementonfloatingice = double(elementonfloatingice) ++ md.mask.vertexonfloatingice = double(vertexonfloatingice) ++ md.mask.elementongroundedice = double(elementongroundedice) ++ md.mask.vertexongroundedice = double(vertexongroundedice) ++ md.mask.vertexonwater = zeros(md.mesh.numberofvertices) ++ md.mask.elementonwater = zeros(md.mesh.numberofelements) ++ return md +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Geometry/FlagElements.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Geometry/FlagElements.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Geometry/FlagElements.py (revision 12112) +@@ -0,0 +1,54 @@ ++from numpy import * ++def FlagElements(md,region): ++#FLAGELEMENTS - flag the elements in an region ++# ++# The region can be given with an exp file, a list of elements. ++# ++# Usage: ++# flag=FlagElements(md,region); ++# ++# Example: ++# flag=FlagElements(md,'all'); ++# flag=FlagElements(md,''); ++# flag=FlagElements(md,'Domain.exp'); ++# flag=FlagElements(md,'~Domain.exp'); ++# flag=FlagElements(md,md.mask.elementongroundedice); ++ ++ if isinstance(region,basestring): ++ if not(region): ++ flag=zeros(md.mesh.numberofelements,'bool') ++ invert=0; ++ elif region=='all': ++ flag=ones(md.mesh.numberofelements,'bool') ++ invert=0; ++ else: ++ #make sure that we actually don't want the elements outside the domain outline! ++ if region[0]=='~': ++ region=region[1:] ++ invert=1; ++ else: ++ invert=0; ++ ++ #does the region domain outline exist or do we have to look for xlim,ylim in basinzoom? ++ if not os.path.isfile(region): ++ [xlim,ylim]=basinzoom('basin',region); ++ flag_nodes=double(md.mesh.xxlim(1) & md.mesh.yylim(1)); ++ flag=prod(flag_nodes(md.mesh.elements),2); ++ else: ++ #ok, flag elements ++ flag=ContourToMesh(md.mesh.elements[:,0:3],md.mesh.x,md.mesh.y,region,'element',1); ++ ++ if invert: ++ flag=~flag; ++ ++ elif isinstance(region,nparray): ++ if len(region)!=md.mesh.numberofelements: ++ print FlagElements.__doc__ ++ print 'Flaglist for region must be of same size as number of elements in model' ++ return [] ++ flag=region; ++ else: ++ print 'Invalid region option' ++ return [] ++ ++ return flag; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 12112) +@@ -1,6 +1,6 @@ + #!/bin/sh + +-pythonversion=2.7 ++pythonversion=3.2 + + ./configure \ + --prefix=$ISSM_TIER \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12111) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12112) +@@ -82,6 +82,7 @@ + from miscellaneous import * + from private import * + from triangle import * ++from setmask import * + + #}}} + Index: /issm/oecreview/Archive/12101-12120/ISSM-12112-12113.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12112-12113.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12112-12113.diff (revision 12325) @@ -0,0 +1,91 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py (revision 12112) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py (revision 12113) +@@ -1,7 +1,9 @@ + from model import * + from triangle import * + from setmask import * ++from parameterize import * + + md=model(); + md=triangle(md,'../Exp/Square.exp',150000); + md=setmask(md,'all',''); ++md=parameterize(md,'../Par/SquareShelfConstrained.par') +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/parameterization/parameterize.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/parameterization/parameterize.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/parameterization/parameterize.py (revision 12113) +@@ -0,0 +1,27 @@ ++import os ++def parameterize(md,parametername): ++ #PARAMETERIZE - parameterize a model ++ # ++ # from a parameter matlab file, start filling in all the model fields that were not ++ # filled in by the mesh.py and setmask.py model methods. ++ # Warning: the parameter file must be able to be run in Python ++ # ++ # Usage: ++ # md=parameterize(md,parametername) ++ # ++ # Example: ++ # md=parameterize(md,'Square.par'); ++ ++ #some checks ++ if not os.path.isfile(parametername): ++ print 'parameterize error message: file '+parametername+' not found.' ++ return [] ++ ++ #Try and run parameter file. ++ execfile(parametername) ++ ++ #ame and notes ++ if len(md.miscellaneous.name)==0: ++ md.miscellaneous.name=os.path.basename(parametername) ++ ++ md=addnote(md,'Model created by using parameter file: '+parametername+' on: '+str(datetime.datetime.now())) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/addnote.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/addnote.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/addnote.py (revision 12113) +@@ -0,0 +1,29 @@ ++def addnote(md, string): ++ ++ # Local Variables: md, string, i, notes, miscellaneous, newnotes ++ # Function calls: ischar, nargout, cell, nargin, length, addnote, error ++ #ADDNOTE - add a note to the existing model notes field ++ # ++ # Usage: ++ # md=addnote(md,string); ++ # ++ # Example: ++ # md=addnote(md,'Pine Island, Geometry of 2007'); ++ ++ if not isinstance(string,basetring): ++ print 'addnote error message: second input argument should be a string' ++ return [] ++ ++ notes = md.miscellaneous.notes ++ ++ if isinstance(notes,basestring): ++ newnotes=[notes,string] ++ else: ++ newnotes=[]; ++ for i in range(len(notes)): ++ newnotes=newnotes+notes[i] ++ ++ newnotes=newnotes+nodes; ++ ++ md.miscellaneous.notes = newnotes ++ return md +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model.py (revision 12112) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model.py (revision 12113) +@@ -110,6 +110,5 @@ + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("results","[%s,%s]" % ("1x1",obj.results.__class__.__name__),"model results'")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("radaroverlay","[%s,%s]" % ("1x1",obj.radaroverlay.__class__.__name__),"radar image for plot overlay")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("miscellaneous","[%s,%s]" % ("1x1",obj.miscellaneous.__class__.__name__),"miscellaneous fields")) +- string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("miscellaneous","[%s,%s]" % ("1x1",obj.miscellaneous.__class__.__name__),"miscellaneous fields")) + return string; + #}}} Index: /issm/oecreview/Archive/12101-12120/ISSM-12114-12115.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12114-12115.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12114-12115.diff (revision 12325) @@ -0,0 +1,80 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12114) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12115) +@@ -64,6 +64,10 @@ + export CXX=icpc + export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ " + export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ " ++ elif test $VENDOR = arm-linux; then ++ export CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-cc ++ export CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-cc ++ + else + AC_MSG_ERROR([unknow compiler vendor!]) + fi +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-android-4.0.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-android-4.0.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-android-4.0.sh (revision 12115) +@@ -0,0 +1,35 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf src install gsl-1.15 ++mkdir src install ++ ++#Untar ++tar -zxvf gsl-1.15.tar.gz ++ ++#Move gsl into src directory ++mv gsl-1.15/* src ++rm -rf gsl-1.15 ++ ++#Configure gsl ++cd src ++ ++./configure \ ++ CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc\ ++ LD=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ld\ ++ AR=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ar\ ++ RANLIB=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib\ ++ NM=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-nm\ ++ OBJ_EXT=o\ ++ LIB_EXT=a\ ++ --host="arm-linux"\ ++ --prefix="$ISSM_TIER/externalpackages/gsl/install" ++ ++#Compile gsl ++if [ -z $1 ]; then ++ make ++else ++ make -j $1 ++fi ++ ++make install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-android-4.0.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/configs/android/android-4.0/configure.make +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/configs/android/android-4.0/configure.make (revision 12114) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/configs/android/android-4.0/configure.make (revision 12115) +@@ -10,10 +10,10 @@ + # http://www.codesourcery.com/gnu_toolchains/arm/arm_gnu_linux_abi.pdf + + ANDROID_BIN=$(ISSM_TIER)/src/android/tmp/android-14-toolchain/bin +-CC=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-gcc +-AR=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-ar +-RANLIB=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-ranlib +-CSWITCHES = $(CFLAGS) -I/usr/X11R6/include -L/usr/X11R6/lib -I$(MATLAB_DIR)/extern/include -fPIC -I$(MATLAB_DIR)/include ++CC=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc ++AR=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-ar ++RANLIB=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib ++CSWITCHES = $(CFLAGS) + TRILIBDEFS = -DTRILIBRARY + OBJ_EXT=o + LIB_EXT=a Index: /issm/oecreview/Archive/12101-12120/ISSM-12115-12116.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12115-12116.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12115-12116.diff (revision 12325) @@ -0,0 +1,28 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py (revision 12115) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py (revision 12116) +@@ -35,12 +35,13 @@ + #Mesh using TriMesh + [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=tm.TriMesh(domainname,riftname,area) + ++ + #Fill in rest of fields: + md.mesh.numberofelements = size(md.mesh.elements) + md.mesh.numberofvertices = size(md.mesh.x) + md.mesh.z = zeros(md.mesh.numberofvertices) + md.mesh.vertexonboundary = zeros(md.mesh.numberofvertices) +- md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)] = 1. ++ md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)-1] = 1. + md.mesh.vertexonbed = ones(md.mesh.numberofvertices) + md.mesh.vertexonsurface = ones(md.mesh.numberofvertices) + md.mesh.elementonbed = ones(md.mesh.numberofelements) +@@ -49,7 +50,7 @@ + #Now, build the connectivity tables for this mesh. + [md.mesh.vertexconnectivity]= nc.NodeConnectivity(md.mesh.elements, md.mesh.numberofvertices) + [md.mesh.elementconnectivity] = ec.ElementConnectivity(md.mesh.elements, md.mesh.vertexconnectivity) +- ++ + #type of model + md.mesh.dimension = 2. + return md Index: /issm/oecreview/Archive/12101-12120/ISSM-12116-12117.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12116-12117.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12116-12117.diff (revision 12325) @@ -0,0 +1,54 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py (revision 12116) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py (revision 12117) +@@ -18,6 +18,8 @@ + self.rheology_B = float('NaN') + self.rheology_n = float('NaN') + self.rheology_law = ""; ++ ++ self.setdefaultparameters() + #}}} + def __repr__(obj): + # {{{ Display +@@ -39,3 +41,40 @@ + + return string + #}}} ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ #ice density (kg/m^3) ++ obj.rho_ice=917 ++ ++ #water density (kg/m^3) ++ obj.rho_water=1023 ++ ++ #water viscosity (N.s/m^2) ++ obj.mu_water=0.001787 ++ ++ #ice heat capacity cp (J/kg/K) ++ obj.heatcapacity=2093 ++ ++ #ice latent heat of fusion L (J/kg) ++ obj.latentheat=3.34*10**5 ++ ++ #ice thermal conductivity (W/m/K) ++ obj.thermalconductivity=2.4 ++ ++ #the melting point of ice at 1 atmosphere of pressure in K ++ obj.meltingpoint=273.15 ++ ++ #rate of change of melting point with pressure (K/Pa) ++ obj.beta=9.8*10**-8 ++ ++ #mixed layer (ice-water interface) heat capacity (J/kg/K) ++ obj.mixed_layer_capacity=3974 ++ ++ #thermal exchange velocity (ice-water interface) (m/s) ++ obj.thermal_exchange_velocity=1.00*10**-4 ++ ++ #Rheology law: what is the temperature dependence of B with T ++ #available: none, paterson and arrhenius ++ obj.rheology_law='Paterson' ++ return obj ++ #}}} Index: /issm/oecreview/Archive/12101-12120/ISSM-12117-12118.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12117-12118.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12117-12118.diff (revision 12325) @@ -0,0 +1,283 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am (revision 12117) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/python/Makefile.am (revision 12118) +@@ -2,9 +2,10 @@ + EXEEXT=$(PYTHONWRAPPEREXT) + #Bin programs {{{1 + if MODULES +-bin_PROGRAMS = TriMesh \ +- NodeConnectivity \ +- ElementConnectivity ++bin_PROGRAMS = ElementConnectivity\ ++ InterpFromMeshToMesh2d \ ++ NodeConnectivity\ ++ TriMesh + endif + #}}} + #Flags and libraries {{{1 +@@ -30,6 +31,9 @@ + ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\ + ../ElementConnectivity/ElementConnectivity.h + ++InterpFromMeshToMesh2d_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\ ++ ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h ++ + NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\ + ../NodeConnectivity/NodeConnectivity.h + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12117) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (revision 12118) +@@ -3,44 +3,30 @@ + */ + #include "./InterpFromMeshToMesh2d.h" + +-void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + +- int i; ++WRAPPER(InterpFromMeshToMesh2d){ + + /*input: */ + double* index=NULL; + int index_cols; +- + double* x_data=NULL; + int x_data_rows; +- + double* y_data=NULL; + int y_data_rows; +- + double* data=NULL; + int data_rows; + int data_cols; +- + double* x_interp=NULL; +- double* y_interp=NULL; +- + int x_interp_rows; ++ double* y_interp=NULL; + int y_interp_rows; +- ++ char* contourname=NULL; + double* default_values=NULL; + int num_default_values=0; ++ DataSet *contours = NULL; + +- //contours +- mxArray* matlabstructure=NULL; +- Contour** contours=NULL; +- int numcontours; +- Contour* contouri=NULL; +- + /*Intermediary*/ +- int nods_data; + int nels_data; +- int nods_interp; +- int verbose=0; + + /* output: */ + double* data_interp=NULL; +@@ -48,67 +34,41 @@ + /*Boot module: */ + MODULEBOOT(); + +- /*checks on arguments on the matlab side: */ ++ /*checks on output arguments on the matlab side: */ ++ #ifdef _HAVE_MATLAB_MODULES_ + if(nlhs!=NLHS){ + InterpFromMeshToMesh2dUsage(); + _error_("InterpFromMeshToMesh2dUsage usage error"); + } ++ #endif ++ /*check on input arguments: */ + if((nrhs!=6) & (nrhs!=8)){ + InterpFromMeshToMesh2dUsage(); + _error_("InterpFromMeshToMesh2dUsage usage error"); + } + + /*Input datasets: */ +- if (verbose) printf("Fetching inputs\n"); +- FetchData(&index,&nels_data,&index_cols,INDEXHANDLE); +- FetchData(&x_data,&x_data_rows,NULL,XHANDLE); +- FetchData(&y_data,&y_data_rows,NULL,YHANDLE); +- FetchData(&data,&data_rows,&data_cols,DATAHANDLE); +- FetchData(&x_interp,&x_interp_rows,NULL,XINTERPHANDLE); +- FetchData(&y_interp,&y_interp_rows,NULL,YINTERPHANDLE); ++ FetchData(&index,&nels_data,&index_cols,INDEX); ++ FetchData(&x_data,&x_data_rows,NULL,X); ++ FetchData(&y_data,&y_data_rows,NULL,Y); ++ FetchData(&data,&data_rows,&data_cols,DATA); ++ FetchData(&x_interp,&x_interp_rows,XINTERP); ++ FetchData(&y_interp,&y_interp_rows,YINTERP); + ++ /*Figure out contours and default values: */ + if(nrhs==8){ +- +- /*Call expread on filename to build a contour array in the matlab workspace: */ +- mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); +- +- /*default values: */ +- FetchData(&default_values,&num_default_values,DEFAULTHANDLE); +- +- /*contours: */ +- numcontours=mxGetNumberOfElements(matlabstructure); +- contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); +- for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); +- //set pointers. +- contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); +- contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); +- *(contours+i)=contouri; +- } +- +- /* Debugging of contours :{{{1*/ +- /*for(i=0;inods); +- for (j=0;jnods;j++){ +- printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); +- } +- }*/ +- /*}}}*/ ++ FetchData(&default_values,&num_default_values,DEFAULT); ++ FetchData(&contourname,CONTOURNAME); ++ contours=DomainOutlineRead(contourname); + } + else{ + num_default_values=0; + default_values=NULL; +- numcontours=0; +- contours=NULL; ++ contours=new DataSet(); + } + ++ + /*some checks*/ +- if (verbose) printf("Checking inputs\n"); + if (x_data_rows!=y_data_rows){ + _error_("vectors x and y should have the same length!"); + } +@@ -119,22 +79,18 @@ + _error_("index should have 3 columns (input provided has %i columns)",index_cols); + } + +- /*get number of elements and number of nodes in the data*/ +- nods_data=x_data_rows; +- nods_interp=x_interp_rows; +- + /* Run core computations: */ +- if (verbose) printf("Call core\n"); +- InterpFromMeshToMesh2dx(&data_interp,index,x_data,y_data,nods_data,nels_data,data,data_rows,data_cols,x_interp,y_interp,nods_interp,default_values,num_default_values,contours,numcontours); ++ InterpFromMeshToMesh2dx(&data_interp,index,x_data,y_data,x_data_rows,nels_data,data,data_rows,data_cols,x_interp,y_interp,x_interp_rows,default_values,num_default_values,contours); + + /*Write data: */ +- WriteData(DATAINTERP,data_interp,nods_interp,data_cols); ++ WriteData(DATAINTERP,data_interp,x_interp_rows,data_cols); + + /*end module: */ + MODULEEND(); + } + +-void InterpFromMeshToMesh2dUsage(void) ++void InterpFromMeshToMesh2dUsage(void)//{{{1 ++ + { + _printf_(true,"INTERFROMMESHTOMESH2D - interpolation from a 2d triangular mesh onto a list of point\n"); + _printf_(true,"\n"); +@@ -160,3 +116,4 @@ + _printf_(true," md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y,253,'Contour.exp');\n"); + _printf_(true,"\n"); + } ++//}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 12117) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 12118) +@@ -5,34 +5,67 @@ + #ifndef _INTERPFROMMESHTOMESH2d_H + #define _INTERPFROMMESHTOMESH2d_H + +-/* local prototypes: */ +-void InterpFromMeshToMesh2dUsage(void); ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif + ++/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ ++#ifdef _HAVE_PYTHON_ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#endif ++ ++/*Header files: */ + #include "../../c/include/globals.h" ++#include "../../c/toolkits/toolkits.h" ++#include "../../c/include/include.h" + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" + #include "../../c/issm-binding.h" ++#include "../../c/io/io.h" ++#include "../../c/EnumDefinitions/EnumDefinitions.h" + +-#undef __FUNCT__ +-#define __FUNCT__ "InterpFromMeshToMesh2d" +- +- ++#ifdef _HAVE_MATLAB_MODULES_ + /* serial input macros: */ +-#define INDEXHANDLE prhs[0] +-#define XHANDLE prhs[1] +-#define YHANDLE prhs[2] +-#define DATAHANDLE prhs[3] +-#define XINTERPHANDLE prhs[4] +-#define YINTERPHANDLE prhs[5] +-#define DEFAULTHANDLE prhs[6] +-#define FILENAME prhs[7] ++#define INDEX prhs[0] ++#define X prhs[1] ++#define Y prhs[2] ++#define DATA prhs[3] ++#define XINTERP prhs[4] ++#define YINTERP prhs[5] ++#define DEFAULT prhs[6] ++#define CONTOURNAME prhs[7] + + /* serial output macros: */ + #define DATAINTERP (mxArray**)&plhs[0] ++#endif + ++#ifdef _HAVE_PYTHON_MODULES_ ++/* serial input macros: */ ++#define INDEX PyTuple_GetItem(args,0) ++#define X PyTuple_GetItem(args,1) ++#define Y PyTuple_GetItem(args,2) ++#define DATA PyTuple_GetItem(args,3) ++#define XINTERP PyTuple_GetItem(args,4) ++#define YINTERP PyTuple_GetItem(args,5) ++#define DEFAULT PyTuple_GetItem(args,6) ++#define CONTOURNAME PyTuple_GetItem(args,7) ++/* serial output macros: */ ++#define DATAINTERP output,0 ++#endif ++ ++#undef __FUNCT__ ++#define __FUNCT__ "InterpFromMeshToMesh2d" ++ + /* serial arg counts: */ + #undef NLHS + #define NLHS 1 ++#undef NRHS ++#define NRHS 6 //can be 8 though + ++/* local prototypes: */ ++void InterpFromMeshToMesh2dUsage(void); ++ + #endif Index: /issm/oecreview/Archive/12101-12120/ISSM-12118-12119.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12118-12119.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12118-12119.diff (revision 12325) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h (revision 12118) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/include/python_macros.h (revision 12119) +@@ -22,7 +22,8 @@ + * will be trapped. Really nifty!*/ + + #define MODULEBOOT(); ModuleBoot(); \ +- PyObject* output = PyTuple_New(NLHS); if (!output) return NULL; ++ PyObject* output = PyTuple_New(NLHS); if (!output) return NULL;\ ++ int nrhs = (int)PyTuple_Size(args); + + #define MODULEEND(); ModuleEnd(); \ + return output; Index: /issm/oecreview/Archive/12101-12120/ISSM-12119-12120.diff =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-12119-12120.diff (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-12119-12120.diff (revision 12325) @@ -0,0 +1,52 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h (revision 12119) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/pythonio.h (revision 12120) +@@ -40,11 +40,11 @@ + //void FetchData(Matrix** pmatrix,PyObject* py_ref); + //void FetchData(int** pvector,int* pM,PyObject* py_ref); + //void FetchData(float** pvector,int* pM,PyObject* py_ref); +-//void FetchData(double** pvector,int* pM,PyObject* py_ref); + //void FetchData(bool** pvector,int* pM,PyObject* py_ref); + //void FetchData(Vector** pvector,PyObject* py_ref); + //void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); + //void FetchData(Parameters** pparameters, DataHandle py_ref); ++void FetchData(double** pvector,int* pM,PyObject* py_ref); + void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_array); + void FetchData(char** pstring,PyObject* py_unicode); + void FetchData(double* pscalar,PyObject* py_float); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12119) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 12120) +@@ -80,7 +80,30 @@ + if(pmatrix)*pmatrix=matrix; + } + /*}}}*/ ++/*FUNCTION FetchData(double** pvector,int* pM, PyObject* py_vector){{{1*/ ++void FetchData(double** pvector,int* pM,PyObject* py_vector){ + ++ /*output: */ ++ double* vector=NULL; ++ int M; ++ int ndim; ++ npy_intp* dims=NULL; ++ ++ /*retrive dimensions: */ ++ ndim=PyArray_NDIM((const PyArrayObject*)py_vector); ++ if(ndim!=1)_error_("expecting an Mx1 vector in input!"); ++ dims=PyArray_DIMS((PyArrayObject*)py_vector); ++ M=dims[0]; ++ ++ /*retrieve internal value: */ ++ vector=(double*)PyArray_DATA((PyArrayObject*)py_vector); ++ ++ /*output: */ ++ if(pM)*pM=M; ++ if(pvector)*pvector=vector; ++} ++/*}}}*/ ++ + /*Python version dependent: */ + #if _PYTHON_MAJOR_ >= 3 + /*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{1*/ Index: /issm/oecreview/Archive/12101-12120/ISSM-DocReview-12101-12120.tex =================================================================== --- /issm/oecreview/Archive/12101-12120/ISSM-DocReview-12101-12120.tex (revision 12325) +++ /issm/oecreview/Archive/12101-12120/ISSM-DocReview-12101-12120.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12101-12120/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12101-12120/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12101-12120/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12101-12120 Index: /issm/oecreview/Archive/12101-12120/Makefile =================================================================== --- /issm/oecreview/Archive/12101-12120/Makefile (revision 12325) +++ /issm/oecreview/Archive/12101-12120/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12101-12120 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12101-12120/log.tex =================================================================== --- /issm/oecreview/Archive/12101-12120/log.tex (revision 12325) +++ /issm/oecreview/Archive/12101-12120/log.tex (revision 12325) @@ -0,0 +1,36 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12101-12102.diff: \\ Function name: \\A /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp A /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/petscpatches.h \\ Export determination: 6. \\Rationale: Relocation from matlab to petsc patches +M /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh M /issm/trunk-jpl/externalpackages/nose/install-macosx64sh M /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh M /issm/trunk-jpl/m4/issm\_options.m4 M /issm/trunk-jpl/src/Makefile.am M /issm/trunk-jpl/src/c/Container/Constraints.cpp M /issm/trunk-jpl/src/c/Container/Elements.cpp M /issm/trunk-jpl/src/c/Container/Loads.cpp M /issm/trunk-jpl/src/c/Container/Nodes.cpp M /issm/trunk-jpl/src/c/Container/Vertices.cpp M /issm/trunk-jpl/src/c/Makefile.am D /issm/trunk-jpl/src/c/matlab/io/PetscMatrixToDoubleMatrix.cpp D /issm/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp M /issm/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp M /issm/trunk-jpl/src/c/matlab/io/matlabio.h M /issm/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp M /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp M /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp M /issm/trunk-jpl/src/c/modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.cpp M /issm/trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp M /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp M /issm/trunk-jpl/src/c/modules/IceVolumex/IceVolumex.cpp M /issm/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp M /issm/trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp M /issm/trunk-jpl/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp M /issm/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp M /issm/trunk-jpl/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp M /issm/trunk-jpl/src/c/modules/MaxVelx/MaxVelx.cpp M /issm/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp M /issm/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp M /issm/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp M /issm/trunk-jpl/src/c/modules/MeshPartitionx/MeshPartitionx.cpp M /issm/trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp M /issm/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp M /issm/trunk-jpl/src/c/modules/MinVyx/MinVyx.cpp M /issm/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp M /issm/trunk-jpl/src/c/modules/NodalValuex/NodalValuex.cpp M /issm/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp M /issm/trunk-jpl/src/c/modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceAreax/SurfaceAreax.cpp M /issm/trunk-jpl/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp M /issm/trunk-jpl/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp M /issm/trunk-jpl/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp M /issm/trunk-jpl/src/c/modules/TimeAdaptx/TimeAdaptx.cpp M /issm/trunk-jpl/src/c/objects/Bamg/Metric.h M /issm/trunk-jpl/src/c/objects/IoModel.cpp M /issm/trunk-jpl/src/c/objects/Patch.cpp M /issm/trunk-jpl/src/c/solutions/issm.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp M /issm/trunk-jpl/src/c/toolkits/toolkits.h A /issm/trunk-jpl/src/m/model/mesh/triangle.py M /issm/trunk-jpl/startup.py M /issm/trunk-jpl/test/NightlyRun/test101.py Stripped out the following layers: METIS: if not running with MPI, do not partition! MPI: can now run without PETSC and MPI, just using the gsl matrix format. PETSC and MPI: idem. Can not run MPI and PETSC separately. \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12102-12103.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh M /issm/trunk-jpl/externalpackages/nose/install-macosx64sh M /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh M /issm/trunk-jpl/m4/issm\_options.m4 M /issm/trunk-jpl/src/Makefile.am M /issm/trunk-jpl/src/c/Container/Constraints.cpp M /issm/trunk-jpl/src/c/Container/Elements.cpp M /issm/trunk-jpl/src/c/Container/Loads.cpp M /issm/trunk-jpl/src/c/Container/Nodes.cpp M /issm/trunk-jpl/src/c/Container/Vertices.cpp M /issm/trunk-jpl/src/c/Makefile.am D /issm/trunk-jpl/src/c/matlab/io/PetscMatrixToDoubleMatrix.cpp D /issm/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp M /issm/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp M /issm/trunk-jpl/src/c/matlab/io/matlabio.h M /issm/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp M /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp M /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp M /issm/trunk-jpl/src/c/modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.cpp M /issm/trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp M /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp M /issm/trunk-jpl/src/c/modules/IceVolumex/IceVolumex.cpp M /issm/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp M /issm/trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp M /issm/trunk-jpl/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp M /issm/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp M /issm/trunk-jpl/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp M /issm/trunk-jpl/src/c/modules/MaxVelx/MaxVelx.cpp M /issm/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp M /issm/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp M /issm/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp M /issm/trunk-jpl/src/c/modules/MeshPartitionx/MeshPartitionx.cpp M /issm/trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp M /issm/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp M /issm/trunk-jpl/src/c/modules/MinVyx/MinVyx.cpp M /issm/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp M /issm/trunk-jpl/src/c/modules/NodalValuex/NodalValuex.cpp M /issm/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp M /issm/trunk-jpl/src/c/modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceAreax/SurfaceAreax.cpp M /issm/trunk-jpl/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp M /issm/trunk-jpl/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp M /issm/trunk-jpl/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp M /issm/trunk-jpl/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp M /issm/trunk-jpl/src/c/modules/TimeAdaptx/TimeAdaptx.cpp M /issm/trunk-jpl/src/c/objects/Bamg/Metric.h M /issm/trunk-jpl/src/c/objects/IoModel.cpp M /issm/trunk-jpl/src/c/objects/Patch.cpp M /issm/trunk-jpl/src/c/solutions/issm.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp M /issm/trunk-jpl/src/c/toolkits/toolkits.h A /issm/trunk-jpl/src/m/model/mesh/triangle.py M /issm/trunk-jpl/startup.py M /issm/trunk-jpl/test/NightlyRun/test101.py \\ Export determination: 6. \\Rationale: Stripped out the following layers: METIS: if not running with MPI, do not partition! MPI: can now run without PETSC and MPI, just using the gsl matrix format. PETSC and MPI: idem. Can not run MPI and PETSC separately. +M /issm/trunk-jpl/configs/config-arm.sh Arm processor configuration \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12103-12104.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-arm.sh \\ Export determination: 6. \\Rationale: Arm processor configuration +M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp Create dense matrix if sparsity=1 \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12104-12105.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp \\ Export determination: 6. \\Rationale: Create dense matrix if sparsity=1 +M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp oops, wrong file \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12105-12106.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp \\ Export determination: 6. \\Rationale: oops, wrong file +M /issm/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp Create dense matrix if sparsity=1 \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12106-12107.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp \\ Export determination: 6. \\Rationale: Create dense matrix if sparsity=1 +M /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh Added spai install \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12107-12108.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh \\ Export determination: 6. \\Rationale: Added spai install +M /issm/trunk-jpl/src/c/Container/Nodes.cpp Bug in MPI\_Gather \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12108-12109.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Nodes.cpp \\ Export determination: 6. \\Rationale: Bug in MPI\_Gather +M /issm/trunk-jpl/src/c/Container/Nodes.cpp Fixed bug introduced while stripping MPI \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12109-12110.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Nodes.cpp \\ Export determination: 6. \\Rationale: Fixed bug introduced while stripping MPI +M /issm/trunk-jpl/test/NightlyRun/test101.py triangle now working completely in python \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12110-12111.diff: \\ Function name: \\M /issm/trunk-jpl/test/NightlyRun/test101.py \\ Export determination: 6. \\Rationale: triangle now working completely in python +D /issm/trunk-jpl/test/NightlyRun/test101.py A /issm/trunk-jpl/test/NightlyRun/test102.py (from /issm/trunk-jpl/test/NightlyRun/test101.py:12110) Moving to 102 \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12111-12112.diff: \\ Function name: \\D /issm/trunk-jpl/test/NightlyRun/test101.py A /issm/trunk-jpl/test/NightlyRun/test102.py (from /issm/trunk-jpl/test/NightlyRun/test101.py:12110) \\ Export determination: 6. \\Rationale: Moving to 102 +M /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh M /issm/trunk-jpl/src/c/python/io/FetchPythonData.cpp M /issm/trunk-jpl/src/c/python/io/WritePythonData.cpp M /issm/trunk-jpl/src/c/python/io/pythonio.h M /issm/trunk-jpl/src/m/model/mesh M /issm/trunk-jpl/src/m/model/mesh/triangle.py A /issm/trunk-jpl/src/m/model/setmask.py A /issm/trunk-jpl/src/m/utils/Geometry/FlagElements.py M /issm/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp M /issm/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h M /issm/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp M /issm/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h M /issm/trunk-jpl/src/modules/TriMesh/TriMesh.cpp M /issm/trunk-jpl/src/modules/python/Makefile.am M /issm/trunk-jpl/startup.py M /issm/trunk-jpl/test/NightlyRun/test102.py Finished python version of setmask.py and FlagElements.py Also finished triangle.py, with addition of 2 python modules NodeConnectivity and ElementConnectivity. \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-12112-12113.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh M /issm/trunk-jpl/src/c/python/io/FetchPythonData.cpp M /issm/trunk-jpl/src/c/python/io/WritePythonData.cpp M /issm/trunk-jpl/src/c/python/io/pythonio.h M /issm/trunk-jpl/src/m/model/mesh M /issm/trunk-jpl/src/m/model/mesh/triangle.py A /issm/trunk-jpl/src/m/model/setmask.py A /issm/trunk-jpl/src/m/utils/Geometry/FlagElements.py M /issm/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp M /issm/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h M /issm/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp M /issm/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h M /issm/trunk-jpl/src/modules/TriMesh/TriMesh.cpp M /issm/trunk-jpl/src/modules/python/Makefile.am M /issm/trunk-jpl/startup.py M /issm/trunk-jpl/test/NightlyRun/test102.py \\ Export determination: 6. \\Rationale: Finished python version of setmask.py and FlagElements.py Also finished triangle.py, with addition of 2 python modules NodeConnectivity and ElementConnectivity. +M /issm/trunk-jpl/src/m/classes/model.py A /issm/trunk-jpl/src/m/model/addnote.py A /issm/trunk-jpl/src/m/model/parameterization/parameterize.py M /issm/trunk-jpl/test/NightlyRun/test102.py Implemented parameterize routine in python \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-12113-12114.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/model.py A /issm/trunk-jpl/src/m/model/addnote.py A /issm/trunk-jpl/src/m/model/parameterization/parameterize.py M /issm/trunk-jpl/test/NightlyRun/test102.py \\ Export determination: 6. \\Rationale: Implemented parameterize routine in python \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-12114-12115.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/gsl/install-android-4.0.sh M /issm/trunk-jpl/externalpackages/triangle/configs/android/android-4.0/configure.make M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: Created the install script for GSL to cross-compile for arm-linux-android and made minor modifications to other scripts. \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-12115-12116.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/gsl/install-android-4.0.sh M /issm/trunk-jpl/externalpackages/triangle/configs/android/android-4.0/configure.make M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: Created the install script for GSL to cross-compile for arm-linux-android and made minor modifications to other scripts. +M /issm/trunk-jpl/src/m/model/mesh/triangle.py Indexing bug \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-12116-12117.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/mesh/triangle.py \\ Export determination: 6. \\Rationale: Indexing bug +M /issm/trunk-jpl/src/m/classes/materials.py Added defaults for materials class \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-12117-12118.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/materials.py \\ Export determination: 6. \\Rationale: Added defaults for materials class +M /issm/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp M /issm/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h M /issm/trunk-jpl/src/modules/python/Makefile.am Adapted InterpFromMeshToMesh2d to python \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-12118-12119.diff: \\ Function name: \\M /issm/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp M /issm/trunk-jpl/src/modules/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h M /issm/trunk-jpl/src/modules/python/Makefile.am \\ Export determination: 6. \\Rationale: Adapted InterpFromMeshToMesh2d to python +M /issm/trunk-jpl/src/c/python/include/python\_macros.h Added nrhs as input argument for all python modules to access \\\\ +\noindent \textbf{Change \#19} with diff file ISSM-12119-12120.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/python/include/python\_macros.h \\ Export determination: 6. \\Rationale: Added nrhs as input argument for all python modules to access +M /issm/trunk-jpl/src/c/python/io/FetchPythonData.cpp M /issm/trunk-jpl/src/c/python/io/pythonio.h Added fetch data capability for double* vector \\\\ Index: /issm/oecreview/Archive/12101-12120/r1.tex =================================================================== --- /issm/oecreview/Archive/12101-12120/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12101-12120/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12101 Index: /issm/oecreview/Archive/12101-12120/r2.tex =================================================================== --- /issm/oecreview/Archive/12101-12120/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12101-12120/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12120 Index: /issm/oecreview/Archive/12121-12140/Date.tex =================================================================== --- /issm/oecreview/Archive/12121-12140/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12121-12140/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12121-12140/ISSM-12121-12122.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12121-12122.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12121-12122.diff (revision 12325) @@ -0,0 +1,75 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Par/SquareShelfConstrained.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Par/SquareShelfConstrained.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Par/SquareShelfConstrained.py (revision 12122) +@@ -0,0 +1,57 @@ ++from numpy import * ++import scipy.io as matio ++import InterpFromMeshToMesh2d as im ++ ++#Start defining model parameters here ++#Geometry ++hmin = 300. ++hmax = 1000. ++ymin = min(md.mesh.y) ++ymax = max(md.mesh.y) ++ ++md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin) ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; ++md.geometry.surface = md.geometry.bed+md.geometry.thickness ++ ++#%Initial velocity ++mat=matio.loadmat('../Data/SquareShelfConstrained.data') ++#deal with 'F' oriented matlab matrices! ++index=mat['index'].astype(float) ++index=reshape(index.T,(len(index),3),order='F') ++ ++md.initialization.vx = im.InterpFromMeshToMesh2d(index, mat['x'], mat['y'], mat['vx'], md.mesh.x, md.mesh.y) ++md.initialization.vy = im.InterpFromMeshToMesh2d(index, mat['x'], mat['y'], mat['vy'], md.mesh.x, md.mesh.y) ++md.initialization.vz = zeros(md.mesh.numberofvertices) ++md.initialization.pressure = zeros(md.mesh.numberofvertices) ++#%Materials ++md.initialization.temperature = (273.-20)*ones(md.mesh.numberofvertices) ++md.materials.rheology_B = paterson(md.initialization.temperature) ++md.materials.rheology_n = 3.*ones(md.mesh.numberofelements) ++#%Surface mass balance and basal melting ++md.surfaceforcings.mass_balance = 10.*ones(md.mesh.numberofvertices) ++md.basalforcings.melting_rate = 5.*ones(md.mesh.numberofvertices) ++#%Friction ++pos = nonzero(md.mask.elementonfloatingice) ++md.friction.coefficient = 20.*ones(md.mesh.numberofvertices) ++md.friction.coefficient[(md.mesh.elements[int(pos)-1,:])] = 0. ++md.friction.p = ones(md.mesh.numberofelements) ++md.friction.q = ones(md.mesh.numberofelements) ++#%Numerical parameters ++md.diagnostic.viscosity_overshoot = 0.0 ++md.prognostic.stabilization = 1. ++md.thermal.stabilization = 1. ++md.verbose = verbose[-1] ++md.settings.waitonlock = 30. ++md.diagnostic.restol = 0.05 ++md.diagnostic.reltol = 0.05 ++md.steadystate.reltol = 0.05 ++md.diagnostic.abstol = nan ++md.timestepping.time_step = 1. ++md.timestepping.final_time = 3. ++#%Deal with boundary conditions: ++md = SetIceShelfBC(md) ++#%Change name so that no test have the same name ++A = dbstack ++if length(A) > 2.: ++ md.miscellaneous.name = A[2].file[0:0-2.] ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py (revision 12121) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test102.py (revision 12122) +@@ -4,6 +4,6 @@ + from parameterize import * + + md=model(); +-md=triangle(md,'../Exp/Square.exp',150000); ++md=triangle(md,'../Exp/Square.exp',50000); + md=setmask(md,'all',''); +-md=parameterize(md,'../Par/SquareShelfConstrained.par') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') Index: /issm/oecreview/Archive/12121-12140/ISSM-12122-12123.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12122-12123.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12122-12123.diff (revision 12325) @@ -0,0 +1,922 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/thermal.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/thermal.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/thermal.py (revision 12123) +@@ -12,6 +12,10 @@ + self.penalty_lock = 0 + self.penalty_factor = 0 + self.isenthalpy = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -24,3 +28,25 @@ + string="%s\n%s"%(string,fielddisplay(obj,'isenthalpy','use an enthalpy formulation to include temperate ice (default is 0)')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #Number of unstable constraints acceptable ++ obj.penalty_threshold=0 ++ ++ #Type of stabilization used ++ obj.stabilization=1 ++ ++ #Maximum number of iterations ++ obj.maxiter=100 ++ ++ #factor used to compute the values of the penalties: kappa=max(stiffness matrix)*10^penalty_factor ++ obj.penalty_factor=3 ++ ++ #Should we use cold ice (default) or enthalpy formulation ++ obj.isenthalpy=0 ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/settings.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/settings.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/settings.py (revision 12123) +@@ -5,11 +5,15 @@ + #properties + def __init__(self): + # {{{ Properties +- self.io_gather = 0; +- self.lowmem = 0; +- self.results_as_patches = 0; +- self.output_frequency = 0; +- self.waitonlock = 0; ++ self.io_gather = 0 ++ self.lowmem = 0 ++ self.results_as_patches = 0 ++ self.output_frequency = 0 ++ self.waitonlock = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -22,3 +26,28 @@ + string="%s\n%s"%(string,fielddisplay(obj,"waitonlock","maximum number of minutes to wait for batch results, or return 0")) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #are we short in memory ? (0 faster but requires more memory) ++ obj.lowmem=0 ++ ++ #i/o: ++ obj.io_gather=1 ++ ++ #results frequency by default every step ++ obj.output_frequency=1 ++ ++ #do not use patches by default (difficult to plot) ++ obj.results_as_patches=0 ++ ++ #this option can be activated to load automatically the results ++ #onto the model after a parallel run by waiting for the lock file ++ #N minutes that is generated once the solution has converged ++ #0 to desactivate ++ obj.waitonlock=float('Inf') ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/balancethickness.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/balancethickness.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/balancethickness.py (revision 12123) +@@ -7,6 +7,10 @@ + self.spcthickness = float('NaN') + self.thickening_rate = float('NaN') + self.stabilization = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -18,3 +22,12 @@ + string="%s\n%s"%(string,fielddisplay(obj,'stabilization','0: None, 1: SU, 2: MacAyeal''s artificial diffusivity, 3:DG')) + return string + #}}} ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #Type of stabilization used ++ obj.stabilization=1 ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.py (revision 12123) +@@ -7,6 +7,10 @@ + # {{{ Properties + self.migration='' + self.melting_rate=float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -15,4 +19,16 @@ + string="%s\n\n%s"%(string,fielddisplay(obj,'migration','type of grounding line migration: ''SoftMigration'',''AgressiveMigration'' or ''None''')) + string="%s\n%s"%(string,fielddisplay(obj,'melting_rate','melting rate applied when previously grounded parts start floating')) + return string +- #}}} ++ #}}} ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #Type of migration ++ obj.migration='None' ++ ++ #basal melting rate correction: ++ obj.melting_rate=0; ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/transient.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/transient.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/transient.py (revision 12123) +@@ -10,6 +10,10 @@ + self.isthermal = 0 + self.isgroundingline = 0 + self.requested_outputs = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -21,3 +25,16 @@ + string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','list of additional outputs requested')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #full analysis: Diagnostic, Prognostic and Thermal but no groundingline migration for now ++ obj.isprognostic=1 ++ obj.isdiagnostic=1 ++ obj.isthermal=1 ++ obj.isgroundingline=0 ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/hydrology.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/hydrology.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/hydrology.py (revision 12123) +@@ -12,6 +12,10 @@ + self.q = 0 + self.kn = 0 + self.stabilization = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ + + #}}} + def __repr__(obj): +@@ -27,3 +31,20 @@ + string="%s\n%s"%(string,fielddisplay(obj,'stabilization','artificial diffusivity (default is 1). can be more than 1 to increase diffusivity.')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #Parameters from Johnson's 2002 thesis, section 3.5.4 ++ obj.n=.02 ++ obj.CR=.01 ++ obj.p=2 ++ obj.q=1 ++ obj.kn=0 ++ ++ #Type of stabilization to use 0:nothing 1:artificial_diffusivity ++ obj.stabilization=1 ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/surfaceforcings.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/surfaceforcings.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/surfaceforcings.py (revision 12123) +@@ -7,6 +7,10 @@ + # {{{ Properties + self.precipitation = float('NaN') + self.mass_balance = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -17,3 +21,9 @@ + + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/rifts.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/rifts.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/rifts.py (revision 12123) +@@ -7,6 +7,10 @@ + # {{{ Properties + self.riftstruct = float('NaN') + self.riftproperties = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -16,3 +20,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,'riftproperties','')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.py (revision 12123) +@@ -45,6 +45,9 @@ + self.extractedvertices = float('NaN'); + self.extractedelements = float('NaN'); + ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -106,3 +109,17 @@ + string="%s\n%s"%(string,fielddisplay(obj,"hemisphere","Indicate hemisphere ""n"" or ""s"" ")) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #the connectivity is the avergaded number of nodes linked to a ++ #given node through an edge. This connectivity is used to initially ++ #allocate memory to the stiffness matrix. A value of 16 seems to ++ #give a good memory/time ration. This value can be checked in ++ #trunk/test/Miscellaneous/runme.m ++ obj.average_vertex_connectivity=25 ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/timestepping.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/timestepping.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/timestepping.py (revision 12123) +@@ -5,10 +5,14 @@ + #properties + def __init__(self): + # {{{ Properties +- self.time_step = 0; +- self.final_time = 0; +- self.time_adapt = 0; +- self.cfl_coefficient = 0; ++ self.time_step = 0 ++ self.final_time = 0 ++ self.time_adapt = 0 ++ self.cfl_coefficient = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -19,3 +23,19 @@ + string="%s\n%s"%(string,fielddisplay(obj,"cfl_coefficient","coefficient applied to cfl condition")) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #time between 2 time steps ++ obj.time_step=1/2 ++ ++ #final time ++ obj.final_time=10*obj.time_step ++ ++ #time adaptation? ++ obj.time_adapt=0 ++ obj.cfl_coefficient=.5 ++ ++ return obj ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/constants.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/constants.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/constants.py (revision 12123) +@@ -8,6 +8,10 @@ + self.g = 0 + self.yts = 0 + self.referencetemperature = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -19,3 +23,19 @@ + + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #acceleration due to gravity (m/s^2) ++ obj.g=9.81 ++ ++ #converstion from year to seconds ++ obj.yts=365*24*3600 ++ ++ #the reference temperature for enthalpy model (cf Aschwanden) ++ obj.referencetemperature=223.15 ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.py (revision 12123) +@@ -8,6 +8,10 @@ + self.coefficient = float('NaN') + self.p = float('NaN') + self.q = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -17,3 +21,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,"q","q exponent")) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/materials.py (revision 12123) +@@ -43,38 +43,38 @@ + #}}} + def setdefaultparameters(obj): + # {{{setdefaultparameters +- #ice density (kg/m^3) +- obj.rho_ice=917 ++ #ice density (kg/m^3) ++ obj.rho_ice=917 + +- #water density (kg/m^3) +- obj.rho_water=1023 ++ #water density (kg/m^3) ++ obj.rho_water=1023 + +- #water viscosity (N.s/m^2) +- obj.mu_water=0.001787 ++ #water viscosity (N.s/m^2) ++ obj.mu_water=0.001787 + +- #ice heat capacity cp (J/kg/K) +- obj.heatcapacity=2093 ++ #ice heat capacity cp (J/kg/K) ++ obj.heatcapacity=2093 + +- #ice latent heat of fusion L (J/kg) +- obj.latentheat=3.34*10**5 ++ #ice latent heat of fusion L (J/kg) ++ obj.latentheat=3.34*10**5 + +- #ice thermal conductivity (W/m/K) +- obj.thermalconductivity=2.4 ++ #ice thermal conductivity (W/m/K) ++ obj.thermalconductivity=2.4 + +- #the melting point of ice at 1 atmosphere of pressure in K +- obj.meltingpoint=273.15 ++ #the melting point of ice at 1 atmosphere of pressure in K ++ obj.meltingpoint=273.15 + +- #rate of change of melting point with pressure (K/Pa) +- obj.beta=9.8*10**-8 ++ #rate of change of melting point with pressure (K/Pa) ++ obj.beta=9.8*10**-8 + +- #mixed layer (ice-water interface) heat capacity (J/kg/K) +- obj.mixed_layer_capacity=3974 ++ #mixed layer (ice-water interface) heat capacity (J/kg/K) ++ obj.mixed_layer_capacity=3974 + +- #thermal exchange velocity (ice-water interface) (m/s) +- obj.thermal_exchange_velocity=1.00*10**-4 ++ #thermal exchange velocity (ice-water interface) (m/s) ++ obj.thermal_exchange_velocity=1.00*10**-4 + +- #Rheology law: what is the temperature dependence of B with T +- #available: none, paterson and arrhenius +- obj.rheology_law='Paterson' +- return obj ++ #Rheology law: what is the temperature dependence of B with T ++ #available: none, paterson and arrhenius ++ obj.rheology_law='Paterson' ++ return obj + #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/diagnostic.py (revision 12123) +@@ -23,6 +23,10 @@ + self.rift_penalty_threshold = 0 + self.referential = float('NaN') + self.requested_outputs = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -61,3 +65,35 @@ + + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ #maximum of non-linear iterations. ++ obj.maxiter=100 ++ ++ #Convergence criterion: absolute, relative and residual ++ obj.restol=10**-4; ++ obj.reltol=0.01 ++ obj.abstol=10 ++ ++ obj.stokesreconditioning=10**13 ++ obj.shelf_dampening=0 ++ ++ #Penalty factor applied kappa=max(stiffness matrix)*10^penalty_factor ++ obj.penalty_factor=3 ++ ++ #coefficient to update the viscosity between each iteration of ++ #a diagnostic according to the following formula ++ #viscosity(n)=viscosity(n)+viscosity_overshoot(viscosity(n)-viscosity(n-1)) ++ obj.viscosity_overshoot=0 ++ ++ #Stop the iterations of rift if below a threshold ++ obj.rift_penalty_threshold=0 ++ ++ #in some solutions, it might be needed to stop a run when only ++ #a few constraints remain unstable. For thermal computation, this ++ #parameter is often used. ++ obj.rift_penalty_lock=10 ++ ++ return obj ++ #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/debug.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/debug.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/debug.py (revision 12123) +@@ -7,6 +7,10 @@ + # {{{ Properties + self.valgrind=False + self.gprof = False ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -16,3 +20,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,"gprof","use gnu-profiler to find out where the time is spent")) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/initialization.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/initialization.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/initialization.py (revision 12123) +@@ -14,6 +14,10 @@ + self.temperature = float('NaN') + self.watercolumn = float('NaN') + self.waterfraction = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -30,3 +34,9 @@ + + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.py (revision 12123) +@@ -11,6 +11,10 @@ + self.stabilization = 0 + self.vertex_pairing = float('NaN') + self.penalty_factor = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -22,3 +26,22 @@ + + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #Type of stabilization to use 0:nothing 1:artificial_diffusivity 3:Discontinuous Galerkin ++ obj.stabilization=1 ++ ++ #Factor applied to compute the penalties kappa=max(stiffness matrix)*10^penalty_factor ++ obj.penalty_factor=3 ++ ++ #Minimum ice thickness that can be used ++ obj.min_thickness=1 ++ ++ #Hydrostatic adjustment ++ obj.hydrostatic_adjustment='Absolute' ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mask.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mask.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mask.py (revision 12123) +@@ -11,6 +11,10 @@ + self.vertexonfloatingice = float('NaN') + self.vertexongroundedice = float('NaN') + self.vertexonwater = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -24,3 +28,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,"vertexonwater","vertex on water flags list")) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/radaroverlay.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/radaroverlay.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/radaroverlay.py (revision 12123) +@@ -8,6 +8,10 @@ + self.pwr = float('NaN') + self.x = float('NaN') + self.y = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -17,3 +21,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,'y','corresponding y coordinates')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/autodiff.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/autodiff.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/autodiff.py (revision 12123) +@@ -8,6 +8,10 @@ + self.isautodiff = False + self.forward = True + self.reverse = False ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -17,3 +21,8 @@ + string="%s\n%s"%(string,fielddisplay(obj,'reverse','backward differentiation')) + return string + #}}} ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/steadystate.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/steadystate.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/steadystate.py (revision 12123) +@@ -8,6 +8,10 @@ + self.reltol = 0 + self.maxiter = 0 + self.requested_outputs = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -17,3 +21,16 @@ + string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','additional requested outputs')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #maximum of steady state iterations ++ obj.maxiter=100 ++ ++ #Relative tolerance for the steadystate convertgence ++ obj.reltol=0.01 ++ ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/geometry.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/geometry.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/geometry.py (revision 12123) +@@ -10,6 +10,10 @@ + self.bed = float('NaN') + self.bathymetry = float('NaN') + self.hydrostatic_ratio = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -23,3 +27,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,'hydrostatic_ratio','coefficient for ice shelves'' thickness correction: hydrostatic_ratio H_obs+ (1-hydrostatic_ratio) H_hydro')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/qmu.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/qmu.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/qmu.py (revision 12123) +@@ -21,9 +21,19 @@ + self.mass_flux_segments = [] + self.adjacency = float('NaN') + self.vertex_weight = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display + string=" qmu parameters: not implemented yet!" + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/miscellaneous.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/miscellaneous.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/miscellaneous.py (revision 12123) +@@ -8,6 +8,10 @@ + self.notes = '' + self.name = '' + self.dummy = {} ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -18,3 +22,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,'dummy','empty field to store some data')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/private.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/private.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/private.py (revision 12123) +@@ -8,6 +8,10 @@ + self.runtimename = '' + self.bamg = {} + self.solution = ''; ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -17,3 +21,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,'solution','type of solution launched')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/inversion.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/inversion.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/inversion.py (revision 12123) +@@ -57,3 +57,48 @@ + string="%s\n%s"%(string,' 503: ThicknessAbsGradient') + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ ++ #default is incomplete adjoint for now ++ obj.incomplete_adjoint=1 ++ ++ #parameter to be inferred by control methods (only ++ #drag and B are supported yet) ++ obj.control_parameters=['FrictionCoefficient'] ++ ++ #number of steps in the control methods ++ obj.nsteps=20 ++ ++ #maximum number of iteration in the optimization algorithm for ++ #each step ++ obj.maxiter_per_step=20*ones(obj.nsteps) ++ ++ #the inversed parameter is updated as follows: ++ #new_par=old_par + gradient_scaling(n)*C*gradient with C in [0 1]; ++ #usually the gradient_scaling must be of the order of magnitude of the ++ #inversed parameter (10^8 for B, 50 for drag) and can be decreased ++ #after the first iterations ++ obj.gradient_scaling=50*ones(obj.nsteps) ++ ++ #several responses can be used: ++ obj.cost_functions=101*ones(obj.nsteps) ++ ++ #step_threshold is used to speed up control method. When ++ #misfit(1)/misfit(0) < obj.step_threshold, we go directly to ++ #the next step ++ obj.step_threshold=.7*ones(obj.nsteps) #30 per cent decrement ++ ++ #stop control solution at the gradient computation and return it? ++ obj.gradient_only=0 ++ ++ #cost_function_threshold is a criteria to stop the control methods. ++ #if J[n]-J[n-1]/J[n] < criteria, the control run stops ++ #NaN if not applied ++ obj.cost_function_threshold=NaN #not activated ++ ++ return obj ++ #}}} ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/basalforcings.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/basalforcings.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/basalforcings.py (revision 12123) +@@ -8,6 +8,10 @@ + self.melting_rate = float('NaN') + self.melting_rate_correction = float('NaN') + self.geothermalflux = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -18,3 +22,8 @@ + string="%s\n%s"%(string,fielddisplay(obj,"geothermalflux","geothermal heat flux [W/m^2]")) + return string + #}}} ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flowequation.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flowequation.py (revision 12122) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/flowequation.py (revision 12123) +@@ -14,6 +14,10 @@ + self.bordermacayeal = float('NaN') + self.borderpattyn = float('NaN') + self.borderstokes = float('NaN') ++ ++ #set defaults ++ self.setdefaultparameters() ++ + #}}} + def __repr__(obj): + # {{{ Display +@@ -29,3 +33,9 @@ + string="%s\n%s"%(string,fielddisplay(obj,'borderstokes','vertices on Stokes'' border (for tiling)')) + return string + #}}} ++ ++ def setdefaultparameters(obj): ++ # {{{setdefaultparameters ++ return obj ++ #}}} ++ Index: /issm/oecreview/Archive/12121-12140/ISSM-12123-12124.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12123-12124.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12123-12124.diff (revision 12325) @@ -0,0 +1,65 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Par/SquareShelfConstrained.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Par/SquareShelfConstrained.py (revision 12123) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Par/SquareShelfConstrained.py (revision 12124) +@@ -1,6 +1,8 @@ + from numpy import * ++from verbose import * + import scipy.io as matio + import InterpFromMeshToMesh2d as im ++from paterson import * + + #Start defining model parameters here + #Geometry +@@ -13,7 +15,7 @@ + md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; + md.geometry.surface = md.geometry.bed+md.geometry.thickness + +-#%Initial velocity ++#Initial velocity + mat=matio.loadmat('../Data/SquareShelfConstrained.data') + #deal with 'F' oriented matlab matrices! + index=mat['index'].astype(float) +@@ -23,24 +25,24 @@ + md.initialization.vy = im.InterpFromMeshToMesh2d(index, mat['x'], mat['y'], mat['vy'], md.mesh.x, md.mesh.y) + md.initialization.vz = zeros(md.mesh.numberofvertices) + md.initialization.pressure = zeros(md.mesh.numberofvertices) +-#%Materials ++#Materials + md.initialization.temperature = (273.-20)*ones(md.mesh.numberofvertices) + md.materials.rheology_B = paterson(md.initialization.temperature) + md.materials.rheology_n = 3.*ones(md.mesh.numberofelements) +-#%Surface mass balance and basal melting ++#Surface mass balance and basal melting + md.surfaceforcings.mass_balance = 10.*ones(md.mesh.numberofvertices) + md.basalforcings.melting_rate = 5.*ones(md.mesh.numberofvertices) +-#%Friction ++#Friction + pos = nonzero(md.mask.elementonfloatingice) + md.friction.coefficient = 20.*ones(md.mesh.numberofvertices) +-md.friction.coefficient[(md.mesh.elements[int(pos)-1,:])] = 0. ++md.friction.coefficient[md.mesh.elements[pos,:].astype(int)-1] =0. + md.friction.p = ones(md.mesh.numberofelements) + md.friction.q = ones(md.mesh.numberofelements) +-#%Numerical parameters ++#Numerical parameters + md.diagnostic.viscosity_overshoot = 0.0 + md.prognostic.stabilization = 1. + md.thermal.stabilization = 1. +-md.verbose = verbose[-1] ++md.verbose = verbose() + md.settings.waitonlock = 30. + md.diagnostic.restol = 0.05 + md.diagnostic.reltol = 0.05 +@@ -48,9 +50,9 @@ + md.diagnostic.abstol = nan + md.timestepping.time_step = 1. + md.timestepping.final_time = 3. +-#%Deal with boundary conditions: ++#Deal with boundary conditions: + md = SetIceShelfBC(md) +-#%Change name so that no test have the same name ++#Change name so that no test have the same name + A = dbstack + if length(A) > 2.: + md.miscellaneous.name = A[2].file[0:0-2.] Index: /issm/oecreview/Archive/12121-12140/ISSM-12124-12125.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12124-12125.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12124-12125.diff (revision 12325) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py (revision 12124) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/triangle.py (revision 12125) +@@ -37,8 +37,8 @@ + + + #Fill in rest of fields: +- md.mesh.numberofelements = size(md.mesh.elements) +- md.mesh.numberofvertices = size(md.mesh.x) ++ md.mesh.numberofelements = len(md.mesh.elements) ++ md.mesh.numberofvertices = len(md.mesh.x) + md.mesh.z = zeros(md.mesh.numberofvertices) + md.mesh.vertexonboundary = zeros(md.mesh.numberofvertices) + md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)-1] = 1. Index: /issm/oecreview/Archive/12121-12140/ISSM-12125-12126.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12125-12126.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12125-12126.diff (revision 12325) @@ -0,0 +1,55 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Meca/paterson.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Meca/paterson.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Meca/paterson.py (revision 12126) +@@ -0,0 +1,50 @@ ++from numpy import * ++ ++def paterson(temperature): ++ ++ # Local Variables: pos11, pos5, pos10, temperature, pos, T, pos8, pos9, pos6, pos7, pos4, rigidity, pos2, pos3, pos1 ++ # Function calls: length, zeros, argwhere, paterson, error ++ #PATERSON - figure out the rigidity of ice for a given temperature ++ # ++ # rigidigty (in s^(1/3)Pa) is the flow law paramter in the flow law sigma=B*e(1/3) (Paterson, p97). ++ # temperature is in Kelvin degrees ++ # ++ # Usage: ++ # rigidity=paterson(temperature) ++ ++ pos=argwhere(temperature<0.) ++ if len(pos): ++ print 'input temperature should be in Kelvin (positive)' ++ return [] ++ ++ T = temperature-273.15 ++ #The routine below is equivalent to: ++ # n=3; T=temperature-273; ++ # %From paterson, ++ # Temp=[0;-2;-5;-10;-15;-20;-25;-30;-35;-40;-45;-50]; ++ # A=[6.8*10^-15;2.4*10^-15;1.6*10^-15;4.9*10^-16;2.9*10^-16;1.7*10^-16;9.4* ++ # 10^-17;5.1*10^-17;2.7*10^-17;1.4*10^-17;7.3*10^-18;3.6*10^-18];;%s-1(kPa-3) ++ # %Convert into rigidity B ++ # B=A.^(-1/n)*10^3; %s^(1/3)Pa ++ # %Now, do a cubic fit between Temp and B: ++ # fittedmodel=fit(Temp,B,'cubicspline'); ++ # rigidity=fittedmodel(temperature); ++ ++ rigidity=zeros(len(T)) ++ pos1=argwhere(T<=-45); rigidity[pos1]=10**8*(-0.000292866376675*(T[pos1]+50)**3+ 0.011672640664130*(T[pos1]+50)**2 -0.325004442485481*(T[pos1]+50)+ 6.524779401948101) ++ pos2=argwhere(logical_and(-45<=T,T<-40)); rigidity[pos2]=10**8*(-0.000292866376675*(T[pos2]+45)**3+ 0.007279645014004*(T[pos2]+45)**2 -0.230243014094813*(T[pos2]+45)+ 5.154964909039554) ++ pos3=argwhere(logical_and(-40<=T,T<-35)); rigidity[pos3]=10**8*(0.000072737147457*(T[pos3]+40)**3+ 0.002886649363879*(T[pos3]+40)**2 -0.179411542205399*(T[pos3]+40)+ 4.149132666831214) ++ pos4=argwhere(logical_and(-35<=T,T<-30)); rigidity[pos4]=10**8*(-0.000086144770023*(T[pos4]+35)**3+ 0.003977706575736*(T[pos4]+35)**2 -0.145089762507325*(T[pos4]+35)+ 3.333333333333331) ++ pos5=argwhere(logical_and(-30<=T,T<-25)); rigidity[pos5]=10**8*(-0.000043984685769*(T[pos5]+30)**3+ 0.002685535025386*(T[pos5]+30)**2 -0.111773554501713*(T[pos5]+30)+ 2.696559088937191) ++ pos6=argwhere(logical_and(-25<=T,T<-20)); rigidity[pos6]=10**8*(-0.000029799523463*(T[pos6]+25)**3+ 0.002025764738854*(T[pos6]+25)**2 -0.088217055680511*(T[pos6]+25)+ 2.199331606342181) ++ pos7=argwhere(logical_and(-20<=T,T<-15)); rigidity[pos7]=10**8*(0.000136920904777*(T[pos7]+20)**3+ 0.001578771886910*(T[pos7]+20)**2 -0.070194372551690*(T[pos7]+20)+ 1.805165505978111) ++ pos8=argwhere(logical_and(-15<=T,T<-10)); rigidity[pos8]=10**8*(-0.000899763781026*(T[pos8]+15)**3+ 0.003632585458564*(T[pos8]+15)**2 -0.044137585824322*(T[pos8]+15)+ 1.510778053489523) ++ pos9=argwhere(logical_and(-10<=T,T<-5)); rigidity[pos9]=10**8*(0.001676964325070*(T[pos9]+10)**3- 0.009863871256831*(T[pos9]+10)**2 -0.075294014815659*(T[pos9]+10)+ 1.268434288203714) ++ pos10=argwhere(logical_and(-5<=T,T<-2)); rigidity[pos10]=10**8*(-0.003748937622487*(T[pos10]+5)**3+0.015290593619213*(T[pos10]+5)**2 -0.048160403003748*(T[pos10]+5)+ 0.854987973338348) ++ pos11=argwhere(-2<=T); rigidity[pos11]=10**8*(-0.003748937622488*(T[pos11]+2)**3-0.018449844983174*(T[pos11]+2)**2 -0.057638157095631*(T[pos11]+2)+ 0.746900791092860) ++ ++ #Now make sure that rigidity is positive ++ pos=argwhere(rigidity<0); rigidity[pos]=1**6 ++ ++ return rigidity ++ Index: /issm/oecreview/Archive/12121-12140/ISSM-12126-12127.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12126-12127.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12126-12127.diff (revision 12325) @@ -0,0 +1,395 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 12126) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 12127) +@@ -10,7 +10,7 @@ + + #include "./ContourToMeshx.h" + +-int ContourToMeshx( Vector** pin_nod,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue) { ++int ContourToMeshx( Vector** pin_nod,Vector** pin_elem, double* index, double* x, double* y,DataSet* contours,char* interptype,int nel,int nods, int edgevalue) { + + int noerr=1; + int i; +@@ -36,7 +36,6 @@ + in_elem=new Vector(nel); + + /*initialize thread parameters: */ +- gate.numcontours=numcontours; + gate.contours=contours; + gate.nods=nods; + gate.edgevalue=edgevalue; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 12126) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 12127) +@@ -25,15 +25,9 @@ + int i; + + /*Contour:*/ +- Contour* contouri=NULL; +- int numnodes; +- double* xc=NULL; +- double* yc=NULL; ++ DataSet* contours=NULL; + +- + /*parameters: */ +- int numcontours; +- Contour** contours=NULL; + int nods; + int edgevalue; + double* x=NULL; +@@ -48,7 +42,6 @@ + num_threads=handle->num; + + /*recover parameters :*/ +- numcontours=gate->numcontours; + contours=gate->contours; + nods=gate->nods; + edgevalue=gate->edgevalue; +@@ -60,12 +53,9 @@ + PartitionRange(&i0,&i1,nods,num_threads,my_thread); + + /*Loop through all contours: */ +- for (i=0;inods; +- xc=contouri->x; +- yc=contouri->y; +- IsInPoly(in_nod,xc,yc,numnodes,x,y,i0,i1,edgevalue); ++ for (i=0;iSize();i++){ ++ Contour* contour=(Contour*)contours->GetObjectByOffset(i); ++ IsInPoly(in_nod,contour->x,contour->y,contour->nods,x,y,i0,i1,edgevalue); + } + + return NULL; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 12126) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 12127) +@@ -12,8 +12,7 @@ + /*threading: */ + typedef struct{ + +- int numcontours; +- Contour** contours; ++ DataSet* contours; + int nods; + int edgevalue; + Vector* in_nod; +@@ -24,7 +23,7 @@ + + + /* local prototypes: */ +-int ContourToMeshx( Vector** pin_nods,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue); ++int ContourToMeshx( Vector** pin_nods,Vector** pin_elem, double* index, double* x, double* y,DataSet* contours,char* interptype,int nel,int nods, int edgevalue); + + void* ContourToMeshxt(void* vContourToMeshxThreadStruct); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.h (revision 12126) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.h (revision 12127) +@@ -7,41 +7,66 @@ + #ifndef _CONTOURTOMESH_H + #define _CONTOURTOMESH_H + +-/* local prototypes: */ +-void ContourToMeshUsage(void); + ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/ ++#ifdef _HAVE_PYTHON_ ++#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol ++#endif ++ ++/*Header files: */ + #include "../../c/include/globals.h" ++#include "../../c/toolkits/toolkits.h" ++#include "../../c/include/include.h" + #include "../../c/modules/modules.h" + #include "../../c/Container/Container.h" + #include "../../c/shared/shared.h" + #include "../../c/issm-binding.h" ++#include "../../c/io/io.h" ++#include "../../c/EnumDefinitions/EnumDefinitions.h" + +-#undef __FUNCT__ +-#define __FUNCT__ "ContourToMesh" ++#ifdef _HAVE_MATLAB_MODULES_ ++/* serial input macros: */ ++#define INDEX (mxArray *)prhs[0] ++#define X (mxArray *)prhs[1] ++#define Y (mxArray *)prhs[2] ++#define CONTOURNAME (mxArray *)prhs[3] ++#define INTERPTYPE (mxArray *)prhs[4] ++#define EDGEVALUE (mxArray *)prhs[5] ++/* serial output macros: */ ++#define PLHS0 (mxArray**)&plhs[0] ++#define PLHS1 (mxArray**)&plhs[1] ++#endif + +- +-#ifndef ALL +-#define ALL 0 ++#ifdef _HAVE_PYTHON_MODULES_ ++/* serial input macros: */ ++#define INDEX PyTuple_GetItem(args,0) ++#define X PyTuple_GetItem(args,1) ++#define Y PyTuple_GetItem(args,2) ++#define CONTOURNAME PyTuple_GetItem(args,3) ++#define INTERPTYPE PyTuple_GetItem(args,4) ++#define EDGEVALUE PyTuple_GetItem(args,5) ++/* serial output macros: */ ++#define PLHS0 output,0 ++#define PLHS1 output,1 + #endif + +-/* input macros: */ +-#define INDEXHANDLE prhs[0] +-#define XHANDLE prhs[1] +-#define YHANDLE prhs[2] +-#define FILENAME prhs[3] +-#define INTERPTYPEHANDLE prhs[4] +-#define EDGEVALUEHANDLE prhs[5] ++#undef __FUNCT__ ++#define __FUNCT__ "ContourToMesh" + +-/* serial output macros: */ +-#define PLHS0 (mxArray**)&plhs[0] +-#define PLHS1 (mxArray**)&plhs[1] +- + /* serial arg counts: */ + #undef NLHS + #define NLHS 2 + #undef NRHS + #define NRHS 6 + ++/* local prototypes: */ ++void ContourToMeshUsage(void); + + #endif /* _CONTOURTOMESH_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12126) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 12127) +@@ -20,78 +20,55 @@ + + #include "./ContourToMesh.h" + +-void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { ++WRAPPER(ContourToMesh){ + + int i,j; + + /* required input: */ + int edgevalue; + double *index = NULL; ++ int nel; + double *x = NULL; ++ int nods; + double *y = NULL; + char *interptype = NULL; ++ char* contourname = NULL; ++ DataSet* contours = NULL; + + /* output: */ + Vector *in_nod = NULL; +- int nods; + Vector *in_elem = NULL; +- int nel; + +- //contours +- mxArray *matlabstructure = NULL; +- int numcontours; +- Contour **contours = NULL; +- Contour *contouri = NULL; +- + /*Boot module: */ + MODULEBOOT(); + +- /*checks on arguments on the matlab side: */ +- //CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ContourToMeshUsage); Cant' use it here, as we have variable outputs. +- if((nlhs!=1 && nlhs!=2) || (nrhs!=NRHS)){ ++ /*checks on output arguments on the matlab side: */ ++ #ifdef _HAVE_MATLAB_MODULES_ ++ if(nlhs!=1 && nlhs!=2){ + ContourToMeshUsage(); + _error_(" usage. See above"); + } ++ #endif ++ /*check on input arguments: */ ++ if(nrhs!=NRHS){ ++ ContourToMeshUsage(); ++ _error_(" usage. See above"); ++ } + +- /*First, call expread on filename to build a contour array in the matlab workspace: */ +- mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); + + /*Fetch inputs: */ +- FetchData(&index,&nel,NULL,INDEXHANDLE); +- FetchData(&x,&nods,NULL,XHANDLE); +- FetchData(&y,NULL,NULL,YHANDLE); +- FetchData(&edgevalue,EDGEVALUEHANDLE); ++ FetchData(&index,&nel,NULL,INDEX); ++ FetchData(&x,&nods,NULL,X); ++ FetchData(&y,NULL,NULL,Y); ++ FetchData(&edgevalue,EDGEVALUE); ++ FetchData(&contourname,CONTOURNAME); ++ contours=DomainOutlineRead(contourname); + +- //Fetch contours +- numcontours=mxGetNumberOfElements(matlabstructure); +- contours=(Contour**)xmalloc(numcontours*sizeof(Contour*)); +- for(i=0;inods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); +- //set pointers. +- contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); +- contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); +- *(contours+i)=contouri; +- } +- + /*Fetch interptype: */ +- FetchData(&interptype,INTERPTYPEHANDLE); ++ FetchData(&interptype,INTERPTYPE); + +- /* Debugging of contours :{{{1*/ +- /*for(i=0;inods); +- for (j=0;jnods;j++){ +- printf(" %lf %lf\n",*(contouri->x+j),*(contouri->y+j)); +- } +- }*/ +- /*}}}*/ +- + /*Run interpolation routine: */ +- ContourToMeshx( &in_nod,&in_elem,index,x,y,contours,numcontours,interptype,nel,nods,edgevalue); ++ ContourToMeshx( &in_nod,&in_elem,index,x,y,contours,interptype,nel,nods,edgevalue); + + /* output: */ + if (strcmp(interptype,"node")==0){ +@@ -111,7 +88,7 @@ + + } + +-void ContourToMeshUsage(void) ++void ContourToMeshUsage(void)//{{{1 + { + printf("CONTOURTOMESH - Flag the elements or nodes inside a contour\n"); + printf("\n"); +@@ -133,3 +110,4 @@ + printf(" [in_nodes,in_elements]=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element and node',0)\n"); + printf("\n"); + } ++//}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/BC/SetIceShelfBC.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/BC/SetIceShelfBC.py (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/BC/SetIceShelfBC.py (revision 12127) +@@ -0,0 +1,93 @@ ++def SetIceShelfBC(md,icefrontfile='') ++ #SETICESHELFBC - Create the boundary conditions for diagnostic and thermal models for a Ice Shelf with Ice Front ++ # ++ # Neumann BC are used on the ice front (an ANRGUS contour around the ice front ++ # must be given in input) ++ # Dirichlet BC are used elsewhere for diagnostic ++ # ++ # Usage: ++ # md=SetIceShelfBC(md,varargin) ++ # ++ # Example: ++ # md=SetIceShelfBC(md); ++ # md=SetIceShelfBC(md,'Front.exp'); ++ # ++ # See also: SETICESHEETBC, SETMARINEICESHEETBC ++ ++ #node on Dirichlet (boundary and ~icefront) ++ if not icefrontfile: ++ nodeonicefront=zeros(md.mesh.numberofvertices) ++ else: ++ if not os.path.isfile(icefrontfile): ++ print 'SetIceShelfBC error message: ice front file '+icefrontfile+ ' not found' ++ return [] ++ nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2); ++ nodeonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront); ++ ++ pos=find(md.mesh.vertexonboundary & ~nodeonicefront); ++ md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); ++ md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); ++ md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); ++ md.diagnostic.spcvx(pos)=0; ++ md.diagnostic.spcvy(pos)=0; ++ md.diagnostic.spcvz(pos)=0; ++ md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6); ++ ++ #Dirichlet Values ++ if (length(md.inversion.vx_obs)==md.mesh.numberofvertices & length(md.inversion.vy_obs)==md.mesh.numberofvertices) ++ disp(' boundary conditions for diagnostic model: spc set as observed velocities'); ++ md.diagnostic.spcvx(pos)=md.inversion.vx_obs(pos); ++ md.diagnostic.spcvy(pos)=md.inversion.vy_obs(pos); ++ else ++ disp(' boundary conditions for diagnostic model: spc set as zero'); ++ end ++ ++ #segment on Ice Front ++ #segment on Neumann (Ice Front) ++ pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); ++ if (md.mesh.dimension==2) ++ pressureload=md.mesh.segments(pos,:); ++ elseif md.mesh.dimension==3 ++ pressureload_layer1=[md.mesh.segments(pos,1:2) md.mesh.segments(pos,2)+md.mesh.numberofvertices2d md.mesh.segments(pos,1)+md.mesh.numberofvertices2d md.mesh.segments(pos,3)]; ++ pressureload=[]; ++ for i=1:md.mesh.numberoflayers-1, ++ pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d ]; ++ end ++ end ++ ++ #Add water or air enum depending on the element ++ pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))]; ++ ++ #plug onto model ++ md.diagnostic.icefront=pressureload; ++ ++ #Create zeros basalforcings and surfaceforcings ++ if isnan(md.surfaceforcings.precipitation), ++ md.surfaceforcings.precipitation=zeros(md.mesh.numberofvertices,1); ++ disp(' no surfaceforcings.precipitation specified: values set as zero'); ++ end ++ if isnan(md.surfaceforcings.mass_balance), ++ md.surfaceforcings.mass_balance=zeros(md.mesh.numberofvertices,1); ++ disp(' no surfaceforcings.mass_balance specified: values set as zero'); ++ end ++ if isnan(md.basalforcings.melting_rate), ++ md.basalforcings.melting_rate=zeros(md.mesh.numberofvertices,1); ++ disp(' no basalforcings.melting_rate specified: values set as zero'); ++ end ++ if isnan(md.balancethickness.thickening_rate), ++ md.balancethickness.thickening_rate=zeros(md.mesh.numberofvertices,1); ++ disp(' no balancethickness.thickening_rate specified: values set as zero'); ++ end ++ ++ md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices,1); ++ md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); ++ ++ if (length(md.initialization.temperature)==md.mesh.numberofvertices), ++ md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1); ++ pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); #impose observed temperature on surface ++ if (length(md.basalforcings.geothermalflux)~=md.mesh.numberofvertices), ++ md.basalforcings.geothermalflux=zeros(md.mesh.numberofvertices,1); ++ end ++ else ++ disp(' no thermal boundary conditions created: no observed temperature found'); ++ end Index: /issm/oecreview/Archive/12121-12140/ISSM-12127-12128.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12127-12128.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12127-12128.diff (revision 12325) @@ -0,0 +1,39 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/python/pythonincludes.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/python/pythonincludes.h (revision 12127) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/python/pythonincludes.h (revision 12128) +@@ -6,6 +6,19 @@ + #define _PYTHON_INCLUDES_H_ + + ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#if _PYTHON_MAJOR_ == 2 ++#undef NPY_NO_DEPRECATED_API ++#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION ++#else ++#define NPY_NO_DEPRECATED_API ++#endif ++ + #include "Python.h" + #include "arrayobject.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12127) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12128) +@@ -949,10 +949,7 @@ + if PYTHON + libISSMPython_a_SOURCES = $(python_sources) + libISSMPython_a_CXXFLAGS= $(ALLCXXFLAGS) +-if PYTHON3 +-libISSMPython_a_CXXFLAGS+= -DNPY_NO_DEPRECATED_API + endif +-endif + + if MATLAB + libISSMMatlab_a_SOURCES = $(matlab_sources) Index: /issm/oecreview/Archive/12121-12140/ISSM-12128-12129.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12128-12129.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12128-12129.diff (revision 12325) @@ -0,0 +1,55 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/triangle.c.patch.python +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/triangle.c.patch.python (revision 12128) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/triangle.c.patch.python (revision 12129) +@@ -4,8 +4,8 @@ + > * matlab, we had to change the allocation routine trimalloc, as well as the + > * double precision activation in exactinit(); The rest is not changed. + > * We also created the ice_makefile to compile Triangle into a library. */ +-> #include +-> #include ++> /* #include ++> #include */ + > #define ANSI_DECLARATORS + > #define NO_TIMER + > +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh (revision 12128) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm.sh (revision 12129) +@@ -1,12 +0,0 @@ +-#!/bin/sh +- +-pythonversion=2.7 +- +-./configure \ +- --prefix=$ISSM_TIER \ +- --with-python-dir=$ISSM_TIER/externalpackages/python/install\ +- --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ +- --with-vendor=arm \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12129) +@@ -0,0 +1,12 @@ ++#!/bin/sh ++ ++pythonversion=2.7 ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --with-python-dir=$ISSM_TIER/externalpackages/python/install\ ++ --with-python-version=$pythonversion \ ++ --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-vendor=arm-linux\ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12121-12140/ISSM-12129-12130.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12129-12130.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12129-12130.diff (revision 12325) @@ -0,0 +1,25 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh (revision 12129) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh (revision 12130) +@@ -1,7 +1,7 @@ + #This installs the Android SDK (Software Development Kit) + #which is needed for the compilation of the Java project. + +-step=3; ++step=2; + + #Different steps here. + #1: install sdk, ant and sdk tools +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12129) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12130) +@@ -7,6 +7,6 @@ + --with-python-dir=$ISSM_TIER/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ +- --with-vendor=arm-linux\ ++ --with-vendor=arm-linux \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install Index: /issm/oecreview/Archive/12121-12140/ISSM-12130-12131.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12130-12131.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12130-12131.diff (revision 12325) @@ -0,0 +1,47 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/freetype/freetype-2.4.9.tar.gz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/freetype/freetype-2.4.9.tar.gz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/freetype/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/freetype/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/freetype/install.sh (revision 12131) +@@ -0,0 +1,26 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf src ++rm -rf install ++rm -rf freetype-2.4.9 ++mkdir src install ++ ++#Untar ++tar -zxvf freetype-2.4.9.tar.gz ++ ++#Move freetype into src directory ++mv freetype-2.4.9/* src ++rm -rf freetype-2.4.9 ++ ++#Configure freetype ++cd src ++sudo ./configure ++ ++#Compile and install freetype ++if [ -z $1 ]; then ++ sudo make ++else ++ sudo make -j $1 ++fi ++sudo make install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/freetype/install.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12121-12140/ISSM-12131-12132.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12131-12132.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12131-12132.diff (revision 12325) @@ -0,0 +1,8 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/freetype +___________________________________________________________________ +Added: svn:ignore + + install +src + + Index: /issm/oecreview/Archive/12121-12140/ISSM-12132-12133.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12132-12133.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12132-12133.diff (revision 12325) @@ -0,0 +1,13 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/scipy +___________________________________________________________________ +Modified: svn:ignore + - scipy +numpy + + + scipy +scipy-* +numpy +numpy-* + + Index: /issm/oecreview/Archive/12121-12140/ISSM-12133-12134.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12133-12134.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12133-12134.diff (revision 12325) @@ -0,0 +1,20 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/nose/nose-1.1.2.tar.gz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/nose/nose-1.1.2.tar.gz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/nose +___________________________________________________________________ +Modified: svn:ignore + - py3k + + + py3k +src-* + + Index: /issm/oecreview/Archive/12121-12140/ISSM-12134-12135.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12134-12135.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12134-12135.diff (revision 12325) @@ -0,0 +1,32 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/distribute/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/distribute/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/distribute/install.sh (revision 12135) +@@ -0,0 +1,4 @@ ++#!/bin/bash ++ ++curl -O http://python-distribute.org/distribute_setup.py ++python distribute_setup.py + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/distribute/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/distribute/distribute-0.6.26.tar.gz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/distribute/distribute-0.6.26.tar.gz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/distribute +___________________________________________________________________ +Added: svn:ignore + + distribute_setup.py + + Index: /issm/oecreview/Archive/12121-12140/ISSM-12135-12136.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12135-12136.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12135-12136.diff (revision 12325) @@ -0,0 +1,48 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ipython/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ipython/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ipython/install.sh (revision 12136) +@@ -0,0 +1,19 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf src ++rm -rf install ++rm -rf ipython-0.12 ++mkdir src install ++ ++#Untar ++tar -zxvf ipython-0.12.tar.gz ++ ++#Move ipython into src directory ++mv ipython-0.12/* src ++rm -rf ipython-0.12 ++ ++#install ipython ++cd src ++python setup.py build ++python setup.py install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ipython/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ipython/ipython-0.12.tar.gz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ipython/ipython-0.12.tar.gz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ipython +___________________________________________________________________ +Added: svn:ignore + + src-* +install + + Index: /issm/oecreview/Archive/12121-12140/ISSM-12136-12137.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12136-12137.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12136-12137.diff (revision 12325) @@ -0,0 +1,34 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libermate/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libermate/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libermate/install.sh (revision 12137) +@@ -0,0 +1,13 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf install ++rm -rf libermate-0.4 ++mkdir install ++ ++#Untar ++tar -zxvf libermate-0.4.tgz ++ ++#Move libermate into install directory ++mv libermate-0.4/* install ++rm -rf libermate-0.4 + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libermate/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libermate/libermate-0.4.tgz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libermate/libermate-0.4.tgz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + Index: /issm/oecreview/Archive/12121-12140/ISSM-12137-12138.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12137-12138.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12137-12138.diff (revision 12325) @@ -0,0 +1,7 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libermate +___________________________________________________________________ +Added: svn:ignore + + install + + Index: /issm/oecreview/Archive/12121-12140/ISSM-12138-12139.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12138-12139.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12138-12139.diff (revision 12325) @@ -0,0 +1,39 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pyclips/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pyclips/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pyclips/install.sh (revision 12139) +@@ -0,0 +1,18 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf install ++rm -rf pyclips-1.0.7.348 ++mkdir install ++ ++#Untar ++tar -zxvf pyclips-1.0.7.348.tar.gz ++ ++#Move pyclips into install directory ++mv pyclips/* install ++rm -rf pyclips ++ ++#install ++cd install ++python setup.py build ++sudo python setup.py install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pyclips/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pyclips/pyclips-1.0.7.348.tar.gz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pyclips/pyclips-1.0.7.348.tar.gz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + Index: /issm/oecreview/Archive/12121-12140/ISSM-12139-12140.diff =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-12139-12140.diff (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-12139-12140.diff (revision 12325) @@ -0,0 +1,7 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pyclips +___________________________________________________________________ +Added: svn:ignore + + install + + Index: /issm/oecreview/Archive/12121-12140/ISSM-DocReview-12121-12140.tex =================================================================== --- /issm/oecreview/Archive/12121-12140/ISSM-DocReview-12121-12140.tex (revision 12325) +++ /issm/oecreview/Archive/12121-12140/ISSM-DocReview-12121-12140.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12121-12140/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12121-12140/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12121-12140/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12121-12140 Index: /issm/oecreview/Archive/12121-12140/Makefile =================================================================== --- /issm/oecreview/Archive/12121-12140/Makefile (revision 12325) +++ /issm/oecreview/Archive/12121-12140/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12121-12140 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12121-12140/log.tex =================================================================== --- /issm/oecreview/Archive/12121-12140/log.tex (revision 12325) +++ /issm/oecreview/Archive/12121-12140/log.tex (revision 12325) @@ -0,0 +1,38 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12121-12122.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.cpp M /issm/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.h M /issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h \\ Export determination: 6. \\Rationale: Added new ContourToNodesx prototype to handle same functionality, but with DataSet* contours in input instead of just a simple Contour struct Adapted InterpFromMeshToMesh2dx accordingly. +M /issm/trunk-jpl/test/NightlyRun/test102.py A /issm/trunk-jpl/test/Par/SquareShelfConstrained.py Converting SquareShelfConstrained.par to SquareShelfConstrained.py Pushing test102.py forward. \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12122-12123.diff: \\ Function name: \\M /issm/trunk-jpl/test/NightlyRun/test102.py A /issm/trunk-jpl/test/Par/SquareShelfConstrained.py \\ Export determination: 6. \\Rationale: Converting SquareShelfConstrained.par to SquareShelfConstrained.py Pushing test102.py forward. +M /issm/trunk-jpl/src/m/classes/autodiff.py M /issm/trunk-jpl/src/m/classes/balancethickness.py M /issm/trunk-jpl/src/m/classes/basalforcings.py M /issm/trunk-jpl/src/m/classes/constants.py M /issm/trunk-jpl/src/m/classes/debug.py M /issm/trunk-jpl/src/m/classes/diagnostic.py M /issm/trunk-jpl/src/m/classes/flowequation.py M /issm/trunk-jpl/src/m/classes/friction.py M /issm/trunk-jpl/src/m/classes/geometry.py M /issm/trunk-jpl/src/m/classes/groundingline.py M /issm/trunk-jpl/src/m/classes/hydrology.py M /issm/trunk-jpl/src/m/classes/initialization.py M /issm/trunk-jpl/src/m/classes/inversion.py M /issm/trunk-jpl/src/m/classes/mask.py M /issm/trunk-jpl/src/m/classes/materials.py M /issm/trunk-jpl/src/m/classes/mesh.py M /issm/trunk-jpl/src/m/classes/miscellaneous.py M /issm/trunk-jpl/src/m/classes/private.py M /issm/trunk-jpl/src/m/classes/prognostic.py M /issm/trunk-jpl/src/m/classes/qmu.py M /issm/trunk-jpl/src/m/classes/radaroverlay.py M /issm/trunk-jpl/src/m/classes/rifts.py M /issm/trunk-jpl/src/m/classes/settings.py M /issm/trunk-jpl/src/m/classes/steadystate.py M /issm/trunk-jpl/src/m/classes/surfaceforcings.py M /issm/trunk-jpl/src/m/classes/thermal.py M /issm/trunk-jpl/src/m/classes/timestepping.py M /issm/trunk-jpl/src/m/classes/transient.py Added setdefaultparameters routines to python classes \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12123-12124.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/autodiff.py M /issm/trunk-jpl/src/m/classes/balancethickness.py M /issm/trunk-jpl/src/m/classes/basalforcings.py M /issm/trunk-jpl/src/m/classes/constants.py M /issm/trunk-jpl/src/m/classes/debug.py M /issm/trunk-jpl/src/m/classes/diagnostic.py M /issm/trunk-jpl/src/m/classes/flowequation.py M /issm/trunk-jpl/src/m/classes/friction.py M /issm/trunk-jpl/src/m/classes/geometry.py M /issm/trunk-jpl/src/m/classes/groundingline.py M /issm/trunk-jpl/src/m/classes/hydrology.py M /issm/trunk-jpl/src/m/classes/initialization.py M /issm/trunk-jpl/src/m/classes/inversion.py M /issm/trunk-jpl/src/m/classes/mask.py M /issm/trunk-jpl/src/m/classes/materials.py M /issm/trunk-jpl/src/m/classes/mesh.py M /issm/trunk-jpl/src/m/classes/miscellaneous.py M /issm/trunk-jpl/src/m/classes/private.py M /issm/trunk-jpl/src/m/classes/prognostic.py M /issm/trunk-jpl/src/m/classes/qmu.py M /issm/trunk-jpl/src/m/classes/radaroverlay.py M /issm/trunk-jpl/src/m/classes/rifts.py M /issm/trunk-jpl/src/m/classes/settings.py M /issm/trunk-jpl/src/m/classes/steadystate.py M /issm/trunk-jpl/src/m/classes/surfaceforcings.py M /issm/trunk-jpl/src/m/classes/thermal.py M /issm/trunk-jpl/src/m/classes/timestepping.py M /issm/trunk-jpl/src/m/classes/transient.py \\ Export determination: 6. \\Rationale: Added setdefaultparameters routines to python classes +M /issm/trunk-jpl/test/Par/SquareShelfConstrained.py Almost finished translated to python \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12124-12125.diff: \\ Function name: \\M /issm/trunk-jpl/test/Par/SquareShelfConstrained.py \\ Export determination: 6. \\Rationale: Almost finished translated to python +M /issm/trunk-jpl/src/m/model/mesh/triangle.py Bug fix. \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12125-12126.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/mesh/triangle.py \\ Export determination: 6. \\Rationale: Bug fix. +A /issm/trunk-jpl/src/m/utils/Meca/paterson.py Converted paterson.m to paterson.py \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12126-12127.diff: \\ Function name: \\A /issm/trunk-jpl/src/m/utils/Meca/paterson.py \\ Export determination: 6. \\Rationale: Converted paterson.m to paterson.py +M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp A /issm/trunk-jpl/src/m/utils/BC/SetIceShelfBC.py M /issm/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp M /issm/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.h Starting conversion of SetIceShelfBC Needs ContourToMesh python module, so converted this module to python interface. Also simplified Contours* treatment. \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12127-12128.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp A /issm/trunk-jpl/src/m/utils/BC/SetIceShelfBC.py M /issm/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp M /issm/trunk-jpl/src/modules/ContourToMesh/ContourToMesh.h \\ Export determination: 6. \\Rationale: Starting conversion of SetIceShelfBC Needs ContourToMesh python module, so converted this module to python interface. Also simplified Contours* treatment. +M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/toolkits/python/pythonincludes.h Folded NPY\_DEPRECATED python stuff into pythonincludes header file \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12128-12129.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/toolkits/python/pythonincludes.h \\ Export determination: 6. \\Rationale: Folded NPY\_DEPRECATED python stuff into pythonincludes header file +A /issm/trunk-jpl/configs/config-arm-linux.sh (from /issm/trunk-jpl/configs/config-arm.sh:12114) D /issm/trunk-jpl/configs/config-arm.sh M /issm/trunk-jpl/externalpackages/triangle/triangle.c.patch.python Minor modification to Triangle.c python patch and the arm-linux configuration script. \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12129-12130.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-arm-linux.sh (from /issm/trunk-jpl/configs/config-arm.sh:12114) D /issm/trunk-jpl/configs/config-arm.sh M /issm/trunk-jpl/externalpackages/triangle/triangle.c.patch.python \\ Export determination: 6. \\Rationale: Minor modification to Triangle.c python patch and the arm-linux configuration script. +M /issm/trunk-jpl/configs/config-arm-linux.sh M /issm/trunk-jpl/externalpackages/android/android-sdk/install.sh Minor modification to config-arm-linux.sh \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12130-12131.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-arm-linux.sh M /issm/trunk-jpl/externalpackages/android/android-sdk/install.sh \\ Export determination: 6. \\Rationale: Minor modification to config-arm-linux.sh +A /issm/trunk-jpl/externalpackages/freetype A /issm/trunk-jpl/externalpackages/freetype/freetype-2.4.9.tar.gz A /issm/trunk-jpl/externalpackages/freetype/install.sh Freetype package \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12131-12132.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/freetype A /issm/trunk-jpl/externalpackages/freetype/freetype-2.4.9.tar.gz A /issm/trunk-jpl/externalpackages/freetype/install.sh \\ Export determination: 6. \\Rationale: Freetype package +M /issm/trunk-jpl/externalpackages/freetype Ignoring src and install for svn \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-12132-12133.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/freetype \\ Export determination: 6. \\Rationale: Ignoring src and install for svn +M /issm/trunk-jpl/externalpackages/scipy Ignoring some svn files \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-12133-12134.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/scipy \\ Export determination: 6. \\Rationale: Ignoring some svn files +M /issm/trunk-jpl/externalpackages/nose A /issm/trunk-jpl/externalpackages/nose/nose-1.1.2.tar.gz nose package \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-12134-12135.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/nose A /issm/trunk-jpl/externalpackages/nose/nose-1.1.2.tar.gz \\ Export determination: 6. \\Rationale: nose package +A /issm/trunk-jpl/externalpackages/distribute A /issm/trunk-jpl/externalpackages/distribute/distribute-0.6.26.tar.gz A /issm/trunk-jpl/externalpackages/distribute/install.sh distribute package for installing python packages in 3.2.2 \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-12135-12136.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/distribute A /issm/trunk-jpl/externalpackages/distribute/distribute-0.6.26.tar.gz A /issm/trunk-jpl/externalpackages/distribute/install.sh \\ Export determination: 6. \\Rationale: distribute package for installing python packages in 3.2.2 +A /issm/trunk-jpl/externalpackages/ipython A /issm/trunk-jpl/externalpackages/ipython/install.sh A /issm/trunk-jpl/externalpackages/ipython/ipython-0.12.tar.gz ipython package \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-12136-12137.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/ipython A /issm/trunk-jpl/externalpackages/ipython/install.sh A /issm/trunk-jpl/externalpackages/ipython/ipython-0.12.tar.gz \\ Export determination: 6. \\Rationale: ipython package +A /issm/trunk-jpl/externalpackages/libermate A /issm/trunk-jpl/externalpackages/libermate/install.sh A /issm/trunk-jpl/externalpackages/libermate/libermate-0.4.tgz matlab to python scripts \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-12137-12138.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/libermate A /issm/trunk-jpl/externalpackages/libermate/install.sh A /issm/trunk-jpl/externalpackages/libermate/libermate-0.4.tgz \\ Export determination: 6. \\Rationale: matlab to python scripts +M /issm/trunk-jpl/externalpackages/libermate Ignoring install directory \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-12138-12139.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/libermate \\ Export determination: 6. \\Rationale: Ignoring install directory +A /issm/trunk-jpl/externalpackages/pyclips A /issm/trunk-jpl/externalpackages/pyclips/install.sh A /issm/trunk-jpl/externalpackages/pyclips/pyclips-1.0.7.348.tar.gz py clips package \\\\ +\noindent \textbf{Change \#19} with diff file ISSM-12139-12140.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/pyclips A /issm/trunk-jpl/externalpackages/pyclips/install.sh A /issm/trunk-jpl/externalpackages/pyclips/pyclips-1.0.7.348.tar.gz \\ Export determination: 6. \\Rationale: py clips package +M /issm/trunk-jpl/externalpackages/pyclips Ignoring install directory \\\\ Index: /issm/oecreview/Archive/12121-12140/r1.tex =================================================================== --- /issm/oecreview/Archive/12121-12140/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12121-12140/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12121 Index: /issm/oecreview/Archive/12121-12140/r2.tex =================================================================== --- /issm/oecreview/Archive/12121-12140/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12121-12140/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12140 Index: /issm/oecreview/Archive/12141-12160/Date.tex =================================================================== --- /issm/oecreview/Archive/12141-12160/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12141-12160/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12141-12160/ISSM-12141-12142.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12141-12142.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12141-12142.diff (revision 12325) @@ -0,0 +1,11 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle +___________________________________________________________________ +Modified: svn:ignore + - install + + + install +install-matlab +install-python + + Index: /issm/oecreview/Archive/12141-12160/ISSM-12142-12143.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12142-12143.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12142-12143.diff (revision 12325) @@ -0,0 +1,27 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matplotlib/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matplotlib/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matplotlib/install.sh (revision 12143) +@@ -0,0 +1,7 @@ ++#/bin/bash ++ ++git clone https://github.com/matplotlib/matplotlib ++mv matplotlib src ++cd src ++python setup.py build ++python setup.py install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matplotlib/install.sh +___________________________________________________________________ +Added: svn:executable + + * + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matplotlib +___________________________________________________________________ +Added: svn:ignore + + src-* +src +install + + Index: /issm/oecreview/Archive/12141-12160/ISSM-12143-12144.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12143-12144.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12143-12144.diff (revision 12325) @@ -0,0 +1,55 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libpng/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libpng/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libpng/install.sh (revision 12144) +@@ -0,0 +1,26 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf src ++rm -rf install ++rm -rf libpng-1.5.10 ++mkdir src install ++ ++#Untar ++tar -zxvf libpng-1.5.10.tar.gz ++ ++#Move libpng into src directory ++mv libpng-1.5.10/* src ++rm -rf libpng-1.5.10 ++ ++#Configure libpng ++cd src ++sudo ./configure ++ ++#Compile and install libpng ++if [ -z $1 ]; then ++ sudo make ++else ++ sudo make -j $1 ++fi ++sudo make install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libpng/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libpng/libpng-1.5.10.tar.gz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libpng/libpng-1.5.10.tar.gz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libpng +___________________________________________________________________ +Added: svn:ignore + + src +install + + Index: /issm/oecreview/Archive/12141-12160/ISSM-12144-12145.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12144-12145.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12144-12145.diff (revision 12325) @@ -0,0 +1,100 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.4.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.4.sh (revision 12144) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.4.sh (revision 12145) +@@ -1,31 +0,0 @@ +-#!/bin/sh +- +-#External packages versions: +-#petsc 3.1 or 3.2 +-#mpich 1.4 +- +-./configure \ +- --prefix=$ISSM_TIER \ +- --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ +- --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ +- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ +- --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \ +- --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ +- --with-graphics-lib=/usr/lib64/libX11.so \ +- --with-cxxoptflags="-march=opteron -O2" \ +- --with-numthreads=32 \ +- --enable-debugging +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh (revision 12145) +@@ -0,0 +1,31 @@ ++#!/bin/sh ++ ++#External packages versions: ++#petsc 3.1 or 3.2 ++#mpich 1.0.2 ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ ++ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich " \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ ++ --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \ ++ --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ ++ --with-graphics-lib=/usr/lib64/libX11.so \ ++ --with-cxxoptflags="-march=opteron -O2" \ ++ --with-numthreads=32 \ ++ --enable-debugging + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid.sh (revision 12144) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid.sh (revision 12145) +@@ -2,7 +2,7 @@ + + #External packages versions: + #petsc 3.1 or 3.2 +-#mpich 1.0.2 ++#mpich 1.4 + + ./configure \ + --prefix=$ISSM_TIER \ +@@ -12,7 +12,7 @@ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich " \ ++ --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ Index: /issm/oecreview/Archive/12141-12160/ISSM-12146-12147.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12146-12147.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12146-12147.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/Makefile.am (revision 12146) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/Makefile.am (revision 12147) +@@ -13,7 +13,6 @@ + ./planet/*.m \ + ./qmu/*.m \ + ./utils/*.m \ +- ./utils/Analysis/*.m \ + ./utils/Array/*.m \ + ./utils/BC/*.m \ + ./utils/Basins/*.m \ Index: /issm/oecreview/Archive/12141-12160/ISSM-12147-12148.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12147-12148.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12147-12148.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/expdisp.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/expdisp.m (revision 12147) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/expdisp.m (revision 12148) +@@ -40,7 +40,7 @@ + unitmultiplier=varargin{4}; if isnan(unitmultiplier), unitmultiplier=1; end + end + +-domain=expread(domainoutline,1); ++domain=expread(domainoutline); + + figure(figurenumber),hold on + for i=1:length(domain), Index: /issm/oecreview/Archive/12141-12160/ISSM-12148-12149.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12148-12149.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12148-12149.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.m (revision 12148) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/groundingline.m (revision 12149) +@@ -36,7 +36,7 @@ + checkmessage(['requesting grounding line migration, but bathymetry is absent!']); + end + pos=find(md.mask.vertexongroundedice); +- if any(md.geometry.bed(pos)-md.geometry.bathymetry(pos)), ++ if any(abs(md.geometry.bed(pos)-md.geometry.bathymetry(pos))>10^-10), + checkmessage(['bathymetry not equal to bed on grounded ice !']); + end + pos=find(md.mask.vertexonfloatingice); Index: /issm/oecreview/Archive/12141-12160/ISSM-12149-12150.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12149-12150.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12149-12150.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_section.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_section.m (revision 12149) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_section.m (revision 12150) +@@ -35,7 +35,7 @@ + end + + %read contours: +-profiles=expread(getfieldvalue(options,'sectionvalue'),1); ++profiles=expread(getfieldvalue(options,'sectionvalue')); + numprofiles=length(profiles); + + %Loop over number of profiles: Index: /issm/oecreview/Archive/12141-12160/ISSM-12150-12151.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12150-12151.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12150-12151.diff (revision 12325) @@ -0,0 +1,169 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/mail +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/mail (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/mail (revision 12151) +@@ -0,0 +1,158 @@ ++#!/bin/sh ++ ++# This is a shell script to emulate the standard mail(1) aka mailx(1) ++# aka Mail(1) tool usage for sending emails. This shell script is not ++# a client for checking or reading mail. Also, this version of mail ++# does not touch any mail boxes. ++ ++# Copyright (c) 2003 by Jeremy C. Reed ++# This software is provided "as is" without any warranties. You may ++# redistribute and use this source, with or without modification, ++# as long as you include this copyright and disclaimer. ++ ++# To do: some switches to consider: ++# -v display details of delivery ++# -E do not send empty messages ++# -c send carbon copies to users ++# -b send blind carbon copies ++ ++# todo: test if read can read in long enough lines ++# some shells may have limit of 256 characters per read? ++ ++SENDMAIL=sendmail # set to path of your sendmail(8) command ++SENDMAIL_ARGS="-t -i" # -i is so dot doesn't terminate message ++ # -t is to get recipients from headers ++ ++unset subject ++unset to_addr ++dontsendempty=0 ++ ++about () ++{ ++ echo "This is mailx.sh version 0.03. This is simple, shell script" ++ echo "to implement mailx(1) functionality for sending mail. It does" ++ echo "not provide an interface for checking or reading email messages." ++ echo ++ ++ # maybe do this without forking a command ++ mailname=$( basename $0 ) ++ ++ if [ -n "$1" ] ; then ++ echo "$mailname: $1" 1>&2 ++ fi ++ ++ echo "Usage: $mailname [-s subject] to-addr ..." 1>&2 ++ ++ if [ -n "$1" ] ; then ++ if [ -n "$2" ] ; then ++ exit $2 ++ fi ++ exit 100 ++ fi ++ ++ exit 0 ++} ++ ++if [ $# -eq 0 ] ; then ++ about "Sorry, this is not a mail reader." 1 ++fi ++ ++while [ -n "$1" ] ; do ++ case "$1" in ++ -*) ++ if [ "$1" = "-s" ] ; then ++ if [ -z "$2" ] ; then ++ about "The \"-s\" option requires an argument." 4 ++ fi ++ subject="$2" ++ shift ++ elif [ "$1" = "-u" -o "$1" = "-f" ] ; then ++ about "Sorry, this is not a mail reader." 2 ++# elif [ "$1" = "-E" ] ; then ++# this probably needs to have entire message saved to temp file first ++# dontsendempty=1 ++ else ++# about "unknown option -- $1" 3 ++ about "Switch \"$1\" is not implemented." 3 ++ fi ++ ;; ++ *) if [ -n "$to_addr" ] ; then ++ to_addr="${to_addr}, $1" ++ else ++ to_addr="$1" ++ fi ++ ;; ++ esac ++ shift ++done ++ ++ ++if [ -t 0 ] ; then # no piped in standard input ++ if [ -z "$subject" ] ; then ++ echo -n "Subject: " ++ OLD_IFS=$IFS ++ IFS="" ++ read -r subject ++ IFS=$OLD_IFS ++ fi ++fi ++ ++if [ -z "$to_addr" ] ; then ++ about "No recipients specified." 6 ++# about "You must specify recipients." 6 ++fi ++ ++# generate SMTP headers ++ ++# mail(1) doesn't seem to set date ++#date +"Date: %a, %e %b %G %T %z" ++## maybe pipe though sed to get rid of extra space ++## before single digit day of month? ++ ++{ ++# if [ -n "$to_addr" ] ; then ++echo "To: ${to_addr}" ++# fi ++ ++if [ -n "$subject" ] ; then ++ echo "Subject: $subject" ++fi ++ ++# end of headers ++echo "" ++ ++# output ++line_count=0 ++OLD_IFS=$IFS ++IFS="" ++while read -r line ; do ++ # finish if manual, non-piped input is a period on a line by itself ++ if [ "$line" = "." -a -t 0 ] ; then ++ break ++ fi ++ echo "$line" ++ line_count=$(( line_count + 1 )) ++done ++ ++IFS=$OLD_IFS ++ ++if [ -t 0 ] ; then # no piped in standard input ++ echo "EOT" 1>&2 ++fi ++ ++# later add switch to not send mail by exiting ++if [ "$line_count" -eq 0 ] ; then ++# if [ "$dontsendempty" -eq 1 ] ; then ++# todo this, have it save to temp file and then send to sendmail as needed ++# # No message, so just exit cleanly ++# exit 0 ++# fi ++ if [ -z "$subject" ] ; then ++ echo "No message, no subject; hope that's ok" 1>&2 ++ else ++ echo "Null message body; hope that's ok" 1>&2 ++ fi ++fi ++ ++} | $SENDMAIL $SENDMAIL_ARGS ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/mail +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12141-12160/ISSM-12151-12152.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12151-12152.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12151-12152.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp (revision 12151) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp (revision 12152) +@@ -1,6 +1,7 @@ + #include "../Alloc/alloc.h" + #include "../../include/include.h" + #include "../Exceptions/exceptions.h" ++#include "./isnan.h" + #include + + void XZvectorsToCoordinateSystem(double* T,double* xzvectors){ Index: /issm/oecreview/Archive/12141-12160/ISSM-12152-12153.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12152-12153.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12152-12153.diff (revision 12325) @@ -0,0 +1,94 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732 (revision 12152) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732 (revision 12153) +@@ -5,8 +5,8 @@ + #-------------------------------# + + #ISSM main directory (full path) +-ISSM_DIR="/cygdrive/c/issm" +-ISSM_TIER="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl" ++ISSM_DIR="/cygdrive/c/issm-uci" ++ISSM_TIER="/cygdrive/c/issm-uci/trunk-jpl/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="cygwin-intel" +@@ -15,7 +15,7 @@ + MACHINE="win7" + + #MATLAB path +-MATLAB_PATH="C:/MATLAB/R2011b32/" ++MATLAB_PATH="C:/MATLAB/R2012a/" + + #COMPILATION CONFIGURATION FILE + COMPILE_CONFIG_FILE="config-win7-32.sh" +@@ -31,13 +31,13 @@ + # ->skip to section 3 + # - "none" leave ISSM as is in its directory + # ->skip to section 3 +-ISSM_INSTALLATION="none" ++ISSM_INSTALLATION="checkout" + + #SVN repository + REPOSITORY="http://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" + + #execution path used for parallel runs +-EXECUTION_PATH="/cygdrive/c/issm/ExecutionNightlyRun" ++EXECUTION_PATH="/cygdrive/c/issm-uci/ExecutionNightlyRun" + + #-----------------------------------# + # 3: External packages installation # +@@ -48,8 +48,8 @@ + # - "copy" copy existing directories (EXTERNALPACKAGESDIR) + # - "none" leave external packages as is + # ->skip to section 4 +-ISSM_EXTERNALPACKAGES="none" +-EXTERNALPACKAGESDIR="/cygdrive/c/issm/trunk-jpl/externalpackages" ++ISSM_EXTERNALPACKAGES="link" ++EXTERNALPACKAGESDIR="/cygdrive/c/issm-uci/trunk-jpl/externalpackages" + + #List of external pakages to be installed + EXTERNALPACKAGES=" autoconf automake petsc metis triangle cccl" +@@ -65,7 +65,7 @@ + #ISSM_COMPILATION can have 2 values: + # - "yes" compile ISSM + # - "no" do not compile ISSM +-ISSM_COMPILATION="no" ++ISSM_COMPILATION="yes" + + #----------------------# + # 5: Mail notification # +@@ -73,10 +73,10 @@ + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be + #sent to the adresses present in $ISSM_TIER/cron/mailinglist. +-SKIPMAIL="no" ++SKIPMAIL="yes" + + #Sender email address +-EMAIL_ADRESS="eric.larour@jpl.nasa.gov" ++EMAIL_ADRESS="eric.larour@gmail.com" + + #------------------------# + # 6: Nightly run options # +@@ -84,7 +84,7 @@ + + #number of cpus used in ISSM installation and compilation (one is usually + #safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=8 ++NUMCPUS_INSTALL=1 + + #number of cpus used in the nightly runs. + NUMCPUS_RUN=1 +@@ -94,9 +94,9 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="'benchmark','all'" ++NROPTIONS="'benchmark',102:2:120" + + #------------------------# + # 7: Matlab# + #------------------------# +-MATLABBIN=/cygdrive/c/MATLAB/R2011b32/bin/matlab ++MATLABBIN=/cygdrive/c/MATLAB/R2012a/bin/matlab Index: /issm/oecreview/Archive/12141-12160/ISSM-12153-12154.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12153-12154.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12153-12154.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh (revision 12153) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh (revision 12154) +@@ -14,7 +14,7 @@ + declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework64\\v3.5;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;" + declare -x LOCALAPPDATA="C:\\Users\\schlegel\\AppData\\Local" + declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" +-declare -x PATH="/usr/local/bin:/usr/bin:/usr/include:/cygdrive/c/cygwin/usr/bin:/cygdrive/c/cygwin/usr/include:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/b/MATLAB/R2011b/bin:/cygdrive/c/MATLAB/R2011b/extern/include:/cygdrive/c/MATLAB/R2011a/runtime/win64:/cygdrive/c/MATLAB/R2011a/bin:/cygdrive/c/MATLAB/R2011a/extern/include" ++declare -x PATH="/usr/local/bin:/usr/bin:/usr/include:/cygdrive/c/cygwin/usr/bin:/cygdrive/c/cygwin/usr/include:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2012a/runtime/win64:/cygdrive/c/MATLAB/R2012a/bin:/cygdrive/c/MATLAB/R2012a/extern/include:/cygdrive/c/MATLAB/R2011a/runtime/win64:/cygdrive/c/MATLAB/R2011a/bin:/cygdrive/c/MATLAB/R2011a/extern/include" + declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC" + declare -x PROCESSOR_ARCHITECTURE="x86" + declare -x PROCESSOR_ARCHITEW6432="AMD64" Index: /issm/oecreview/Archive/12141-12160/ISSM-12154-12155.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12154-12155.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12154-12155.diff (revision 12325) @@ -0,0 +1,437 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh (revision 12155) +@@ -5,16 +5,16 @@ + cat EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-zA-Z]Enum," | grep -v include | sed -e "s/,//g" | awk '{ printf "%s %s\n", NR, $0 }' > temp + + #Removed existing files +-rm $ISSM_TIER/src/m/enum/*.m +-rm $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp +-rm $ISSM_TIER/src/c/modules/StringToEnumx/StringToEnumx.cpp ++rm $ISSM_DIR/src/m/enum/*.m ++rm $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp ++rm $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp + + #Get number of enums + NUMENUMS=$(wc -l temp | awk '{printf("%s",$1);}'); + + #Build EnumToStringx.cpp {{{1 + #Header +-cat < $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp ++cat < $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp + /* + * \file EnumToStringx.cpp: + * \brief: output string associated with enum +@@ -34,9 +34,9 @@ + + END + #core +-cat temp | awk '{print "\t\t" "case " $2" : return \"" substr($2,1,length($2)-4) "\";"}' >> $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp ++cat temp | awk '{print "\t\t" "case " $2" : return \"" substr($2,1,length($2)-4) "\";"}' >> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp + #Footer +-cat <> $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp ++cat <> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp + default : return "unknown"; + + } +@@ -56,7 +56,7 @@ + #}}} + #Build StringToEnumx.cpp {{{1 + #Header +-cat < $ISSM_TIER/src/c/modules/StringToEnumx/StringToEnumx.cpp ++cat < $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp + /* + * \file StringToEnumx.cpp: + * \brief: output enum associated with string +@@ -80,11 +80,11 @@ + i1=1; + i2=120; + for (( i=1 ; i<=100 ; i++ )); do +- echo " if(stage==$i){" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp ++ echo " if(stage==$i){" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + awk -v i1=$i1 -v i2=$i2 '{if(NR>=i1 && NR<=i2) print $0 }' temp | +- awk '{print "\t" ((NR==1)?" if":" else if") " (strcmp(name,\"" substr($2,1,length($2)-4) "\")==0) return " $2 ";"}' >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp +- echo " else stage=$(($i+1));" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp +- echo " }" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp ++ awk '{print "\t" ((NR==1)?" if":" else if") " (strcmp(name,\"" substr($2,1,length($2)-4) "\")==0) return " $2 ";"}' >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp ++ echo " else stage=$(($i+1));" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp ++ echo " }" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + + if [ $i2 -ge $NUMENUMS ]; then break; fi + let i1=$i1+120 +@@ -92,7 +92,7 @@ + done + + #footer +-cat <> $ISSM_TIER/src/c/modules/StringToEnumx/StringToEnumx.cpp ++cat <> $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp + /*If we reach this point, the string provided has not been found*/ + _error_("Enum %s not found",name); + } +@@ -126,7 +126,7 @@ + fi + #}}} + #Add case to matlabenum file{{{ +- cat < $ISSM_TIER"/src/m/enum/"$(echo $NAMEENUM".m") ++ cat < $ISSM_DIR"/src/m/enum/"$(echo $NAMEENUM".m") + function macro=$(echo $NAMEENUM)() + %$(echo $NAMEENUM | awk {'print toupper($1)'}) - Enum of $(echo $NAME) + % +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Synchronize.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Synchronize.sh (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/Synchronize.sh (revision 12155) +@@ -1,7 +1,7 @@ + #!/bin/bash + #Synchronize Verbosity + #first remove existing files +-rm $ISSM_TIER/src/m/shared/Verb*.m ++rm $ISSM_DIR/src/m/shared/Verb*.m + + echo "Synchronizing Verbosity levels..." + +@@ -50,7 +50,7 @@ + echo "$FILENAME -> 2^$POWER = $BINARY" + + #Add Verbosity Matlab file{{{ +- cat < $ISSM_TIER"/src/m/shared/"$(echo $FILENAME".m") ++ cat < $ISSM_DIR"/src/m/shared/"$(echo $FILENAME".m") + function bool=$(echo $FILENAME)() + %$(echo $FILENAME | awk {'print toupper($1)'}) - Return true if $(echo $LEVELNAME | awk {'print tolower($1)'}) level is activated + % +@@ -147,7 +147,7 @@ + END + #}}} + #Complete verbose.m {{{1 +-VERBOSEPATH="$ISSM_TIER/src/m/classes/verbose.m" ++VERBOSEPATH="$ISSM_DIR/src/m/classes/verbose.m" + cat $VERBOSEPATH | sed "/%BEGINFIELDS/,$ d" > temp_begin + cat $VERBOSEPATH | sed "1,/%ENDFIELDS/d" > temp_end + cat temp_begin FIELDS temp_end > $VERBOSEPATH +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp (revision 12155) +@@ -5,7 +5,7 @@ + + int SegmentIntersect(double* palpha, double* pbeta, double* x1, double* y1, double* x2, double* y2){ + +- /*See ISSM_TIER/src/m/utils/Geometry/SegIntersect.m for matlab routine from which we take this routine: */ ++ /*See ISSM_DIR/src/m/utils/Geometry/SegIntersect.m for matlab routine from which we take this routine: */ + + /*output: */ + double alpha=-1; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/petscversion.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/petscversion.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/petscversion.m (revision 12155) +@@ -7,7 +7,7 @@ + %default + PETSC_VERSION=3; + +-configfile=[issmtier() '/config.h']; ++configfile=[issmdir() '/config.h']; + if ~exist(configfile,'file'), + error(['File ' configfile ' not found. ISSM has not been configured yet!']); + end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/modis.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/modis.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/modis.m (revision 12155) +@@ -13,11 +13,11 @@ + y1=max(ylim); + + %Get path to gdal binaries +-path_gdal=[issmtier() '/externalpackages/gdal/install/bin/']; ++path_gdal=[issmdir() '/externalpackages/gdal/install/bin/']; + + %Was gdal compiled? + if ~exist([path_gdal 'gdal_translate']), +- error(['modis error message: GDAL library needs to be compiled to use this routine. Compile GDAL in ' issmtier() '/externalpackages/gdal to use this routine.']); ++ error(['modis error message: GDAL library needs to be compiled to use this routine. Compile GDAL in ' issmdir() '/externalpackages/gdal to use this routine.']); + end + + inputname='./temp.tif'; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmscpin.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmscpin.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmscpin.m (revision 12155) +@@ -31,18 +31,18 @@ + if ispc, + %use the putty project pscp.exe: it should be in the path. + +- %get ISSM_TIER variable +- [status,ISSM_TIER]=system('echo [%ISSM_TIER_WIN%]'); ++ %get ISSM_DIR variable ++ [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); + if status, +- error('scpin error message: could not find ISSM_TIER_WIN envirnoment variable'); ++ error('scpin error message: could not find ISSM_DIR_WIN envirnoment variable'); + end +- ISSM_TIER=ISSM_TIER(2:end-2); ++ ISSM_DIR=ISSM_DIR(2:end-2); + + username=input('Username: (quoted string) '); + key=input('Key: (quoted string) '); + + for i=1:numel(packages), +- [status,result]=system([ISSM_TIER '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' host ':' path '/' packages{i} ' ./']); ++ [status,result]=system([ISSM_DIR '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' host ':' path '/' packages{i} ' ./']); + if status, + error('scpin error message: could not call putty pscp'); + end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmscpout.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmscpout.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmscpout.m (revision 12155) +@@ -22,18 +22,18 @@ + if ispc, + %use the putty project pscp.exe: it should be in the path. + +- %get ISSM_TIER variable +- [status,ISSM_TIER]=system('echo [%ISSM_TIER_WIN%]'); ++ %get ISSM_DIR variable ++ [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); + if status, +- error('scpout error message: could not find ISSM_TIER_WIN envirnoment variable'); ++ error('scpout error message: could not find ISSM_DIR_WIN envirnoment variable'); + end +- ISSM_TIER=ISSM_TIER(2:end-2); ++ ISSM_DIR=ISSM_DIR(2:end-2); + + username=input('Username: (quoted string) '); + key=input('Key: (quoted string) '); + + for i=1:numel(packages), +- [status,result]=system([ISSM_TIER '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' packages{i} ' ' host ':' path]); ++ [status,result]=system([ISSM_DIR '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' packages{i} ' ' host ':' path]); + if status, + error('scpout error message: could not call putty pscp'); + end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmssh.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmssh.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/issmssh.m (revision 12155) +@@ -14,17 +14,17 @@ + if ispc, + %use the putty project plink.exe: it should be in the path. + +- %get ISSM_TIER variable +- [status,ISSM_TIER]=system('echo [%ISSM_TIER_WIN%]'); ++ %get ISSM_DIR variable ++ [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); + if status, +- error('issmssh error message: could not find ISSM_TIER_WIN envirnoment variable'); ++ error('issmssh error message: could not find ISSM_DIR_WIN envirnoment variable'); + end +- ISSM_TIER=ISSM_TIER(2:end-2); ++ ISSM_DIR=ISSM_DIR(2:end-2); + + username=input('Username: (quoted string) '); + key=input('Key: (quoted string) '); + +- system([ISSM_TIER '/externalpackages/ssh/plink.exe -ssh -l "' username '" -pw "' key '" ' host ' "' command '"']); ++ system([ISSM_DIR '/externalpackages/ssh/plink.exe -ssh -l "' username '" -pw "' key '" ' host ' "' command '"']); + + else + %just use standard unix ssh +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ispetsc.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ispetsc.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ispetsc.m (revision 12155) +@@ -5,7 +5,7 @@ + % flag=ispetsc(); + + +-configfile=[issmtier() '/bin/config.h']; %should find it in the install target ++configfile=[issmdir() '/bin/config.h']; %should find it in the install target + if ~exist(configfile,'file'), + error(['File ' configfile ' not found. ISSM has not been configured yet!']); + end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ismumps.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ismumps.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ismumps.m (revision 12155) +@@ -5,7 +5,7 @@ + % flag=ismumps(); + + +-configfile=[issmtier() '/bin/config.h']; %should find it in the install target ++configfile=[issmdir() '/bin/config.h']; %should find it in the install target + if ~exist(configfile,'file'), + error(['File ' configfile ' not found. ISSM has not been configured yet!']); + end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Miscellaneous/issmdoc.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Miscellaneous/issmdoc.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Miscellaneous/issmdoc.m (revision 12155) +@@ -1,11 +1,11 @@ + %Quick documentation for ISSM + + %First get ISSM tier: +-ISSM_TIER=issmtier; ++ISSM_DIR=issmdir; + + disp(sprintf('\n%s',' A comprehensive documentation is available on http://issm.jpl.nasa.gov')); + disp(sprintf('\n%s',' Example: how to create a square ice shelf')); +-disp(sprintf('%s',' go to ',ISSM_TIER,'/examples/SquareIceshelf')); ++disp(sprintf('%s',' go to ',ISSM_DIR,'/examples/SquareIceshelf')); + disp(sprintf('%s',' md=model; %creates a new empty model structure')); + disp(sprintf('%s',' md=triangle(md,''DomainOutline.exp'',50000); %creates a mesh of the domain outline with a resolution of 50000m')); + disp(sprintf('%s',' md=geography(md,''all'',''''); %defines the glacier system as an ice shelf (no island)')); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/TracksToMatrix.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/TracksToMatrix.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/TracksToMatrix.m (revision 12155) +@@ -25,7 +25,7 @@ + end + + %Add path to dace +-addpath([issmtier() '/externalpackages/dace/install']) ++addpath([issmdir() '/externalpackages/dace/install']) + + %First create the x_m and y_m fot the matrix + x_f=[xmin:posting:xmin+posting*nx]'; +@@ -81,4 +81,4 @@ + MatData=reshape(VecData,ny,nx); + + %remove DACE path +-rmpath([issmtier() '/externalpackages/dace/install']); ++rmpath([issmdir() '/externalpackages/dace/install']); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmtier.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmtier.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmtier.m (revision 12155) +@@ -1,18 +0,0 @@ +-function ISSM_TIER=issmtier() +-%ISSMTIER - Get ISSM_TIER environment variable contents. +-% +-% Usage: +-% ISSM_TIER=issmtier() +- +-if ~ispc, +- ISSM_TIER =getenv('ISSM_TIER'); +-else +- ISSM_TIER =getenv('ISSM_TIER_WIN'); +- if strcmpi(ISSM_TIER(end),'/') | strcmpi(ISSM_TIER(end),'\'), +- ISSM_TIER = ISSM_TIER(1:end-1); %shave off the last '/' +- end +-end +- +-if (isempty(ISSM_TIER)), +- error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); +-end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/flaimdir.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/flaimdir.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/flaimdir.m (revision 12155) +@@ -4,4 +4,4 @@ + % Usage: + % FLAIM_DIR=flaimdir() + +-FLAIM_DIR=[issmtier '/externalpackages/flaim/install']; ++FLAIM_DIR=[issmdir '/externalpackages/flaim/install']; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/ucisvn.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/ucisvn.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/ucisvn.m (revision 12155) +@@ -0,0 +1,15 @@ ++function UCI_SVN=ucisvn() ++%ISSMDIR - Get UCI_SVN environment variable ++% ++% Usage: ++% UCI_SVN=ucisvn() ++ ++if ~ispc, ++ UCI_SVN =getenv('UCI_SVN'); ++else ++ UCI_SVN =getenv('UCI_SVN_WIN'); ++end ++ ++if (isempty(UCI_SVN)), ++ error('ucisvn error message: ''UCI_SVN'' environment variable is empty! You should define UCI_SVN in your .cshrc or .bashrc'); ++end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmdir.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmdir.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmdir.m (revision 12155) +@@ -1,5 +1,5 @@ + function ISSM_DIR=issmdir() +-%ISSMDIR - Get ISSM_DIR environment variable contents. ++%ISSMDIR - Get ISSM_DIR environment variable + % + % Usage: + % ISSM_DIR=issmdir() +@@ -8,6 +8,9 @@ + ISSM_DIR =getenv('ISSM_DIR'); + else + ISSM_DIR =getenv('ISSM_DIR_WIN'); ++ if strcmpi(ISSM_DIR(end),'/') | strcmpi(ISSM_DIR(end),'\'), ++ ISSM_DIR = ISSM_DIR(1:end-1); %shave off the last '/' ++ end + end + + if (isempty(ISSM_DIR)), +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/jplsvn.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/jplsvn.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/jplsvn.m (revision 12155) +@@ -0,0 +1,15 @@ ++function JPL_SVN=jplsvn() ++%ISSMDIR - Get JPL_SVN environment variable ++% ++% Usage: ++% JPL_SVN=jplsvn() ++ ++if ~ispc, ++ JPL_SVN =getenv('JPL_SVN'); ++else ++ JPL_SVN =getenv('JPL_SVN_WIN'); ++end ++ ++if (isempty(JPL_SVN)), ++ error('jplsvn error message: ''JPL_SVN'' environment variable is empty! You should define JPL_SVN in your .cshrc or .bashrc'); ++end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.py (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.py (revision 12155) +@@ -15,11 +15,11 @@ + self.np=1 + self.port=0 + self.interactive=1 +- self.codepath=issmtier() + '/bin' +- self.executionpath=issmtier() + '/execution' +- self.valgrind=issmtier() + '/externalpackages/valgrind/install/bin/valgrind' +- self.valgrindlib=issmtier() + '/externalpackages/valgrind/install/lib/libmpidebug.so' +- self.valgrindsup=issmtier() + '/externalpackages/valgrind/issm.supp' ++ self.codepath=issmdir() + '/bin' ++ self.executionpath=issmdir() + '/execution' ++ self.valgrind=issmdir() + '/externalpackages/valgrind/install/bin/valgrind' ++ self.valgrindlib=issmdir() + '/externalpackages/valgrind/install/lib/libmpidebug.so' ++ self.valgrindsup=issmdir() + '/externalpackages/valgrind/issm.supp' + #}}} + def __repr__(obj): + # {{{ Display +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.m (revision 12154) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters/generic.m (revision 12155) +@@ -12,11 +12,11 @@ + np=1; + port=0; + interactive=1; +- codepath=[issmtier() '/bin']; +- executionpath=[issmtier() '/execution']; +- valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind']; +- valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so']; +- valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp']; ++ codepath=[issmdir() '/bin']; ++ executionpath=[issmdir() '/execution']; ++ valgrind=[issmdir() '/externalpackages/valgrind/install/bin/valgrind']; ++ valgrindlib=[issmdir() '/externalpackages/valgrind/install/lib/libmpidebug.so']; ++ valgrindsup=[issmdir() '/externalpackages/valgrind/issm.supp']; + %}}} + end + methods Index: /issm/oecreview/Archive/12141-12160/ISSM-12155-12156.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12155-12156.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12155-12156.diff (revision 12325) @@ -0,0 +1,1179 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cppcheck/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cppcheck/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cppcheck/install.sh (revision 12156) +@@ -16,5 +16,5 @@ + else + make -j $1 + fi +-make install PREFIX=$ISSM_TIER/externalpackages/cppcheck/install ++make install PREFIX=$ISSM_DIR/externalpackages/cppcheck/install + cd .. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh (revision 12156) +@@ -41,7 +41,7 @@ + if [[ $step == "2" ]]; then + + #Once this is done, we need to install an emulator. Location will default to ~/.android/avd, +- #which we will move to $ISSM_TIER/externalpackages/android-emulators. ++ #which we will move to $ISSM_DIR/externalpackages/android-emulators. + #For now, it's called: Android-4.0.3 + + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cmake/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cmake/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cmake/install.sh (revision 12156) +@@ -13,7 +13,7 @@ + + #Compile cmake + cd install +-./bootstrap --prefix=$ISSM_TIER/externalpackages/cmake/install ++./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install + if [ -z $1 ]; then + make + else +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh (revision 12156) +@@ -19,7 +19,7 @@ + + #Configure doxygen + cd src +-./configure --prefix="$ISSM_TIER/externalpackages/python/install" --enable-framework="$ISSM_TIER/externalpackages/python/install" ++./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" + if [ -z $1 ]; then + make + else +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx64.sh (revision 12156) +@@ -18,7 +18,7 @@ + export CFLAGS=" -arch x86_64" + export CXXFLAGS=" -arch x86_64" + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-f91 \ + --enable-sharedlibs=osx-gcc \ + --enable-shared \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-linux64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 12156) +@@ -17,7 +17,7 @@ + export CFLAGS="$CFLAGS -fPIC" + export FFLAGS="$FFLAGS -fPIC" + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-altix64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 12156) +@@ -17,7 +17,7 @@ + export CFLAGS="$CFLAGS -fPIC" + export FFLAGS="$FFLAGS -fPIC" + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-linux64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-linux64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-linux64.sh (revision 12156) +@@ -16,7 +16,7 @@ + export CFLAGS="$CFLAGS -fPIC" + export FFLAGS="$FFLAGS -fPIC" + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-shared \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-macosx32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 12156) +@@ -16,7 +16,7 @@ + make distclean + export CFLAGS=" -m32" + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-f91=gfortran \ + --enable-sharedlibs=osx-gcc + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-win32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-win32.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.0.2-win32.sh (revision 12156) +@@ -16,7 +16,7 @@ + make distclean + export CFLAGS="$CFLAGS -fPIC" + export FFLAGS="$FFLAGS -fPIC" +-./configure --prefix="$ISSM_TIER/externalpackages/mpich2/install" ++./configure --prefix="$ISSM_DIR/externalpackages/mpich2/install" + + #Apply Patch to examples + patch ./examples/Makefile ../configs/1.0.2/win32/Examples.Makefile.patch +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx32.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx32.sh (revision 12156) +@@ -18,7 +18,7 @@ + export CXXFLAGS=" -arch i386" + export CPPFLAGS=" -arch i386" + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --prefix="$ISSM_DIR/externalpackages/mpich2/install" \ + --enable-f91=gfortran \ + --enable-sharedlibs=osx-gcc \ + --enable-shared \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/install.sh (revision 12156) +@@ -15,7 +15,7 @@ + cd src + + #Configure and compile: +-./configure --prefix=$ISSM_TIER/externalpackages/gmake/install ++./configure --prefix=$ISSM_DIR/externalpackages/gmake/install + + if [ -z $1 ]; then + make +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adic/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adic/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adic/install.sh (revision 12156) +@@ -18,13 +18,13 @@ + mkdir build + cd build + ../source/configure \ +- --with-rose=$ISSM_TIER/externalpackages/rose/install \ +- --with-openanalysis=$ISSM_TIER/externalpackages/openanalysis/openanalysis/x86_64-Linux \ +- --with-boost=$ISSM_TIER/externalpackages/boost/install \ +- --with-xerces=$ISSM_TIER/externalpackages/xerces/src \ +- --with-xaifbooster=$ISSM_TIER/externalpackages/xaifbooster/xaifBooster \ +- --with-colpack=$ISSM_TIER/externalpackages/colpack/install\ +- --prefix=$ISSM_TIER/externalpackages/adic/install ++ --with-rose=$ISSM_DIR/externalpackages/rose/install \ ++ --with-openanalysis=$ISSM_DIR/externalpackages/openanalysis/openanalysis/x86_64-Linux \ ++ --with-boost=$ISSM_DIR/externalpackages/boost/install \ ++ --with-xerces=$ISSM_DIR/externalpackages/xerces/src \ ++ --with-xaifbooster=$ISSM_DIR/externalpackages/xaifbooster/xaifBooster \ ++ --with-colpack=$ISSM_DIR/externalpackages/colpack/install\ ++ --prefix=$ISSM_DIR/externalpackages/adic/install + if [ -z $1 ]; then + make + else +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-win32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-win32.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-win32.sh (revision 12156) +@@ -13,7 +13,7 @@ + + #configure + cd install +-./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" ++./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" + + #Compile valgrind + make -j 4 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-macosx64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-macosx64.sh (revision 12156) +@@ -13,7 +13,7 @@ + + #configure + cd install +-./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" --enable-only64bit ++./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only64bit + + #Compile valgrind + make -j 4 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-linux64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-linux64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-linux64.sh (revision 12156) +@@ -13,7 +13,7 @@ + + #configure + cd install +-./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" ++./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" + + #Compile valgrind + make -j 4 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-altix64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-altix64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-altix64.sh (revision 12156) +@@ -13,7 +13,7 @@ + + #configure + cd install +-./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" ++./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" + + #Compile valgrind + make -j 4 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-macosx32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-macosx32.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/valgrind/install-macosx32.sh (revision 12156) +@@ -13,7 +13,7 @@ + + #configure + cd install +-./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" --enable-only32bit ++./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only32bit + + #Compile valgrind + make -j 4 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/rose/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/rose/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/rose/install.sh (revision 12156) +@@ -14,9 +14,9 @@ + #Configure + cd build + ../source/configure \ +- --prefix=$ISSM_TIER/externalpackages/rose/install \ +- --with-boost=$ISSM_TIER/externalpackages/boost/install\ +- --srcdir=$ISSM_TIER/externalpackages/rose/source ++ --prefix=$ISSM_DIR/externalpackages/rose/install \ ++ --with-boost=$ISSM_DIR/externalpackages/boost/install\ ++ --srcdir=$ISSM_DIR/externalpackages/rose/source + + if [ -z $1 ]; then + make +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/doxygen/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/doxygen/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/doxygen/install.sh (revision 12156) +@@ -7,7 +7,7 @@ + svn co https://doxygen.svn.sourceforge.net/svnroot/doxygen/trunk install + + #Configure doxygen +-cd install && ./configure --prefix "$ISSM_TIER/externalpackages/doxygen/install" ++cd install && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install" + if [ -z $1 ]; then + make + else +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/autoconf/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/autoconf/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/autoconf/install.sh (revision 12156) +@@ -14,6 +14,6 @@ + + #Compile autoconf + cd src +-./configure --prefix="$ISSM_TIER/externalpackages/autoconf/install" ++./configure --prefix="$ISSM_DIR/externalpackages/autoconf/install" + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/install-5.0.1-linux64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/install-5.0.1-linux64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/install-5.0.1-linux64.sh (revision 12156) +@@ -16,5 +16,5 @@ + cd install + + #Compile metis +-make config prefix="$ISSM_TIER/externalpackages/metis/install" ++make config prefix="$ISSM_DIR/externalpackages/metis/install" + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pcre/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pcre/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/pcre/install.sh (revision 12156) +@@ -12,6 +12,6 @@ + + #Configure doxygen + cd install +-./configure --prefix "$ISSM_TIER/externalpackages/python/install" ++./configure --prefix "$ISSM_DIR/externalpackages/python/install" + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libtool/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libtool/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/libtool/install.sh (revision 12156) +@@ -12,6 +12,6 @@ + + #Compile libtool + cd src +-./configure --prefix="$ISSM_TIER/externalpackages/libtool/install" ++./configure --prefix="$ISSM_DIR/externalpackages/libtool/install" + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/swig/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/swig/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/swig/install.sh (revision 12156) +@@ -12,15 +12,15 @@ + + #Copy pcre prototype in include directory + cd install +-#cp $ISSM_TIER/externalpackages/pcre/install/pcre.h ./Source/Include/ +-#cp $ISSM_TIER/externalpackages/pcre/install/.libs/* ./Source/Include/ +-export CFLAGS="$CFLAGS -I$ISSM_TIER/externalpackages/pcre/install" +-export LDFLAGS="-L$ISSM_TIER/externalpackages/pcre/install/.libs/" ++#cp $ISSM_DIR/externalpackages/pcre/install/pcre.h ./Source/Include/ ++#cp $ISSM_DIR/externalpackages/pcre/install/.libs/* ./Source/Include/ ++export CFLAGS="$CFLAGS -I$ISSM_DIR/externalpackages/pcre/install" ++export LDFLAGS="-L$ISSM_DIR/externalpackages/pcre/install/.libs/" + export LIBS="-lpcre" + #Configure doxygen + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/python/install" \ +- --with-pcre-prefix="$ISSM_TIER/externalpackages/pcre/install" \ +- --with-pcre-exec-prefix="$ISSM_TIER/externalpackages/pcre/install" ++ --prefix="$ISSM_DIR/externalpackages/python/install" \ ++ --with-pcre-prefix="$ISSM_DIR/externalpackages/pcre/install" \ ++ --with-pcre-exec-prefix="$ISSM_DIR/externalpackages/pcre/install" + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/rats/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/rats/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/rats/install.sh (revision 12156) +@@ -11,7 +11,7 @@ + + #compile + cd src +-./configure --prefix=$ISSM_TIER/externalpackages/rats/install ++./configure --prefix=$ISSM_DIR/externalpackages/rats/install + make + make install + cd .. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adolc/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adolc/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adolc/install.sh (revision 12156) +@@ -19,7 +19,7 @@ + cd src + + ./configure \ +- --prefix=$ISSM_TIER/externalpackages/adolc/install \ ++ --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --enable-sparse \ + --enable-docexa \ + --enable-addexa \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/graphviz/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/graphviz/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/graphviz/install.sh (revision 12156) +@@ -13,7 +13,7 @@ + + #Configure dakota + cd src +-./configure --prefix="$ISSM_TIER/externalpackages/graphviz/install" ++./configure --prefix="$ISSM_DIR/externalpackages/graphviz/install" + cd .. + + #Compile and install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/bbftp/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/bbftp/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/bbftp/install.sh (revision 12156) +@@ -18,6 +18,6 @@ + + #Configure and compile + cd bbftpc +-./configure --prefix=$ISSM_TIER/externalpackages/bbftp/install ++./configure --prefix=$ISSM_DIR/externalpackages/bbftp/install + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh (revision 12156) +@@ -28,12 +28,12 @@ + #Configure dakota + cd src + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/dakota/install" \ ++ --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ +- --with-blas="-L$ISSM_TIER/externalpackages/petsc/install/lib -lfblas " \ +- --with-lapack="-L$ISSM_TIER/externalpackages/petsc/install/lib -lflapack -lPLAPACK " ++ --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ ++ --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack -lPLAPACK " + cd .. + + #Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-pleiades.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-pleiades.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-pleiades.sh (revision 12156) +@@ -28,7 +28,7 @@ + #Configure dakota + cd src + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/dakota/install" \ ++ --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-altix64-cosmos.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-altix64-cosmos.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-altix64-cosmos.sh (revision 12156) +@@ -28,7 +28,7 @@ + #Configure dakota + cd src + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/dakota/install" \ ++ --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-astrid.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-astrid.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-astrid.sh (revision 12156) +@@ -28,7 +28,7 @@ + #Configure dakota + cd src + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/dakota/install" \ ++ --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh (revision 12156) +@@ -28,7 +28,7 @@ + #Configure dakota + cd src + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/dakota/install" \ ++ --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/install-win7.orig.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/install-win7.orig.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/install-win7.orig.sh (revision 12156) +@@ -14,7 +14,7 @@ + cd src + + #Compile +-./configure --prefix="$ISSM_TIER/externalpackages/cccl/install" ++./configure --prefix="$ISSM_DIR/externalpackages/cccl/install" + + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gdal/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gdal/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gdal/install.sh (revision 12156) +@@ -16,7 +16,7 @@ + #Configure gdal + cd src + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/gdal/install" \ ++ --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --with-netcdf=no \ + --with-jasper=no \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/latex2rtf/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/latex2rtf/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/latex2rtf/install.sh (revision 12156) +@@ -9,5 +9,5 @@ + + #Compile + cd install +-export PREFIX="$ISSM_TIER/externalpackages/latex2rtf/install/" ++export PREFIX="$ISSM_DIR/externalpackages/latex2rtf/install/" + make +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-cosmos.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-cosmos.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-cosmos.sh (revision 12156) +@@ -12,8 +12,8 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no COPTFLAGS=-O3 FOPTFLAGS=-O3 \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-cosmos.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 12156) +@@ -11,7 +11,7 @@ + + #configure + cd install +-PETSC_DIR=$ISSM_TIER/externalpackages/petsc/install ++PETSC_DIR=$ISSM_DIR/externalpackages/petsc/install + ./config/configure.py \ + --prefix=$PETSC_DIR \ + --with-batch=1 \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-macosx64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-macosx64.sh (revision 12156) +@@ -12,10 +12,10 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH=macosx-gnu \ +- --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --download-mumps=yes \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-greenplanet.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-greenplanet.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-greenplanet.sh (revision 12156) +@@ -12,8 +12,8 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --with-batch=1 \ + --with-debugging=0 \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 12156) +@@ -12,10 +12,10 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH=macosx-gnu \ +- --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --download-mumps=yes \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-ogive.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 12156) +@@ -12,9 +12,9 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ +- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH=macosx-gnu \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ +@@ -29,7 +29,7 @@ + --COPTFLAGS="-march=opteron -O2 " \ + --FOPTFLAGS="-march=opteron -O2 " \ + --CXXOPTFLAGS="-march=opteron -O2 " \ +- --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran " ++ --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran " + + #Compile petsc and install it + make +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 12156) +@@ -11,10 +11,10 @@ + + #configure + cd install +-./config/configure.py --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++./config/configure.py --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH=macosx-gnu \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ + --with-shared=0 \ +@@ -23,7 +23,7 @@ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ +- --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran" \ ++ --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran" \ + --download-plapack=yes + + #Compile petsc and install it +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-linux64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-linux64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-linux64.sh (revision 12156) +@@ -12,11 +12,11 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --with-clanguage=C++ \ + --PETSC_ARCH=linux-gnu-amd64 \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --download-mumps=yes \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-eric.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 12156) +@@ -16,10 +16,10 @@ + #configure + cd install + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH=macosx-gnu \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ + --with-shared=0 \ +@@ -28,7 +28,7 @@ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ +- --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ ++ --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ + --download-plapack=yes \ + --CXXFLAGS=" -fPIC -arch i386" \ + --CFLAGS=" -fPIC -arch i386" \ +@@ -42,19 +42,19 @@ + if [ $STEP -eq 2 ]; then + cd install + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH=macosx-gnu \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ + --with-shared=0 \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3 \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3 \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ +- --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ ++ --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ + --download-plapack=yes \ + --CXXFLAGS=" -fPIC -arch i386" \ + --CFLAGS=" -fPIC -arch i386" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-win32-eric.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 12156) +@@ -13,9 +13,9 @@ + cd install + ./config/configure.py \ + --with-parallel-no \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH=cygwin-intel \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ + --with-debugging=0 \ + --with-mpi=0 \ + --download-c-blas-lapack=1 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-win7.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-win7.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-win7.sh (revision 12156) +@@ -13,9 +13,9 @@ + cd src + ./config/configure.py \ + --with-parallel-no \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH=cygwin-intel \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-mpi=0 \ + --download-c-blas-lapack=yes \ +@@ -25,10 +25,10 @@ + --with-clanguage=cxx + + #./config/configure.py \ +-# --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +-# --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++# --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++# --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + # --PETSC_ARCH=macosx-gnu \ +-# --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++# --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + # --with-debugging=0 \ + # --with-shared=0 \ + # --download-mumps=yes \ +@@ -37,7 +37,7 @@ + # --download-blas=yes \ + # --download-f-blas-lapack=yes \ + # --download-plapack=yes \ +-# --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -arch i386" \ ++# --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -arch i386" \ + # --COPTFLAGS="-march=opteron -O2 -arch i386" \ + # --FOPTFLAGS="-march=opteron -O2 -arch i386" \ + # --CXXOPTFLAGS="-march=opteron -O2 -arch i386" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-altix64-castor.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 12156) +@@ -16,8 +16,8 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no \ + --with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \ +@@ -40,8 +40,8 @@ + if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-altix64-castor.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 12156) +@@ -16,7 +16,7 @@ + #configure + cd install + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ +@@ -40,7 +40,7 @@ + if [ $STEP -eq 2 ]; then + cd install + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-win7.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-win7.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-win7.sh (revision 12156) +@@ -13,9 +13,9 @@ + cd install + ./config/configure.py \ + --with-parallel-no \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH=cygwin-intel \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ + --with-debugging=0 \ + --with-mpi=0 \ + --download-c-blas-lapack=1 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-pleiades.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-pleiades.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-pleiades.sh (revision 12156) +@@ -16,10 +16,10 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=no \ + --with-shared=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ +@@ -43,10 +43,10 @@ + if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=no \ + --with-shared=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ +@@ -56,7 +56,7 @@ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ +- --with-plapack-dir=$ISSM_TIER/externalpackages/petsc/src/$ISSM_ARCH \ ++ --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ + --download-parmetis=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh (revision 12156) +@@ -28,11 +28,11 @@ + rm -rf install + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \ + --with-clanguage=C++ \ + --PETSC_ARCH=linux-gnu-amd64 \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --download-metis=yes \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-pleiades.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 12156) +@@ -16,7 +16,7 @@ + #configure + cd install + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ +@@ -43,7 +43,7 @@ + if [ $STEP -eq 2 ]; then + cd install + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh (revision 12156) +@@ -16,10 +16,10 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ +@@ -43,10 +43,10 @@ + if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ +@@ -56,7 +56,7 @@ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ +- --with-plapack-dir=$ISSM_TIER/externalpackages/petsc/src/$ISSM_ARCH \ ++ --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ + --download-parmetis=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-mathieu.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 12156) +@@ -12,10 +12,10 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH=macosx-gnu \ +- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ +@@ -24,7 +24,7 @@ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ +- --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -arch i386" \ ++ --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -arch i386" \ + --COPTFLAGS="-march=opteron -O2 -arch i386" \ + --FOPTFLAGS="-march=opteron -O2 -arch i386" \ + --CXXOPTFLAGS="-march=opteron -O2 -arch i386" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-linux64-astrid.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 12156) +@@ -12,10 +12,10 @@ + #configure + cd src + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH=linux-gnu-amd64 \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ +@@ -24,7 +24,7 @@ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-parmetis=yes \ +- --FFLAGS=-I$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \ + --download-plapack=yes \ + --COPTFLAGS="-march=opteron -O2" \ + --FOPTFLAGS="-march=opteron -O2" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-linux64-astrid.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 12156) +@@ -12,10 +12,10 @@ + #configure + cd install + ./config/configure.py \ +- --prefix="$ISSM_TIER/externalpackages/petsc/install" \ +- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH=linux-gnu-amd64 \ +- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \ + --with-fc=gfortran \ + --with-debugging=1 \ + --with-shared=0 \ +@@ -24,7 +24,7 @@ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ +- --FFLAGS=-I$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \ + --download-plapack=yes \ + --COPTFLAGS="-march=opteron -O2" \ + --FOPTFLAGS="-march=opteron -O2" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/bsdtar/install-win7.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/bsdtar/install-win7.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/bsdtar/install-win7.sh (revision 12156) +@@ -12,6 +12,6 @@ + rm -rf libarchive-3.0.3 + + cd src +-./configure --prefix="$ISSM_TIER/externalpackages/bsdtar/install" ++./configure --prefix="$ISSM_DIR/externalpackages/bsdtar/install" + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/tao/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/tao/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/tao/install.sh (revision 12156) +@@ -13,7 +13,7 @@ + mv tao-2.0-p3/* install/ + rm -rf tao-2.0-p3 + cd install +-export TAO_DIR="$ISSM_TIER/externalpackages/tao/install/" ++export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/" + + #petsc needs to be compiled with --with-clanguage=C++ + make +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/qhull/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/qhull/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/qhull/install.sh (revision 12156) +@@ -14,6 +14,6 @@ + + #Configure qhull + cd src +-./configure --prefix="$ISSM_TIER/externalpackages/qhull/install" ++./configure --prefix="$ISSM_DIR/externalpackages/qhull/install" + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh (revision 12156) +@@ -17,7 +17,7 @@ + export CFLAGS=" -arch x86_64" + + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/gsl/install" ++ --prefix="$ISSM_DIR/externalpackages/gsl/install" + + #Compile gsl + if [ -z $1 ]; then +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-linux64-murdo.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-linux64-murdo.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-linux64-murdo.sh (revision 12156) +@@ -15,7 +15,7 @@ + cd src + + ./configure \ +- --prefix="$ISSM_TIER/externalpackages/gsl/install" ++ --prefix="$ISSM_DIR/externalpackages/gsl/install" + + #Compile gsl + if [ -z $1 ]; then +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-android-4.0.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-android-4.0.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-android-4.0.sh (revision 12156) +@@ -23,7 +23,7 @@ + OBJ_EXT=o\ + LIB_EXT=a\ + --host="arm-linux"\ +- --prefix="$ISSM_TIER/externalpackages/gsl/install" ++ --prefix="$ISSM_DIR/externalpackages/gsl/install" + + #Compile gsl + if [ -z $1 ]; then +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh (revision 12156) +@@ -21,9 +21,9 @@ + #Configure and compile + cd src + ./bootstrap.sh \ +- --prefix="$ISSM_TIER/externalpackages/boost/install" \ ++ --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ +- --with-python-root="$ISSM_TIER/externalpackages/python/install" ++ --with-python-root="$ISSM_DIR/externalpackages/python/install" + + #Compile boost + ./bjam install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ncview/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ncview/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/ncview/install.sh (revision 12156) +@@ -14,11 +14,11 @@ + #Configure doxygen + cd install + ./configure \ +- --prefix "$ISSM_TIER/externalpackages/ncview/install" \ ++ --prefix "$ISSM_DIR/externalpackages/ncview/install" \ + --x-libraries=/usr/X11/lib/ \ + --x-includes=/usr/X11/include/ \ +- --with-netcdf_incdir="$ISSM_TIER/externalpackages/netcdf/install/include/" \ +- --with-netcdf_libdir="$ISSM_TIER/externalpackages/netcdf/install/lib/" ++ --with-netcdf_incdir="$ISSM_DIR/externalpackages/netcdf/install/include/" \ ++ --with-netcdf_libdir="$ISSM_DIR/externalpackages/netcdf/install/lib/" + + make + make install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/install.sh (revision 12156) +@@ -18,7 +18,7 @@ + export CC=gcc + cd src/src + ./configure \ +- --prefix "$ISSM_TIER/externalpackages/vim/install" \ ++ --prefix "$ISSM_DIR/externalpackages/vim/install" \ + --with-gcc "/usr/bin/gcc" + + #Compile vim +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/netcdf/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/netcdf/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/netcdf/install.sh (revision 12156) +@@ -14,7 +14,7 @@ + + #Configure and compile + cd install +-./configure --prefix="$ISSM_TIER/externalpackages/netcdf/install" ++./configure --prefix="$ISSM_DIR/externalpackages/netcdf/install" + if [ -z $1 ]; then + make + else +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/automake/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/automake/install.sh (revision 12155) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/automake/install.sh (revision 12156) +@@ -12,6 +12,6 @@ + + #Compile automake + cd src +-./configure --prefix="$ISSM_TIER/externalpackages/automake/install" ++./configure --prefix="$ISSM_DIR/externalpackages/automake/install" + make + make install Index: /issm/oecreview/Archive/12141-12160/ISSM-12156-12157.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12156-12157.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12156-12157.diff (revision 12325) @@ -0,0 +1,953 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-cosmos.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-cosmos.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-cosmos.sh (revision 12157) +@@ -1,3 +1,3 @@ + #!/bin/csh + +-./configure --prefix=$ISSM_TIER --with-serial=no --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=/opt/mpich/gm/intel10.1/include --with-mpi-lib="-L/opt/mpich/gm/intel10.1/lib -lmpich -L/usr/local/gm/lib/ -lgm -lpthread -lrt" --with-petsc-arch=$ISSM_ARCH --with-mkl-dir=/opt/intel/mkl/10.0.5.025/lib/32/ --with-plapack-dir="-L$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH --with-vendor=intel-linux --with-graphics-lib=/usr/X11R6/lib/libX11.so ++./configure --prefix=$ISSM_DIR --with-serial=no --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=/opt/mpich/gm/intel10.1/include --with-mpi-lib="-L/opt/mpich/gm/intel10.1/lib -lmpich -L/usr/local/gm/lib/ -lgm -lpthread -lrt" --with-petsc-arch=$ISSM_ARCH --with-mkl-dir=/opt/intel/mkl/10.0.5.025/lib/32/ --with-plapack-dir="-L$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH --with-vendor=intel-linux --with-graphics-lib=/usr/X11R6/lib/libX11.so +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-greenplanet.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-greenplanet.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-greenplanet.sh (revision 12157) +@@ -4,21 +4,21 @@ + #MPI /sopt/mpi/openmpi-1.5.4_psm/intel + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-modules=no \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include="/sopt/mpi/openmpi-1.5.4_psm/intel/include/" \ + --with-mpi-lib="-L/sopt/mpi/openmpi-1.5.4_psm/intel/lib/ -lmpi -lmpi_f77" \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mkl-dir=/opt/intel/mkl/10.2.4.032/ \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS" \ + --with-vendor=intel-linux +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh (revision 12157) +@@ -1,16 +1,16 @@ + #!/bin/sh + + #Dos style path needed for the windows sdk 7.1 cl compiler: +-ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` ++ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"` + + #get configure.sh to pick up the win7 Visual Studio compiler +-./configure --prefix=$ISSM_TIER \ ++./configure --prefix=$ISSM_DIR \ + --with-vendor=intel-win7-32 \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir="$ISSM_TIER_WIN/externalpackages/triangle/install" \ +- --with-metis-dir="$ISSM_TIER_WIN/externalpackages/metis/install" \ +- --with-petsc-dir="$ISSM_TIER_WIN/externalpackages/petsc/install" \ ++ --with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \ ++ --with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \ ++ --with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ \ +- --with-mpi-lib="$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ +- --with-mpi-include="$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni" ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ ++ --with-mpi-lib="$ISSM_DIR_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ ++ --with-mpi-include="$ISSM_DIR_WIN/externalpackages/petsc/install/include/mpiuni" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 12157) +@@ -4,24 +4,24 @@ + #mpich 1.4 + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ +- --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ +- #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ ++ #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh (revision 12157) +@@ -1,27 +1,27 @@ + #!/bin/sh + + ./configure \ +- --prefix=$ISSM_TIER \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ ++ --prefix=$ISSM_DIR \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib \ + --with-graphics-lib=/usr/lib64/libX11.so \ +- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ +- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ ++ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-numthreads=18 \ + --enable-debugging \ +- --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install + + +-# --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++# --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + # --with-petsc-arch=$ISSM_ARCH \ +-# --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +-# --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +-# --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +-# --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +-# --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +-# --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++# --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++# --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++# --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++# --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++# --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++# --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx32-ogive.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx32-ogive.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx32-ogive.sh (revision 12157) +@@ -4,21 +4,21 @@ + #mpich 1.4 + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh (revision 12157) +@@ -5,25 +5,25 @@ + #mpich 1.0.2 + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich " \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich " \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ +- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ +- --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ ++ --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh (revision 12157) +@@ -1,16 +1,16 @@ + #!/bin/sh + + #Dos style path needed for the windows sdk 7.1 cl compiler: +-ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` ++ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"` + + #get configure.sh to pick up the win7 Visual Studio compiler +-./configure --prefix=$ISSM_TIER \ ++./configure --prefix=$ISSM_DIR \ + --with-vendor=intel-win7-64 \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir="$ISSM_TIER_WIN/externalpackages/triangle/install" \ +- --with-metis-dir="$ISSM_TIER_WIN/externalpackages/metis/install" \ +- --with-petsc-dir="$ISSM_TIER_WIN/externalpackages/petsc/install" \ ++ --with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \ ++ --with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \ ++ --with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ \ +- --with-mpi-lib="$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ +- --with-mpi-include="$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni" ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ ++ --with-mpi-lib="$ISSM_DIR_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ ++ --with-mpi-include="$ISSM_DIR_WIN/externalpackages/petsc/install/include/mpiuni" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-ogive.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-ogive.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-ogive.sh (revision 12157) +@@ -8,21 +8,21 @@ + export CXXFLAGS=" -arch x86_64" + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/gfortran/lib/x86_64/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-nicole.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-nicole.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-nicole.sh (revision 12157) +@@ -4,23 +4,23 @@ + #mpich 1.4 + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ +- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12157) +@@ -3,10 +3,10 @@ + pythonversion=2.7 + + ./configure \ +- --prefix=$ISSM_TIER \ +- --with-python-dir=$ISSM_TIER/externalpackages/python/install\ ++ --prefix=$ISSM_DIR \ ++ --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-vendor=arm-linux \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-bothapis.sh (revision 12157) +@@ -6,28 +6,28 @@ + pythonversion=2.7 + + ./configure \ +- --prefix=$ISSM_TIER \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --prefix=$ISSM_DIR \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-python-dir=$ISSM_TIER/externalpackages/python/install\ ++ --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ +- --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ +- #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- #--with-boost-dir=$ISSM_TIER/externalpackages/boost/install/ \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ ++ #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-ad.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-ad.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-ad.sh (revision 12157) +@@ -1,24 +1,24 @@ + #!/bin/sh + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-serial=no\ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ +- --with-rose-dir=$ISSM_TIER/externalpackages/rose/install/ \ +- --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ ++ --with-rose-dir=$ISSM_DIR/externalpackages/rose/install/ \ ++ --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ + --with-numthreads=24 \ + --without-thermal \ + --without-control \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-ad.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-ad.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-ad.sh (revision 12157) +@@ -1,25 +1,25 @@ + #!/bin/sh + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-serial=no\ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-hypre-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-ml-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-ml-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -lg2c /usr/lib/gcc/x86_64-redhat-linux/4.1.1/libgfortran.a" \ +- --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ ++ --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ + --with-numthreads=24 \ + --without-thermal \ + --without-control \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 12157) +@@ -3,13 +3,13 @@ + pythonversion=3.2 + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-python-dir=$ISSM_TIER/externalpackages/python/install\ ++ --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ +- --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win32-eric.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win32-eric.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win32-eric.sh (revision 12157) +@@ -3,4 +3,4 @@ + + #get configure.sh to pick up the intel compiler + +-./configure --prefix=$ISSM_TIER --with-parallel=no --with-vendor=intel-win --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/f2cblaslapack/$ISSM_ARCH ++./configure --prefix=$ISSM_DIR --with-parallel=no --with-vendor=intel-win --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/f2cblaslapack/$ISSM_ARCH +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-altix64-castor.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-altix64-castor.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-altix64-castor.sh (revision 12157) +@@ -1,3 +1,3 @@ + #!/bin/csh + +-./configure --prefix=$ISSM_TIER --with-serial=no --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=/usr/include --with-mpi-lib="-L/usr/lib -lmpi" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install --with-mkl-dir=/opt/intel/mkl/9.1.023/lib/64 --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH --with-graphics-lib=/usr/X11R6/lib/libX11.so ++./configure --prefix=$ISSM_DIR --with-serial=no --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=/usr/include --with-mpi-lib="-L/usr/lib -lmpi" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-mkl-dir=/opt/intel/mkl/9.1.023/lib/64 --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH --with-graphics-lib=/usr/X11R6/lib/libX11.so +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-pleiades-petsc2.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-pleiades-petsc2.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-pleiades-petsc2.sh (revision 12157) +@@ -1,21 +1,21 @@ + #!/bin/csh + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-modules=no \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --with-mpi-lib="-L/nasa/sgi/mpt/1.25/lib/ -lmpi -lpthread -lgfortran" \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS" \ + --with-vendor=intel-pleiades +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-python.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-python.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-python.sh (revision 12157) +@@ -4,26 +4,26 @@ + #mpich 1.4 + + ./configure \ +- --prefix=$ISSM_TIER \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-python-dir=$ISSM_TIER/externalpackages/python/install\ +- --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ +- --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --prefix=$ISSM_DIR \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-python-dir=$ISSM_DIR/externalpackages/python/install\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ +- #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- #--with-boost-dir=$ISSM_TIER/externalpackages/boost/install/ \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ ++ #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-pleiades.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-pleiades.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-pleiades.sh (revision 12157) +@@ -1,22 +1,22 @@ + #!/bin/csh + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-modules=no \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --with-mpi-lib="-L/nasa/sgi/mpt/1.25/lib/ -lmpi -lpthread -lgfortran" \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS" \ + --with-vendor=intel-pleiades +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh (revision 12157) +@@ -5,19 +5,19 @@ + + ./configure \ + --with-serial=no\ +- --prefix=$ISSM_TIER \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --prefix=$ISSM_DIR \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --without-blas-lapack-dir \ +- --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ +- --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ +- --with-adolc-dir=$ISSM_TIER/externalpackages/adolc/install/ \ ++ --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ ++ --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install/ \ + --with-numthreads=8 \ + --without-thermal \ + --without-control \ +@@ -33,11 +33,11 @@ + --without-groundingline + + #--without-prognostic \ +-#--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++#--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + #--with-petsc-arch=$ISSM_ARCH \ +-#--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +-#--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +-#--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +-#--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +-#--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +-#--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++#--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++#--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++#--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++#--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++#--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++#--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx32-mathieu.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx32-mathieu.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx32-mathieu.sh (revision 12157) +@@ -9,21 +9,21 @@ + export CXXFLAGS=" -arch i386" + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-sophie.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-sophie.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-sophie.sh (revision 12157) +@@ -8,21 +8,21 @@ + export CXXFLAGS=" -arch x86_64" + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-fortran-lib="/sw/usr/local/lib/x86_64/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-petsc2.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-petsc2.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid-petsc2.sh (revision 12157) +@@ -4,4 +4,4 @@ + #petsc 2.6 + #mpich 1.0.2 + +-./configure --prefix=$ISSM_TIER --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-scotch-dir=$ISSM_TIER/externalpackages/scotch/install --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install --enable-debugging --with-shapelib-dir=$ISSM_TIER/externalpackages/shapelib/install\ ++./configure --prefix=$ISSM_DIR --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-scotch-dir=$ISSM_DIR/externalpackages/scotch/install --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install --enable-debugging --with-shapelib-dir=$ISSM_DIR/externalpackages/shapelib/install\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo.sh (revision 12157) +@@ -1,26 +1,26 @@ + #!/bin/sh + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ +- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-numthreads=18 \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --enable-debugging + + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-astrid.sh (revision 12157) +@@ -5,25 +5,25 @@ + #mpich 1.4 + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ +- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ +- --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ ++ --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-mathieu.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-mathieu.sh (revision 12156) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-mathieu.sh (revision 12157) +@@ -4,21 +4,21 @@ + #mpich 1.4 + + ./configure \ +- --prefix=$ISSM_TIER \ ++ --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ Index: /issm/oecreview/Archive/12141-12160/ISSM-12157-12158.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12157-12158.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12157-12158.diff (revision 12325) @@ -0,0 +1,113 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12157) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.py (revision 12158) +@@ -4,23 +4,23 @@ + # startup.py is a script run by python at the beginning of a session, just + # before handing over the prompt to the user if the environment variable + # PYTHONSTARTUP is defined: +-# export PYTHONSTARTUP=$ISSM_TIER/startup.py ++# export PYTHONSTARTUP=$ISSM_DIR/startup.py + # This startup script should be run by users before trying to use ISSM. + + import os,sys + +-#Recover ISSM_TIER, ISSM_DIR and USERNAME +-ISSM_TIER=os.getenv('ISSM_TIER') ++#Recover ISSM_DIR and USERNAME ++ISSM_DIR=os.getenv('ISSM_DIR') + USERNAME =os.getenv('USER') +-if(ISSM_TIER==None): +- raise NameError('"ISSM_TIER" environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!') ++if(ISSM_DIR==None): ++ raise NameError('"ISSM_DIR" environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!') + + #Now add all issm code paths necessary to run issm smoothly. + #We capture the error output, so that we can warn the user to update +-#the variable ISSM_TIER in this file, in case it is not correctly setup. ++#the variable ISSM_DIR in this file, in case it is not correctly setup. + + #ISSM path. Go through src/py and load everything we find that looks like a python file +-for root,dirs,files in os.walk(ISSM_TIER+ '/src/py'): ++for root,dirs,files in os.walk(ISSM_DIR+ '/src/py'): + for file in files: + if file.find(".py") != -1: + if file.find(".pyc") == -1: +@@ -29,7 +29,7 @@ + file=os.path.splitext(file)[0] + #__import__(file) + +-for root,dirs,files in os.walk(ISSM_TIER+ '/src/m'): ++for root,dirs,files in os.walk(ISSM_DIR+ '/src/m'): + for file in files: + if file.find(".py") != -1: + if file.find(".pyc") == -1: +@@ -38,7 +38,7 @@ + file=os.path.splitext(file)[0] + #__import__(file) + +-sys.path.append(ISSM_TIER + '/src/modules/python') ++sys.path.append(ISSM_DIR + '/src/modules/python') + + #Deal with scipy import: + import scipy +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m (revision 12157) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m (revision 12158) +@@ -10,37 +10,37 @@ + % clear the last warning to focus on the warnings of the ISSM path + lastwarn(''); + +-%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN ++%Recover ISSM_DIR , or if on a Windows machine, ISSM_DIR_WIN + if ~ispc, +- ISSM_TIER=getenv('ISSM_TIER'); ++ ISSM_DIR=getenv('ISSM_DIR'); + else +- ISSM_TIER=getenv('ISSM_TIER_WIN'); +- %ISSM_TIER=''; ++ ISSM_DIR=getenv('ISSM_DIR_WIN'); ++ %ISSM_DIR=''; + end +-if (isempty(ISSM_TIER)), +- error('''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); ++if (isempty(ISSM_DIR)), ++ error('''ISSM_DIR'' environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!'); + end + + %Now add all issm code paths necessary to run issm smoothly. + %We capture the error output, so that we can warn the user to update +-%the variable ISSM_TIER in this file, in case it is not correctly setup. ++%the variable ISSM_DIR in this file, in case it is not correctly setup. + + %ISSM path +-addpath([ISSM_TIER '/src/m/utils/']); %loads recursivepath +-addpath([ISSM_TIER '/bin']); +-addpath(recursivepath([ISSM_TIER '/src/m'])); +-addpath(recursivepath([ISSM_TIER '/externalpackages/scotch'])); +-addpath(recursivepath([ISSM_TIER '/externalpackages/canos'])); +-addpath(recursivepath([ISSM_TIER '/externalpackages/kml'])); +-addpath(recursivepath([ISSM_TIER '/externalpackages/export_fig'])); +-addpath(recursivepath([ISSM_TIER '/externalpackages/googleearthtoolbox'])); +-addpath(recursivepath([ISSM_TIER '/externalpackages/cm_and_cb_utilities'])); ++addpath([ISSM_DIR '/src/m/utils/']); %loads recursivepath ++addpath([ISSM_DIR '/bin']); ++addpath(recursivepath([ISSM_DIR '/src/m'])); ++addpath(recursivepath([ISSM_DIR '/externalpackages/scotch'])); ++addpath(recursivepath([ISSM_DIR '/externalpackages/canos'])); ++addpath(recursivepath([ISSM_DIR '/externalpackages/kml'])); ++addpath(recursivepath([ISSM_DIR '/externalpackages/export_fig'])); ++addpath(recursivepath([ISSM_DIR '/externalpackages/googleearthtoolbox'])); ++addpath(recursivepath([ISSM_DIR '/externalpackages/cm_and_cb_utilities'])); + +-clear ISSM_TIER; ++clear ISSM_DIR; + + %Check on any warning messages that might indicate that the paths were not correct. + if ~isempty(lastwarn), +- fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); ++ fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_DIR variable in your .cshrc or .bashrc!\n'); + fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); + else + fprintf('\n To get started with ISSM, type issmdoc at the command prompt.\n\n'); Index: /issm/oecreview/Archive/12141-12160/ISSM-12158-12159.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12158-12159.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12158-12159.diff (revision 12325) @@ -0,0 +1,334 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/windowsbuild.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/windowsbuild.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/windowsbuild.sh (revision 12159) +@@ -10,7 +10,7 @@ + #Create tar file, with today's date in the title; + today=`today_date` + +-cd $ISSM_TIER/bin ++cd $ISSM_DIR/bin + + #Filter out .svn files + rm -rf list +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/report.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/report.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/report.sh (revision 12159) +@@ -48,7 +48,7 @@ + BODY_FONTL=`echo $BODY_FONT | sed -e "s/style=\"/style=\"text-align:left; /g"` + + #create some variables +-if [ $(ls -1 $ISSM_TIER/bin | wc -l) -le 20 ]; ++if [ $(ls -1 $ISSM_DIR/bin | wc -l) -le 20 ]; + then + IS_INSTALL=0 + else +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/getloc.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/getloc.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/getloc.sh (revision 12159) +@@ -1,13 +1,13 @@ + #!/bin/bash + #get number of lines of code +-cloc-1.55.pl $ISSM_TIER/src $ISSM_TIER/m4 --exclude-dir=.svn --exclude-ext=exp --exclude-lang=make --out=temp ++cloc-1.55.pl $ISSM_DIR/src $ISSM_DIR/m4 --exclude-dir=.svn --exclude-ext=exp --exclude-lang=make --out=temp + cat temp + ./cloc2html.py + rm temp + +-cat $ISSM_TIER/src/dox/issm.dox | sed '/ input1 +-cat $ISSM_TIER/src/dox/issm.dox | sed '1,/<\/table>/d' > input2 +-cat input1 temp.html input2 > $ISSM_TIER/src/dox/issm.dox ++cat $ISSM_DIR/src/dox/issm.dox | sed '/
input1 ++cat $ISSM_DIR/src/dox/issm.dox | sed '1,/<\/table>/d' > input2 ++cat input1 temp.html input2 > $ISSM_DIR/src/dox/issm.dox + rm input1 input2 temp.html + + exit 1 +@@ -18,12 +18,12 @@ + + #OLDER MANUAL VESION + #get Matlab number of lines +-cd $ISSM_TIER/src/m ++cd $ISSM_DIR/src/m + M_LOC=$(find . -name "*.m" -exec wc -l '{}' \; | awk '{ sum += $1 } END { print sum}'); + echo "Matlab code: $M_LOC" + + #get C/CPP number of lines +-cd $ISSM_TIER/src ++cd $ISSM_DIR/src + CPP_LOC=$(find . -name "*.cpp" -exec wc -l '{}' \; | awk '{ sum += $1 } END { print sum}'); + echo "C++ code: $CPP_LOC" + C_LOC=$(find . -name "*.c" -exec wc -l '{}' \; | awk '{ sum += $1 } END { print sum}'); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/archive.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/archive.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/archive.sh (revision 12159) +@@ -9,7 +9,7 @@ + } + + #Cleanup code +-cd $ISSM_TIER ++cd $ISSM_DIR + make clean + make distclean + +@@ -17,6 +17,6 @@ + rm -rf externalpackages + + #Create tar file, with today's date in the title; +-cd $ISSM_TIER/.. ++cd $ISSM_DIR/.. + today=`today_date` +-tar zcvf issm-3.0-$today.tar.gz `basename $ISSM_TIER` ++tar zcvf issm-3.0-$today.tar.gz `basename $ISSM_DIR` +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/automakererun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/automakererun.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/automakererun.sh (revision 12159) +@@ -3,10 +3,10 @@ + # archive. + + +- ACLOCAL="$ISSM_TIER/externalpackages/automake/install/bin/aclocal" +-AUTOCONF="$ISSM_TIER/externalpackages/autoconf/install/bin/autoconf" +-AUTOHEAD="$ISSM_TIER/externalpackages/autoconf/install/bin/autoheader" +-AUTOMAKE="$ISSM_TIER/externalpackages/automake/install/bin/automake" ++ ACLOCAL="$ISSM_DIR/externalpackages/automake/install/bin/aclocal" ++AUTOCONF="$ISSM_DIR/externalpackages/autoconf/install/bin/autoconf" ++AUTOHEAD="$ISSM_DIR/externalpackages/autoconf/install/bin/autoheader" ++AUTOMAKE="$ISSM_DIR/externalpackages/automake/install/bin/automake" + + echo "removing config.cach" + rm -rf config.cach +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/dailyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/dailyrun.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/dailyrun.sh (revision 12159) +@@ -53,25 +53,25 @@ + + #Prepare run + #Windows hack for startup.m {{{1 +-#windows environments: ISSM_TIER_WIN variable not correctly picked up when using +-#the cron job. just get startup to take the ISSM_TIER variable as the pwd: ++#windows environments: ISSM_DIR_WIN variable not correctly picked up when using ++#the cron job. just get startup to take the ISSM_DIR variable as the pwd: + if [ "$OS" = "winxp32" ] + then +- cat startup.m | sed 's/clear status/clear status; ISSM_TIER=pwd;/g' > startup.m.bak ++ cat startup.m | sed 's/clear status/clear status; ISSM_DIR=pwd;/g' > startup.m.bak + mv startup.m.bak startup.m + fi + #}}} + #create softlink to startup {{{1 +-cd $ISSM_TIER/test/NightlyRun/ +-ln -s $ISSM_TIER/startup.m . ++cd $ISSM_DIR/test/NightlyRun/ ++ln -s $ISSM_DIR/startup.m . + #}}} + #Create dailylog directory and info.log {{{1 + #put installation elapsed time in info.log + INSTALL_TIME=$(timer) + ELAPSED_INSTALL=$(timer $START_TIME) +-rm -rf $ISSM_TIER/dailylog +-mkdir $ISSM_TIER/dailylog +-cat << END > $ISSM_TIER/dailylog/info.log ++rm -rf $ISSM_DIR/dailylog ++mkdir $ISSM_DIR/dailylog ++cat << END > $ISSM_DIR/dailylog/info.log + today: $(echo $TODAY) + user: $(echo $USER) + host: $(echo $HOST_NAME) +@@ -94,10 +94,10 @@ + for (( i=1;i<=$NUMCPUS_RUN;i++ )) + do + #Launch matlab and the daily run script +- cat > $ISSM_TIER/dailylog/matlab_run$i.m << EOF ++ cat > $ISSM_DIR/dailylog/matlab_run$i.m << EOF + warning off %necessary to avoid a info.log of several Go for parallel runs + try, +- cd $ISSM_TIER/test/NightlyRun ++ cd $ISSM_DIR/test/NightlyRun + startup; + $(if [ "$NROPTIONS" = "" ] + then +@@ -110,7 +110,7 @@ + %An error occured, get report and exit + directory=strsplit(pwd,'/'); + message=getReport(me) +- fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at'); ++ fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at'); + fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); + fprintf(fid,'%s',message); + fclose(fid); +@@ -120,7 +120,7 @@ + EOF + + #Start run from dailylog directory +- cd $ISSM_TIER/dailylog/ ++ cd $ISSM_DIR/dailylog/ + + #Start test + MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8 +@@ -131,7 +131,7 @@ + wait + #}}} + #concatenate all reports {{{1 +-cd $ISSM_TIER/dailylog/ ++cd $ISSM_DIR/dailylog/ + mv matlab_log1.log matlab_log.log + for (( i=2;i<=$NUMCPUS_RUN;i++ )) + do +@@ -148,7 +148,7 @@ + fi + ELAPSED_RUN=$(timer $INSTALL_TIME) + ELAPSED_TOTAL=$(timer $START_TIME) +-cat << END >> $ISSM_TIER/dailylog/info.log ++cat << END >> $ISSM_DIR/dailylog/info.log + elapsed_run: $(echo $ELAPSED_RUN) + elapsed_total: $(echo $ELAPSED_TOTAL) + matlab_crash: $(echo $MATLABCRASH) +@@ -157,8 +157,8 @@ + + #Send Report + #Build html report {{{1 +-cd $ISSM_TIER/dailylog/ ++cd $ISSM_DIR/dailylog/ + sh ../scripts/report.sh +-ln -s $ISSM_TIER/dailylog/report.html $INIT_PATH +-echo "html report located in $ISSM_TIER/dailylog/report.html and $INIT_PATH/report.html" ++ln -s $ISSM_DIR/dailylog/report.html $INIT_PATH ++echo "html report located in $ISSM_DIR/dailylog/report.html and $INIT_PATH/report.html" + #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/GenerateReferences.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/GenerateReferences.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/GenerateReferences.sh (revision 12159) +@@ -15,7 +15,7 @@ + \bibliographystyle{agu} + \begin{document} + \nocite{$CITE} +-\bibliography{$ISSM_DIR/publications/bibtex/references} ++\bibliography{$JPL_SVN/publications/bibtex/references} + \end{document} + END + #Generate pdf +@@ -28,7 +28,7 @@ + cat references.bak1 | sed -e "/ibitem/,/]/d" > references.bak2 #delete labels that are on multiple lines + mv references.bak2 references.bbl + echo "Converting to rtf" +-$ISSM_TIER/externalpackages/latex2rtf/install/latex2rtf -P $ISSM_TIER/externalpackages/latex2rtf/install/cfg/ references ++$ISSM_DIR/externalpackages/latex2rtf/install/latex2rtf -P $ISSM_DIR/externalpackages/latex2rtf/install/cfg/ references + + #Remove all but rtf file + rm -rf references.[!rtf]* +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/convertmatlabclasses.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/convertmatlabclasses.py (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/convertmatlabclasses.py (revision 12159) +@@ -3,10 +3,10 @@ + import sys, re, os, shutil + + #get names of all directories to process +-ISSM_TIER=os.getenv('ISSM_TIER'); +-if(not ISSM_TIER): raise NameError('ISSM_TIER undefined') +-newclassesdir = ISSM_TIER + '/src/m/classes/' +-oldclassesdir = ISSM_TIER + '/src/m/oldclasses/' ++ISSM_DIR=os.getenv('ISSM_DIR'); ++if(not ISSM_DIR): raise NameError('ISSM_DIR undefined') ++newclassesdir = ISSM_DIR + '/src/m/classes/' ++oldclassesdir = ISSM_DIR + '/src/m/oldclasses/' + + #make new directory + if(os.path.exists(oldclassesdir)):shutil.rmtree(oldclassesdir) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/issmconfiguration.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/issmconfiguration.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/issmconfiguration.sh (revision 12159) +@@ -6,8 +6,8 @@ + #keep track of present directory: + presendir=`pwd` + +-if test -d "$ISSM_TIER/configs" ; then +- cd $ISSM_TIER/configs ++if test -d "$ISSM_DIR/configs" ; then ++ cd $ISSM_DIR/configs + LIST=`ls` + + if [[ $# == "0" ]]; then +@@ -39,7 +39,7 @@ + echo "Configuring ISSM with following configs: $configurename" + echo "" + +- cd $ISSM_TIER ++ cd $ISSM_DIR + source ./scripts/automakererun.sh + source configs/$configurename + +@@ -55,4 +55,4 @@ + + + +-#alias aut='a=`pwd` && cd $ISSM_TIER && ./scripts/automakererun.sh && ./configs/config-macosx64-larour-nopetsc.sh' ++#alias aut='a=`pwd` && cd $ISSM_DIR && ./scripts/automakererun.sh && ./configs/config-macosx64-larour-nopetsc.sh' +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/run.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/run.sh (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/run.sh (revision 12159) +@@ -5,18 +5,18 @@ + NROPTIONS=""; + MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8 + #create softlink to startup {{{1 +-cd $ISSM_TIER/test/NightlyRun/ +-ln -s $ISSM_TIER/startup.m . ++cd $ISSM_DIR/test/NightlyRun/ ++ln -s $ISSM_DIR/startup.m . + #}}} + + #Launch all tests on different cpus + for (( i=1;i<=$NUMCPUS_RUN;i++ )) + do + #Launch matlab and the daily run script +- cat > $ISSM_TIER/dailylog/matlab_run$i.m << EOF ++ cat > $ISSM_DIR/dailylog/matlab_run$i.m << EOF + warning off %necessary to avoid a daily.log of several Go for parallel runs + try, +- cd $ISSM_TIER/test/NightlyRun ++ cd $ISSM_DIR/test/NightlyRun + startup; + $(if [ "$NROPTIONS" = "" ] + then +@@ -29,7 +29,7 @@ + %An error occured, get report and exit + directory=strsplit(pwd,'/'); + message=getReport(me) +- fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at'); ++ fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at'); + fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); + fprintf(fid,'%s',message); + fclose(fid); +@@ -38,7 +38,7 @@ + EOF + + #Start run from dailylog directory +- cd $ISSM_TIER/dailylog/ ++ cd $ISSM_DIR/dailylog/ + + #Start test + /usr/local/pkgs/matlab-$MATLAB_VERSION/bin/matlab -nojvm -nosplash -r matlab_run$i -logfile matlab_log$i.log & +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/cloc2html.py +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/cloc2html.py (revision 12158) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/cloc2html.py (revision 12159) +@@ -3,8 +3,8 @@ + #inspired from http://qwiki.stanford.edu/images/d/df/Latex2qwiki.txt + import sys, re, os + +-ISSM_TIER=os.getenv('ISSM_TIER'); +-if(not ISSM_TIER): raise NameError('ISSM_TIER undefined') ++ISSM_DIR=os.getenv('ISSM_DIR'); ++if(not ISSM_DIR): raise NameError('ISSM_DIR undefined') + + infile = open('temp','r') + outfile = open('temp.html','w') Index: /issm/oecreview/Archive/12141-12160/ISSM-12159-12160.diff =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-12159-12160.diff (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-12159-12160.diff (revision 12325) @@ -0,0 +1,161 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_nightly +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_nightly (revision 12159) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_nightly (revision 12160) +@@ -5,8 +5,7 @@ + #-------------------------------# + + #ISSM main directory (full path) +-ISSM_DIR="/path/to/issm/" +-ISSM_TIER="/path/to/issm/trunk-jpl/cron/trunk-jpl" ++ISSM_DIR="/path/to/issm/trunk-jpl/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="macosx-gnu" +@@ -71,7 +70,7 @@ + #----------------------# + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++#sent to the adresses present in $ISSM_DIR/cron/mailinglist. + SKIPMAIL="no" + + #Sender email address +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_daily (revision 12159) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_daily (revision 12160) +@@ -5,8 +5,7 @@ + #-------------------------------# + + #ISSM main directory (full path) +-ISSM_DIR="/path/to/issm/" +-ISSM_TIER="/path/to/issm/trunk-jpl/cron/trunk-jpl" ++ISSM_DIR="/path/to/issm/trunk-jpl/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="macosx-gnu" +@@ -71,7 +70,7 @@ + #----------------------# + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++#sent to the adresses present in $ISSM_DIR/cron/mailinglist. + SKIPMAIL="no" + + #Sender email address +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_nightly +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_nightly (revision 12159) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_nightly (revision 12160) +@@ -5,8 +5,7 @@ + #-------------------------------# + + #ISSM main directory (full paths) +-ISSM_DIR="/path/to/issm" +-ISSM_TIER="/path/to/issm/cron/trunk-jpl" ++ISSM_DIR="/path/to/issm/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="linux-gnu-amd64" +@@ -71,7 +70,7 @@ + #----------------------# + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++#sent to the adresses present in $ISSM_DIR/cron/mailinglist. + SKIPMAIL="no" + + #Sender email address +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732 (revision 12159) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732 (revision 12160) +@@ -5,8 +5,7 @@ + #-------------------------------# + + #ISSM main directory (full path) +-ISSM_DIR="/cygdrive/c/issm-uci" +-ISSM_TIER="/cygdrive/c/issm-uci/trunk-jpl/cron/trunk-jpl" ++ISSM_DIR="/cygdrive/c/issm-uci/trunk-jpl/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="cygwin-intel" +@@ -72,7 +71,7 @@ + #----------------------# + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++#sent to the adresses present in $ISSM_DIR/cron/mailinglist. + SKIPMAIL="yes" + + #Sender email address +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/winxp32 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/winxp32 (revision 12159) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/winxp32 (revision 12160) +@@ -5,8 +5,7 @@ + #-------------------------------# + + #ISSM main directory (full path) +-ISSM_DIR="C:/home/issm/trunk-jpl" +-ISSM_TIER="C:/home/issm/trunk-jpl/cron/trunk-jpl" ++ISSM_DIR="C:/home/issm/trunk-jpl/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="cygwin-intel" +@@ -65,7 +64,7 @@ + #----------------------# + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++#sent to the adresses present in $ISSM_DIR/cron/mailinglist. + SKIPMAIL="no" + + #Sender email address +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_daily (revision 12159) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_daily (revision 12160) +@@ -5,8 +5,7 @@ + #-------------------------------# + + #ISSM main directory (full paths) +-ISSM_DIR="/path/to/issm" +-ISSM_TIER="/path/to/issm/cron/trunk-jpl" ++ISSM_DIR="/path/to/issm/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="linux-gnu-amd64" +@@ -71,7 +70,7 @@ + #----------------------# + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++#sent to the adresses present in $ISSM_DIR/cron/mailinglist. + SKIPMAIL="no" + + #Sender email address +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win764 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win764 (revision 12159) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win764 (revision 12160) +@@ -5,8 +5,7 @@ + #-------------------------------# + + #ISSM main directory (full path) +-ISSM_DIR="/cygdrive/c/issm" +-ISSM_TIER="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl" ++ISSM_DIR="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="cygwin-intel" +@@ -72,7 +71,7 @@ + #----------------------# + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++#sent to the adresses present in $ISSM_DIR/cron/mailinglist. + SKIPMAIL="no" + + #Sender email address Index: /issm/oecreview/Archive/12141-12160/ISSM-DocReview-12141-12160.tex =================================================================== --- /issm/oecreview/Archive/12141-12160/ISSM-DocReview-12141-12160.tex (revision 12325) +++ /issm/oecreview/Archive/12141-12160/ISSM-DocReview-12141-12160.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12141-12160/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12141-12160/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12141-12160/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12141-12160 Index: /issm/oecreview/Archive/12141-12160/Makefile =================================================================== --- /issm/oecreview/Archive/12141-12160/Makefile (revision 12325) +++ /issm/oecreview/Archive/12141-12160/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12141-12160 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12141-12160/log.tex =================================================================== --- /issm/oecreview/Archive/12141-12160/log.tex (revision 12325) +++ /issm/oecreview/Archive/12141-12160/log.tex (revision 12325) @@ -0,0 +1,38 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12141-12142.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/readline A /issm/trunk-jpl/externalpackages/readline/install.sh A /issm/trunk-jpl/externalpackages/readline/readline-6.2.2.tar.gz \\ Export determination: 6. \\Rationale: readline python package +M /issm/trunk-jpl/externalpackages/triangle Ignoring install directories \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12142-12143.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/triangle \\ Export determination: 6. \\Rationale: Ignoring install directories +A /issm/trunk-jpl/externalpackages/matplotlib A /issm/trunk-jpl/externalpackages/matplotlib/install.sh matplotlib python package \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12143-12144.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/matplotlib A /issm/trunk-jpl/externalpackages/matplotlib/install.sh \\ Export determination: 6. \\Rationale: matplotlib python package +A /issm/trunk-jpl/externalpackages/libpng A /issm/trunk-jpl/externalpackages/libpng/install.sh A /issm/trunk-jpl/externalpackages/libpng/libpng-1.5.10.tar.gz python libpng package \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12144-12145.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/libpng A /issm/trunk-jpl/externalpackages/libpng/install.sh A /issm/trunk-jpl/externalpackages/libpng/libpng-1.5.10.tar.gz \\ Export determination: 6. \\Rationale: python libpng package +A /issm/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh D /issm/trunk-jpl/configs/config-linux64-astrid-mpich1.4.sh M /issm/trunk-jpl/configs/config-linux64-astrid.sh Changing mpich version \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12145-12146.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh D /issm/trunk-jpl/configs/config-linux64-astrid-mpich1.4.sh M /issm/trunk-jpl/configs/config-linux64-astrid.sh \\ Export determination: 6. \\Rationale: Changing mpich version +D /issm/trunk-jpl/src/m/utils/Analysis not needed anymore \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12146-12147.diff: \\ Function name: \\D /issm/trunk-jpl/src/m/utils/Analysis \\ Export determination: 6. \\Rationale: not needed anymore +M /issm/trunk-jpl/src/m/Makefile.am removed Analysis \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12147-12148.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/Makefile.am \\ Export determination: 6. \\Rationale: removed Analysis +M /issm/trunk-jpl/src/m/utils/Exp/expdisp.m minor \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12148-12149.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/Exp/expdisp.m \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/src/m/classes/groundingline.m bathymetry approximately equal to bed (10$^-10$) \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12149-12150.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/groundingline.m \\ Export determination: 6. \\Rationale: bathymetry approximately equal to bed (10$^-10$) +M /issm/trunk-jpl/src/m/model/plot/plot\_section.m expread has only one argument now \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12150-12151.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/plot/plot\_section.m \\ Export determination: 6. \\Rationale: expread has only one argument now +A /issm/trunk-jpl/scripts/mail Needed for some platforms that don't carry mailx \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12151-12152.diff: \\ Function name: \\A /issm/trunk-jpl/scripts/mail \\ Export determination: 6. \\Rationale: Needed for some platforms that don't carry mailx +M /issm/trunk-jpl/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp isnan missing \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-12152-12153.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp \\ Export determination: 6. \\Rationale: isnan missing +M /issm/trunk-jpl/cron/configs/win732 win732 configuration \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-12153-12154.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/win732 \\ Export determination: 6. \\Rationale: win732 configuration +M /issm/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh Updated configuration \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-12154-12155.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh \\ Export determination: 6. \\Rationale: Updated configuration +M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh M /issm/trunk-jpl/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp M /issm/trunk-jpl/src/c/shared/Numerics/Synchronize.sh M /issm/trunk-jpl/src/m/classes/clusters/generic.m M /issm/trunk-jpl/src/m/classes/clusters/generic.py M /issm/trunk-jpl/src/m/model/modis.m M /issm/trunk-jpl/src/m/model/petscversion.m M /issm/trunk-jpl/src/m/utils/DataProcessing/TracksToMatrix.m M /issm/trunk-jpl/src/m/utils/Miscellaneous/issmdoc.m M /issm/trunk-jpl/src/m/utils/OS/ismumps.m M /issm/trunk-jpl/src/m/utils/OS/ispetsc.m M /issm/trunk-jpl/src/m/utils/OS/issmscpin.m M /issm/trunk-jpl/src/m/utils/OS/issmscpout.m M /issm/trunk-jpl/src/m/utils/OS/issmssh.m M /issm/trunk-jpl/src/m/utils/Shell/flaimdir.m M /issm/trunk-jpl/src/m/utils/Shell/issmdir.m D /issm/trunk-jpl/src/m/utils/Shell/issmtier.m A /issm/trunk-jpl/src/m/utils/Shell/jplsvn.m A /issm/trunk-jpl/src/m/utils/Shell/ucisvn.m Changing ISSM\_TIER to ISSM\_DIR \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-12155-12156.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh M /issm/trunk-jpl/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp M /issm/trunk-jpl/src/c/shared/Numerics/Synchronize.sh M /issm/trunk-jpl/src/m/classes/clusters/generic.m M /issm/trunk-jpl/src/m/classes/clusters/generic.py M /issm/trunk-jpl/src/m/model/modis.m M /issm/trunk-jpl/src/m/model/petscversion.m M /issm/trunk-jpl/src/m/utils/DataProcessing/TracksToMatrix.m M /issm/trunk-jpl/src/m/utils/Miscellaneous/issmdoc.m M /issm/trunk-jpl/src/m/utils/OS/ismumps.m M /issm/trunk-jpl/src/m/utils/OS/ispetsc.m M /issm/trunk-jpl/src/m/utils/OS/issmscpin.m M /issm/trunk-jpl/src/m/utils/OS/issmscpout.m M /issm/trunk-jpl/src/m/utils/OS/issmssh.m M /issm/trunk-jpl/src/m/utils/Shell/flaimdir.m M /issm/trunk-jpl/src/m/utils/Shell/issmdir.m D /issm/trunk-jpl/src/m/utils/Shell/issmtier.m A /issm/trunk-jpl/src/m/utils/Shell/jplsvn.m A /issm/trunk-jpl/src/m/utils/Shell/ucisvn.m \\ Export determination: 6. \\Rationale: Changing ISSM\_TIER to ISSM\_DIR +M /issm/trunk-jpl/externalpackages/adic/install.sh M /issm/trunk-jpl/externalpackages/adolc/install.sh M /issm/trunk-jpl/externalpackages/android/android-sdk/install.sh M /issm/trunk-jpl/externalpackages/autoconf/install.sh M /issm/trunk-jpl/externalpackages/automake/install.sh M /issm/trunk-jpl/externalpackages/bbftp/install.sh M /issm/trunk-jpl/externalpackages/boost/install.sh M /issm/trunk-jpl/externalpackages/bsdtar/install-win7.sh M /issm/trunk-jpl/externalpackages/cccl/install-win7.orig.sh M /issm/trunk-jpl/externalpackages/cmake/install.sh M /issm/trunk-jpl/externalpackages/cppcheck/install.sh M /issm/trunk-jpl/externalpackages/dakota/install-altix64-cosmos.sh M /issm/trunk-jpl/externalpackages/dakota/install-linux64-astrid.sh M /issm/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh M /issm/trunk-jpl/externalpackages/dakota/install-macosx64.sh M /issm/trunk-jpl/externalpackages/dakota/install-pleiades.sh M /issm/trunk-jpl/externalpackages/doxygen/install.sh M /issm/trunk-jpl/externalpackages/gdal/install.sh M /issm/trunk-jpl/externalpackages/gmake/install.sh M /issm/trunk-jpl/externalpackages/graphviz/install.sh M /issm/trunk-jpl/externalpackages/gsl/install-android-4.0.sh M /issm/trunk-jpl/externalpackages/gsl/install-linux64-murdo.sh M /issm/trunk-jpl/externalpackages/gsl/install-macosx64.sh M /issm/trunk-jpl/externalpackages/latex2rtf/install.sh M /issm/trunk-jpl/externalpackages/libtool/install.sh M /issm/trunk-jpl/externalpackages/metis/install-5.0.1-linux64.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.0.2-altix64.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.0.2-linux64.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.0.2-macosx32.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.0.2-win32.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.4-linux64.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.4-macosx32.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.4-macosx64.sh M /issm/trunk-jpl/externalpackages/ncview/install.sh M /issm/trunk-jpl/externalpackages/netcdf/install.sh M /issm/trunk-jpl/externalpackages/pcre/install.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-altix64-castor.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-cosmos.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-linux64-astrid.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-eric.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-pleiades.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-win32-eric.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-win7.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-altix64-castor.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-cosmos.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-linux64-astrid.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-mathieu.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-ogive.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-pleiades.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-win7.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.2-greenplanet.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.2-linux64.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.2-macosx64.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh M /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh M /issm/trunk-jpl/externalpackages/python/install.sh M /issm/trunk-jpl/externalpackages/qhull/install.sh M /issm/trunk-jpl/externalpackages/rats/install.sh M /issm/trunk-jpl/externalpackages/rose/install.sh M /issm/trunk-jpl/externalpackages/swig/install.sh M /issm/trunk-jpl/externalpackages/tao/install.sh M /issm/trunk-jpl/externalpackages/valgrind/install-altix64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-linux64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-macosx32.sh M /issm/trunk-jpl/externalpackages/valgrind/install-macosx64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-win32.sh M /issm/trunk-jpl/externalpackages/vim/install.sh Changing ISSM\_TIER to ISSM\_DIR \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-12156-12157.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/adic/install.sh M /issm/trunk-jpl/externalpackages/adolc/install.sh M /issm/trunk-jpl/externalpackages/android/android-sdk/install.sh M /issm/trunk-jpl/externalpackages/autoconf/install.sh M /issm/trunk-jpl/externalpackages/automake/install.sh M /issm/trunk-jpl/externalpackages/bbftp/install.sh M /issm/trunk-jpl/externalpackages/boost/install.sh M /issm/trunk-jpl/externalpackages/bsdtar/install-win7.sh M /issm/trunk-jpl/externalpackages/cccl/install-win7.orig.sh M /issm/trunk-jpl/externalpackages/cmake/install.sh M /issm/trunk-jpl/externalpackages/cppcheck/install.sh M /issm/trunk-jpl/externalpackages/dakota/install-altix64-cosmos.sh M /issm/trunk-jpl/externalpackages/dakota/install-linux64-astrid.sh M /issm/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh M /issm/trunk-jpl/externalpackages/dakota/install-macosx64.sh M /issm/trunk-jpl/externalpackages/dakota/install-pleiades.sh M /issm/trunk-jpl/externalpackages/doxygen/install.sh M /issm/trunk-jpl/externalpackages/gdal/install.sh M /issm/trunk-jpl/externalpackages/gmake/install.sh M /issm/trunk-jpl/externalpackages/graphviz/install.sh M /issm/trunk-jpl/externalpackages/gsl/install-android-4.0.sh M /issm/trunk-jpl/externalpackages/gsl/install-linux64-murdo.sh M /issm/trunk-jpl/externalpackages/gsl/install-macosx64.sh M /issm/trunk-jpl/externalpackages/latex2rtf/install.sh M /issm/trunk-jpl/externalpackages/libtool/install.sh M /issm/trunk-jpl/externalpackages/metis/install-5.0.1-linux64.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.0.2-altix64.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.0.2-linux64.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.0.2-macosx32.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.0.2-win32.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.4-linux64.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.4-macosx32.sh M /issm/trunk-jpl/externalpackages/mpich2/install-1.4-macosx64.sh M /issm/trunk-jpl/externalpackages/ncview/install.sh M /issm/trunk-jpl/externalpackages/netcdf/install.sh M /issm/trunk-jpl/externalpackages/pcre/install.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-altix64-castor.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-cosmos.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-linux64-astrid.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-eric.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-pleiades.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-win32-eric.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-win7.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-altix64-castor.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-cosmos.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-linux64-astrid.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-mathieu.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-ogive.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-pleiades.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-win7.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.2-greenplanet.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.2-linux64.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.2-macosx64.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh M /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh M /issm/trunk-jpl/externalpackages/python/install.sh M /issm/trunk-jpl/externalpackages/qhull/install.sh M /issm/trunk-jpl/externalpackages/rats/install.sh M /issm/trunk-jpl/externalpackages/rose/install.sh M /issm/trunk-jpl/externalpackages/swig/install.sh M /issm/trunk-jpl/externalpackages/tao/install.sh M /issm/trunk-jpl/externalpackages/valgrind/install-altix64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-linux64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-macosx32.sh M /issm/trunk-jpl/externalpackages/valgrind/install-macosx64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-win32.sh M /issm/trunk-jpl/externalpackages/vim/install.sh \\ Export determination: 6. \\Rationale: Changing ISSM\_TIER to ISSM\_DIR +M /issm/trunk-jpl/configs/config-altix64-castor.sh M /issm/trunk-jpl/configs/config-arm-linux.sh M /issm/trunk-jpl/configs/config-cosmos.sh M /issm/trunk-jpl/configs/config-greenplanet.sh M /issm/trunk-jpl/configs/config-linux64-astrid-ad.sh M /issm/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh M /issm/trunk-jpl/configs/config-linux64-astrid-petsc2.sh M /issm/trunk-jpl/configs/config-linux64-astrid.sh M /issm/trunk-jpl/configs/config-linux64-murdo-ad.sh M /issm/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh M /issm/trunk-jpl/configs/config-linux64-murdo.sh M /issm/trunk-jpl/configs/config-macosx32-mathieu.sh M /issm/trunk-jpl/configs/config-macosx32-ogive.sh M /issm/trunk-jpl/configs/config-macosx64-larour-ad.sh M /issm/trunk-jpl/configs/config-macosx64-larour-bothapis.sh M /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh M /issm/trunk-jpl/configs/config-macosx64-larour-python.sh M /issm/trunk-jpl/configs/config-macosx64-larour.sh M /issm/trunk-jpl/configs/config-macosx64-mathieu.sh M /issm/trunk-jpl/configs/config-macosx64-nicole.sh M /issm/trunk-jpl/configs/config-macosx64-ogive.sh M /issm/trunk-jpl/configs/config-macosx64-sophie.sh M /issm/trunk-jpl/configs/config-pleiades-petsc2.sh M /issm/trunk-jpl/configs/config-pleiades.sh M /issm/trunk-jpl/configs/config-win32-eric.sh M /issm/trunk-jpl/configs/config-win7-32.sh M /issm/trunk-jpl/configs/config-win7-64.sh Changing ISSM\_TIER to ISSM\_DIR \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-12157-12158.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-altix64-castor.sh M /issm/trunk-jpl/configs/config-arm-linux.sh M /issm/trunk-jpl/configs/config-cosmos.sh M /issm/trunk-jpl/configs/config-greenplanet.sh M /issm/trunk-jpl/configs/config-linux64-astrid-ad.sh M /issm/trunk-jpl/configs/config-linux64-astrid-mpich1.0.sh M /issm/trunk-jpl/configs/config-linux64-astrid-petsc2.sh M /issm/trunk-jpl/configs/config-linux64-astrid.sh M /issm/trunk-jpl/configs/config-linux64-murdo-ad.sh M /issm/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh M /issm/trunk-jpl/configs/config-linux64-murdo.sh M /issm/trunk-jpl/configs/config-macosx32-mathieu.sh M /issm/trunk-jpl/configs/config-macosx32-ogive.sh M /issm/trunk-jpl/configs/config-macosx64-larour-ad.sh M /issm/trunk-jpl/configs/config-macosx64-larour-bothapis.sh M /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh M /issm/trunk-jpl/configs/config-macosx64-larour-python.sh M /issm/trunk-jpl/configs/config-macosx64-larour.sh M /issm/trunk-jpl/configs/config-macosx64-mathieu.sh M /issm/trunk-jpl/configs/config-macosx64-nicole.sh M /issm/trunk-jpl/configs/config-macosx64-ogive.sh M /issm/trunk-jpl/configs/config-macosx64-sophie.sh M /issm/trunk-jpl/configs/config-pleiades-petsc2.sh M /issm/trunk-jpl/configs/config-pleiades.sh M /issm/trunk-jpl/configs/config-win32-eric.sh M /issm/trunk-jpl/configs/config-win7-32.sh M /issm/trunk-jpl/configs/config-win7-64.sh \\ Export determination: 6. \\Rationale: Changing ISSM\_TIER to ISSM\_DIR +M /issm/trunk-jpl/startup.m M /issm/trunk-jpl/startup.py Changing ISSM\_TIER to ISSM\_DIR \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-12158-12159.diff: \\ Function name: \\M /issm/trunk-jpl/startup.m M /issm/trunk-jpl/startup.py \\ Export determination: 6. \\Rationale: Changing ISSM\_TIER to ISSM\_DIR +M /issm/trunk-jpl/scripts/GenerateReferences.sh M /issm/trunk-jpl/scripts/archive.sh M /issm/trunk-jpl/scripts/automakererun.sh M /issm/trunk-jpl/scripts/cloc2html.py M /issm/trunk-jpl/scripts/convertmatlabclasses.py M /issm/trunk-jpl/scripts/dailyrun.sh M /issm/trunk-jpl/scripts/getloc.sh M /issm/trunk-jpl/scripts/issmconfiguration.sh M /issm/trunk-jpl/scripts/report.sh M /issm/trunk-jpl/scripts/run.sh M /issm/trunk-jpl/scripts/windowsbuild.sh Changing ISSM\_TIER to ISSM\_DIR \\\\ +\noindent \textbf{Change \#19} with diff file ISSM-12159-12160.diff: \\ Function name: \\M /issm/trunk-jpl/scripts/GenerateReferences.sh M /issm/trunk-jpl/scripts/archive.sh M /issm/trunk-jpl/scripts/automakererun.sh M /issm/trunk-jpl/scripts/cloc2html.py M /issm/trunk-jpl/scripts/convertmatlabclasses.py M /issm/trunk-jpl/scripts/dailyrun.sh M /issm/trunk-jpl/scripts/getloc.sh M /issm/trunk-jpl/scripts/issmconfiguration.sh M /issm/trunk-jpl/scripts/report.sh M /issm/trunk-jpl/scripts/run.sh M /issm/trunk-jpl/scripts/windowsbuild.sh \\ Export determination: 6. \\Rationale: Changing ISSM\_TIER to ISSM\_DIR +M /issm/trunk-jpl/cron/configs/linux64\_daily M /issm/trunk-jpl/cron/configs/linux64\_nightly M /issm/trunk-jpl/cron/configs/macosx64\_daily M /issm/trunk-jpl/cron/configs/macosx64\_nightly M /issm/trunk-jpl/cron/configs/win732 M /issm/trunk-jpl/cron/configs/win764 M /issm/trunk-jpl/cron/configs/winxp32 Changing ISSM\_TIER to ISSM\_DIR \\\\ Index: /issm/oecreview/Archive/12141-12160/r1.tex =================================================================== --- /issm/oecreview/Archive/12141-12160/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12141-12160/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12141 Index: /issm/oecreview/Archive/12141-12160/r2.tex =================================================================== --- /issm/oecreview/Archive/12141-12160/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12141-12160/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12160 Index: /issm/oecreview/Archive/12161-12180/Date.tex =================================================================== --- /issm/oecreview/Archive/12161-12180/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12161-12180/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12161-12180/ISSM-12162-12163.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12162-12163.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12162-12163.diff (revision 12325) @@ -0,0 +1,47 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/runme.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/runme.m (revision 12162) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/runme.m (revision 12163) +@@ -29,8 +29,8 @@ + % runme('exclude',101); + % md=runme('id',102,'procedure','model'); + +-%Get ISSM_TIER variable +-ISSM_TIER=issmtier(); ++%Get ISSM_DIR variable ++ISSM_DIR=issmdir(); + + %Check inputs + % {{{1 +@@ -167,13 +167,13 @@ + directory=strsplit(pwd,'/'); + message=getReport(me2); + if strcmpi(output,'nightly') +- fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); ++ fid=fopen([ISSM_DIR '/nightlylog/matlaberror.log'], 'at'); + fprintf(fid,'%s',message); + fprintf(fid,'\n------------------------------------------------------------------\n'); + fclose(fid); + disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,fieldname)); + elseif strcmpi(output,'daily'); +- fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at'); ++ fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at'); + fprintf(fid,'%s',message); + fprintf(fid,'\n------------------------------------------------------------------\n'); + fclose(fid); +@@ -192,13 +192,13 @@ + directory=strsplit(pwd,'/'); + message=getReport(me); + if strcmpi(output,'nightly') +- fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); ++ fid=fopen([ISSM_DIR '/nightlylog/matlaberror.log'], 'at'); + fprintf(fid,'%s',message); + fprintf(fid,'\n------------------------------------------------------------------\n'); + fclose(fid); + disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,'N/A')); + elseif strcmpi(output,'daily'); +- fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at'); ++ fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at'); + fprintf(fid,'%s',message); + fprintf(fid,'\n------------------------------------------------------------------\n'); + fclose(fid); Index: /issm/oecreview/Archive/12161-12180/ISSM-12163-12164.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12163-12164.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12163-12164.diff (revision 12325) @@ -0,0 +1,191 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h (revision 12163) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h (revision 12164) +@@ -61,6 +61,7 @@ + #include "./Ll2xyx/Ll2xyx.h" + #include "./Exp2Kmlx/Exp2Kmlx.h" + #include "./Kml2Expx/Kml2Expx.h" ++#include "./Krigingx/Krigingx.h" + #include "./Shp2Kmlx/Shp2Kmlx.h" + #include "./MassFluxx/MassFluxx.h" + #include "./MaxAbsVxx/MaxAbsVxx.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12164) +@@ -0,0 +1,22 @@ ++/*!\file: Kriging.cpp ++ * \brief "c" core code for Kriging ++ */ ++ ++#include "./Krigingx.h" ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++#include "../../toolkits/toolkits.h" ++#include "../../objects/objects.h" ++#include "../modules.h" ++ ++int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp){ ++ ++ /*output*/ ++ double *predictions = NULL; ++ ++ /*Allocate output*/ ++ predictions=(double*)xmalloc(n_interp*sizeof(double)); ++ ++ /*Assign output pointer*/ ++ *ppredictions=predictions; ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12164) +@@ -0,0 +1,15 @@ ++/*!\file Kriging.h ++ * \brief: header file for Kriging ++ */ ++ ++#ifndef _KRIGINGX_H ++#define _KRIGINGX_H ++ ++#include "../../objects/objects.h" ++#include "../../toolkits/toolkits.h" ++ ++ ++int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp); ++ ++#endif /* _KRIGINGX_H */ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12163) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12164) +@@ -819,6 +819,8 @@ + ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.h\ + ./modules/HoleFillerx/HoleFillerx.cpp\ + ./modules/HoleFillerx/HoleFillerx.h\ ++ ./modules/Krigingx/Krigingx.cpp\ ++ ./modules/Krigingx/Krigingx.h\ + ./modules/AverageFilterx/AverageFilterx.cpp\ + ./modules/AverageFilterx/AverageFilterx.h\ + ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.h (revision 12164) +@@ -0,0 +1,35 @@ ++/* ++ KrigingUsage.h ++*/ ++ ++#ifndef _KRIGING_H_ ++#define _KRIGING_H_ ++ ++/* local prototypes: */ ++void KrigingUsage(void); ++ ++#include "../../c/include/globals.h" ++#include "../../c/modules/modules.h" ++#include "../../c/shared/shared.h" ++#include "../../c/issm-binding.h" ++ ++#undef __FUNCT__ ++#define __FUNCT__ "Kriging" ++ ++/* serial input macros: */ ++#define X (mxArray *)prhs[0] ++#define Y (mxArray *)prhs[1] ++#define OBSERVATIONS (mxArray *)prhs[2] ++#define XINTERP (mxArray *)prhs[3] ++#define YINTERP (mxArray *)prhs[4] ++ ++/* serial output macros: */ ++#define PREDICTIONS (mxArray**)&plhs[0] ++ ++/* serial arg counts: */ ++#undef NLHS ++#define NLHS 1 ++#undef NRHS ++#define NRHS 5 ++ ++#endif /* _KRIGING_H_ */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.cpp (revision 12164) +@@ -0,0 +1,52 @@ ++/*\file Kriging.c ++ *\brief: best linear predictor ++ */ ++#include "./Kriging.h" ++ ++void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ ++ ++ /*Outputs*/ ++ double *x = NULL; ++ double *y = NULL; ++ double *observations = NULL; ++ double *x_interp = NULL; ++ double *y_interp = NULL; ++ double *predictions = NULL; ++ int n_interp,n,n_obs; ++ ++ /*Boot module: */ ++ MODULEBOOT(); ++ ++ /*checks on arguments on the matlab side: */ ++ CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&KrigingUsage); ++ ++ /*Fetch inputs: */ ++ FetchData(&x,&n_obs,X); ++ FetchData(&y,&n,Y); if(n_obs!=n) _error_("x and y should have the same size"); ++ FetchData(&observations,&n,OBSERVATIONS); if(n_obs!=n) _error_("x and observations should have the same size"); ++ FetchData(&x_interp,&n_interp,XINTERP); ++ FetchData(&y_interp,&n,YINTERP); if(n_interp!=n) _error_("x_interp and y_interp should have the same size"); ++ ++ /*Call x layer*/ ++ Krigingx(&predictions,x,y,observations,n_obs,x_interp,y_interp,n_interp); ++ ++ /*Generate output Matlab Structures*/ ++ WriteData(PREDICTIONS,predictions,n_interp); ++ ++ /*Free ressources: */ ++ xfree((void**)&x); ++ xfree((void**)&y); ++ xfree((void**)&observations); ++ xfree((void**)&x_interp); ++ xfree((void**)&y_interp); ++ xfree((void**)&predictions); ++ ++ /*end module: */ ++ MODULEEND(); ++} ++ ++void KrigingUsage(void){ ++ _printf_(true,"\n"); ++ _printf_(true," usage: predictions=%s(x,y,observations,x_interp,y_interp);\n",__FUNCT__); ++ _printf_(true,"\n"); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am (revision 12163) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/matlab/Makefile.am (revision 12164) +@@ -23,6 +23,7 @@ + KMLMeshWrite \ + KMLOverlay \ + Kml2Exp \ ++ Kriging \ + Ll2xy \ + NodeConnectivity \ + MeshPartition\ +@@ -127,6 +128,9 @@ + Kml2Exp_SOURCES = ../Kml2Exp/Kml2Exp.cpp\ + ../Kml2Exp/Kml2Exp.h + ++Kriging_SOURCES = ../Kriging/Kriging.cpp\ ++ ../Kriging/Kriging.h ++ + MeshPartition_SOURCES = ../MeshPartition/MeshPartition.cpp\ + ../MeshPartition/MeshPartition.h + Index: /issm/oecreview/Archive/12161-12180/ISSM-12164-12165.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12164-12165.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12164-12165.diff (revision 12325) @@ -0,0 +1,112 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/ImageProcessing/gradient_perso.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/ImageProcessing/gradient_perso.m (revision 12164) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/ImageProcessing/gradient_perso.m (revision 12165) +@@ -1,91 +0,0 @@ +-function [ax,ay ]=gradient_perso(a,dx,dy,n); +-%GRADIENT_PERSO - gradient computation +-% +-% INPUT a,dx,dy,n where a is the scalar value, dx and dy the spacing of one pixel +-% in a and n is the width wanted in the gradient computation, in pixels. +-% +-% Usage: +-% [ax,ay ]=gradient_perso(a,dx,dy,n) +- +-s=size(a); +-ax=zeros(s(1),s(2)); +-ay=zeros(s(1),s(2)); +- +-for k=n+1:s(1)-n, +- if mod(k,10)==0, +- disp(k/s(1)*100); +- end +- +- for j=n+1:s(2)-n, +- if isnan(a(k,j)), +- ax(k,j)=NaN; +- ay(k,j)=NaN; +- else +- temp=a(k,j); +- temp2=a(k,j); +- +- count=1; +- while ~isnan(a(k,j+count)), +- temp=[temp a(k,j+count)]; +- count=count+1; +- if count>n, +- count=count-1; +- break; +- end +- +- end +- count=1; +- while ~isnan(a(k,j-count)), +- temp=[a(k,j-count) temp]; +- count=count+1; +- if count>n, +- count=count-1; +- break; +- end +- +- end +- +- count=1; +- while ~isnan(a(k+count,j)), +- temp2=[temp2 a(k+count,j)]; +- count=count+1; +- if count>n, +- count=count-1; +- break; +- end +- +- end +- count=1; +- while ~isnan(a(k-count,j)), +- temp2=[a(k-count,j) temp2]; +- count=count+1; +- if count>n, +- count=count-1; +- break; +- end +- +- end +- +- if length(temp)==1, +- ax(k,j)=NaN; +- else +- ax(k,j)=(temp(length(temp))-temp(1))/(length(temp)-1)/dx; +- end +- +- if length(temp2)==1, +- ay(k,j)=NaN; +- else +- ay(k,j)=(temp2(length(temp2))-temp2(1))/(length(temp2)-1)/dy; +- end +- +- end +- end +-end +- +- +- +- +- +- +- +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/ImageProcessing/transp.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/ImageProcessing/transp.m (revision 12164) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/ImageProcessing/transp.m (revision 12165) +@@ -1,10 +0,0 @@ +-bg = uint8(255.*rand(100, 100, 3)); +-imview(bg); +- +-fg(:, :, 1) = uint8(255 .*(cumsum(ones(100, 100)) ./ 100));% +-fg(:, :, 2) = uint8(zeros(100)); +-fg(:, :, 3) = flipud(fg(:, :, 1)); +-imview(fg); +- +-res=immerge(bg, fg, .3); +-imview(res); +\ No newline at end of file Index: /issm/oecreview/Archive/12161-12180/ISSM-12165-12166.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12165-12166.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12165-12166.diff (revision 12325) @@ -0,0 +1,26 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m (revision 12165) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plot_gridded.m (revision 12166) +@@ -39,6 +39,7 @@ + data_min=min(data_grid(:)); + data_max=max(data_grid(:)); + end ++options=changefieldvalue(options,'cbYLim',[data_min data_max]); + if whitepos==1, + white =data_max + (data_max-data_min)/55; + options=changefieldvalue(options,'caxis',[data_min white]); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m (revision 12165) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m (revision 12166) +@@ -218,6 +218,9 @@ + end + warning on MATLAB:log:logOfZero; + set(c,'YTickLabel',labels); ++ end ++ if exist(options,'cbYLim'); ++ set(c,'YLim',getfieldvalue(options,'cbYLim')); + end + if exist(options,'colorbartitle'), + set(get(c,'title'),'FontSize',getfieldvalue(options,'colorbarfontsize',fontsize),'String',getfieldvalue(options,'colorbartitle'),... Index: /issm/oecreview/Archive/12161-12180/ISSM-12168-12169.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12168-12169.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12168-12169.diff (revision 12325) @@ -0,0 +1,42 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/radarpower.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/radarpower.m (revision 12168) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/radarpower.m (revision 12169) +@@ -33,11 +33,11 @@ + %figure out if we should go look for Greenland or Antarctica geotiff, or if user provided one. + if ~exist(options,'overlay_image'), + if strcmpi(md.mesh.hemisphere,'n'), +- if ~exist([issmdir() '/projects/ModelData/MOG/mog150_greenland_map.jpg']), +- error(['radarpower error message: file ' issmdir() '/projects/ModelData/MOG/mog150_greenland_map.jpg not found.']); ++ if ~exist([jplsvn() '/projects/ModelData/MOG/mog150_greenland_map.jpg']), ++ error(['radarpower error message: file ' jplsvn() '/projects/ModelData/MOG/mog150_greenland_map.jpg not found.']); + end +- jpgim=[issmdir() '/projects/ModelData/MOG/mog150_greenland_map.jpg']; +- geom=load([issmdir() '/projects/ModelData/MOG/mog150_greenland_map.jpgw'],'ascii'); ++ jpgim=[jplsvn() '/projects/ModelData/MOG/mog150_greenland_map.jpg']; ++ geom=load([jplsvn() '/projects/ModelData/MOG/mog150_greenland_map.jpgw'],'ascii'); + + %geom: xposting nbcols nbrows yposting xmin ymax + xmin=max(geom(5),x0); +@@ -61,15 +61,15 @@ + + elseif strcmpi(md.mesh.hemisphere,'s'), + if highres, +- if ~exist([issmdir() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']), +- error(['radarpower error message: file ' issmdir() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif not found.']); ++ if ~exist([jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']), ++ error(['radarpower error message: file ' jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif not found.']); + end +- geotiff_name=[issmdir() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']; ++ geotiff_name=[jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']; + else +- if ~exist([issmdir() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif']), +- error(['radarpower error message: file ' issmdir() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif not found.']); ++ if ~exist([jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif']), ++ error(['radarpower error message: file ' jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif not found.']); + end +- geotiff_name=[issmdir() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif']; ++ geotiff_name=[jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif']; + end + + %Name of image Index: /issm/oecreview/Archive/12161-12180/ISSM-12169-12170.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12169-12170.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12169-12170.diff (revision 12325) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/collapse.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/collapse.m (revision 12169) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/collapse.m (revision 12170) +@@ -100,8 +100,8 @@ + md.mask.vertexonwater=project2d(md,md.mask.vertexonwater,1); + + %lat long +-if numel(md.mesh.lat)>1, md.mesh.lat=project2d(md,md.mesh.lat,1); end +-if numel(md.mesh.long)>1, md.mesh.long=project2d(md,md.mesh.long,1); end ++if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end ++if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end + + %Initialize with the 2d mesh + md.mesh.x=md.mesh.x2d; Index: /issm/oecreview/Archive/12161-12180/ISSM-12170-12171.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12170-12171.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12170-12171.diff (revision 12325) @@ -0,0 +1,18 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12170) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12171) +@@ -1,12 +1,8 @@ + #!/bin/sh + +-pythonversion=2.7 +- + ./configure \ + --prefix=$ISSM_DIR \ +- --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --without-modules \ + --with-vendor=arm-linux \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install Index: /issm/oecreview/Archive/12161-12180/ISSM-12171-12172.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12171-12172.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12171-12172.diff (revision 12325) @@ -0,0 +1,48 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12171) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12172) +@@ -65,10 +65,12 @@ + export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ " + export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ " + elif test $VENDOR = arm-linux; then +- export CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-cc +- export CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-cc +- +- else ++ export CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc ++ export GCC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc ++ export CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-g++ ++ export AR=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ar ++ export RANLIB=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib ++ else + AC_MSG_ERROR([unknow compiler vendor!]) + fi + fi +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh (revision 12171) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh (revision 12172) +@@ -1,8 +1,8 @@ + #!/bin/bash + #wget http://python.org/ftp/python/version/Python-version.tgz + +-version=3.2.2 +-#version=2.7.2 ++#version=3.2.2 ++version=2.7.2 + + #Some cleanup + rm -rf install src +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12171) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12172) +@@ -2,6 +2,7 @@ + + ./configure \ + --prefix=$ISSM_DIR \ ++ --host="arm-linux" \ + --without-modules \ + --with-vendor=arm-linux \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: /issm/oecreview/Archive/12161-12180/ISSM-12172-12173.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12172-12173.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12172-12173.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/partition/AreaAverageOntoPartition.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/partition/AreaAverageOntoPartition.m (revision 12172) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/partition/AreaAverageOntoPartition.m (revision 12173) +@@ -28,7 +28,7 @@ + + %finally, project vector: + vector=project2d(md3d,vector,layer); +- md.qmu.partition=project2d(md3d,md3d.part,layer); ++ md.qmu.partition=project2d(md3d,md3d.qmu.partition,layer); + end + + %ok, first check that part is Matlab indexed Index: /issm/oecreview/Archive/12161-12180/ISSM-12173-12174.diff =================================================================== --- /issm/oecreview/Archive/12161-12180/ISSM-12173-12174.diff (revision 12325) +++ /issm/oecreview/Archive/12161-12180/ISSM-12173-12174.diff (revision 12325) @@ -0,0 +1,156 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12173) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12174) +@@ -14,9 +14,133 @@ + /*output*/ + double *predictions = NULL; + +- /*Allocate output*/ +- predictions=(double*)xmalloc(n_interp*sizeof(double)); ++ /*Intermediaries*/ ++ int i,j; ++ double numerator,denominator,ratio; ++ double *Gamma = NULL; ++ double *GinvG0 = NULL; ++ double *Ginv1 = NULL; ++ double *GinvZ = NULL; ++ double *gamma0 = NULL; ++ double *ones = NULL; + +- /*Assign output pointer*/ ++ /*Memory allocation*/ ++ predictions =(double*)xmalloc(n_interp*sizeof(double)); ++ Gamma =(double*)xmalloc(n_obs*n_obs*sizeof(double)); ++ gamma0 =(double*)xmalloc(n_obs*sizeof(double)); ++ ones =(double*)xmalloc(n_obs*sizeof(double)); ++ ++ /*First: Create semivariogram matrix for observations*/ ++ for(i=0;i + +-int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp){ ++int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options){ + + /*output*/ + double *predictions = NULL; +@@ -48,9 +49,9 @@ + for(i=0;i6 +- error('plotmodel error message: to many input arguments for northarrow: [x0 y0 length [ratio [width]]]'); ++ error('plotmodel error message: to many input arguments for northarrow: [x0 y0 length [ratio width fontsize]]'); + end + + %retrieve north arrow parameters +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plotdoc.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plotdoc.m (revision 12192) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/plotdoc.m (revision 12193) +@@ -129,7 +129,7 @@ + disp(' ''latlonnumbering'': ''on'' or {latgap longap colornumber latangle lonangle} where latgap and longap are pixel gaps for the numbers,'); + disp(' ''latlonclick'': ''on'' to click on latlon ticks positions'); + disp(' colornumber is a [r g b] array and latangle and lonangle are angles to flip the numbers'); +-disp(' ''northarrow'': add an arrow pointing north, ''on'' for default value or [x0 y0 length [ratio [width]]] where (x0,y0) are the coordinates of the base, and ratio=headlength/length'); ++disp(' ''northarrow'': add an arrow pointing north, ''on'' for default value or [x0 y0 length [ratio width fontsize]] where (x0,y0) are the coordinates of the base, ratio=headlength/length'); + disp(' ''offset'': mesh offset used by ''rifts'', default is 500'); + disp(' ''scaleruler'': add a scale ruler, ''on'' for default value or [x0 y0 length width numberofticks] where (x0,y0) are the coordinates of the lower left corner'); + disp(' ''showregion'': show domain in Antarctica on an inset, use ''insetpos'' properties'); Index: /issm/oecreview/Archive/12181-12200/ISSM-12195-12196.diff =================================================================== --- /issm/oecreview/Archive/12181-12200/ISSM-12195-12196.diff (revision 12325) +++ /issm/oecreview/Archive/12181-12200/ISSM-12195-12196.diff (revision 12325) @@ -0,0 +1,216 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 12195) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 12196) +@@ -64,7 +64,6 @@ + #}}} + #Export ISSM_* variables{{{1 + export ISSM_DIR +-export ISSM_TIER + export ISSM_ARCH + #}}} + #Initialize variables {{{1 +@@ -89,7 +88,7 @@ + then + + #only update ISSM +- cd $ISSM_TIER ++ cd $ISSM_DIR + svn update + + elif [ "$ISSM_INSTALLATION" == "none" ] +@@ -108,20 +107,20 @@ + #}}} + #Create cluster's settings{{{1 + #create simpler cluster.rc file, with only the cluster we are interested in. +-cd $ISSM_TIER/test/NightlyRun/ ++cd $ISSM_DIR/test/NightlyRun/ + if [ "$MACHINE" = "win7" ]; then + cat << END > $HOST_NAME"_settings.m" + cluster.login='$USER'; +-cluster.codepath='`cygpath -m $ISSM_TIER/bin`'; ++cluster.codepath='`cygpath -m $ISSM_DIR/bin`'; + cluster.executionpath='`cygpath -m $EXECUTION_PATH`'; + END + else + cat << END > $HOST_NAME"_settings.m" + cluster.login='$USER'; +-cluster.codepath='$ISSM_TIER/bin'; ++cluster.codepath='$ISSM_DIR/bin'; + cluster.executionpath='$EXECUTION_PATH'; + END +- cat << END > $ISSM_TIER/externalpackages/matlab/install.sh ++ cat << END > $ISSM_DIR/externalpackages/matlab/install.sh + #!/bin/bash + rm -rf install + ln -s $MATLAB_PATH install +@@ -130,14 +129,14 @@ + fi + #}}} + #Source environment variables with new matlab path {{{1 +-cd $ISSM_TIER/etc ++cd $ISSM_DIR/etc + source environment.sh MATLAB_DIR=$MATLAB_PATH + #}}} + #install/copy/none external packages (ISSM_EXTERNALPACKAGES){{{1 + if [ "$ISSM_EXTERNALPACKAGES" == "install" ] + then + +- cd $ISSM_TIER/externalpackages ++ cd $ISSM_DIR/externalpackages + #number of packages: + numpackages=`echo $EXTERNALPACKAGES | wc -w` + +@@ -155,7 +154,7 @@ + then + + #erase externapackages, and link with externalpackages_dir +- cd $ISSM_TIER ++ cd $ISSM_DIR + rm -rf externalpackages + cp -Rf $EXTERNALPACKAGESDIR ./ + +@@ -163,7 +162,7 @@ + then + + #erase externapackages, and link with externalpackages_dir +- cd $ISSM_TIER ++ cd $ISSM_DIR + rm -rf externalpackages + ln -s $EXTERNALPACKAGESDIR . + +@@ -185,7 +184,7 @@ + if [ "$ISSM_COMPILATION" == "yes" ] + then + +- cd $ISSM_TIER ++ cd $ISSM_DIR + make clean + make distclean + ./scripts/automakererun.sh +@@ -213,17 +212,17 @@ + + #Prepare run + #create softlink to startup {{{1 +-cd $ISSM_TIER/test/NightlyRun/ ++cd $ISSM_DIR/test/NightlyRun/ + rm startup.m #in case it alreade exists +-cp $ISSM_TIER/startup.m . ++cp $ISSM_DIR/startup.m . + #}}} + #Create nightlylog directory and info.log {{{1 + #put installation elapsed time in info.log + INSTALL_TIME=$(timer) + ELAPSED_INSTALL=$(timer $START_TIME) +-rm -rf $ISSM_TIER/nightlylog +-mkdir $ISSM_TIER/nightlylog +-cat << END > $ISSM_TIER/nightlylog/info.log ++rm -rf $ISSM_DIR/nightlylog ++mkdir $ISSM_DIR/nightlylog ++cat << END > $ISSM_DIR/nightlylog/info.log + today: $(echo $TODAY) + user: $(echo $USER) + host: $(echo $HOST_NAME) +@@ -244,16 +243,16 @@ + #Run tests + #on Matlab and windows machines, we'll need a windows style path: {{{ + if [ "$MACHINE" = "win7" ]; then +- MATLAB_TIER=`cygpath -m $ISSM_TIER` ++ MATLAB_TIER=`cygpath -m $ISSM_DIR` + else +- MATLAB_TIER=$ISSM_TIER ++ MATLAB_TIER=$ISSM_DIR + fi + #}}} + #Launch all tests on different cpus {{{1 + for (( i=1;i<=$NUMCPUS_RUN;i++ )) + do + #Launch matlab and the nightly run script +- cat > $ISSM_TIER/nightlylog/matlab_run$i.m << EOF ++ cat > $ISSM_DIR/nightlylog/matlab_run$i.m << EOF + warning off %necessary to avoid a info.log of several Go for parallel runs + try, + cd $MATLAB_TIER/test/NightlyRun +@@ -262,7 +261,6 @@ + then + echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" + else +- #echo "runme('id',[101 102]);" + echo "runme($NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" + fi + ) +@@ -270,7 +268,7 @@ + %An error occured, get report and exit + message=getReport(me) + directory=strsplit(pwd,'/'); +- fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); ++ fid=fopen([issmdir '/nightlylog/matlaberror.log'], 'at'); + fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); + fprintf(fid,'%s',message); + fclose(fid); +@@ -280,7 +278,7 @@ + EOF + + #Start run from nightlylog directory +- cd $ISSM_TIER/nightlylog/ ++ cd $ISSM_DIR/nightlylog/ + + MATLABBIN=$MATLAB_PATH/bin/matlab + #Start test +@@ -297,7 +295,7 @@ + + #}}} + #concatenate all reports {{{1 +-cd $ISSM_TIER/nightlylog/ ++cd $ISSM_DIR/nightlylog/ + cp matlab_log1.log matlab_log.log + for (( i=2;i<=$NUMCPUS_RUN;i++ )) + do +@@ -314,7 +312,7 @@ + fi + ELAPSED_RUN=$(timer $INSTALL_TIME) + ELAPSED_TOTAL=$(timer $START_TIME) +-cat << END >> $ISSM_TIER/nightlylog/info.log ++cat << END >> $ISSM_DIR/nightlylog/info.log + elapsed_run: $(echo $ELAPSED_RUN) + elapsed_total: $(echo $ELAPSED_TOTAL) + matlab_crash: $(echo $MATLABCRASH) +@@ -323,24 +321,24 @@ + + #Send Report + #Build html report {{{1 +-cd $ISSM_TIER/nightlylog/ ++cd $ISSM_DIR/nightlylog/ + sh ../scripts/report.sh +-echo "html report located in $ISSM_TIER/nightlylog/report.html" ++echo "html report located in $ISSM_DIR/nightlylog/report.html" + #}}} + #send mail if requested (SKIPMAIL) {{{1 + if [ "$SKIPMAIL" != "yes" ] + then + echo "sending report..." +- source $ISSM_TIER/cron/mailinglist ++ source $ISSM_DIR/cron/mailinglist + for i in `echo $MAILINGLIST`; do + + if [ "$MACHINE" = "win7" ] + then +- email -html -s "Nightly runs on $HOST_NAME (version: $ISSM_RELEASE)" -n "ISSM Nightly run" -f echo $EMAIL_ADRESS $i < $ISSM_TIER/nightlylog/report.html ++ email -html -s "Nightly runs on $HOST_NAME (version: $ISSM_RELEASE)" -n "ISSM Nightly run" -f echo $EMAIL_ADRESS $i < $ISSM_DIR/nightlylog/report.html + else + if [ "$MACHINE" = "astrid" ] + then +-cat - $ISSM_TIER/nightlylog/report.html < + To: $i + Subject: Nightly runs on $HOST_NAME (version: $ISSM_RELEASE) +@@ -348,7 +346,7 @@ + Content-Type: text/html + HERE + else +-cat - $ISSM_TIER/nightlylog/report.html < + To: $i + Subject: Nightly runs on $HOST_NAME (version: $ISSM_RELEASE) Index: /issm/oecreview/Archive/12181-12200/ISSM-12199-12200.diff =================================================================== --- /issm/oecreview/Archive/12181-12200/ISSM-12199-12200.diff (revision 12325) +++ /issm/oecreview/Archive/12181-12200/ISSM-12199-12200.diff (revision 12325) @@ -0,0 +1,573 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12199) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12200) +@@ -10,20 +10,23 @@ + #include "../modules.h" + #include + ++#include "../../objects/Kriging/GaussianVariogram.h" + int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options){ + + /*output*/ + double *predictions = NULL; + + /*Intermediaries*/ +- int i,j; +- double numerator,denominator,ratio; +- double *Gamma = NULL; +- double *GinvG0 = NULL; +- double *Ginv1 = NULL; +- double *GinvZ = NULL; +- double *gamma0 = NULL; +- double *ones = NULL; ++ int i,j; ++ double numerator,denominator,ratio; ++ char *model = NULL; ++ double *Gamma = NULL; ++ double *GinvG0 = NULL; ++ double *Ginv1 = NULL; ++ double *GinvZ = NULL; ++ double *gamma0 = NULL; ++ double *ones = NULL; ++ Variogram *variogram = NULL; + + /*Memory allocation*/ + predictions =(double*)xmalloc(n_interp*sizeof(double)); +@@ -31,10 +34,21 @@ + gamma0 =(double*)xmalloc(n_obs*sizeof(double)); + ones =(double*)xmalloc(n_obs*sizeof(double)); + ++ /*Create Semi-Variogram object*/ ++ if(options->GetOption("model")){ ++ options->Get(&model,"model"); ++ if (strcmp(model,"gaussian")==0) variogram = new GaussianVariogram(options); ++ else if(strcmp(model,"exponential")==0) variogram = new ExponentialVariogram(options); ++ else if(strcmp(model,"spherical")==0) variogram = new SphericalVariogram(options); ++ else _error_("only gaussian semivariogram models supported yet"); ++ } ++ else variogram = new GaussianVariogram(options); ++ variogram->Echo(); ++ + /*First: Create semivariogram matrix for observations*/ + for(i=0;iSemiVariogram(x[i]-x[j],y[i]-y[j]); + Gamma[j*n_obs+i] = Gamma[i*n_obs+j]; + } + } +@@ -46,7 +60,7 @@ + if(idx%100==0) printf("\b\b\b\b\b\b\b%5.2lf %%",(double)idx/n_interp*100); + + /*Get semivariogram vector associated to this location*/ +- for(i=0;iSemiVariogram(x[i]-x_interp[idx],y[i]-y_interp[idx]); + + /*Solve the three linear systems*/ + GslSolve(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0 +@@ -70,39 +84,14 @@ + printf("\b\b\b\b\b\b\b\b%5.2lf %%\n",100.0); + + /*clean-up and Assign output pointer*/ ++ delete variogram; + xfree((void**)&Gamma); + xfree((void**)&gamma0); + xfree((void**)&ones); ++ xfree((void**)&model); + *ppredictions=predictions; + } + +-void SemiVariogram(double* gamma,double x1,double y1,double x2,double y2){ +- +- /*Intermediaries*/ +- double a,c0,c1; +- +- /*Calculate distance*/ +- double r=sqrt(pow(x1-x2,2.)+pow(y1-y2,2.)); +- +- /*Switch between variogram models*/ +- switch(2){ +- case 1:/*Exponential*/ +- c0=0.2; +- c1=0.8; +- a =1; +- *gamma = c0 + c1*(1-exp(-r/a)); +- return; +- case 2:/*Gaussian*/ +- c0=0.2; +- c1=0.8; +- a =1; +- *gamma = c0 + c1*(1-exp(-pow(r,2.)/pow(a,2.))); +- return; +- default: +- _error_("Not implemented yet"); +- } +-} +- + void GslSolve(double** pX,double* A,double* B,int n){ + #ifdef _HAVE_GSL_ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12199) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12200) +@@ -9,7 +9,6 @@ + #include "../../toolkits/toolkits.h" + + int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options); +-void SemiVariogram(double* gamma,double x1,double y1,double x2,double y2); + void GslSolve(double** pX,double* A,double* B,int n); + + #endif /* _KRIGINGX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12199) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12200) +@@ -608,6 +608,18 @@ + ./modules/BamgTriangulatex/BamgTriangulatex.cpp\ + ./modules/BamgTriangulatex/BamgTriangulatex.h + #}}} ++#Kriging sources {{{1 ++kriging_sources = ./objects/Kriging/Variogram.h \ ++ ./objects/Kriging/GaussianVariogram.h\ ++ ./objects/Kriging/GaussianVariogram.cpp\ ++ ./objects/Kriging/ExponentialVariogram.h\ ++ ./objects/Kriging/ExponentialVariogram.cpp\ ++ ./objects/Kriging/SphericalVariogram.h\ ++ ./objects/Kriging/SphericalVariogram.cpp\ ++ ./modules/Krigingx/Krigingx.cpp\ ++ ./modules/Krigingx/Krigingx.h ++ ++#}}} + #Kml sources {{{1 + kml_sources = ./modules/Exp2Kmlx/Exp2Kmlx.h\ + ./modules/Exp2Kmlx/Exp2Kmlx.cpp\ +@@ -819,8 +831,6 @@ + ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.h\ + ./modules/HoleFillerx/HoleFillerx.cpp\ + ./modules/HoleFillerx/HoleFillerx.h\ +- ./modules/Krigingx/Krigingx.cpp\ +- ./modules/Krigingx/Krigingx.h\ + ./modules/AverageFilterx/AverageFilterx.cpp\ + ./modules/AverageFilterx/AverageFilterx.h\ + ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp\ +@@ -945,6 +955,7 @@ + if MODULES + libISSMModules_a_SOURCES = $(module_sources) + libISSMModules_a_SOURCES += $(bamg_sources) ++libISSMModules_a_SOURCES += $(kriging_sources) + libISSMModules_a_SOURCES += $(kml_sources) + libISSMModules_a_CXXFLAGS = $(ALLCXXFLAGS) + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 12199) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 12200) +@@ -172,4 +172,10 @@ + #include "./Bamg/QuadTree.h" + #include "./Bamg/SetOfE4.h" + ++/*Kriging*/ ++#include "./Kriging/Variogram.h" ++#include "./Kriging/GaussianVariogram.h" ++#include "./Kriging/ExponentialVariogram.h" ++#include "./Kriging/SphericalVariogram.h" ++ + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp (revision 12200) +@@ -0,0 +1,74 @@ ++/*!\file ExponentialVariogram.c ++ * \brief: implementation of the ExponentialVariogram object ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++ ++/*ExponentialVariogram constructors and destructor*/ ++/*FUNCTION ExponentialVariogram::ExponentialVariogram(){{{1*/ ++ExponentialVariogram::ExponentialVariogram(){ ++ this->nugget = 0.2; ++ this->sill = 1; ++ this->range = SQRT3; ++ return; ++} ++/*}}}*/ ++/*FUNCTION ExponentialVariogram::ExponentialVariogram(Options* options){{{1*/ ++ExponentialVariogram::ExponentialVariogram(Options* options){ ++ ++ /*Defaults*/ ++ this->nugget = 0.2; ++ this->sill = 1; ++ this->range = SQRT3; ++ ++ /*Overwrite from options*/ ++ if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); ++ if(options->GetOption("sill")) options->Get(&this->sill,"sill"); ++ if(options->GetOption("range")) options->Get(&this->range,"range"); ++ ++ /*Checks*/ ++ if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); ++} ++/*}}}*/ ++/*FUNCTION ExponentialVariogram::~ExponentialVariogram(){{{1*/ ++ExponentialVariogram::~ExponentialVariogram(){ ++ return; ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION ExponentialVariogram::Echo {{{1*/ ++void ExponentialVariogram::Echo(void){ ++ printf("ExponentialVariogram\n"); ++ printf(" nugget: %g\n",this->nugget); ++ printf(" sill : %g\n",this->sill); ++ printf(" range : %g\n",this->range); ++} ++/*}}}*/ ++ ++/*Variogram function*/ ++/*FUNCTION ExponentialVariogram::SemiVariogram{{{1*/ ++double ExponentialVariogram::SemiVariogram(double deltax,double deltay){ ++ /*http://en.wikipedia.org/wiki/Variogram*/ ++ double h,a,gamma; ++ ++ /*Calculate length*/ ++ h=sqrt(pow(deltax,2.)+pow(deltay,2.)); ++ ++ /*return semi-variogram*/ ++ a = 1./3.; ++ gamma = (sill-nugget)*(1-exp(-h/(a*range))) + nugget; ++ return gamma; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12200) +@@ -0,0 +1,74 @@ ++/*!\file GaussianVariogram.c ++ * \brief: implementation of the GaussianVariogram object ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++ ++/*GaussianVariogram constructors and destructor*/ ++/*FUNCTION GaussianVariogram::GaussianVariogram(){{{1*/ ++GaussianVariogram::GaussianVariogram(){ ++ this->nugget = 0.2; ++ this->sill = 1; ++ this->range = SQRT3; ++ return; ++} ++/*}}}*/ ++/*FUNCTION GaussianVariogram::GaussianVariogram(Options* options){{{1*/ ++GaussianVariogram::GaussianVariogram(Options* options){ ++ ++ /*Defaults*/ ++ this->nugget = 0.2; ++ this->sill = 1; ++ this->range = SQRT3; ++ ++ /*Overwrite from options*/ ++ if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); ++ if(options->GetOption("sill")) options->Get(&this->sill,"sill"); ++ if(options->GetOption("range")) options->Get(&this->range,"range"); ++ ++ /*Checks*/ ++ if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); ++} ++/*}}}*/ ++/*FUNCTION GaussianVariogram::~GaussianVariogram(){{{1*/ ++GaussianVariogram::~GaussianVariogram(){ ++ return; ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION GaussianVariogram::Echo {{{1*/ ++void GaussianVariogram::Echo(void){ ++ printf("GaussianVariogram\n"); ++ printf(" nugget: %g\n",this->nugget); ++ printf(" sill : %g\n",this->sill); ++ printf(" range : %g\n",this->range); ++} ++/*}}}*/ ++ ++/*Variogram function*/ ++/*FUNCTION GaussianVariogram::SemiVariogram{{{1*/ ++double GaussianVariogram::SemiVariogram(double deltax,double deltay){ ++ /*http://en.wikipedia.org/wiki/Variogram*/ ++ double h2,a,gamma; ++ ++ /*Calculate length square*/ ++ h2=pow(deltax,2.)+pow(deltay,2.); ++ ++ /*return semi-variogram*/ ++ a = 1./3.; ++ gamma = (sill-nugget)*(1-exp(-h2/(a*pow(range,2.)))) + nugget; ++ return gamma; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp (revision 12200) +@@ -0,0 +1,77 @@ ++/*!\file SphericalVariogram.c ++ * \brief: implementation of the SphericalVariogram object ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++ ++/*SphericalVariogram constructors and destructor*/ ++/*FUNCTION SphericalVariogram::SphericalVariogram(){{{1*/ ++SphericalVariogram::SphericalVariogram(){ ++ this->nugget = 0.2; ++ this->sill = 1; ++ this->range = SQRT3; ++ return; ++} ++/*}}}*/ ++/*FUNCTION SphericalVariogram::SphericalVariogram(Options* options){{{1*/ ++SphericalVariogram::SphericalVariogram(Options* options){ ++ ++ /*Defaults*/ ++ this->nugget = 0.2; ++ this->sill = 1; ++ this->range = SQRT3; ++ ++ /*Overwrite from options*/ ++ if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); ++ if(options->GetOption("sill")) options->Get(&this->sill,"sill"); ++ if(options->GetOption("range")) options->Get(&this->range,"range"); ++ ++ /*Checks*/ ++ if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); ++} ++/*}}}*/ ++/*FUNCTION SphericalVariogram::~SphericalVariogram(){{{1*/ ++SphericalVariogram::~SphericalVariogram(){ ++ return; ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION SphericalVariogram::Echo {{{1*/ ++void SphericalVariogram::Echo(void){ ++ printf("SphericalVariogram\n"); ++ printf(" nugget: %g\n",this->nugget); ++ printf(" sill : %g\n",this->sill); ++ printf(" range : %g\n",this->range); ++} ++/*}}}*/ ++ ++/*Variogram function*/ ++/*FUNCTION SphericalVariogram::SemiVariogram{{{1*/ ++double SphericalVariogram::SemiVariogram(double deltax,double deltay){ ++ /*http://en.wikipedia.org/wiki/Variogram*/ ++ double h,gamma; ++ ++ /*Calculate length square*/ ++ h=sqrt(pow(deltax,2.)+pow(deltay,2.)); ++ ++ /*return semi-variogram*/ ++ if(h<=range) ++ gamma = (sill-nugget)*( (3*h)/(2*range) - pow(h,3.)/(2*pow(range,3.)) ) + nugget; ++ else ++ gamma = sill; ++ ++ return gamma; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h (revision 12200) +@@ -0,0 +1,34 @@ ++/*! \file ExponentialVariogram.h ++ * \brief: header file for triavertexinput object ++ */ ++ ++#ifndef _EXPONENTIALVARIOGRAM_H_ ++#define _EXPONENTIALVARIOGRAM_H_ ++ ++/*Headers:*/ ++#include "./Variogram.h" ++ ++class ExponentialVariogram: public Variogram{ ++ ++ public: ++ double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin ++ double sill; //Limit of the variogram tending to infinity lag distances ++ double range; //The distance in which the difference of the variogram from the sill becomes negligible ++ ++ /*ExponentialVariogram constructors, destructors*/ ++ ExponentialVariogram(); ++ ExponentialVariogram(Options* options); ++ ~ExponentialVariogram(); ++ ++ /*Object virtual functions definitions*/ ++ void Echo(); ++ void DeepEcho(){_error_("Not implemented yet");}; ++ int Id(){_error_("Not implemented yet");}; ++ int MyRank(){_error_("Not implemented yet");}; ++ int ObjectEnum(){_error_("Not implemented yet");}; ++ Object* copy(){_error_("Not implemented yet");}; ++ ++ /*Variogram functions*/ ++ double SemiVariogram(double deltax,double deltay); ++}; ++#endif /* _EXPONENTIALVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h (revision 12200) +@@ -0,0 +1,34 @@ ++/*! \file GaussianVariogram.h ++ * \brief: header file for triavertexinput object ++ */ ++ ++#ifndef _GAUSSIANVARIOGRAM_H_ ++#define _GAUSSIANVARIOGRAM_H_ ++ ++/*Headers:*/ ++#include "./Variogram.h" ++ ++class GaussianVariogram: public Variogram{ ++ ++ public: ++ double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin ++ double sill; //Limit of the variogram tending to infinity lag distances ++ double range; //The distance in which the difference of the variogram from the sill becomes negligible ++ ++ /*GaussianVariogram constructors, destructors*/ ++ GaussianVariogram(); ++ GaussianVariogram(Options* options); ++ ~GaussianVariogram(); ++ ++ /*Object virtual functions definitions*/ ++ void Echo(); ++ void DeepEcho(){_error_("Not implemented yet");}; ++ int Id(){_error_("Not implemented yet");}; ++ int MyRank(){_error_("Not implemented yet");}; ++ int ObjectEnum(){_error_("Not implemented yet");}; ++ Object* copy(){_error_("Not implemented yet");}; ++ ++ /*Variogram functions*/ ++ double SemiVariogram(double deltax,double deltay); ++}; ++#endif /* _GAUSSIANVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h (revision 12200) +@@ -0,0 +1,34 @@ ++/*! \file SphericalVariogram.h ++ * \brief: header file for triavertexinput object ++ */ ++ ++#ifndef _SPHERICALVARIOGRAM_H_ ++#define _SPHERICALVARIOGRAM_H_ ++ ++/*Headers:*/ ++#include "./Variogram.h" ++ ++class SphericalVariogram: public Variogram{ ++ ++ public: ++ double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin ++ double sill; //Limit of the variogram tending to infinity lag distances ++ double range; //The distance in which the difference of the variogram from the sill becomes negligible ++ ++ /*SphericalVariogram constructors, destructors*/ ++ SphericalVariogram(); ++ SphericalVariogram(Options* options); ++ ~SphericalVariogram(); ++ ++ /*Object virtual functions definitions*/ ++ void Echo(); ++ void DeepEcho(){_error_("Not implemented yet");}; ++ int Id(){_error_("Not implemented yet");}; ++ int MyRank(){_error_("Not implemented yet");}; ++ int ObjectEnum(){_error_("Not implemented yet");}; ++ Object* copy(){_error_("Not implemented yet");}; ++ ++ /*Variogram functions*/ ++ double SemiVariogram(double deltax,double deltay); ++}; ++#endif /* _SPHERICALVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h (revision 12200) +@@ -0,0 +1,18 @@ ++/*!\file: Variogram.h ++ * \brief abstract class for Variogram object ++ */ ++ ++ ++#ifndef _VARIOGRAM_H_ ++#define _VARIOGRAM_H_ ++ ++#include "../Object.h" ++ ++class Variogram: public Object{ ++ ++ public: ++ virtual ~Variogram(){}; ++ virtual double SemiVariogram(double deltax,double deltay)=0; ++ ++}; ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/Constraint.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/Constraint.h (revision 12199) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Constraints/Constraint.h (revision 12200) +@@ -10,10 +10,8 @@ + + /*Headers:*/ + /*{{{1*/ +-#include "../Object.h" +- + class Nodes; +- ++#include "../Object.h" + #include "../../toolkits/toolkits.h" + /*}}}*/ + Index: /issm/oecreview/Archive/12181-12200/ISSM-DocReview-12181-12200.tex =================================================================== --- /issm/oecreview/Archive/12181-12200/ISSM-DocReview-12181-12200.tex (revision 12325) +++ /issm/oecreview/Archive/12181-12200/ISSM-DocReview-12181-12200.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12181-12200/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12181-12200/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12181-12200/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12181-12200 Index: /issm/oecreview/Archive/12181-12200/Makefile =================================================================== --- /issm/oecreview/Archive/12181-12200/Makefile (revision 12325) +++ /issm/oecreview/Archive/12181-12200/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12181-12200 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12181-12200/log.tex =================================================================== --- /issm/oecreview/Archive/12181-12200/log.tex (revision 12325) +++ /issm/oecreview/Archive/12181-12200/log.tex (revision 12325) @@ -0,0 +1,28 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12181-12182.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h \\ Export determination: 6. \\Rationale: Enable GSL and PETSc simultaneously +M /issm/trunk-jpl/configs/config-linux64-astrid.sh Added gsl \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12182-12183.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-linux64-astrid.sh \\ Export determination: 6. \\Rationale: Added gsl +M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.h added options and GSL support \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12183-12184.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.h \\ Export determination: 6. \\Rationale: added options and GSL support +M /issm/trunk-jpl/src/modules/Kriging/Kriging.cpp Added options \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12184-12185.diff: \\ Function name: \\M /issm/trunk-jpl/src/modules/Kriging/Kriging.cpp \\ Export determination: 6. \\Rationale: Added options +M /issm/trunk-jpl/etc/environment.sh Added GSL to LD\_LIBRARY\_PATH \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12185-12186.diff: \\ Function name: \\M /issm/trunk-jpl/etc/environment.sh \\ Export determination: 6. \\Rationale: Added GSL to LD\_LIBRARY\_PATH +M /issm/trunk-jpl/scripts/DownloadExternalPackage.py Do not delete file if it already exists \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12186-12187.diff: \\ Function name: \\M /issm/trunk-jpl/scripts/DownloadExternalPackage.py \\ Export determination: 6. \\Rationale: Do not delete file if it already exists +M /issm/trunk-jpl/scripts/DownloadExternalPackage.py minor \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12187-12188.diff: \\ Function name: \\M /issm/trunk-jpl/scripts/DownloadExternalPackage.py \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/scripts/DownloadExternalPackage.py minor \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12188-12189.diff: \\ Function name: \\M /issm/trunk-jpl/scripts/DownloadExternalPackage.py \\ Export determination: 6. \\Rationale: minor +D /issm/trunk-jpl/externalpackages/adolc/ADOL-C-2.2.0.tar.gz M /issm/trunk-jpl/externalpackages/adolc/install.sh D /issm/trunk-jpl/externalpackages/android/android-ndk/android-ndk-r7b-darwin-x86.tar.bz2 M /issm/trunk-jpl/externalpackages/android/android-ndk/install.sh D /issm/trunk-jpl/externalpackages/android/android-sdk/android-sdk-r16-macosx.zip D /issm/trunk-jpl/externalpackages/android/android-sdk/apache-ant-1.8.2-bin.zip M 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/issm/trunk-jpl/externalpackages/triangle/install-macosx64.sh M /issm/trunk-jpl/externalpackages/triangle/install-pleiades.sh M /issm/trunk-jpl/externalpackages/triangle/install-win32.sh M /issm/trunk-jpl/externalpackages/triangle/install-win7.sh D /issm/trunk-jpl/externalpackages/triangle/triangle.zip M /issm/trunk-jpl/externalpackages/valgrind/install-altix64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-linux64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-macosx32.sh M /issm/trunk-jpl/externalpackages/valgrind/install-macosx64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-win32.sh D /issm/trunk-jpl/externalpackages/valgrind/valgrind-3.7.0.tar.bz2 M /issm/trunk-jpl/externalpackages/vim/install.sh D /issm/trunk-jpl/externalpackages/vim/vim-7.2.tar.bz2 A /issm/trunk-jpl/externalpackages/windows/install.sh D /issm/trunk-jpl/externalpackages/windows/win7.sdk7.1.exe M /issm/trunk-jpl/externalpackages/xerces/install.sh D /issm/trunk-jpl/externalpackages/xerces/xerces-c-src\_2\_8\_0.tar.gz M /issm/trunk-jpl/externalpackages/yams/install.sh D /issm/trunk-jpl/externalpackages/yams/yams2-linux.gz D /issm/trunk-jpl/externalpackages/yams/yams2-osx.gz D /issm/trunk-jpl/externalpackages/yams/yams2-win.exe Deleted all externalpackage from trunk, use python script to download from issm website \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12189-12190.diff: \\ Function name: \\D /issm/trunk-jpl/externalpackages/adolc/ADOL-C-2.2.0.tar.gz M /issm/trunk-jpl/externalpackages/adolc/install.sh D /issm/trunk-jpl/externalpackages/android/android-ndk/android-ndk-r7b-darwin-x86.tar.bz2 M /issm/trunk-jpl/externalpackages/android/android-ndk/install.sh D /issm/trunk-jpl/externalpackages/android/android-sdk/android-sdk-r16-macosx.zip D /issm/trunk-jpl/externalpackages/android/android-sdk/apache-ant-1.8.2-bin.zip M /issm/trunk-jpl/externalpackages/android/android-sdk/install.sh D 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/issm/trunk-jpl/externalpackages/pcre/pcre-8.21.tar.gz M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-altix64-castor.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-cosmos.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-linux64-astrid.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-eric.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-pleiades.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-win32-eric.sh M /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-win7.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-altix64-castor.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-cosmos.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-linux64-astrid.sh M /issm/trunk-jpl/externalpackages/petsc/install-3.1-macosx32-mathieu.sh M 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/issm/trunk-jpl/externalpackages/python/Python-3.2.2.tgz M /issm/trunk-jpl/externalpackages/python/install.sh M /issm/trunk-jpl/externalpackages/qhull/install.sh D /issm/trunk-jpl/externalpackages/qhull/qhull-2003.1.tar.gz M /issm/trunk-jpl/externalpackages/rats/install.sh D /issm/trunk-jpl/externalpackages/rats/rats-2.3.tar.gz M /issm/trunk-jpl/externalpackages/readline/install.sh D /issm/trunk-jpl/externalpackages/readline/readline-6.2.2.tar.gz M /issm/trunk-jpl/externalpackages/rose/install.sh D /issm/trunk-jpl/externalpackages/rose/rose-0.9.5a-13219.tar.gz D /issm/trunk-jpl/externalpackages/satstress/SatStress-0.1.2.tar.gz M /issm/trunk-jpl/externalpackages/satstress/install.sh M /issm/trunk-jpl/externalpackages/scotch/install.sh D /issm/trunk-jpl/externalpackages/scotch/scotch\_5.1.6.tar.gz D /issm/trunk-jpl/externalpackages/scotch/scotch\_5.1.6\_esmumps.tar.gz M /issm/trunk-jpl/externalpackages/shapelib/install.sh D /issm/trunk-jpl/externalpackages/shapelib/shape\_eg\_data.zip D /issm/trunk-jpl/externalpackages/shapelib/shapelib-1.2.10.tar.gz M /issm/trunk-jpl/externalpackages/slepc/install.sh D /issm/trunk-jpl/externalpackages/slepc/slepc-2.3.2.tgz D /issm/trunk-jpl/externalpackages/ssh/plink.exe D /issm/trunk-jpl/externalpackages/ssh/pscp.exe M /issm/trunk-jpl/externalpackages/swig/install.sh D /issm/trunk-jpl/externalpackages/swig/swig-2.0.4.tar.gz D /issm/trunk-jpl/externalpackages/swig/swigwin-2.0.4.zip M /issm/trunk-jpl/externalpackages/tao/install.sh D /issm/trunk-jpl/externalpackages/tao/tao-2.0-p3.tar.gz M /issm/trunk-jpl/externalpackages/tex2im/install.sh D /issm/trunk-jpl/externalpackages/tex2im/tex2im-1.8.tar.gz M /issm/trunk-jpl/externalpackages/triangle/install-altix64.sh M /issm/trunk-jpl/externalpackages/triangle/install-android-4.0.sh M /issm/trunk-jpl/externalpackages/triangle/install-linux64.sh M /issm/trunk-jpl/externalpackages/triangle/install-macosx32.sh M /issm/trunk-jpl/externalpackages/triangle/install-macosx64.sh M /issm/trunk-jpl/externalpackages/triangle/install-pleiades.sh M /issm/trunk-jpl/externalpackages/triangle/install-win32.sh M /issm/trunk-jpl/externalpackages/triangle/install-win7.sh D /issm/trunk-jpl/externalpackages/triangle/triangle.zip M /issm/trunk-jpl/externalpackages/valgrind/install-altix64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-linux64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-macosx32.sh M /issm/trunk-jpl/externalpackages/valgrind/install-macosx64.sh M /issm/trunk-jpl/externalpackages/valgrind/install-win32.sh D /issm/trunk-jpl/externalpackages/valgrind/valgrind-3.7.0.tar.bz2 M /issm/trunk-jpl/externalpackages/vim/install.sh D /issm/trunk-jpl/externalpackages/vim/vim-7.2.tar.bz2 A /issm/trunk-jpl/externalpackages/windows/install.sh D /issm/trunk-jpl/externalpackages/windows/win7.sdk7.1.exe M /issm/trunk-jpl/externalpackages/xerces/install.sh D /issm/trunk-jpl/externalpackages/xerces/xerces-c-src\_2\_8\_0.tar.gz M /issm/trunk-jpl/externalpackages/yams/install.sh D /issm/trunk-jpl/externalpackages/yams/yams2-linux.gz D /issm/trunk-jpl/externalpackages/yams/yams2-osx.gz D /issm/trunk-jpl/externalpackages/yams/yams2-win.exe \\ Export determination: 6. \\Rationale: Deleted all externalpackage from trunk, use python script to download from issm website +D /issm/trunk-jpl/externalpackages/windows/Sdk1.png D /issm/trunk-jpl/externalpackages/windows/Sdk2.png not needed \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12190-12191.diff: \\ Function name: \\D /issm/trunk-jpl/externalpackages/windows/Sdk1.png D /issm/trunk-jpl/externalpackages/windows/Sdk2.png \\ Export determination: 6. \\Rationale: not needed +M /issm/trunk-jpl/src/m/utils/BC/SetIceShelfBC.py Further translation of SetIceShelfBC.m to python \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12191-12192.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/BC/SetIceShelfBC.py \\ Export determination: 6. \\Rationale: Further translation of SetIceShelfBC.m to python +M /issm/trunk-jpl/src/modules/matlab Ignore Win7 files \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-12192-12193.diff: \\ Function name: \\M /issm/trunk-jpl/src/modules/matlab \\ Export determination: 6. \\Rationale: Ignore Win7 files +M /issm/trunk-jpl/src/m/model/plot/northarrow.m M /issm/trunk-jpl/src/m/model/plot/plotdoc.m clarified northarrow plot documentation \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-12193-12194.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/plot/northarrow.m M /issm/trunk-jpl/src/m/model/plot/plotdoc.m \\ Export determination: 6. \\Rationale: clarified northarrow plot documentation \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-12195-12196.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: Replaced ISSM\_TIER by ISSM\_DIR \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-12196-12197.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: Replaced ISSM\_TIER by ISSM\_DIR \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-12199-12200.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.h M /issm/trunk-jpl/src/c/objects/Constraints/Constraint.h A /issm/trunk-jpl/src/c/objects/Kriging A /issm/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp A /issm/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h A /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp A /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h A /issm/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp A /issm/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h A /issm/trunk-jpl/src/c/objects/Kriging/Variogram.h M /issm/trunk-jpl/src/c/objects/objects.h \\ Export determination: 6. \\Rationale: Added Kriging object for semivariograms \\\\ Index: /issm/oecreview/Archive/12181-12200/r1.tex =================================================================== --- /issm/oecreview/Archive/12181-12200/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12181-12200/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12181 Index: /issm/oecreview/Archive/12181-12200/r2.tex =================================================================== --- /issm/oecreview/Archive/12181-12200/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12181-12200/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12200 Index: /issm/oecreview/Archive/12201-12220/Date.tex =================================================================== --- /issm/oecreview/Archive/12201-12220/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12201-12220/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12201-12220/ISSM-12201-12202.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12201-12202.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12201-12202.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12201) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12202) +@@ -129,6 +129,6 @@ + gsl_vector_free(x); + *pX=X; + #else +- error_("GSL support required"); ++ _error_("GSL support required"); + #endif + } Index: /issm/oecreview/Archive/12201-12220/ISSM-12202-12203.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12202-12203.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12202-12203.diff (revision 12325) @@ -0,0 +1,23 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh (revision 12202) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh (revision 12203) +@@ -1,7 +1,7 @@ + #This file sources all relevant scripts to setup the paths to windows compilers. + + #Where are the configuration files for each compiler: +-config_dir="$ISSM_TIER/externalpackages/windows/configs" ++config_dir="$ISSM_DIR/externalpackages/windows/configs" + + #your choise of compiler: + # 1: sdk 7.1 32 bits on Win7 +@@ -23,6 +23,6 @@ + source $config_dir/intel-winXP.sh + fi + +-#finally, out of ISSM_TIER, we need to create an ISSM_TIER_WIN variable for Matlab to pick up on. +-ISSM_TIER_WIN=`cygpath -m $ISSM_TIER` +-export ISSM_TIER_WIN ++#finally, out of ISSM_DIR, we need to create an ISSM_DIR_WIN variable for Matlab to pick up on. ++ISSM_DIR_WIN=`cygpath -m $ISSM_DIR` ++export ISSM_DIR_WIN Index: /issm/oecreview/Archive/12201-12220/ISSM-12203-12204.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12203-12204.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12203-12204.diff (revision 12325) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12203) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12204) +@@ -8,7 +8,10 @@ + #include "../../toolkits/toolkits.h" + #include "../../objects/objects.h" + #include "../modules.h" ++ ++#ifdef _HAVE_GSL_ + #include ++#endif + + #include "../../objects/Kriging/GaussianVariogram.h" + int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options){ Index: /issm/oecreview/Archive/12201-12220/ISSM-12204-12205.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12204-12205.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12204-12205.diff (revision 12325) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh (revision 12204) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh (revision 12205) +@@ -12,7 +12,6 @@ + declare -x LANG="C.UTF-8" + declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib\\X64;" + declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework64\\v3.5;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;" +-declare -x LOCALAPPDATA="C:\\Users\\schlegel\\AppData\\Local" + declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" + declare -x PATH="/usr/local/bin:/usr/bin:/usr/include:/cygdrive/c/cygwin/usr/bin:/cygdrive/c/cygwin/usr/include:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2012a/runtime/win64:/cygdrive/c/MATLAB/R2012a/bin:/cygdrive/c/MATLAB/R2012a/extern/include:/cygdrive/c/MATLAB/R2011a/runtime/win64:/cygdrive/c/MATLAB/R2011a/bin:/cygdrive/c/MATLAB/R2011a/extern/include" + declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC" +@@ -40,8 +39,6 @@ + declare -x TERM="cygwin" + declare -x TMP="/tmp" + declare -x ToolsVersion="4.0" +-declare -x USER="schlegel" +-declare -x USERNAME="schlegel" + declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" + declare -x WINDIR="C:\\Windows" + declare -x WindowsSDKDir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" Index: /issm/oecreview/Archive/12201-12220/ISSM-12205-12206.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12205-12206.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12205-12206.diff (revision 12325) @@ -0,0 +1,63 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim (revision 12205) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim (revision 12206) +@@ -546,6 +546,12 @@ + syn keyword cType Geometry + syn keyword cType QuadTree + syn keyword cType SetOfE4 ++syn keyword cType Variogram ++syn keyword cType GaussianVariogram ++syn keyword cType ExponentialVariogram ++syn keyword cType SphericalVariogram ++syn keyword cType Quadtree ++syn keyword cType Observation + "ISSM's objects end + + "ISSM's Enums begin +@@ -685,6 +691,10 @@ + syn keyword cConstant SettingsOutputFrequencyEnum + syn keyword cConstant SettingsResultsAsPatchesEnum + syn keyword cConstant SettingsWaitonlockEnum ++syn keyword cConstant DebugPetscProfilingEnum ++syn keyword cConstant PetscProfilingCurrentMemEnum ++syn keyword cConstant PetscProfilingCurrentFlopsEnum ++syn keyword cConstant PetscProfilingSolutionTimeEnum + syn keyword cConstant SteadystateMaxiterEnum + syn keyword cConstant SteadystateNumRequestedOutputsEnum + syn keyword cConstant SteadystateReltolEnum +@@ -700,8 +710,9 @@ + syn keyword cConstant ThermalStabilizationEnum + syn keyword cConstant ThermalIsenthalpyEnum + syn keyword cConstant ThicknessEnum ++syn keyword cConstant TimesteppingStartTimeEnum ++syn keyword cConstant TimesteppingFinalTimeEnum + syn keyword cConstant TimesteppingCflCoefficientEnum +-syn keyword cConstant TimesteppingFinalTimeEnum + syn keyword cConstant TimesteppingTimeAdaptEnum + syn keyword cConstant TimesteppingTimeStepEnum + syn keyword cConstant TransientIsdiagnosticEnum +@@ -763,6 +774,7 @@ + syn keyword cConstant ResultsEnum + syn keyword cConstant BoolInputEnum + syn keyword cConstant BoolParamEnum ++syn keyword cConstant ContourEnum + syn keyword cConstant ControlInputEnum + syn keyword cConstant DatasetInputEnum + syn keyword cConstant DofIndexingEnum +@@ -903,6 +915,7 @@ + syn keyword cConstant P0Enum + syn keyword cConstant P1Enum + syn keyword cConstant P1DGEnum ++syn keyword cConstant SaveResultsEnum + syn keyword cConstant BoolElementResultEnum + syn keyword cConstant BoolExternalResultEnum + syn keyword cConstant DoubleElementResultEnum +@@ -917,6 +930,7 @@ + syn keyword cConstant PentaP1ElementResultEnum + syn keyword cConstant PetscVecExternalResultEnum + syn keyword cConstant StringExternalResultEnum ++syn keyword cConstant StepEnum + syn keyword cConstant TimeEnum + syn keyword cConstant TriaP1ElementResultEnum + syn keyword cConstant WaterColumnOldEnum Index: /issm/oecreview/Archive/12201-12220/ISSM-12206-12207.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12206-12207.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12206-12207.diff (revision 12325) @@ -0,0 +1,559 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12206) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12207) +@@ -14,61 +14,64 @@ + #endif + + #include "../../objects/Kriging/GaussianVariogram.h" +-int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options){ ++int Krigingx(double** ppredictions,double* obs_x, double* obs_y, double* obs_list, int obs_length,double* x_interp,double* y_interp,int n_interp,Options* options){ + + /*output*/ + double *predictions = NULL; + + /*Intermediaries*/ +- int i,j; ++ int i,j,n_obs; + double numerator,denominator,ratio; +- char *model = NULL; +- double *Gamma = NULL; +- double *GinvG0 = NULL; +- double *Ginv1 = NULL; +- double *GinvZ = NULL; +- double *gamma0 = NULL; +- double *ones = NULL; +- Variogram *variogram = NULL; ++ double *x = NULL; ++ double *y = NULL; ++ double *obs = NULL; ++ double *Gamma = NULL; ++ double *GinvG0 = NULL; ++ double *Ginv1 = NULL; ++ double *GinvZ = NULL; ++ double *gamma0 = NULL; ++ double *ones = NULL; ++ Variogram *variogram = NULL; ++ DataSet *observations = NULL; + +- /*Memory allocation*/ +- predictions =(double*)xmalloc(n_interp*sizeof(double)); +- Gamma =(double*)xmalloc(n_obs*n_obs*sizeof(double)); +- gamma0 =(double*)xmalloc(n_obs*sizeof(double)); +- ones =(double*)xmalloc(n_obs*sizeof(double)); ++ /*Get Variogram from Options*/ ++ ProcessVariogram(&variogram,options); + +- /*Create Semi-Variogram object*/ +- if(options->GetOption("model")){ +- options->Get(&model,"model"); +- if (strcmp(model,"gaussian")==0) variogram = new GaussianVariogram(options); +- else if(strcmp(model,"exponential")==0) variogram = new ExponentialVariogram(options); +- else if(strcmp(model,"spherical")==0) variogram = new SphericalVariogram(options); +- else _error_("only gaussian semivariogram models supported yet"); +- } +- else variogram = new GaussianVariogram(options); +- variogram->Echo(); ++ /*Process observation dataset*/ ++ ProcessObservations(&observations,obs_list,obs_x,obs_y,obs_length); + +- /*First: Create semivariogram matrix for observations*/ +- for(i=0;iSemiVariogram(x[i]-x[j],y[i]-y[j]); +- Gamma[j*n_obs+i] = Gamma[i*n_obs+j]; +- } +- } +- for(i=0;iSemiVariogram(x[i]-x[j],y[i]-y[j]); ++ Gamma[j*n_obs+i] = Gamma[i*n_obs+j]; ++ } ++ } ++ for(i=0;iSemiVariogram(x[i]-x_interp[idx],y[i]-y_interp[idx]); + + /*Solve the three linear systems*/ + GslSolve(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0 + GslSolve(&Ginv1, Gamma,ones,n_obs); // Gamma^-1 ones +- GslSolve(&GinvZ, Gamma,observations,n_obs); // Gamma^-1 Z ++ GslSolve(&GinvZ, Gamma,obs,n_obs); // Gamma^-1 Z + + /*Prepare predictor*/ + numerator=-1.; denominator=0.; +@@ -80,6 +83,12 @@ + for(i=0;iGetOption("model")){ ++ options->Get(&model,"model"); ++ if (strcmp(model,"gaussian")==0) variogram = new GaussianVariogram(options); ++ else if(strcmp(model,"exponential")==0) variogram = new ExponentialVariogram(options); ++ else if(strcmp(model,"spherical")==0) variogram = new SphericalVariogram(options); ++ else _error_("variogram %s not supported yet (list of supported variogram: gaussian, exponential and spherical)",model); ++ } ++ else variogram = new GaussianVariogram(options); ++ ++ /*Assign output pointer*/ ++ xfree((void**)&model); ++ *pvariogram = variogram; ++}/*}}}*/ ++void ProcessObservations(DataSet **pobservations,double* observations_list,double* x,double* y,int n){/*{{{*/ ++ ++ int i; ++ DataSet* observations = NULL; ++ ++ /*Initialize Observation Dataset*/ ++ observations = new DataSet(); ++ ++ /*Add observations one by one*/ ++ for(i=0;iAddObject(new Observation(x[i],y[i],0,0,observations_list[i])); ++ } ++ ++ /*Assign output pointer*/ ++ *pobservations = observations; ++}/*}}}*/ ++void ObservationList(double **px,double **py,double **pobs,int* pnobs,DataSet* observations,double x_interp,double y_interp){/*{{{*/ ++ ++ /*Output and Intermediaries*/ ++ int nobs,i; ++ double *x = NULL; ++ double *y = NULL; ++ double *obs = NULL; ++ Observation *observation = NULL; ++ ++ /*Get number of observations*/ ++ nobs = observations->Size(); ++ ++ /*Allocate vectors*/ ++ x = (double*)xmalloc(nobs*sizeof(double)); ++ y = (double*)xmalloc(nobs*sizeof(double)); ++ obs = (double*)xmalloc(nobs*sizeof(double)); ++ ++ /*Loop over all observations and fill in x, y and obs*/ ++ for (i=0;iSize();i++){ ++ observation=(Observation*)observations->GetObjectByOffset(i); ++ observation->WriteXYObs(&x[i],&y[i],&obs[i]); ++ } ++ ++ /*Assign output pointer*/ ++ *px=x; ++ *py=y; ++ *pobs=obs; ++ *pnobs=nobs; ++}/*}}}*/ ++void GslSolve(double** pX,double* A,double* B,int n){/*{{{*/ + #ifdef _HAVE_GSL_ + +- /*GSL Matrices and vectors: */ +- int s; +- gsl_matrix_view a; +- gsl_vector_view b; +- gsl_vector *x = NULL; +- gsl_permutation *p = NULL; ++ /*GSL Matrices and vectors: */ ++ int s; ++ gsl_matrix_view a; ++ gsl_vector_view b; ++ gsl_vector *x = NULL; ++ gsl_permutation *p = NULL; + +- /*A will be modified by LU decomposition. Use copy*/ +- double* Acopy = (double*)xmalloc(n*n*sizeof(double)); +- memcpy(Acopy,A,n*n*sizeof(double)); ++ /*A will be modified by LU decomposition. Use copy*/ ++ double* Acopy = (double*)xmalloc(n*n*sizeof(double)); ++ memcpy(Acopy,A,n*n*sizeof(double)); + +- /*Initialize gsl matrices and vectors: */ +- a = gsl_matrix_view_array (Acopy,n,n); +- b = gsl_vector_view_array (B,n); +- x = gsl_vector_alloc (n); ++ /*Initialize gsl matrices and vectors: */ ++ a = gsl_matrix_view_array (Acopy,n,n); ++ b = gsl_vector_view_array (B,n); ++ x = gsl_vector_alloc (n); + +- /*Run LU and solve: */ +- p = gsl_permutation_alloc (n); +- gsl_linalg_LU_decomp (&a.matrix, p, &s); +- gsl_linalg_LU_solve (&a.matrix, p, &b.vector, x); ++ /*Run LU and solve: */ ++ p = gsl_permutation_alloc (n); ++ gsl_linalg_LU_decomp (&a.matrix, p, &s); ++ gsl_linalg_LU_solve (&a.matrix, p, &b.vector, x); + +- //printf ("x = \n"); +- //gsl_vector_fprintf (stdout, x, "%g"); ++ //printf ("x = \n"); ++ //gsl_vector_fprintf (stdout, x, "%g"); + +- /*Copy result*/ +- double* X = (double*)xmalloc(n*sizeof(double)); +- memcpy(X,gsl_vector_ptr(x,0),n*sizeof(double)); ++ /*Copy result*/ ++ double* X = (double*)xmalloc(n*sizeof(double)); ++ memcpy(X,gsl_vector_ptr(x,0),n*sizeof(double)); + +- /*Clean up and assign output pointer*/ +- xfree((void**)&Acopy); +- gsl_permutation_free(p); +- gsl_vector_free(x); +- *pX=X; ++ /*Clean up and assign output pointer*/ ++ xfree((void**)&Acopy); ++ gsl_permutation_free(p); ++ gsl_vector_free(x); ++ *pX=X; + #else +- _error_("GSL support required"); ++ _error_("GSL support required"); + #endif +-} ++ }/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12206) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12207) +@@ -9,6 +9,9 @@ + #include "../../toolkits/toolkits.h" + + int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options); ++void ProcessVariogram(Variogram **pvariogram,Options* options); ++void ProcessObservations(DataSet **pobservations,double* observations_list,double* x,double* y,int n); ++void ObservationList(double **px,double **py,double **pobs,int* pnobs,DataSet* observations,double x_interp,double y_interp); + void GslSolve(double** pX,double* A,double* B,int n); + + #endif /* _KRIGINGX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12206) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12207) +@@ -616,6 +616,10 @@ + ./objects/Kriging/ExponentialVariogram.cpp\ + ./objects/Kriging/SphericalVariogram.h\ + ./objects/Kriging/SphericalVariogram.cpp\ ++ ./objects/Kriging/Quadtree.h\ ++ ./objects/Kriging/Quadtree.cpp\ ++ ./objects/Kriging/Observation.h\ ++ ./objects/Kriging/Observation.cpp\ + ./modules/Krigingx/Krigingx.cpp\ + ./modules/Krigingx/Krigingx.h + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 12206) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 12207) +@@ -177,5 +177,7 @@ + #include "./Kriging/GaussianVariogram.h" + #include "./Kriging/ExponentialVariogram.h" + #include "./Kriging/SphericalVariogram.h" ++#include "./Kriging/Quadtree.h" ++#include "./Kriging/Observation.h" + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12207) +@@ -0,0 +1,43 @@ ++ ++#ifndef _QUADTREEK_H ++#define _QUADTREEK_H ++ ++class Quadtree{ ++ ++ private: ++ /* A quadtree box contains up to 4 points (locations). 4 new quadtree boxes are ++ * created if a fifth point is added to the same box. A Quadtree box is therefore ++ * composed of EITHER: ++ * - up to 4 vertices ++ * - 4 "sub" quadtree boxes*/ ++ ++ class QuadtreeBox: public Object{ ++ public: ++ int nbitems; // number of current vertices in the box ++ union{ ++ QuadtreeBox *box[4]; ++ int index[4]; ++ }; ++ ++ /*Object functions (Needed because the Quadtree uses a Container*/ ++ void Echo() {_error_("not implemented yet"); }; ++ void DeepEcho() {_error_("not implemented yet"); }; ++ int Id() {_error_("not implemented yet"); }; ++ int MyRank() {_error_("not implemented yet"); }; ++ int ObjectEnum(){_error_("not implemented yet"); }; ++ Object *copy() {_error_("not implemented yet"); }; ++ }; ++ ++ /*Quadtree private Fields*/ ++ DataSet* boxcontainer; ++ ++ public: ++ QuadtreeBox* root; // main box ++ long NbQuadtreeBox; // total number of boxes ++ long NbPoints; // number of points ++ ++ Quadtree(); ++ ~Quadtree(); ++ QuadtreeBox* NewQuadtreeBox(void); ++}; ++#endif //_QUADTREEK_H +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h (revision 12207) +@@ -0,0 +1,33 @@ ++/*! \file Observation.h ++ * \brief: header file for Observation object ++ */ ++ ++#ifndef _OBSERVATION_H_ ++#define _OBSERVATION_H_ ++ ++#include "../Object.h" ++ ++class Observation: public Object{ ++ ++ public: ++ double x,y; ++ int xi,yi; ++ double value; ++ ++ /*Observation constructors, destructors*/ ++ Observation(); ++ Observation(double x_in,double y_in,int xi_in,int yi_in,double value_in); ++ ~Observation(); ++ ++ /*Object virtual functions definitions*/ ++ void Echo(); ++ void DeepEcho() {_error_("Not implemented yet"); }; ++ int Id() {_error_("Not implemented yet"); }; ++ int MyRank() {_error_("Not implemented yet"); }; ++ int ObjectEnum(){_error_("Not implemented yet"); }; ++ Object *copy() {_error_("Not implemented yet"); }; ++ ++ /*Management*/ ++ void WriteXYObs(double* px,double* py,double* pobs); ++}; ++#endif /* _EXPONENTIALVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12207) +@@ -0,0 +1,98 @@ ++#include "../objects.h" ++/*DOCUMENTATION What is a Quadtree? {{{1 ++ * A Quadtree is a very simple way to group vertices according ++ * to their locations. A square that holds all the points of the mesh ++ * (or the geometry) is divided into 4 boxes. As soon as one box ++ * hold more than 4 vertices, it is divided into 4 new boxes, etc... ++ * There cannot be more than MAXDEEP (=30) subdivision. ++ * This process is like a Dichotomy in dimension 2 ++ * ++ * + - - - - - - - - + - - + - + - + - - - - + ++ * | | | | X | | ++ * + - + - + ++ * | | | | | | ++ * + - - + - + - + + ++ * | | | | | ++ * ++ * | | | | | ++ * + - - - - - - - - + - - + - - + - - - - + ++ * | | | | ++ * ++ * | | | | ++ * ++ * | | | | ++ * | | | | ++ * + - - - - - - - - + - - - - + - - - - + ++ * | | | ++ * ++ * | | | ++ * ++ * | | | ++ * ++ * | | | ++ * | | | ++ * | | | ++ * | | | ++ * | | | ++ * + - - - - - - - - + - - - - - - - - + ++ * ++ * The coordinate system used in a quadtree are integers to avoid ++ * round-off errors. The vertex in the lower left box has the coordinates ++ * (0 0) ++ * The upper right vertex has the follwing coordinates: ++ * 2^30 -1 2^30 -1 in decimal ++ * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary ++ * \-- 29 --/ \-- 29 --/ ++ * Using binaries is therefore very easy to locate a vertex in a box: ++ * we just need to look at the bits from the left to the right (See ::Add) ++ }}}1*/ ++ ++ /*Constructors/Destructors*/ ++ /*FUNCTION Quadtree::Quadtree(){{{1*/ ++ Quadtree::Quadtree(){ ++ ++ /*Number of boxes and vertices*/ ++ NbQuadtreeBox=0; ++ NbPoints=0; ++ ++ /*Create container*/ ++ boxcontainer=new DataSet(); ++ ++ /*Create Root, pointer toward the main box*/ ++ root=NewQuadtreeBox(); ++ ++ } ++ /*}}}1*/ ++ /*FUNCTION Quadtree::~Quadtree(){{{1*/ ++ Quadtree::~Quadtree() { ++ ++ delete boxcontainer; ++ root=NULL; ++ ++ } ++ /*}}}1*/ ++ ++ /*Methods*/ ++ /*FUNCTION Quadtree::NewQuadtreeBox {{{1*/ ++ Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(void){ ++ ++ /*Output*/ ++ QuadtreeBox* newbox=NULL; ++ ++ /*Create and initialize a new box*/ ++ newbox=new QuadtreeBox(); ++ newbox->nbitems=0; ++ newbox->box[0]=NULL; ++ newbox->box[1]=NULL; ++ newbox->box[2]=NULL; ++ newbox->box[3]=NULL; ++ ++ /*Add root to the container*/ ++ boxcontainer->AddObject(newbox); ++ ++ /*Increase counter*/ ++ NbQuadtreeBox++; ++ ++ /*currentbox now points toward next quadtree box*/ ++ return newbox; ++ }/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp (revision 12207) +@@ -0,0 +1,49 @@ ++/*!\file Observation.c ++ * \brief: implementation of the Observation object ++ */ ++ ++#include "../objects.h" ++ ++/*Observation constructors and destructor*/ ++/*FUNCTION Observation::Observation(){{{1*/ ++Observation::Observation(){ ++ return; ++} ++/*}}}*/ ++/*FUNCTION Observation::Observation(double x,double y,int xi,int yi,double value){{{1*/ ++Observation::Observation(double x_in,double y_in,int xi_in,int yi_in,double value_in){ ++ ++ this->x = x_in; ++ this->y = y_in; ++ this->xi = xi_in; ++ this->yi = yi_in; ++ this->value = value_in; ++ ++} ++/*}}}*/ ++/*FUNCTION Observation::~Observation(){{{1*/ ++Observation::~Observation(){ ++ return; ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION Observation::Echo {{{1*/ ++void Observation::Echo(void){ ++ printf("Observation\n"); ++ printf(" x : %g\n",this->x); ++ printf(" y : %g\n",this->y); ++ printf(" xi : %i\n",this->xi); ++ printf(" yi : %i\n",this->yi); ++ printf(" value : %g\n",this->value); ++} ++/*}}}*/ ++ ++/*Observations functions*/ ++/*FUNCTION Observation::WriteXYObs(double* px,double* py,double* pobs){{{1*/ ++void Observation::WriteXYObs(double* px,double* py,double* pobs){ ++ *px = this->x; ++ *py = this->y; ++ *pobs = this->value; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h (revision 12206) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h (revision 12207) +@@ -2,7 +2,6 @@ + * \brief abstract class for Variogram object + */ + +- + #ifndef _VARIOGRAM_H_ + #define _VARIOGRAM_H_ + Index: /issm/oecreview/Archive/12201-12220/ISSM-12207-12208.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12207-12208.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12207-12208.diff (revision 12325) @@ -0,0 +1,56 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-32.sh (revision 12207) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-32.sh (revision 12208) +@@ -1,38 +1,38 @@ + declare -x ALLUSERSPROFILE="C:\\ProgramData" +-declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319" +-declare -x COMMONPROGRAMFILES="C:\\Program Files (x86)\\Common Files" ++declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319" ++declare -x COMMONPROGRAMFILES="C:\\Program Files\\Common Files" + declare -x COMSPEC="C:\\Windows\\system32\\cmd.exe" +-declare -x CommandPromptType="Cross" +-declare -x CommonProgramW6432="C:\\Program Files\\Common Files" ++declare -x CommandPromptType="Native" + declare -x Configuration="Debug" + declare -x FP_NO_HOST_CHECK="NO" + declare -x FrameworkVersion="v4.0.30319" + declare -x HOMEDRIVE="C:" +-declare -x INCLUDE="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\ATLMFC\\INCLUDE;" ++declare -x INCLUDE="C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;" + declare -x INFOPATH="/usr/local/info:/usr/share/info:/usr/info:" + declare -x LANG="en_US.UTF-8" +-declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\ATLMFC\\LIB;" +-declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib;" ++declare -x LIB="C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\Lib;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;" ++declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\Lib;" + declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" +-declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b32/runtime/win32:/cygdrive/c/MATLAB/R2011b32/bin:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/c/MATLAB/R2011b/bin:/cygdrive/c/Program Files (x86)/Microsoft SQL Server/100/Tools/Binn:/cygdrive/c/Program Files/Microsoft SQL Server/100/Tools/Binn:/cygdrive/c/Program Files/Microsoft SQL Server/100/DTS/Binn:/cygdrive/c/Program Files/Microsoft Network Monitor 3" ++declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/VC/Bin:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/MATLAB/R2012a/runtime/win32:/cygdrive/c/MATLAB/R2012a/bin:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit" + declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC" ++declare -x PRINTER="137.78.140.129#:1" + declare -x PROCESSOR_ARCHITECTURE="x86" +-declare -x PROCESSOR_ARCHITEW6432="AMD64" +-declare -x PROCESSOR_IDENTIFIER="Intel64 Family 6 Model 42 Stepping 7, GenuineIntel" ++declare -x PROCESSOR_IDENTIFIER="x86 Family 6 Model 42 Stepping 7, GenuineIntel" + declare -x PROCESSOR_LEVEL="6" + declare -x PROCESSOR_REVISION="2a07" +-declare -x PROGRAMFILES="C:\\Program Files (x86)" ++declare -x PROGRAMFILES="C:\\Program Files" + declare -x PSModulePath="C:\\Windows\\system32\\WindowsPowerShell\\v1.0\\Modules\\" + declare -x PUBLIC="C:\\Users\\Public" + declare -x PlatformToolset="Windows7.1SDK" + declare -x ProgramData="C:\\ProgramData" +-declare -x ProgramW6432="C:\\Program Files" + declare -x SHELL="/bin/bash" + declare -x SYSTEMDRIVE="C:" + declare -x SYSTEMROOT="C:\\Windows" ++declare -x TARGET_CPU="x86" + declare -x TARGET_PLATFORM="WIN7" + declare -x TERM="cygwin" +-declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" ++declare -x ToolsVersion="4.0" ++declare -x VS100COMNTOOLS="C:\\Program Files\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" + declare -x WINDIR="C:\\Windows" + declare -x WindowsSDKDir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" + declare -x WindowsSDKVersionOverride="v7.1" Index: /issm/oecreview/Archive/12201-12220/ISSM-12208-12209.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12208-12209.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12208-12209.diff (revision 12325) @@ -0,0 +1,24 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh (revision 12208) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh (revision 12209) +@@ -9,8 +9,18 @@ + # 3: intel compiler on Win7 + # 4: intel compiler on WinXP + +-compiler=2; ++#Determine OS version using uname: ++version=`uname -s | grep 64` ++if [[ $version == "" ]];then ++ compiler=1 ++else ++ compiler=2 ++fi + ++#If you want to override and use intel compilers: ++#compiler=3; ++ ++ + #source corresponding environment variables: + + if [[ "$compiler" == "1" ]]; then Index: /issm/oecreview/Archive/12201-12220/ISSM-12209-12210.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12209-12210.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12209-12210.diff (revision 12325) @@ -0,0 +1,454 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12210) +@@ -0,0 +1,79 @@ ++/* ++ * \file Observations.c ++ * \brief: implementation of the Observations class, derived from DataSet class ++ */ ++ ++/*Headers: {{{*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include ++#include ++ ++#include "./DataSet.h" ++#include "./Observations.h" ++#include "../shared/shared.h" ++#include "../include/include.h" ++#include "../EnumDefinitions/EnumDefinitions.h" ++ ++using namespace std; ++/*}}}*/ ++ ++/*Object constructors and destructor*/ ++/*FUNCTION Observations::Observations(){{{*/ ++Observations::Observations(){ ++ return; ++} ++/*}}}*/ ++/*FUNCTION Observations::Observations(double* observations_list,double* x,double* y,int n){{{*/ ++Observations::Observations(double* observations_list,double* x,double* y,int n){ ++ ++ /*Add observations one by one*/ ++ for(int i=0;iAddObject(new Observation(x[i],y[i],0,0,observations_list[i])); ++ } ++ ++} ++/*}}}*/ ++/*FUNCTION Observations::~Observations(){{{*/ ++Observations::~Observations(){ ++ return; ++} ++/*}}}*/ ++ ++/*Methods*/ ++/*FUNCTION Observations::ObservationList{{{*/ ++void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp){/*{{{*/ ++ ++ /*Output and Intermediaries*/ ++ int nobs,i; ++ double *x = NULL; ++ double *y = NULL; ++ double *obs = NULL; ++ Observation *observation = NULL; ++ ++ /*Get number of observations*/ ++ nobs = this->Size(); ++ ++ /*Allocate vectors*/ ++ x = (double*)xmalloc(nobs*sizeof(double)); ++ y = (double*)xmalloc(nobs*sizeof(double)); ++ obs = (double*)xmalloc(nobs*sizeof(double)); ++ ++ /*Loop over all observations and fill in x, y and obs*/ ++ for (i=0;iGetObjectByOffset(i); ++ observation->WriteXYObs(&x[i],&y[i],&obs[i]); ++ } ++ ++ /*Assign output pointer*/ ++ *px=x; ++ *py=y; ++ *pobs=obs; ++ *pnobs=nobs; ++}/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12210) +@@ -0,0 +1,24 @@ ++/*!\file: Observations.h ++ * \brief prototypes for Observations.h ++ */ ++ ++#ifndef _CONTAINER_OBSERVATIONS_H_ ++#define _CONTAINER_OBSERVATIONS_H_ ++ ++class Obsevration; ++ ++class Observations: public DataSet{ ++ ++ public: ++ ++ /*constructors, destructors*/ ++ Observations(); ++ Observations(double* observations_list,double* x,double* y,int n); ++ ~Observations(); ++ ++ /*Methods*/ ++ void ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp); ++ ++}; ++#endif //ifndef _OBSERVATIONS_H_ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12209) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12210) +@@ -7,6 +7,7 @@ + #include "../../include/include.h" + #include "../../toolkits/toolkits.h" + #include "../../objects/objects.h" ++#include "../../Container/Observations.h" + #include "../modules.h" + + #ifdef _HAVE_GSL_ +@@ -20,25 +21,25 @@ + double *predictions = NULL; + + /*Intermediaries*/ +- int i,j,n_obs; +- double numerator,denominator,ratio; +- double *x = NULL; +- double *y = NULL; +- double *obs = NULL; +- double *Gamma = NULL; +- double *GinvG0 = NULL; +- double *Ginv1 = NULL; +- double *GinvZ = NULL; +- double *gamma0 = NULL; +- double *ones = NULL; +- Variogram *variogram = NULL; +- DataSet *observations = NULL; ++ int i,j,n_obs; ++ double numerator,denominator,ratio; ++ double *x = NULL; ++ double *y = NULL; ++ double *obs = NULL; ++ double *Gamma = NULL; ++ double *GinvG0 = NULL; ++ double *Ginv1 = NULL; ++ double *GinvZ = NULL; ++ double *gamma0 = NULL; ++ double *ones = NULL; ++ Variogram *variogram = NULL; ++ Observations *observations = NULL; + + /*Get Variogram from Options*/ + ProcessVariogram(&variogram,options); + + /*Process observation dataset*/ +- ProcessObservations(&observations,obs_list,obs_x,obs_y,obs_length); ++ observations=new Observations(obs_list,obs_x,obs_y,obs_length); + + /*Allocation output*/ + predictions =(double*)xmalloc(n_interp*sizeof(double)); +@@ -49,7 +50,7 @@ + if(idx%10==0) printf("\b\b\b\b\b\b\b%5.2lf %%",(double)idx/n_interp*100); + + /*Get list of observations for current point*/ +- ObservationList(&x,&y,&obs,&n_obs,observations,x_interp[idx],y_interp[idx]); ++ observations->ObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx]); + + /*Allocate intermediary matrix and vectors*/ + Gamma =(double*)xmalloc(n_obs*n_obs*sizeof(double)); +@@ -120,51 +121,6 @@ + xfree((void**)&model); + *pvariogram = variogram; + }/*}}}*/ +-void ProcessObservations(DataSet **pobservations,double* observations_list,double* x,double* y,int n){/*{{{*/ +- +- int i; +- DataSet* observations = NULL; +- +- /*Initialize Observation Dataset*/ +- observations = new DataSet(); +- +- /*Add observations one by one*/ +- for(i=0;iAddObject(new Observation(x[i],y[i],0,0,observations_list[i])); +- } +- +- /*Assign output pointer*/ +- *pobservations = observations; +-}/*}}}*/ +-void ObservationList(double **px,double **py,double **pobs,int* pnobs,DataSet* observations,double x_interp,double y_interp){/*{{{*/ +- +- /*Output and Intermediaries*/ +- int nobs,i; +- double *x = NULL; +- double *y = NULL; +- double *obs = NULL; +- Observation *observation = NULL; +- +- /*Get number of observations*/ +- nobs = observations->Size(); +- +- /*Allocate vectors*/ +- x = (double*)xmalloc(nobs*sizeof(double)); +- y = (double*)xmalloc(nobs*sizeof(double)); +- obs = (double*)xmalloc(nobs*sizeof(double)); +- +- /*Loop over all observations and fill in x, y and obs*/ +- for (i=0;iSize();i++){ +- observation=(Observation*)observations->GetObjectByOffset(i); +- observation->WriteXYObs(&x[i],&y[i],&obs[i]); +- } +- +- /*Assign output pointer*/ +- *px=x; +- *py=y; +- *pobs=obs; +- *pnobs=nobs; +-}/*}}}*/ + void GslSolve(double** pX,double* A,double* B,int n){/*{{{*/ + #ifdef _HAVE_GSL_ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12209) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12210) +@@ -10,8 +10,6 @@ + + int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options); + void ProcessVariogram(Variogram **pvariogram,Options* options); +-void ProcessObservations(DataSet **pobservations,double* observations_list,double* x,double* y,int n); +-void ObservationList(double **px,double **py,double **pobs,int* pnobs,DataSet* observations,double x_interp,double y_interp); + void GslSolve(double** pX,double* A,double* B,int n); + + #endif /* _KRIGINGX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12209) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12210) +@@ -609,19 +609,21 @@ + ./modules/BamgTriangulatex/BamgTriangulatex.h + #}}} + #Kriging sources {{{1 +-kriging_sources = ./objects/Kriging/Variogram.h \ +- ./objects/Kriging/GaussianVariogram.h\ +- ./objects/Kriging/GaussianVariogram.cpp\ +- ./objects/Kriging/ExponentialVariogram.h\ +- ./objects/Kriging/ExponentialVariogram.cpp\ +- ./objects/Kriging/SphericalVariogram.h\ +- ./objects/Kriging/SphericalVariogram.cpp\ +- ./objects/Kriging/Quadtree.h\ +- ./objects/Kriging/Quadtree.cpp\ +- ./objects/Kriging/Observation.h\ +- ./objects/Kriging/Observation.cpp\ +- ./modules/Krigingx/Krigingx.cpp\ +- ./modules/Krigingx/Krigingx.h ++kriging_sources = ./Container/Observations.h\ ++ ./Container/Observations.cpp\ ++ ./objects/Kriging/Variogram.h \ ++ ./objects/Kriging/GaussianVariogram.h\ ++ ./objects/Kriging/GaussianVariogram.cpp\ ++ ./objects/Kriging/ExponentialVariogram.h\ ++ ./objects/Kriging/ExponentialVariogram.cpp\ ++ ./objects/Kriging/SphericalVariogram.h\ ++ ./objects/Kriging/SphericalVariogram.cpp\ ++ ./objects/Kriging/Quadtree.h\ ++ ./objects/Kriging/Quadtree.cpp\ ++ ./objects/Kriging/Observation.h\ ++ ./objects/Kriging/Observation.cpp\ ++ ./modules/Krigingx/Krigingx.cpp\ ++ ./modules/Krigingx/Krigingx.h + + #}}} + #Kml sources {{{1 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12209) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12210) +@@ -2,6 +2,8 @@ + #ifndef _QUADTREEK_H + #define _QUADTREEK_H + ++class Observation; ++ + class Quadtree{ + + private: +@@ -16,7 +18,7 @@ + int nbitems; // number of current vertices in the box + union{ + QuadtreeBox *box[4]; +- int index[4]; ++ Observation *obs[4]; + }; + + /*Object functions (Needed because the Quadtree uses a Container*/ +@@ -34,10 +36,11 @@ + public: + QuadtreeBox* root; // main box + long NbQuadtreeBox; // total number of boxes +- long NbPoints; // number of points ++ long NbObs; // number of points + + Quadtree(); + ~Quadtree(); ++ void Add(Observation* observation); + QuadtreeBox* NewQuadtreeBox(void); + }; + #endif //_QUADTREEK_H +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12209) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12210) +@@ -46,6 +46,37 @@ + * Using binaries is therefore very easy to locate a vertex in a box: + * we just need to look at the bits from the left to the right (See ::Add) + }}}1*/ ++/*MACROS {{{1*/ ++/* ++ * ++ * J j ++ * ^ ^ ++ * | | +--------+--------+ ++ * | | | | | ++ * 1X | | | 2 | 3 | ++ * | | | | | ++ * | | +--------+--------+ ++ * | | | | | ++ * 0X | | | 0 | 1 | ++ * | | | | | ++ * | | +--------+--------+ ++ * | +-----------------------> i ++ * | ++ * |----------------------------> I ++ * X0 X1 ++ * ++ * box 0 -> I=0 J=0 IJ=00 = 0 ++ * box 1 -> I=1 J=0 IJ=01 = 1 ++ * box 2 -> I=0 J=1 IJ=10 = 2 ++ * box 3 -> I=1 J=1 IJ=11 = 3 ++ */ ++//IJ(i,j,l) returns the box number of i and j with respect to l ++//if !j&l and !i&l -> 0 (box zero: lower left ) ++//if !j&l and i&l -> 1 (box one: lower right) ++//if j&l and !i&l -> 2 (box two: upper left ) ++//if j&l and i&l -> 3 (box three:upper right) ++#define IJ(i,j,l) ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 )) ++/*}}}*/ + + /*Constructors/Destructors*/ + /*FUNCTION Quadtree::Quadtree(){{{1*/ +@@ -53,7 +84,7 @@ + + /*Number of boxes and vertices*/ + NbQuadtreeBox=0; +- NbPoints=0; ++ NbObs=0; + + /*Create container*/ + boxcontainer=new DataSet(); +@@ -73,6 +104,89 @@ + /*}}}1*/ + + /*Methods*/ ++/*FUNCTION Quadtree::Add{{{1*/ ++void Quadtree::Add(Observation* observation){ ++ ++ /*Intermediaries*/ ++ const int MaxDeep = 30; ++ int k,ij; ++ long i,j,level; ++ QuadtreeBox **pb = NULL; ++ QuadtreeBox *b = NULL; ++ ++ /*Get integer coodinates*/ ++ i = observation->xi; ++ j = observation->yi; ++ ++ /*Initialize level*/ ++ level=(1L<nbitems<0)){ ++ ++ /*shift b->nbitems by -1 as a counter*/ ++ b->nbitems--; ++ ++ /*Go down one level = 00100 -> 00010*/ ++ level>>=1; ++ ++ /*Get next subbox according to the bit value (level)*/ ++ pb = &b->box[IJ(i,j,level)]; ++ } ++ _assert_(level>0); ++ ++ /*Now, try to add the vertex, if the box is full (nbitems=4), we have to divide it in 4 new boxes*/ ++ while((b=*pb) && (b->nbitems==4)){ ++ ++ /*Copy the 4 observation in the current Quadtreebox*/ ++ Observation* obs[4]; ++ obs[0] = b->obs[0]; ++ obs[1] = b->obs[1]; ++ obs[2] = b->obs[2]; ++ obs[3] = b->obs[3]; ++ ++ /*set nbitems as negative (now holding boxes instead of observations)*/ ++ b->nbitems = -b->nbitems; ++ ++ /*Initialize the 4 pointers toward the 4 subboxes*/ ++ b->box[0]=NULL; ++ b->box[1]=NULL; ++ b->box[2]=NULL; ++ b->box[3]=NULL; ++ ++ /*level = 00100 -> 00010*/ ++ level>>=1; ++ ++ /*Put the four observations in the new boxes*/ ++ for (k=0;k<4;k++){ ++ ++ /*Get box for observation number k*/ ++ ij=IJ(obs[k]->xi,obs[k]->yi,level); ++ QuadtreeBox *bb = b->box[ij]; ++ if(!bb){ ++ b->box[ij]=NewQuadtreeBox(); ++ bb=b->box[ij]; ++ } ++ ++ /*Copy current observations*/ ++ bb->obs[bb->nbitems++] = obs[k]; ++ } ++ ++ /*Get the subbox where the current observation is located*/ ++ ij=IJ(i,j,level); ++ pb=&b->box[ij]; ++ } ++ ++ /*alloc the QuadtreeBox if necessary and add current observation*/ ++ b=*pb; ++ if(!b) b=NewQuadtreeBox(); ++ b->obs[b->nbitems++]=observation; ++ NbObs++; ++ ++}/*}}}*/ + /*FUNCTION Quadtree::NewQuadtreeBox {{{1*/ + Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(void){ + Index: /issm/oecreview/Archive/12201-12220/ISSM-12210-12211.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12210-12211.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12210-12211.diff (revision 12325) @@ -0,0 +1,37 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-ubuntu64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-ubuntu64.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-ubuntu64.sh (revision 12211) +@@ -0,0 +1,26 @@ ++#!/bin/sh ++ ++./configure \ ++ --prefix=$ISSM_DIR \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl -ldl" \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ ++ --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ ++ --with-fortran-lib="-lgfortran"\ ++ --with-numthreads=8 \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --enable-debugging ++ ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-ubuntu64.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12201-12220/ISSM-12211-12212.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12211-12212.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12211-12212.diff (revision 12325) @@ -0,0 +1,50 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-ubuntu64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-ubuntu64.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-ubuntu64.sh (revision 12212) +@@ -0,0 +1,39 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf install petsc-3.1-p7 src ++mkdir install src ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' ++ ++#Untar and move petsc to install directory ++tar -zxvf petsc-3.1-p7.tar.gz ++mv petsc-3.1-p7/* src/ ++rm -rf petsc-3.1-p7 ++ ++#configure ++cd src ++./config/configure.py \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ ++ --PETSC_ARCH=linux-gnu\ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ ++ --with-debugging=0 \ ++ --with-shared=0 \ ++ --download-mumps=yes \ ++ --download-scalapack=yes \ ++ --download-blacs=yes \ ++ --download-blas=yes \ ++ --download-f-blas-lapack=yes \ ++ --download-parmetis=yes \ ++ --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --download-plapack=yes \ ++ --COPTFLAGS="-O2" \ ++ --FOPTFLAGS="-O2" \ ++ --CXXOPTFLAGS="-O2" \ ++ --with-pic=1 ++ ++#Compile petsc and install it ++make ++make install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.1-ubuntu64.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12201-12220/ISSM-12212-12213.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12212-12213.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12212-12213.diff (revision 12325) @@ -0,0 +1,389 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12212) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12213) +@@ -27,28 +27,62 @@ + /*Object constructors and destructor*/ + /*FUNCTION Observations::Observations(){{{*/ + Observations::Observations(){ ++ this->quadtree = NULL; + return; + } + /*}}}*/ + /*FUNCTION Observations::Observations(double* observations_list,double* x,double* y,int n){{{*/ + Observations::Observations(double* observations_list,double* x,double* y,int n){ + ++ const int MaxICoor = 1073741823; // 2^30-1 =111...111 (29 times) ++ ++ /*Intermediaries*/ ++ int i; ++ int xi,yi; ++ double offset; ++ Observation *observation = NULL; ++ ++ /*Initialize Quadtree*/ ++ this->quadtree = new Quadtree(); ++ ++ /*Get extrema*/ ++ this->xmin=x[0]; this->ymin=y[0]; ++ this->xmax=x[0]; this->ymax=y[0]; ++ for(i=1;icoefficient = double(MaxICoor)/max(xmax-xmin,ymax-ymin); _assert_(coefficient>=0); ++ + /*Add observations one by one*/ +- for(int i=0;iAddObject(new Observation(x[i],y[i],0,0,observations_list[i])); ++ for(i=0;iquadtree->Add(observation); ++ this->AddObject(observation); + } +- + } + /*}}}*/ + /*FUNCTION Observations::~Observations(){{{*/ + Observations::~Observations(){ ++ delete quadtree; + return; + } + /*}}}*/ + + /*Methods*/ + /*FUNCTION Observations::ObservationList{{{*/ +-void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp){/*{{{*/ ++void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp){ + + /*Output and Intermediaries*/ + int nobs,i; +@@ -77,3 +111,22 @@ + *pobs=obs; + *pnobs=nobs; + }/*}}}*/ ++/*FUNCTION Observations::QuadtreeColoring{{{*/ ++void Observations::QuadtreeColoring(double* A,double *x,double *y,int n){ ++ ++ /*Convert to integer coordinates*/ ++ int *xi = (int*)xmalloc(n*sizeof(int)); ++ int *yi = (int*)xmalloc(n*sizeof(int)); ++ for(int i=0;iquadtree->QuadtreeColoring(A,xi,yi,n); ++ ++ /*clean-up*/ ++ xfree((void**)&xi); ++ xfree((void**)&yi); ++ ++}/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12212) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12213) +@@ -6,9 +6,18 @@ + #define _CONTAINER_OBSERVATIONS_H_ + + class Obsevration; ++class Quadtree; + + class Observations: public DataSet{ + ++ private: ++ Quadtree* quadtree; ++ double coefficient; //For integer coordinate conversion ++ double xmin; ++ double ymin; ++ double xmax; ++ double ymax; ++ + public: + + /*constructors, destructors*/ +@@ -18,6 +27,7 @@ + + /*Methods*/ + void ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp); ++ void QuadtreeColoring(double* A,double *x,double *y,int n); + + }; + #endif //ifndef _OBSERVATIONS_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.h (revision 12212) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Vertices.h (revision 12213) +@@ -31,7 +31,4 @@ + + }; + +- +- + #endif //ifndef _VERTICES_H_ +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Elements/elements.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Elements/elements.h (revision 12212) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Elements/elements.h (revision 12213) +@@ -46,5 +46,17 @@ + } + printf("\n"); + } ++inline void printbinary(int n) { ++ unsigned int i; ++ i=1<<(sizeof(n)*8-1); + ++ while (i>0) { ++ if (n&i) ++ printf("1"); ++ else ++ printf("0"); ++ i>>=1; ++ } ++} ++ + #endif //ifndef _SHARED_ELEMENTS_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12212) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12213) +@@ -44,6 +44,11 @@ + /*Allocation output*/ + predictions =(double*)xmalloc(n_interp*sizeof(double)); + ++ for(i=0;iQuadtreeColoring(predictions,x_interp,y_interp,n_interp); ++ *ppredictions=predictions; ++ return 1; ++ + /*Loop over all interpolations*/ + printf(" interpolation progress: %5.2lf %%",0.0); + for(int idx=0;idxxi; +- j = observation->yi; ++ xi = observation->xi; ++ yi = observation->yi; + + /*Initialize level*/ + level=(1L<nbitems<0)){ + +- /*shift b->nbitems by -1 as a counter*/ +- b->nbitems--; +- + /*Go down one level = 00100 -> 00010*/ + level>>=1; + + /*Get next subbox according to the bit value (level)*/ +- pb = &b->box[IJ(i,j,level)]; ++ pb = &b->box[IJ(xi,yi,level)]; + } + _assert_(level>0); + +@@ -142,7 +140,6 @@ + while((b=*pb) && (b->nbitems==4)){ + + /*Copy the 4 observation in the current Quadtreebox*/ +- Observation* obs[4]; + obs[0] = b->obs[0]; + obs[1] = b->obs[1]; + obs[2] = b->obs[2]; +@@ -161,52 +158,87 @@ + level>>=1; + + /*Put the four observations in the new boxes*/ +- for (k=0;k<4;k++){ ++ for (int k=0;k<4;k++){ + + /*Get box for observation number k*/ +- ij=IJ(obs[k]->xi,obs[k]->yi,level); +- QuadtreeBox *bb = b->box[ij]; ++ ij = IJ(obs[k]->xi,obs[k]->yi,level); ++ bb = b->box[ij]; + if(!bb){ + b->box[ij]=NewQuadtreeBox(); + bb=b->box[ij]; + } +- +- /*Copy current observations*/ + bb->obs[bb->nbitems++] = obs[k]; + } + + /*Get the subbox where the current observation is located*/ +- ij=IJ(i,j,level); ++ ij=IJ(xi,yi,level); + pb=&b->box[ij]; + } + + /*alloc the QuadtreeBox if necessary and add current observation*/ + b=*pb; +- if(!b) b=NewQuadtreeBox(); ++ if(!b){ ++ b=*pb=NewQuadtreeBox(); ++ } + b->obs[b->nbitems++]=observation; + NbObs++; + + }/*}}}*/ +- /*FUNCTION Quadtree::NewQuadtreeBox {{{1*/ +- Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(void){ ++/*FUNCTION Quadtree::Echo{{{1*/ ++void Quadtree::Echo(void){ + +- /*Output*/ +- QuadtreeBox* newbox=NULL; ++ printf("Quadtree:\n"); ++ printf(" NbQuadtreeBox = %i\n",NbQuadtreeBox); ++ printf(" NbObs = %i\n",NbObs); ++ printf(" root = %p\n",root); + +- /*Create and initialize a new box*/ +- newbox=new QuadtreeBox(); +- newbox->nbitems=0; +- newbox->box[0]=NULL; +- newbox->box[1]=NULL; +- newbox->box[2]=NULL; +- newbox->box[3]=NULL; ++}/*}}}*/ ++/*FUNCTION Quadtree::NewQuadtreeBox {{{1*/ ++Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(void){ + +- /*Add root to the container*/ +- boxcontainer->AddObject(newbox); ++ /*Output*/ ++ QuadtreeBox* newbox=NULL; + +- /*Increase counter*/ +- NbQuadtreeBox++; ++ /*Create and initialize a new box*/ ++ newbox=new QuadtreeBox(); ++ newbox->nbitems=0; ++ newbox->box[0]=NULL; ++ newbox->box[1]=NULL; ++ newbox->box[2]=NULL; ++ newbox->box[3]=NULL; + +- /*currentbox now points toward next quadtree box*/ +- return newbox; +- }/*}}}*/ ++ /*Add to container*/ ++ this->boxcontainer->AddObject(newbox); ++ NbQuadtreeBox++; ++ ++ /*currentbox now points toward next quadtree box*/ ++ return newbox; ++}/*}}}*/ ++/*FUNCTION Quadtree::QuadtreeColoring{{{1*/ ++void Quadtree::QuadtreeColoring(double* A,int *xi,int *yi,int n){ ++ ++ const int MaxDeep = 30; ++ QuadtreeBox **pb = NULL; ++ QuadtreeBox *b = NULL; ++ int level; ++ ++ for(int i=0;inbitems<0)){ ++ ++ /*Color matrix onces more*/ ++ A[i]+=1; ++ ++ /*Go to one box deeper*/ ++ level>>=1; ++ pb = &b->box[IJ(xi[i],yi[i],level)]; ++ } ++ } ++}/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp (revision 12212) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp (revision 12213) +@@ -2,6 +2,7 @@ + * \brief: implementation of the Observation object + */ + ++#include + #include "../objects.h" + + /*Observation constructors and destructor*/ +@@ -30,11 +31,14 @@ + /*Object virtual functions definitions:*/ + /*FUNCTION Observation::Echo {{{1*/ + void Observation::Echo(void){ ++ ++ int bit; ++ + printf("Observation\n"); + printf(" x : %g\n",this->x); + printf(" y : %g\n",this->y); +- printf(" xi : %i\n",this->xi); +- printf(" yi : %i\n",this->yi); ++ printf(" xi : "); printbinary(this->xi); printf("\n"); ++ printf(" yi : "); printbinary(this->yi); printf("\n"); + printf(" value : %g\n",this->value); + } + /*}}}*/ Index: /issm/oecreview/Archive/12201-12220/ISSM-12213-12214.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12213-12214.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12213-12214.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 12213) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 12214) +@@ -214,7 +214,7 @@ + + #APPSCAN + export PATH="$PATH:$APPSCAN_DIR/install/bin" +-export PATH="$PATH:$APPSCAN_DIR/bin"] ++export PATH="$PATH:$APPSCAN_DIR/bin" + + #CPPCHECK + export PATH="$PATH:$CPPCHECK_DIR/bin" Index: /issm/oecreview/Archive/12201-12220/ISSM-12214-12215.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12214-12215.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12214-12215.diff (revision 12325) @@ -0,0 +1,26 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh (revision 12214) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh (revision 12215) +@@ -5,7 +5,7 @@ + mkdir src install + + #Download from ISSM server +-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + + #Untar + tar -zxvf gsl-1.15.tar.gz +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-linux64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-linux64.sh (revision 12214) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-linux64.sh (revision 12215) +@@ -5,7 +5,7 @@ + mkdir src install + + #Download from ISSM server +-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + + #Untar + tar -zxvf gsl-1.15.tar.gz Index: /issm/oecreview/Archive/12201-12220/ISSM-12215-12216.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12215-12216.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12215-12216.diff (revision 12325) @@ -0,0 +1,160 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h (revision 12215) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h (revision 12216) +@@ -6,8 +6,8 @@ + + namespace bamg { + +- const int MaxDeep = 30; +- const long MaxISize = ( 1L << MaxDeep); // = 2^30 : 010000000000..000 (bitwise operation) ++ const int MaxDepth = 30; ++ const long MaxISize = ( 1L << MaxDepth); // = 2^30 : 010000000000..000 (bitwise operation) + + class BamgVertex; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.cpp (revision 12215) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.cpp (revision 12216) +@@ -178,7 +178,7 @@ + if (b->nbitems > 0 && b->v[0] == &w) return; + } + +- /*check that l is not 0 (this should not happen as MaxDeep = 30)*/ ++ /*check that l is not 0 (this should not happen as MaxDepth = 30)*/ + _assert_(level>0); + + /*Now, try to add the vertex, if the subbox is full (nbitems=4), we have to divide it +@@ -235,10 +235,10 @@ + /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/NearestVertex)*/ + + /*Intermediaries*/ +- QuadTreeBox *pb[MaxDeep]; +- int pi[MaxDeep]; +- Icoor1 ii[MaxDeep]; +- Icoor1 jj[MaxDeep]; ++ QuadTreeBox *pb[MaxDepth]; ++ int pi[MaxDepth]; ++ Icoor1 ii[MaxDepth]; ++ Icoor1 jj[MaxDepth]; + int level; + long n0; + QuadTreeBox *b; +@@ -393,9 +393,9 @@ + BamgVertex* QuadTree::NearestVertexWithNormal(Icoor1 i,Icoor1 j) { + /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/NearestVertexWithNormal)*/ + +- QuadTreeBox * pb[ MaxDeep ]; +- int pi[ MaxDeep ]; +- Icoor1 ii[ MaxDeep ], jj [ MaxDeep]; ++ QuadTreeBox * pb[ MaxDepth ]; ++ int pi[ MaxDepth ]; ++ Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; + int l; // level + QuadTreeBox * b; + long h =MaxISize,h0; +@@ -529,9 +529,9 @@ + const R2 X(v.r); + const Metric Mx(v.m); + +- QuadTreeBox * pb[ MaxDeep ]; +- int pi[ MaxDeep ]; +- Icoor1 ii[ MaxDeep ], jj [ MaxDeep]; ++ QuadTreeBox * pb[ MaxDepth ]; ++ int pi[ MaxDepth ]; ++ Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; + register int l=0; // level + register QuadTreeBox * b; + Icoor1 h=MaxISize; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12215) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12216) +@@ -34,9 +34,10 @@ + DataSet* boxcontainer; + + public: +- QuadtreeBox* root; // main box ++ int MaxDepth; // maximum number of subdivision ++ QuadtreeBox *root; // main box + long NbQuadtreeBox; // total number of boxes +- long NbObs; // number of points ++ long NbObs; // number of points + + Quadtree(); + ~Quadtree(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12215) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12216) +@@ -82,20 +82,21 @@ + /*FUNCTION Quadtree::Quadtree(){{{1*/ + Quadtree::Quadtree(){ + +- /*Number of boxes and vertices*/ +- NbQuadtreeBox=0; +- NbObs=0; ++ /*Initialize fields*/ ++ this->MaxDepth=30; ++ this->NbQuadtreeBox=0; ++ this->NbObs=0; + + /*Create container*/ +- boxcontainer=new DataSet(); ++ this->boxcontainer=new DataSet(); + + /*Create Root, pointer toward the main box*/ +- root=NewQuadtreeBox(); ++ this->root=NewQuadtreeBox(); + + } + /*}}}1*/ + /*FUNCTION Quadtree::~Quadtree(){{{1*/ +- Quadtree::~Quadtree() { ++ Quadtree::~Quadtree(){ + + delete boxcontainer; + root=NULL; +@@ -108,7 +109,6 @@ + void Quadtree::Add(Observation* observation){ + + /*Intermediaries*/ +- const int MaxDeep = 30; + int xi,yi,ij,level; + QuadtreeBox **pb = NULL; + QuadtreeBox *b = NULL; +@@ -120,7 +120,7 @@ + yi = observation->yi; + + /*Initialize level*/ +- level=(1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pb=&root; +@@ -188,6 +188,7 @@ + void Quadtree::Echo(void){ + + printf("Quadtree:\n"); ++ printf(" MaxDepth = %i\n",MaxDepth); + printf(" NbQuadtreeBox = %i\n",NbQuadtreeBox); + printf(" NbObs = %i\n",NbObs); + printf(" root = %p\n",root); +@@ -217,7 +218,6 @@ + /*FUNCTION Quadtree::QuadtreeColoring{{{1*/ + void Quadtree::QuadtreeColoring(double* A,int *xi,int *yi,int n){ + +- const int MaxDeep = 30; + QuadtreeBox **pb = NULL; + QuadtreeBox *b = NULL; + int level; +@@ -225,7 +225,7 @@ + for(int i=0;iMaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pb=&root; Index: /issm/oecreview/Archive/12201-12220/ISSM-12216-12217.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12216-12217.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12216-12217.diff (revision 12325) @@ -0,0 +1,91 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test137.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test137.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test137.m (revision 12217) +@@ -0,0 +1,25 @@ ++ ++%Simple mesh ++md=bamg(model,'domain','../Exp/Square.exp','hmax',100000); ++x1=md.mesh.x; ++y1=md.mesh.y; ++ ++%hVertices ++md=bamg(model,'domain','../Exp/Square.exp','hmax',300000,'hvertices',[10000 100000 400000 100000]'); ++x2=md.mesh.x; ++y2=md.mesh.y; ++ ++%big mesh ++t0=clock; ++md=bamg(model,'domain','../Exp/Square.exp','hmax',3000); ++nbelements=md.mesh.numberofelements; ++elapsedtime=etime(clock,t0); ++ ++%Fields and tolerances to track changes ++field_names ={'x1' 'y1' 'x2' 'y2' 'nbelements' 'elapsed time'}; ++field_tolerances={1e-13 1e-13 1e-13 1e-13 1e-13 0.5}; ++field_values={... ++ x1, y1,... ++ x2, y2,... ++ nbelements,elapsedtime... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test527.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test527.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test527.m (revision 12217) +@@ -0,0 +1,56 @@ ++%Simple mesh 1 ++hVertices=10000*ones(27,1); ++hVertices(1:5)=1000; ++md=bamg(model,'domain','../Exp/Pig.exp','hmax',20000,'hVertices',hVertices,'gradation',3,'geometricalmetric',1); ++x1=md.mesh.x; ++y1=md.mesh.y; ++ ++%Simple mesh 2 ++md=bamg(model,'domain','../Exp/Pig.exp','hmax',10000); ++md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); ++md=parameterize(md,'../Par/Pig.par'); ++x2=md.mesh.x; ++y2=md.mesh.y; ++ ++%refine existing mesh 1 ++hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vy_obs,'node'); ++metric=ComputeMetric(hessian,2/9,1,1000,25*10^3,[]); ++md.miscellaneous.dummy=metric; ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1); ++x3=md2.mesh.x; ++y3=md2.mesh.y; ++ ++%refine existing mesh 2 ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1); ++x4=md2.mesh.x; ++y4=md2.mesh.y; ++ ++%refine existing mesh 3 ++hVertices=NaN*ones(md.mesh.numberofvertices,1); ++hVertices(find(md.mesh.vertexonboundary))=500; ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1,'hVertices',hVertices); ++x5=md2.mesh.x; ++y5=md2.mesh.y; ++ ++%refine existing mesh 4 ++md2=bamg(md,'field',md.inversion.vy_obs,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',0,'err',1); ++x6=md2.mesh.x; ++y6=md2.mesh.y; ++ ++%refine existing mesh 5 ++md2=bamg(md,'field',[md.inversion.vy_obs md.geometry.thickness],'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',1,'err',[10 100]); ++x7=md2.mesh.x; ++y7=md2.mesh.y; ++ ++%Fields and tolerances to track changes ++field_names ={'x1' 'y1' 'x2' 'y2' 'x3' 'y3' 'x4' 'y4' 'x5' 'y5' 'x6' 'y6' 'x7' 'y7' }; ++field_tolerances={1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13 1e-13}; ++field_values={... ++ x1, y1,... ++ y2, y2,... ++ y3, y3,... ++ y4, y4,... ++ y5, y5,... ++ y6, y6,... ++ y7, y7,... ++ }; Index: /issm/oecreview/Archive/12201-12220/ISSM-12217-12218.diff =================================================================== --- /issm/oecreview/Archive/12201-12220/ISSM-12217-12218.diff (revision 12325) +++ /issm/oecreview/Archive/12201-12220/ISSM-12217-12218.diff (revision 12325) @@ -0,0 +1,1531 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 12217) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 12218) +@@ -91,7 +91,7 @@ + Mesh BTh(bamggeom_in,bamgmesh_in,bamgopts); + + //Make Quadtree from background mesh +- BTh.MakeQuadTree(); ++ BTh.MakeBamgQuadtree(); + + //Bound hmin and hmax + bamgopts->hmin=Max(bamgopts->hmin,BTh.MinimalHmin()); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12217) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12218) +@@ -571,8 +571,8 @@ + ./objects/Bamg/EigenMetric.cpp\ + ./objects/Bamg/Metric.cpp\ + ./objects/Bamg/Metric.h\ +- ./objects/Bamg/QuadTree.cpp\ +- ./objects/Bamg/QuadTree.h\ ++ ./objects/Bamg/BamgQuadtree.cpp\ ++ ./objects/Bamg/BamgQuadtree.h\ + ./objects/Bamg/R2.h\ + ./objects/Bamg/SetOfE4.cpp\ + ./objects/Bamg/SetOfE4.h\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h (revision 12217) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.h (revision 12218) +@@ -1,61 +0,0 @@ +-/*Original code from Frederic Hecht (BAMG v1.01, QuadTree.h)*/ +-#ifndef _QUADTREE_H +-#define _QUADTREE_H +- +-#include "./include.h" +- +-namespace bamg { +- +- const int MaxDepth = 30; +- const long MaxISize = ( 1L << MaxDepth); // = 2^30 : 010000000000..000 (bitwise operation) +- +- class BamgVertex; +- +- class QuadTree{ +- +- private: +- +- /*A quadtree box contains a maximum of 4 vertices. 4 other quadtree boxes are +- * created if a fifth vertex is added to the same box. A Quadtree box is therefore +- * composed of EITHER: +- * - up to 4 vertices +- * - 4 "sub" quadtree boxes*/ +- class QuadTreeBox: public Object{ +- public: +- int nbitems; // number of current vertices in the box +- union{ +- QuadTreeBox* b[4]; +- BamgVertex* v[4]; +- }; +- /*Object functions*/ +- void Echo(){_error_("not implemented yet");}; +- void DeepEcho(){_error_("not implemented yet");}; +- int Id(){_error_("not implemented yet");}; +- int MyRank(){_error_("not implemented yet");}; +- int ObjectEnum(){_error_("not implemented yet");}; +- Object* copy(){_error_("not implemented yet");}; +- }; +- +- /*QuadTree private Fields*/ +- DataSet* boxcontainer; +- +- public: +- +- /*QuadTree public Fields*/ +- QuadTreeBox* root; +- long NbQuadTreeBox; +- long NbVertices; +- +- QuadTree(); +- QuadTree(Mesh *t,long nbv=-1); +- ~QuadTree(); +- +- BamgVertex* NearestVertex(Icoor1 i,Icoor1 j); +- BamgVertex* NearestVertexWithNormal(Icoor1 i,Icoor1 j); +- QuadTreeBox* NewQuadTreeBox(void); +- BamgVertex* ToClose(BamgVertex & ,double ,Icoor1,Icoor1); +- void Add( BamgVertex & w); +- +- }; +-} +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.cpp (revision 12217) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/QuadTree.cpp (revision 12218) +@@ -1,598 +0,0 @@ +-#include +-#include +-#include +- +-#include "../objects.h" +- +-namespace bamg { +- +- /*MACROS {{{1*/ +- /* +- * +- * J j +- * ^ ^ +- * | | +--------+--------+ +- * | | | | | +- * 1X | | | 2 | 3 | +- * | | | | | +- * | | +--------+--------+ +- * | | | | | +- * 0X | | | 0 | 1 | +- * | | | | | +- * | | +--------+--------+ +- * | +-----------------------> i +- * | +- * |----------------------------> I +- * X0 X1 +- * +- * box 0 -> I=0 J=0 IJ=00 = 0 +- * box 1 -> I=1 J=0 IJ=01 = 1 +- * box 2 -> I=0 J=1 IJ=10 = 2 +- * box 3 -> I=1 J=1 IJ=11 = 3 +- */ +-#define INTER_SEG(a,b,x,y) (((y) > (a)) && ((x) <(b))) +-#define ABS(i) ((i)<0 ?-(i) :(i)) +-#define MAX1(i,j) ((i)>(j) ?(i) :(j)) +-#define NORM(i1,j1,i2,j2) MAX1(ABS((i1)-(j1)),ABS((i2)-(j2))) +- +- //IJ(i,j,l) returns the box number of i and j with respect to l +- //if !j&l and !i&l -> 0 (box zero: lower left ) +- //if !j&l and i&l -> 1 (box one: lower right) +- //if j&l and !i&l -> 2 (box two: upper left ) +- //if j&l and i&l -> 3 (box three:upper right) +-#define IJ(i,j,l) ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 )) +- +- //I_IJ(k,l) returns l if first bit of k is 1, else 0 +-#define I_IJ(k,l) ((k&1) ? l:0) +- //J_IJ(k,l) returns l if second bit of k is 1, else 0 +-#define J_IJ(k,l) ((k&2) ? l:0) +- /*}}}*/ +- /*DOCUMENTATION What is a QuadTree? {{{1 +- * A Quadtree is a very simple way to group vertices according +- * to their locations. A square that holds all the points of the mesh +- * (or the geometry) is divided into 4 boxes. As soon as one box +- * hold more than 4 vertices, it is divided into 4 new boxes, etc... +- * There cannot be more than MAXDEEP (=30) subdivision. +- * This process is like a Dichotomy in dimension 2 +- * +- * + - - - - - - - - + - - + - + - + - - - - + +- * | | | | X | | +- * + - + - + +- * | | | | | | +- * + - - + - + - + + +- * | | | | | +- * +- * | | | | | +- * + - - - - - - - - + - - + - - + - - - - + +- * | | | | +- * +- * | | | | +- * +- * | | | | +- * | | | | +- * + - - - - - - - - + - - - - + - - - - + +- * | | | +- * +- * | | | +- * +- * | | | +- * +- * | | | +- * | | | +- * | | | +- * | | | +- * | | | +- * + - - - - - - - - + - - - - - - - - + +- * +- * The coordinate system used in a quadtree are integers to avoid +- * round-off errors. The vertex in the lower left box has the coordinates +- * (0 0) +- * The upper right vertex has the follwing coordinates: +- * 2^30 -1 2^30 -1 in decimal +- * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary +- * \-- 29 --/ \-- 29 --/ +- * Using binaries is therefore very easy to locate a vertex in a box: +- * we just need to look at the bits from the left to the right (See ::Add) +- }}}1*/ +- +- /*Constructors/Destructors*/ +- /*FUNCTION QuadTree::QuadTree(){{{1*/ +- QuadTree::QuadTree(){ +- +- /*Number of boxes and vertices*/ +- NbQuadTreeBox=0; +- NbVertices=0; +- +- /*Create container*/ +- boxcontainer=new DataSet(); +- +- /*Create Root, pointer toward the main box*/ +- root=NewQuadTreeBox(); +- +- } +- /*}}}1*/ +- /*FUNCTION QuadTree::QuadTree(Mesh * t,long nbv){{{1*/ +- QuadTree::QuadTree(Mesh * t,long nbv){ +- +- /*Number of boxes and vertices*/ +- NbQuadTreeBox=0; +- NbVertices=0; +- +- /*Create container*/ +- boxcontainer=new DataSet(); +- +- /*Create Root, pointer toward the main box*/ +- root=NewQuadTreeBox(); +- +- /*Check Sizes*/ +- _assert_(MaxISize>MaxICoor); +- +- /*Add all vertices of the mesh*/ +- if (nbv==-1) nbv=t->nbv; +- for (int i=0;ivertices[i]); +- +- } +- /*}}}1*/ +- /*FUNCTION QuadTree::~QuadTree(){{{1*/ +- QuadTree::~QuadTree() { +- delete boxcontainer; +- root=NULL; +- } +- /*}}}1*/ +- +- /*Methods*/ +- /*FUNCTION QuadTree::Add{{{1*/ +- void QuadTree::Add(BamgVertex &w){ +- /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/Add)*/ +- QuadTreeBox** pb=NULL; +- QuadTreeBox* b=NULL; +- +- /*Get integer coodinate of current point w*/ +- register long i=w.i.x, j=w.i.y; +- +- /*Initialize level*/ +- register long level=MaxISize; +- +- /*Get inital box (the largest)*/ +- pb = &root; +- +- /*Find the smallest box where w is located*/ +- while((b=*pb) && (b->nbitems<0)){ +- +- //shift b->nbitems by -1 +- b->nbitems--; +- +- //shifted righ by one bit: level=00000010 -> 00000001 +- level >>= 1; +- +- //Get next subbox according to the bit value (level) +- pb = &b->b[IJ(i,j,level)]; +- } +- +- /*OK, we have found b, a Subbox holding vertices (might be full) +- check that the vertex is not already in the box*/ +- if (b){ +- if (b->nbitems > 3 && b->v[3] == &w) return; +- if (b->nbitems > 2 && b->v[2] == &w) return; +- if (b->nbitems > 1 && b->v[1] == &w) return; +- if (b->nbitems > 0 && b->v[0] == &w) return; +- } +- +- /*check that l is not 0 (this should not happen as MaxDepth = 30)*/ +- _assert_(level>0); +- +- /*Now, try to add the vertex, if the subbox is full (nbitems=4), we have to divide it +- in 4 new subboxes*/ +- while ((b= *pb) && (b->nbitems == 4)){ // the QuadTreeBox is full +- +- /*Copy the 4 vertices in the current QuadTreebox*/ +- BamgVertex* v4[4]; +- v4[0]= b->v[0]; +- v4[1]= b->v[1]; +- v4[2]= b->v[2]; +- v4[3]= b->v[3]; +- +- /*set nbitems as negative +- * (box full -> holds 4 pointers toward subboxes and not 4 vertices)*/ +- b->nbitems = -b->nbitems; +- +- /*Initialize the 4 pointers toward the 4 subboxes*/ +- b->b[0]=b->b[1]=b->b[2]=b->b[3]=NULL; +- +- /*level = 0010000 -> 0001000*/ +- level >>= 1; +- +- /*Put the four vertices in the new boxes*/ +- for (int k=0;k<4;k++){ +- +- int ij; +- /*bb is the new "sub"box of b where v4[k] is located*/ +- QuadTreeBox *bb = b->b[ij=IJ(v4[k]->i.x,v4[k]->i.y,level)]; +- +- // alloc the QuadTreeBox +- if (!bb) bb=b->b[ij]=NewQuadTreeBox(); +- +- /*Copy the current vertex*/ +- bb->v[bb->nbitems++] = v4[k]; +- } +- +- /*Get the subbox where w (i,j) is located*/ +- pb = &b->b[IJ(i,j,level)]; +- } +- +- /*alloc the QuadTreeBox if necessary*/ +- if (!(b=*pb)) b=*pb= NewQuadTreeBox(); +- +- /*Add w*/ +- b->v[b->nbitems++]=&w; +- +- //Increase NbVertices by one (we have one new vertex) +- NbVertices++; +- } +- /*}}}1*/ +- /*FUNCTION QuadTree::NearestVertex{{{1*/ +- BamgVertex* QuadTree::NearestVertex(Icoor1 i,Icoor1 j) { +- /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/NearestVertex)*/ +- +- /*Intermediaries*/ +- QuadTreeBox *pb[MaxDepth]; +- int pi[MaxDepth]; +- Icoor1 ii[MaxDepth]; +- Icoor1 jj[MaxDepth]; +- int level; +- long n0; +- QuadTreeBox *b; +- long h0; +- long h = MaxISize; +- long hb= MaxISize; +- Icoor1 i0=0,j0=0; +- +- /*initial output as NULL (no vertex found)*/ +- BamgVertex* nearest_v=NULL; +- +- /*Project w coordinates (i,j) onto [0,MaxISize-1] x [0,MaxISize-1] -> (iplus,jplus)*/ +- Icoor1 iplus( inbitems) return nearest_v; +- +- /*else, find the smallest non-empty QuadTreeBox containing the point (i,j)*/ +- while((n0=b->nbitems)<0){ +- +- Icoor1 hb2 = hb >> 1; //size of the current box +- int k = IJ(iplus,jplus,hb2); //box number (0,1,2 or 3) +- QuadTreeBox *b0 = b->b[k]; //pointer toward current box +- +- /* break if NULL box or empty (Keep previous box b)*/ +- if (( b0 == NULL) || (b0->nbitems == 0)) break; +- +- /*Get next Quadtree box*/ +- b=b0; +- i0 += I_IJ(k,hb2); // i orign of QuadTreeBox (macro) +- j0 += J_IJ(k,hb2); // j orign of QuadTreeBox +- hb = hb2; // size of the box (in Int) +- } +- +- /*The box b, is the smallest box containing the point (i,j) and +- * has the following properties: +- * - n0: number of items (>0 if vertices, else boxes) +- * - hb: box size (int) +- * - i0: x coordinate of the lower left corner +- * - j0: y coordinate of the lower left corner*/ +- +- /* if the current subbox is holding vertices, we are almost done*/ +- if (n0>0){ +- //loop over the vertices of the box and find the closest vertex +- for(int k=0;kv[k]->i; +- +- /*Compute norm with w*/ +- h0=NORM(iplus,i2.x,jplus,i2.y); +- +- /*is it smaller than previous value*/ +- if (h0v[k]; +- } +- } +- /*return closest vertex*/ +- return nearest_v; +- } +- +- /* general case: the current box is empty, we have to go backwards +- and find the closest not-empty box and find the closest vertex*/ +- +- /*Initialize search variables*/ +- pb[0]=b; //pointer toward the box b +- pi[0]=b->nbitems>0?(int)b->nbitems:4;//number of boxes in b +- ii[0]=i0; //i coordinate of the box lowest left corner +- jj[0]=j0; //j coordinate of the box lowest left corner +- +- /*initialize h: smallest box size, containing a vertex close to w*/ +- h=hb; +- +- /*Main loop*/ +- level=0; +- do { +- +- /*get current box*/ +- b= pb[level]; +- +- /*Loop over the items in current box (if not empty!)*/ +- while (pi[level]){ +- +- /*We are looping now over the items of b. k is the current index (in [0 3])*/ +- pi[level]--; +- int k=pi[level]; +- +- /*if the current subbox is holding vertices (b->nbitems<0 is subboxes)*/ +- if (b->nbitems>0){ +- I2 i2=b->v[k]->i; +- h0 = NORM(iplus,i2.x,jplus,i2.y); +- if (h0v[k]; +- } +- } +- /*else: current box b is pointing toward 4 boxes +- * test sub-box k and go deeper into the tree if it is non empty +- * and contains the point w modulo a size h that is either the size of the smallest +- * non empty box containing w, or the closest point to w (so far) */ +- else{ +- QuadTreeBox* b0=b; +- +- /*if the next box exists:*/ +- if (b=b->b[k]){ +- +- /*Get size (hb) and coordinates of the current sub-box lowest left corner*/ +- hb>>=1; +- Icoor1 iii = ii[level]+I_IJ(k,hb); +- Icoor1 jjj = jj[level]+J_IJ(k,hb); +- +- /*if the current point (iplus,jplus) is in b (modulo h), this box is good: +- * it is holding vertices that are close to w */ +- if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)){ +- level++; +- pb[level]= b; +- pi[level]= b->nbitems>0 ?(int) b->nbitems : 4 ; +- ii[level]= iii; +- jj[level]= jjj; +- } +- +- //else go backwards +- else{ +- //shifted righ by one bit: hb=001000000 -> 01000000 +- b=b0; +- hb<<=1; +- } +- } +- else{ +- /*Current box is NULL, go to next subbox of b (k=k-1)*/ +- b=b0; +- } +- } +- } +- +- /*We have found a vertex, now, let's try the other boxes of the previous level +- * in case there is a vertex closest to w that has not yet been tested*/ +- hb <<= 1; +- } while (level--); +- +- /*return nearest_v, nearest vertex*/ +- return nearest_v; +- +- } +- /*}}}1*/ +- /*FUNCTION QuadTree::NearestVertexWithNormal{{{1*/ +- BamgVertex* QuadTree::NearestVertexWithNormal(Icoor1 i,Icoor1 j) { +- /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/NearestVertexWithNormal)*/ +- +- QuadTreeBox * pb[ MaxDepth ]; +- int pi[ MaxDepth ]; +- Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; +- int l; // level +- QuadTreeBox * b; +- long h =MaxISize,h0; +- long hb=MaxISize; +- Icoor1 i0=0,j0=0; +- Icoor1 iplus( inbitems) +- return vn; // empty tree +- +- while( (n0 = b->nbitems) < 0) +- { +- // search the non empty +- // QuadTreeBox containing the point (i,j) +- register Icoor1 hb2 = hb >> 1 ; +- register int k = IJ(iplus,jplus,hb2);// QuadTreeBox number of size hb2 contening i;j +- register QuadTreeBox * b0= b->b[k]; +- if ( ( b0 == 0) || (b0->nbitems == 0) ) +- break; // null box or empty => break +- b=b0; +- i0 += I_IJ(k,hb2); // i orign of QuadTreeBox +- j0 += J_IJ(k,hb2); // j orign of QuadTreeBox +- hb = hb2; +- } +- +- +- if ( n0 > 0) +- { +- for(register int k=0;kv[k]->i; +- // try if is in the right direction -- +- h0 = NORM(iplus,i2.x,jplus,i2.y); +- if (h0 v[k];} +- } +- if (vn) return vn; +- } +- // general case ----- +- // INITIALISATION OF THE HEAP +- l =0; // level +- pb[0]= b; +- pi[0]=b->nbitems>0 ?(int) b->nbitems : 4 ; +- ii[0]=i0; +- jj[0]=j0; +- h=hb; +- do { // walk on the tree +- b= pb[l]; +- while (pi[l]--) // loop on 4 element of the box +- { +- int k = pi[l]; +- +- if (b->nbitems>0) // BamgVertex QuadTreeBox none empty +- { +- I2 i2 = b->v[k]->i; +- // if good direction when try -- +- +- h0 = NORM(iplus,i2.x,jplus,i2.y); +- if (h0 v[k]; +- } +- } +- else // Pointer QuadTreeBox +- { +- register QuadTreeBox *b0=b; +- if ((b=b->b[k])) +- { +- hb >>=1 ; // div by 2 +- register Icoor1 iii = ii[l]+I_IJ(k,hb); +- register Icoor1 jjj = jj[l]+J_IJ(k,hb); +- +- if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)) +- { +- pb[++l]= b; +- pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; +- ii[l]= iii; +- jj[l]= jjj; +- +- } +- else +- b=b0, hb <<=1 ; +- } +- else +- b=b0; +- } +- } +- hb <<= 1; // mul by 2 +- } while (l--); +- +- return vn; +- } +- /*}}}1*/ +- /*FUNCTION QuadTree::NewQuadTreeBox {{{1*/ +- QuadTree::QuadTreeBox* QuadTree::NewQuadTreeBox(void){ +- +- /*Output*/ +- QuadTreeBox* newbox=NULL; +- +- /*Create and initialize a new box*/ +- newbox=new QuadTreeBox; +- newbox->nbitems=0; +- newbox->b[0]=NULL; +- newbox->b[1]=NULL; +- newbox->b[2]=NULL; +- newbox->b[3]=NULL; +- +- /*Add root to the container*/ +- boxcontainer->AddObject(newbox); +- +- /*Increase counter*/ +- NbQuadTreeBox++; +- +- /*currentbox now points toward next quadtree box*/ +- return newbox; +- }/*}}}*/ +- /*FUNCTION QuadTree::ToClose {{{1*/ +- BamgVertex* QuadTree::ToClose(BamgVertex & v,double seuil,Icoor1 hx,Icoor1 hy){ +- /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/ToClose)*/ +- +- const Icoor1 i=v.i.x; +- const Icoor1 j=v.i.y; +- const R2 X(v.r); +- const Metric Mx(v.m); +- +- QuadTreeBox * pb[ MaxDepth ]; +- int pi[ MaxDepth ]; +- Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; +- register int l=0; // level +- register QuadTreeBox * b; +- Icoor1 h=MaxISize; +- Icoor1 hb = MaxISize; +- Icoor1 i0=0,j0=0; +- +- // BamgVertex *vn=0; +- +- if (!root->nbitems) +- return 0; // empty tree +- +- // general case ----- +- pb[0]=root; +- pi[0]=root->nbitems>0 ?(int) root->nbitems : 4 ; +- ii[0]=i0; +- jj[0]=j0; +- h=hb; +- do { +- b= pb[l]; +- while (pi[l]--){ +- register int k = pi[l]; +- +- if (b->nbitems>0){ // BamgVertex QuadTreeBox none empty +- I2 i2 = b->v[k]->i; +- if ( ABS(i-i2.x) v[k]->r); +- double dd; +- if( (dd= LengthInterpole(Mx(XY), b->v[k]->m(XY))) < seuil ){ +- return b->v[k]; +- } +- } +- } +- else{ // Pointer QuadTreeBox +- register QuadTreeBox *b0=b; +- if ((b=b->b[k])){ +- hb >>=1 ; // div by 2 +- register long iii = ii[l]+I_IJ(k,hb); +- register long jjj = jj[l]+J_IJ(k,hb); +- +- if (INTER_SEG(iii,iii+hb,i-hx,i+hx) && INTER_SEG(jjj,jjj+hb,j-hy,j+hy)){ +- pb[++l]= b; +- pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; +- ii[l]= iii; +- jj[l]= jjj; +- +- } +- else{ +- b=b0; +- hb <<=1 ; +- } +- } +- else{ +- b=b0; +- } +- } +- } +- hb <<= 1; // mul by 2 +- } while (l--); +- +- return 0; +- } +- /*}}}1*/ +-} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Geometry.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Geometry.h (revision 12217) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Geometry.h (revision 12218) +@@ -11,7 +11,7 @@ + namespace bamg { + + class Triangle; +- class QuadTree; ++ class BamgQuadtree; + class GeomSubDomain; + class Edge; + +@@ -19,19 +19,19 @@ + + public: + +- long NbRef; // counter of ref on the this class if 0 we can delete +- long nbv; // number of vertices +- long nbe; // number of edges +- long nbsubdomains; +- long nbcurves; ++ long NbRef; // counter of ref on the this class if 0 we can delete ++ long nbv; // number of vertices ++ long nbe; // number of edges ++ long nbsubdomains; ++ long nbcurves; + GeomVertex *vertices; + GeomEdge *edges; +- QuadTree *quadtree; ++ BamgQuadtree *quadtree; + GeomSubDomain *subdomains; +- Curve *curves; +- R2 pmin,pmax; // domain extrema coordinates +- double coefIcoor; // coef to integer Icoor1; +- double MaxCornerAngle; ++ Curve *curves; ++ R2 pmin,pmax; // domain extrema coordinates ++ double coefIcoor; // coef to integer Icoor1; ++ double MaxCornerAngle; + + //Constructor/Destructors + ~Geometry(); +@@ -43,7 +43,7 @@ + const GeomVertex &operator[](long i) const { return vertices[i]; }; + GeomVertex &operator[](long i) { return vertices[i]; }; + const GeomEdge &operator()(long i) const { return edges[i]; }; +- GeomEdge &operator()(long i) { return edges[i]; }; ++ GeomEdge &operator()(long i) { return edges[i]; }; + + //Methods + void Echo(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.h (revision 12218) +@@ -0,0 +1,60 @@ ++/*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.h)*/ ++#ifndef _QUADTREE_H ++#define _QUADTREE_H ++ ++#include "./include.h" ++ ++namespace bamg { ++ ++ const int MaxDepth = 30; ++ const long MaxISize = ( 1L << MaxDepth); // = 2^30 : 010000000000..000 (bitwise operation) ++ ++ class BamgVertex; ++ ++ class BamgQuadtree{ ++ ++ private: ++ ++ /*A quadtree box contains a maximum of 4 vertices. 4 other quadtree boxes are ++ * created if a fifth vertex is added to the same box. A Quadtree box is therefore ++ * composed of EITHER: ++ * - up to 4 vertices ++ * - 4 "sub" quadtree boxes*/ ++ class BamgQuadtreeBox: public Object{ ++ public: ++ int nbitems; // number of current vertices in the box ++ union{ ++ BamgQuadtreeBox* b[4]; ++ BamgVertex* v[4]; ++ }; ++ /*Object functions*/ ++ void Echo() {_error_("not implemented yet"); }; ++ void DeepEcho() {_error_("not implemented yet"); }; ++ int Id() {_error_("not implemented yet"); }; ++ int MyRank() {_error_("not implemented yet"); }; ++ int ObjectEnum() {_error_("not implemented yet"); }; ++ Object *copy() {_error_("not implemented yet"); }; ++ }; ++ ++ /*BamgQuadtree private Fields*/ ++ DataSet* boxcontainer; ++ ++ public: ++ ++ /*BamgQuadtree public Fields*/ ++ BamgQuadtreeBox* root; ++ long NbBamgQuadtreeBox; ++ long NbVertices; ++ ++ BamgQuadtree(); ++ BamgQuadtree(Mesh *t,long nbv=-1); ++ ~BamgQuadtree(); ++ ++ BamgVertex *NearestVertex(Icoor1 i,Icoor1 j); ++ BamgVertex *NearestVertexWithNormal(Icoor1 i,Icoor1 j); ++ BamgQuadtreeBox *NewBamgQuadtreeBox(void); ++ BamgVertex *ToClose(BamgVertex &,double ,Icoor1,Icoor1); ++ void Add(BamgVertex &w); ++ }; ++} ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Geometry.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Geometry.cpp (revision 12217) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Geometry.cpp (revision 12218) +@@ -504,7 +504,7 @@ + long *next_p = new long[2*nbe]; + float *eangle = new float[nbe]; + double eps = 1e-20; +- QuadTree quadtree; // build quadtree to find duplicates ++ BamgQuadtree quadtree; // build quadtree to find duplicates + BamgVertex *v0 = vertices; + GeomVertex *v0g = (GeomVertex*) (void*)v0; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.h (revision 12217) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.h (revision 12218) +@@ -16,7 +16,7 @@ + //classes + class Geometry; + class CrackedEdge; +- class QuadTree; ++ class BamgQuadtree; + class SubDomain; + + class Mesh { +@@ -28,7 +28,7 @@ + BamgVertex *vertices; + Triangle *triangles; + Edge *edges; +- QuadTree *quadtree; ++ BamgQuadtree *quadtree; + BamgVertex **orderedvertices; + SubDomain *subdomains; + long NbRef; // counter of ref on the this class if 0 we can delete +@@ -93,7 +93,7 @@ + long SplitInternalEdgeWithBorderVertices(); + void MakeQuadrangles(double costheta); + int SplitElement(int choice); +- void MakeQuadTree(); ++ void MakeBamgQuadtree(); + void NewPoints(Mesh &,BamgOpts* bamgopts,int KeepVertices=1); + long InsertNewPoints(long nbvold,long & NbTSwap) ; + void TrianglesRenumberBySubDomain(bool justcompress=false); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.cpp (revision 12218) +@@ -0,0 +1,598 @@ ++#include ++#include ++#include ++ ++#include "../objects.h" ++ ++namespace bamg { ++ ++ /*MACROS {{{1*/ ++ /* ++ * ++ * J j ++ * ^ ^ ++ * | | +--------+--------+ ++ * | | | | | ++ * 1X | | | 2 | 3 | ++ * | | | | | ++ * | | +--------+--------+ ++ * | | | | | ++ * 0X | | | 0 | 1 | ++ * | | | | | ++ * | | +--------+--------+ ++ * | +-----------------------> i ++ * | ++ * |----------------------------> I ++ * X0 X1 ++ * ++ * box 0 -> I=0 J=0 IJ=00 = 0 ++ * box 1 -> I=1 J=0 IJ=01 = 1 ++ * box 2 -> I=0 J=1 IJ=10 = 2 ++ * box 3 -> I=1 J=1 IJ=11 = 3 ++ */ ++#define INTER_SEG(a,b,x,y) (((y) > (a)) && ((x) <(b))) ++#define ABS(i) ((i)<0 ?-(i) :(i)) ++#define MAX1(i,j) ((i)>(j) ?(i) :(j)) ++#define NORM(i1,j1,i2,j2) MAX1(ABS((i1)-(j1)),ABS((i2)-(j2))) ++ ++ //IJ(i,j,l) returns the box number of i and j with respect to l ++ //if !j&l and !i&l -> 0 (box zero: lower left ) ++ //if !j&l and i&l -> 1 (box one: lower right) ++ //if j&l and !i&l -> 2 (box two: upper left ) ++ //if j&l and i&l -> 3 (box three:upper right) ++#define IJ(i,j,l) ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 )) ++ ++ //I_IJ(k,l) returns l if first bit of k is 1, else 0 ++#define I_IJ(k,l) ((k&1) ? l:0) ++ //J_IJ(k,l) returns l if second bit of k is 1, else 0 ++#define J_IJ(k,l) ((k&2) ? l:0) ++ /*}}}*/ ++ /*DOCUMENTATION What is a BamgQuadtree? {{{1 ++ * A Quadtree is a very simple way to group vertices according ++ * to their locations. A square that holds all the points of the mesh ++ * (or the geometry) is divided into 4 boxes. As soon as one box ++ * hold more than 4 vertices, it is divided into 4 new boxes, etc... ++ * There cannot be more than MAXDEEP (=30) subdivision. ++ * This process is like a Dichotomy in dimension 2 ++ * ++ * + - - - - - - - - + - - + - + - + - - - - + ++ * | | | | X | | ++ * + - + - + ++ * | | | | | | ++ * + - - + - + - + + ++ * | | | | | ++ * ++ * | | | | | ++ * + - - - - - - - - + - - + - - + - - - - + ++ * | | | | ++ * ++ * | | | | ++ * ++ * | | | | ++ * | | | | ++ * + - - - - - - - - + - - - - + - - - - + ++ * | | | ++ * ++ * | | | ++ * ++ * | | | ++ * ++ * | | | ++ * | | | ++ * | | | ++ * | | | ++ * | | | ++ * + - - - - - - - - + - - - - - - - - + ++ * ++ * The coordinate system used in a quadtree are integers to avoid ++ * round-off errors. The vertex in the lower left box has the coordinates ++ * (0 0) ++ * The upper right vertex has the follwing coordinates: ++ * 2^30 -1 2^30 -1 in decimal ++ * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary ++ * \-- 29 --/ \-- 29 --/ ++ * Using binaries is therefore very easy to locate a vertex in a box: ++ * we just need to look at the bits from the left to the right (See ::Add) ++ }}}1*/ ++ ++ /*Constructors/Destructors*/ ++ /*FUNCTION BamgQuadtree::BamgQuadtree(){{{1*/ ++ BamgQuadtree::BamgQuadtree(){ ++ ++ /*Number of boxes and vertices*/ ++ NbBamgQuadtreeBox=0; ++ NbVertices=0; ++ ++ /*Create container*/ ++ boxcontainer=new DataSet(); ++ ++ /*Create Root, pointer toward the main box*/ ++ root=NewBamgQuadtreeBox(); ++ ++ } ++ /*}}}1*/ ++ /*FUNCTION BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){{{1*/ ++ BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){ ++ ++ /*Number of boxes and vertices*/ ++ NbBamgQuadtreeBox=0; ++ NbVertices=0; ++ ++ /*Create container*/ ++ boxcontainer=new DataSet(); ++ ++ /*Create Root, pointer toward the main box*/ ++ root=NewBamgQuadtreeBox(); ++ ++ /*Check Sizes*/ ++ _assert_(MaxISize>MaxICoor); ++ ++ /*Add all vertices of the mesh*/ ++ if (nbv==-1) nbv=t->nbv; ++ for (int i=0;ivertices[i]); ++ ++ } ++ /*}}}1*/ ++ /*FUNCTION BamgQuadtree::~BamgQuadtree(){{{1*/ ++ BamgQuadtree::~BamgQuadtree() { ++ delete boxcontainer; ++ root=NULL; ++ } ++ /*}}}1*/ ++ ++ /*Methods*/ ++ /*FUNCTION BamgQuadtree::Add{{{1*/ ++ void BamgQuadtree::Add(BamgVertex &w){ ++ /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/Add)*/ ++ BamgQuadtreeBox** pb=NULL; ++ BamgQuadtreeBox* b=NULL; ++ ++ /*Get integer coodinate of current point w*/ ++ register long i=w.i.x, j=w.i.y; ++ ++ /*Initialize level*/ ++ register long level=MaxISize; ++ ++ /*Get inital box (the largest)*/ ++ pb = &root; ++ ++ /*Find the smallest box where w is located*/ ++ while((b=*pb) && (b->nbitems<0)){ ++ ++ //shift b->nbitems by -1 ++ b->nbitems--; ++ ++ //shifted righ by one bit: level=00000010 -> 00000001 ++ level >>= 1; ++ ++ //Get next subbox according to the bit value (level) ++ pb = &b->b[IJ(i,j,level)]; ++ } ++ ++ /*OK, we have found b, a Subbox holding vertices (might be full) ++ check that the vertex is not already in the box*/ ++ if (b){ ++ if (b->nbitems > 3 && b->v[3] == &w) return; ++ if (b->nbitems > 2 && b->v[2] == &w) return; ++ if (b->nbitems > 1 && b->v[1] == &w) return; ++ if (b->nbitems > 0 && b->v[0] == &w) return; ++ } ++ ++ /*check that l is not 0 (this should not happen as MaxDepth = 30)*/ ++ _assert_(level>0); ++ ++ /*Now, try to add the vertex, if the subbox is full (nbitems=4), we have to divide it ++ in 4 new subboxes*/ ++ while ((b= *pb) && (b->nbitems == 4)){ // the BamgQuadtreeBox is full ++ ++ /*Copy the 4 vertices in the current BamgQuadtreebox*/ ++ BamgVertex* v4[4]; ++ v4[0]= b->v[0]; ++ v4[1]= b->v[1]; ++ v4[2]= b->v[2]; ++ v4[3]= b->v[3]; ++ ++ /*set nbitems as negative ++ * (box full -> holds 4 pointers toward subboxes and not 4 vertices)*/ ++ b->nbitems = -b->nbitems; ++ ++ /*Initialize the 4 pointers toward the 4 subboxes*/ ++ b->b[0]=b->b[1]=b->b[2]=b->b[3]=NULL; ++ ++ /*level = 0010000 -> 0001000*/ ++ level >>= 1; ++ ++ /*Put the four vertices in the new boxes*/ ++ for (int k=0;k<4;k++){ ++ ++ int ij; ++ /*bb is the new "sub"box of b where v4[k] is located*/ ++ BamgQuadtreeBox *bb = b->b[ij=IJ(v4[k]->i.x,v4[k]->i.y,level)]; ++ ++ // alloc the BamgQuadtreeBox ++ if (!bb) bb=b->b[ij]=NewBamgQuadtreeBox(); ++ ++ /*Copy the current vertex*/ ++ bb->v[bb->nbitems++] = v4[k]; ++ } ++ ++ /*Get the subbox where w (i,j) is located*/ ++ pb = &b->b[IJ(i,j,level)]; ++ } ++ ++ /*alloc the BamgQuadtreeBox if necessary*/ ++ if (!(b=*pb)) b=*pb= NewBamgQuadtreeBox(); ++ ++ /*Add w*/ ++ b->v[b->nbitems++]=&w; ++ ++ //Increase NbVertices by one (we have one new vertex) ++ NbVertices++; ++ } ++ /*}}}1*/ ++ /*FUNCTION BamgQuadtree::NearestVertex{{{1*/ ++ BamgVertex* BamgQuadtree::NearestVertex(Icoor1 i,Icoor1 j) { ++ /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/NearestVertex)*/ ++ ++ /*Intermediaries*/ ++ BamgQuadtreeBox *pb[MaxDepth]; ++ int pi[MaxDepth]; ++ Icoor1 ii[MaxDepth]; ++ Icoor1 jj[MaxDepth]; ++ int level; ++ long n0; ++ BamgQuadtreeBox *b; ++ long h0; ++ long h = MaxISize; ++ long hb= MaxISize; ++ Icoor1 i0=0,j0=0; ++ ++ /*initial output as NULL (no vertex found)*/ ++ BamgVertex* nearest_v=NULL; ++ ++ /*Project w coordinates (i,j) onto [0,MaxISize-1] x [0,MaxISize-1] -> (iplus,jplus)*/ ++ Icoor1 iplus( inbitems) return nearest_v; ++ ++ /*else, find the smallest non-empty BamgQuadtreeBox containing the point (i,j)*/ ++ while((n0=b->nbitems)<0){ ++ ++ Icoor1 hb2 = hb >> 1; //size of the current box ++ int k = IJ(iplus,jplus,hb2); //box number (0,1,2 or 3) ++ BamgQuadtreeBox *b0 = b->b[k]; //pointer toward current box ++ ++ /* break if NULL box or empty (Keep previous box b)*/ ++ if (( b0 == NULL) || (b0->nbitems == 0)) break; ++ ++ /*Get next Quadtree box*/ ++ b=b0; ++ i0 += I_IJ(k,hb2); // i orign of BamgQuadtreeBox (macro) ++ j0 += J_IJ(k,hb2); // j orign of BamgQuadtreeBox ++ hb = hb2; // size of the box (in Int) ++ } ++ ++ /*The box b, is the smallest box containing the point (i,j) and ++ * has the following properties: ++ * - n0: number of items (>0 if vertices, else boxes) ++ * - hb: box size (int) ++ * - i0: x coordinate of the lower left corner ++ * - j0: y coordinate of the lower left corner*/ ++ ++ /* if the current subbox is holding vertices, we are almost done*/ ++ if (n0>0){ ++ //loop over the vertices of the box and find the closest vertex ++ for(int k=0;kv[k]->i; ++ ++ /*Compute norm with w*/ ++ h0=NORM(iplus,i2.x,jplus,i2.y); ++ ++ /*is it smaller than previous value*/ ++ if (h0v[k]; ++ } ++ } ++ /*return closest vertex*/ ++ return nearest_v; ++ } ++ ++ /* general case: the current box is empty, we have to go backwards ++ and find the closest not-empty box and find the closest vertex*/ ++ ++ /*Initialize search variables*/ ++ pb[0]=b; //pointer toward the box b ++ pi[0]=b->nbitems>0?(int)b->nbitems:4;//number of boxes in b ++ ii[0]=i0; //i coordinate of the box lowest left corner ++ jj[0]=j0; //j coordinate of the box lowest left corner ++ ++ /*initialize h: smallest box size, containing a vertex close to w*/ ++ h=hb; ++ ++ /*Main loop*/ ++ level=0; ++ do { ++ ++ /*get current box*/ ++ b= pb[level]; ++ ++ /*Loop over the items in current box (if not empty!)*/ ++ while (pi[level]){ ++ ++ /*We are looping now over the items of b. k is the current index (in [0 3])*/ ++ pi[level]--; ++ int k=pi[level]; ++ ++ /*if the current subbox is holding vertices (b->nbitems<0 is subboxes)*/ ++ if (b->nbitems>0){ ++ I2 i2=b->v[k]->i; ++ h0 = NORM(iplus,i2.x,jplus,i2.y); ++ if (h0v[k]; ++ } ++ } ++ /*else: current box b is pointing toward 4 boxes ++ * test sub-box k and go deeper into the tree if it is non empty ++ * and contains the point w modulo a size h that is either the size of the smallest ++ * non empty box containing w, or the closest point to w (so far) */ ++ else{ ++ BamgQuadtreeBox* b0=b; ++ ++ /*if the next box exists:*/ ++ if (b=b->b[k]){ ++ ++ /*Get size (hb) and coordinates of the current sub-box lowest left corner*/ ++ hb>>=1; ++ Icoor1 iii = ii[level]+I_IJ(k,hb); ++ Icoor1 jjj = jj[level]+J_IJ(k,hb); ++ ++ /*if the current point (iplus,jplus) is in b (modulo h), this box is good: ++ * it is holding vertices that are close to w */ ++ if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)){ ++ level++; ++ pb[level]= b; ++ pi[level]= b->nbitems>0 ?(int) b->nbitems : 4 ; ++ ii[level]= iii; ++ jj[level]= jjj; ++ } ++ ++ //else go backwards ++ else{ ++ //shifted righ by one bit: hb=001000000 -> 01000000 ++ b=b0; ++ hb<<=1; ++ } ++ } ++ else{ ++ /*Current box is NULL, go to next subbox of b (k=k-1)*/ ++ b=b0; ++ } ++ } ++ } ++ ++ /*We have found a vertex, now, let's try the other boxes of the previous level ++ * in case there is a vertex closest to w that has not yet been tested*/ ++ hb <<= 1; ++ } while (level--); ++ ++ /*return nearest_v, nearest vertex*/ ++ return nearest_v; ++ ++ } ++ /*}}}1*/ ++ /*FUNCTION BamgQuadtree::NearestVertexWithNormal{{{1*/ ++ BamgVertex* BamgQuadtree::NearestVertexWithNormal(Icoor1 i,Icoor1 j) { ++ /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/NearestVertexWithNormal)*/ ++ ++ BamgQuadtreeBox * pb[ MaxDepth ]; ++ int pi[ MaxDepth ]; ++ Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; ++ int l; // level ++ BamgQuadtreeBox * b; ++ long h =MaxISize,h0; ++ long hb=MaxISize; ++ Icoor1 i0=0,j0=0; ++ Icoor1 iplus( inbitems) ++ return vn; // empty tree ++ ++ while( (n0 = b->nbitems) < 0) ++ { ++ // search the non empty ++ // BamgQuadtreeBox containing the point (i,j) ++ register Icoor1 hb2 = hb >> 1 ; ++ register int k = IJ(iplus,jplus,hb2);// BamgQuadtreeBox number of size hb2 contening i;j ++ register BamgQuadtreeBox * b0= b->b[k]; ++ if ( ( b0 == 0) || (b0->nbitems == 0) ) ++ break; // null box or empty => break ++ b=b0; ++ i0 += I_IJ(k,hb2); // i orign of BamgQuadtreeBox ++ j0 += J_IJ(k,hb2); // j orign of BamgQuadtreeBox ++ hb = hb2; ++ } ++ ++ ++ if ( n0 > 0) ++ { ++ for(register int k=0;kv[k]->i; ++ // try if is in the right direction -- ++ h0 = NORM(iplus,i2.x,jplus,i2.y); ++ if (h0 v[k];} ++ } ++ if (vn) return vn; ++ } ++ // general case ----- ++ // INITIALISATION OF THE HEAP ++ l =0; // level ++ pb[0]= b; ++ pi[0]=b->nbitems>0 ?(int) b->nbitems : 4 ; ++ ii[0]=i0; ++ jj[0]=j0; ++ h=hb; ++ do { // walk on the tree ++ b= pb[l]; ++ while (pi[l]--) // loop on 4 element of the box ++ { ++ int k = pi[l]; ++ ++ if (b->nbitems>0) // BamgVertex BamgQuadtreeBox none empty ++ { ++ I2 i2 = b->v[k]->i; ++ // if good direction when try -- ++ ++ h0 = NORM(iplus,i2.x,jplus,i2.y); ++ if (h0 v[k]; ++ } ++ } ++ else // Pointer BamgQuadtreeBox ++ { ++ register BamgQuadtreeBox *b0=b; ++ if ((b=b->b[k])) ++ { ++ hb >>=1 ; // div by 2 ++ register Icoor1 iii = ii[l]+I_IJ(k,hb); ++ register Icoor1 jjj = jj[l]+J_IJ(k,hb); ++ ++ if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)) ++ { ++ pb[++l]= b; ++ pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; ++ ii[l]= iii; ++ jj[l]= jjj; ++ ++ } ++ else ++ b=b0, hb <<=1 ; ++ } ++ else ++ b=b0; ++ } ++ } ++ hb <<= 1; // mul by 2 ++ } while (l--); ++ ++ return vn; ++ } ++ /*}}}1*/ ++ /*FUNCTION BamgQuadtree::NewBamgQuadtreeBox {{{1*/ ++ BamgQuadtree::BamgQuadtreeBox* BamgQuadtree::NewBamgQuadtreeBox(void){ ++ ++ /*Output*/ ++ BamgQuadtreeBox* newbox=NULL; ++ ++ /*Create and initialize a new box*/ ++ newbox=new BamgQuadtreeBox; ++ newbox->nbitems=0; ++ newbox->b[0]=NULL; ++ newbox->b[1]=NULL; ++ newbox->b[2]=NULL; ++ newbox->b[3]=NULL; ++ ++ /*Add root to the container*/ ++ boxcontainer->AddObject(newbox); ++ ++ /*Increase counter*/ ++ NbBamgQuadtreeBox++; ++ ++ /*currentbox now points toward next quadtree box*/ ++ return newbox; ++ }/*}}}*/ ++ /*FUNCTION BamgQuadtree::ToClose {{{1*/ ++ BamgVertex* BamgQuadtree::ToClose(BamgVertex & v,double seuil,Icoor1 hx,Icoor1 hy){ ++ /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/ToClose)*/ ++ ++ const Icoor1 i=v.i.x; ++ const Icoor1 j=v.i.y; ++ const R2 X(v.r); ++ const Metric Mx(v.m); ++ ++ BamgQuadtreeBox * pb[ MaxDepth ]; ++ int pi[ MaxDepth ]; ++ Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; ++ register int l=0; // level ++ register BamgQuadtreeBox * b; ++ Icoor1 h=MaxISize; ++ Icoor1 hb = MaxISize; ++ Icoor1 i0=0,j0=0; ++ ++ // BamgVertex *vn=0; ++ ++ if (!root->nbitems) ++ return 0; // empty tree ++ ++ // general case ----- ++ pb[0]=root; ++ pi[0]=root->nbitems>0 ?(int) root->nbitems : 4 ; ++ ii[0]=i0; ++ jj[0]=j0; ++ h=hb; ++ do { ++ b= pb[l]; ++ while (pi[l]--){ ++ register int k = pi[l]; ++ ++ if (b->nbitems>0){ // BamgVertex BamgQuadtreeBox none empty ++ I2 i2 = b->v[k]->i; ++ if ( ABS(i-i2.x) v[k]->r); ++ double dd; ++ if( (dd= LengthInterpole(Mx(XY), b->v[k]->m(XY))) < seuil ){ ++ return b->v[k]; ++ } ++ } ++ } ++ else{ // Pointer BamgQuadtreeBox ++ register BamgQuadtreeBox *b0=b; ++ if ((b=b->b[k])){ ++ hb >>=1 ; // div by 2 ++ register long iii = ii[l]+I_IJ(k,hb); ++ register long jjj = jj[l]+J_IJ(k,hb); ++ ++ if (INTER_SEG(iii,iii+hb,i-hx,i+hx) && INTER_SEG(jjj,jjj+hb,j-hy,j+hy)){ ++ pb[++l]= b; ++ pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; ++ ii[l]= iii; ++ jj[l]= jjj; ++ ++ } ++ else{ ++ b=b0; ++ hb <<=1 ; ++ } ++ } ++ else{ ++ b=b0; ++ } ++ } ++ } ++ hb <<= 1; // mul by 2 ++ } while (l--); ++ ++ return 0; ++ } ++ /*}}}1*/ ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.cpp (revision 12217) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.cpp (revision 12218) +@@ -2884,7 +2884,7 @@ + triangles[1].link=&triangles[0]; + + //build quadtree +- if (!quadtree) quadtree = new QuadTree(this,0); ++ if (!quadtree) quadtree = new BamgQuadtree(this,0); + quadtree->Add(*v0); + quadtree->Add(*v1); + +@@ -3106,12 +3106,12 @@ + delete [] qq; + } + /*}}}1*/ +- /*FUNCTION Mesh::MakeQuadTree{{{1*/ +- void Mesh::MakeQuadTree() { +- /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MakeQuadTree)*/ ++ /*FUNCTION Mesh::MakeBamgQuadtree{{{1*/ ++ void Mesh::MakeBamgQuadtree() { ++ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MakeBamgQuadtree)*/ + + long int verbose=0; +- if ( !quadtree ) quadtree = new QuadTree(this); ++ if ( !quadtree ) quadtree = new BamgQuadtree(this); + + } + /*}}}1*/ +@@ -3621,7 +3621,7 @@ + triangles[1].link=&triangles[0]; + + if (!quadtree) delete quadtree; //ReInitialise; +- quadtree = new QuadTree(this,0); ++ quadtree = new BamgQuadtree(this,0); + quadtree->Add(*v0); + quadtree->Add(*v1); + +@@ -3899,7 +3899,7 @@ + } + if (quadtree){ + delete quadtree; +- quadtree = new QuadTree(this); ++ quadtree = new BamgQuadtree(this); + } + + for ( it=0;it + + /*forward declarations */ + class Matrix; Index: /issm/oecreview/Archive/12221-12240/ISSM-12222-12223.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12222-12223.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12222-12223.diff (revision 12325) @@ -0,0 +1,34 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/issm/cccl +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/issm/cccl (revision 12222) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/issm/cccl (revision 12223) +@@ -73,6 +73,19 @@ + ;; + esac + ;; ++ -fPIC) ++ #do nothing ++ ;; ++ -g) ++ #do nothing ++ ;; ++ -pthread) ++ #do nothing ++ ;; ++ -fno-omit-frame-pointer) ++ #do nothing ++ ;; ++ + *) + #do nothing + opts="$opts $1" +@@ -82,6 +95,9 @@ + esac + shift + done ++ ++#Some default options: ++opts="$opts /nologo" + + #echo "$prog $opts" + exec $prog $opts Index: /issm/oecreview/Archive/12221-12240/ISSM-12223-12224.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12223-12224.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12223-12224.diff (revision 12325) @@ -0,0 +1,36 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 12223) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 12224) +@@ -41,6 +41,7 @@ + autoconf + python: Python language interpreter + unzip ++cygrunsrv + + + +@@ -143,10 +144,16 @@ + + + How to setup a Cron job? +-Download exim and cron from cygwin setup. Run exim-config (don't forget to launch your cygwin terminal as +-Administrator). If asked for a daemon name, type ntsec. Also, if cron complains about sendmail, +-symlink /usr/lib/sendmail to /usr/sbin/sendmail. Then link /usr/sbin/sendmail +-to /usr/bin/exim. Alternatively, if you have an smtp server, you can download and configure +-ssmtp. Run ssmtp-config +-as Administrator and link /usr/sbin/sendmail to /usr/bin/ssmtp. After the email has been configured, +-run cron-config as Administrator. ++First, make sure you downloaded cygrunsrv, otherwise the cron setup will only work on a per-session ++basis! Also, make sure that you have an email correctly setup. In particular, cron relies on the ++/usr/sbin/sendmail script. If it does not exist, cron will not send emails. Most email management ++systems will create this script, but you need to check on it. ++Run cron-config and fill up the questions. For daemon name, type ntsec. ++Be careful, make sure that you are running your terminal as Administrator, ++otherwise your settings will be only user-based. ++How to setup email? ++ ++Preferred way is through ssmtp. Download it on cygwin, and type ssmtp-config. If the ssmtp ++daemon does not create /usr/sbin/sendmail, be sure to create a symlink from the email client ++to the latter file. Be careful, make sure that you are running your terminal as Administrator, ++otherwise your settings will be only user-based. Index: /issm/oecreview/Archive/12221-12240/ISSM-12224-12225.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12224-12225.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12224-12225.diff (revision 12325) @@ -0,0 +1,537 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp (revision 12224) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/OptionParse.cpp (revision 12225) +@@ -40,7 +40,7 @@ + + /*check and parse the name */ + ological=new OptionLogical; +- ological->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); ++ ological->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ological->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ +@@ -58,8 +58,8 @@ + OptionChar *ochar = NULL; + + /*check and parse the name */ +- ochar=new OptionChar; +- ochar->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); ++ ochar=new OptionChar(); ++ ochar->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ochar->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12224) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 12225) +@@ -403,18 +403,8 @@ + } + else if (mxIsClass(dataref,"char") ){ + +- /*Check dataref is not pointing to NaN: */ +- if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1) ){ +- outmatrix_numel=0; +- outmatrix_ndims=0; +- outmatrix_size =NULL; +- outmatrix=NULL; +- } +- else{ +- +- /*Convert matlab n-dim array to char* matrix: */ +- MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref); +- } ++ /*Convert matlab n-dim array to char* matrix: */ ++ MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref); + } + else{ + /*This is an error: we don't have the correct input!: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12224) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12225) +@@ -34,20 +34,16 @@ + /*FUNCTION Observations::Observations(double* observations_list,double* x,double* y,int n){{{*/ + Observations::Observations(double* observations_list,double* x,double* y,int n){ + +- const int MaxICoor = 1073741823; // 2^30-1 =111...111 (29 times) +- + /*Intermediaries*/ + int i; + int xi,yi; ++ double xmin,xmax,ymin,ymax; + double offset; + Observation *observation = NULL; + +- /*Initialize Quadtree*/ +- this->quadtree = new Quadtree(); +- + /*Get extrema*/ +- this->xmin=x[0]; this->ymin=y[0]; +- this->xmax=x[0]; this->ymax=y[0]; ++ xmin=x[0]; ymin=y[0]; ++ xmax=x[0]; ymax=y[0]; + for(i=1;icoefficient = double(MaxICoor)/max(xmax-xmin,ymax-ymin); _assert_(coefficient>=0); ++ /*Initialize Quadtree*/ ++ this->quadtree = new Quadtree(xmin,xmax,ymin,ymax,30); + + /*Add observations one by one*/ + for(i=0;iquadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); + observation = new Observation(x[i],y[i],xi,yi,observations_list[i]); + this->quadtree->Add(observation); + this->AddObject(observation); +@@ -114,19 +104,11 @@ + /*FUNCTION Observations::QuadtreeColoring{{{*/ + void Observations::QuadtreeColoring(double* A,double *x,double *y,int n){ + +- /*Convert to integer coordinates*/ +- int *xi = (int*)xmalloc(n*sizeof(int)); +- int *yi = (int*)xmalloc(n*sizeof(int)); ++ int xi,yi; ++ + for(int i=0;iquadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); ++ this->quadtree->QuadtreeColoring(&A[i],xi,yi); + } + +- /*Call quadtree method*/ +- this->quadtree->QuadtreeColoring(A,xi,yi,n); +- +- /*clean-up*/ +- xfree((void**)&xi); +- xfree((void**)&yi); +- + }/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12224) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12225) +@@ -12,11 +12,6 @@ + + private: + Quadtree* quadtree; +- double coefficient; //For integer coordinate conversion +- double xmin; +- double ymin; +- double xmax; +- double ymax; + + public: + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12224) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12225) +@@ -15,14 +15,17 @@ + + class QuadtreeBox: public Object{ + public: +- int nbitems; // number of current vertices in the box ++ int nbitems; // number of current vertices in the box ++ double xcenter; // x position of the center (double) ++ double ycenter; // x position of the center (double) ++ double length; // width of the box + union{ + QuadtreeBox *box[4]; + Observation *obs[4]; + }; + + /*Object functions (Needed because the Quadtree uses a Container*/ +- void Echo() {_error_("not implemented yet"); }; ++ void Echo(); + void DeepEcho() {_error_("not implemented yet"); }; + int Id() {_error_("not implemented yet"); }; + int MyRank() {_error_("not implemented yet"); }; +@@ -34,16 +37,21 @@ + DataSet* boxcontainer; + + public: +- int MaxDepth; // maximum number of subdivision +- QuadtreeBox *root; // main box +- long NbQuadtreeBox; // total number of boxes +- long NbObs; // number of points ++ int MaxDepth; // maximum number of subdivision ++ double coordconversion; // Coefficient to convert coordinates to integer ++ QuadtreeBox *root; // main box ++ long NbQuadtreeBox; // total number of boxes ++ long NbObs; // number of points + + Quadtree(); ++ Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth_in); + ~Quadtree(); ++ void Add(Observation *observation); ++ void DeepEcho(void); + void Echo(void); +- void Add(Observation *observation); +- void QuadtreeColoring(double *A,int *xi,int *yi,int n); +- QuadtreeBox *NewQuadtreeBox(void); ++ void IntergerCoordinates(int *xi,int *yi,double x,double y); ++ QuadtreeBox *NewQuadtreeBox(double xcenter,double ycenter,double length); ++ QuadtreeBox *NewQuadtreeBox(QuadtreeBox* master,int index); ++ void QuadtreeColoring(double *A,int xi,int yi); + }; + #endif //_QUADTREEK_H +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12224) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12225) +@@ -79,22 +79,31 @@ + /*}}}*/ + + /*Constructors/Destructors*/ +- /*FUNCTION Quadtree::Quadtree(){{{1*/ +- Quadtree::Quadtree(){ ++/*FUNCTION Quadtree::Quadtree(){{{1*/ ++Quadtree::Quadtree(){ ++ _error_("Constructor not supported"); + +- /*Initialize fields*/ +- this->MaxDepth=30; +- this->NbQuadtreeBox=0; +- this->NbObs=0; ++} ++/*}}}1*/ ++/*FUNCTION Quadtree::Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth){{{1*/ ++Quadtree::Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth){ + +- /*Create container*/ +- this->boxcontainer=new DataSet(); ++ /*Intermediaries*/ ++ double length; + +- /*Create Root, pointer toward the main box*/ +- this->root=NewQuadtreeBox(); ++ /*Initialize fields*/ ++ this->MaxDepth=maxdepth; ++ this->NbQuadtreeBox=0; ++ this->NbObs=0; + +- } +- /*}}}1*/ ++ /*Create container*/ ++ this->boxcontainer=new DataSet(); ++ ++ /*Create Root, pointer toward the main box*/ ++ length=max(xmax-xmin,ymax-ymin); ++ this->root=NewQuadtreeBox(xmin+length/2,ymin+length/2,length); ++} ++/*}}}1*/ + /*FUNCTION Quadtree::~Quadtree(){{{1*/ + Quadtree::~Quadtree(){ + +@@ -109,78 +118,82 @@ + void Quadtree::Add(Observation* observation){ + + /*Intermediaries*/ +- int xi,yi,ij,level; +- QuadtreeBox **pb = NULL; +- QuadtreeBox *b = NULL; +- QuadtreeBox *bb = NULL; ++ int xi,yi,ij,level,levelbin; ++ QuadtreeBox **pbox = NULL; // pointer toward current box b ++ QuadtreeBox **pmaster = NULL; // pointer toward master of b ++ QuadtreeBox *box = NULL; // current box b ++ QuadtreeBox *slave = NULL; // suslaveox of b (if necessary) + Observation *obs[4]; + + /*Get integer coodinates*/ + xi = observation->xi; + yi = observation->yi; + +- /*Initialize level*/ +- level=(1L<MaxDepth);// = 2^30 ++ /*Initialize levels*/ ++ level = 0; ++ levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ +- pb=&root; ++ pmaster = &root; ++ pbox = &root; + + /*Find the smallest box where the observation is located*/ +- while((b=*pb) && (b->nbitems<0)){ ++ while((box=*pbox) && (box->nbitems<0)){ + +- /*Go down one level = 00100 -> 00010*/ +- level>>=1; ++ /*Go down one level (levelbin = 00100 -> 00010)*/ ++ levelbin>>=1; level+=1; _assert_(levelMaxDepth); + +- /*Get next subbox according to the bit value (level)*/ +- pb = &b->box[IJ(xi,yi,level)]; ++ /*Get next box according to the bit value (levelbin)*/ ++ pmaster = pbox; ++ pbox = &box->box[IJ(xi,yi,levelbin)]; + } +- _assert_(level>0); ++ _assert_(levelbin>0); + + /*Now, try to add the vertex, if the box is full (nbitems=4), we have to divide it in 4 new boxes*/ +- while((b=*pb) && (b->nbitems==4)){ ++ while((box=*pbox) && (box->nbitems==4)){ + + /*Copy the 4 observation in the current Quadtreebox*/ +- obs[0] = b->obs[0]; +- obs[1] = b->obs[1]; +- obs[2] = b->obs[2]; +- obs[3] = b->obs[3]; ++ obs[0] = box->obs[0]; ++ obs[1] = box->obs[1]; ++ obs[2] = box->obs[2]; ++ obs[3] = box->obs[3]; + +- /*set nbitems as negative (now holding boxes instead of observations)*/ +- b->nbitems = -b->nbitems; ++ /*set nbitems as -1 (now holding boxes instead of observations)*/ ++ box->nbitems = -1; ++ box->box[0] = NULL; ++ box->box[1] = NULL; ++ box->box[2] = NULL; ++ box->box[3] = NULL; + +- /*Initialize the 4 pointers toward the 4 subboxes*/ +- b->box[0]=NULL; +- b->box[1]=NULL; +- b->box[2]=NULL; +- b->box[3]=NULL; ++ /*Go down one level (levelbin = 00010 -> 00001)*/ ++ levelbin>>=1; level+=1; _assert_(levelMaxDepth); + +- /*level = 00100 -> 00010*/ +- level>>=1; +- + /*Put the four observations in the new boxes*/ + for (int k=0;k<4;k++){ + + /*Get box for observation number k*/ +- ij = IJ(obs[k]->xi,obs[k]->yi,level); +- bb = b->box[ij]; +- if(!bb){ +- b->box[ij]=NewQuadtreeBox(); +- bb=b->box[ij]; ++ ij = IJ(obs[k]->xi,obs[k]->yi,levelbin); ++ slave = box->box[ij]; ++ if(!slave){ ++ box->box[ij] = NewQuadtreeBox(box,ij); ++ slave = box->box[ij]; + } +- bb->obs[bb->nbitems++] = obs[k]; ++ slave->obs[slave->nbitems++] = obs[k]; + } + +- /*Get the subbox where the current observation is located*/ +- ij=IJ(xi,yi,level); +- pb=&b->box[ij]; ++ /*Get the suslaveox where the current observation is located*/ ++ ij = IJ(xi,yi,levelbin); ++ pmaster = pbox; ++ pbox = &box->box[ij]; + } + + /*alloc the QuadtreeBox if necessary and add current observation*/ +- b=*pb; +- if(!b){ +- b=*pb=NewQuadtreeBox(); ++ box = *pbox; ++ if(!box){ ++ ij = IJ(xi,yi,levelbin); ++ box = *pbox = NewQuadtreeBox(*pmaster,ij); + } +- b->obs[b->nbitems++]=observation; ++ box->obs[box->nbitems++]=observation; + NbObs++; + + }/*}}}*/ +@@ -188,21 +201,59 @@ + void Quadtree::Echo(void){ + + printf("Quadtree:\n"); +- printf(" MaxDepth = %i\n",MaxDepth); +- printf(" NbQuadtreeBox = %i\n",NbQuadtreeBox); +- printf(" NbObs = %i\n",NbObs); +- printf(" root = %p\n",root); ++ printf(" MaxDepth = %i\n",this->MaxDepth); ++ printf(" NbQuadtreeBox = %i\n",this->NbQuadtreeBox); ++ printf(" NbObs = %i\n",this->NbObs); ++ printf(" root = %p\n",this->root); + + }/*}}}*/ +-/*FUNCTION Quadtree::NewQuadtreeBox {{{1*/ +-Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(void){ ++/*FUNCTION Quadtree::DeepEcho{{{1*/ ++void Quadtree::DeepEcho(void){ + ++ printf("Quadtree:\n"); ++ printf(" MaxDepth = %i\n",this->MaxDepth); ++ printf(" NbQuadtreeBox = %i\n",this->NbQuadtreeBox); ++ printf(" NbObs = %i\n",this->NbObs); ++ printf(" root = %p\n",this->root); ++ boxcontainer->Echo(); ++ ++}/*}}}*/ ++/*FUNCTION Quadtree::IntergerCoordinates{{{1*/ ++void Quadtree::IntergerCoordinates(int *xi,int *yi,double x,double y){ ++ ++ /*Intermediaries*/ ++ double coefficient; ++ double xmin,ymin; ++ ++ /*Checks in debugging mode*/ ++ _assert_(xi && yi); ++ _assert_(this->root); ++ ++ /*coeffIcoor is the coefficient used for integer coordinates: ++ * (x-xmin) ++ * xi = (2^30 -1) --------- ++ * length ++ * coefficient = (2^30 -1)/length ++ */ ++ coefficient = double((1L<MaxDepth)-1)/(this->root->length); ++ xmin = this->root->xcenter - this->root->length/2; ++ ymin = this->root->ycenter - this->root->length/2; ++ ++ *xi=int(coefficient*(x - xmin)); ++ *yi=int(coefficient*(y - ymin)); ++}/*}}}*/ ++/*FUNCTION Quadtree::NewQuadtreeBox(double xcenter,double ycenter,double length){{{1*/ ++Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(double xcenter,double ycenter,double length){ ++ + /*Output*/ + QuadtreeBox* newbox=NULL; + + /*Create and initialize a new box*/ + newbox=new QuadtreeBox(); + newbox->nbitems=0; ++ newbox->xcenter=xcenter; ++ newbox->ycenter=ycenter; ++ newbox->length=length; + newbox->box[0]=NULL; + newbox->box[1]=NULL; + newbox->box[2]=NULL; +@@ -215,30 +266,88 @@ + /*currentbox now points toward next quadtree box*/ + return newbox; + }/*}}}*/ ++/*FUNCTION Quadtree::NewQuadtreeBox(QuadtreeBox* master,int index) {{{1*/ ++Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(QuadtreeBox* master,int index){ ++ ++ /*Output*/ ++ QuadtreeBox* newbox=NULL; ++ ++ /*Checks in debugging mode*/ ++ _assert_(master); ++ ++ /*Create and initialize a new box*/ ++ newbox=new QuadtreeBox(); ++ newbox->nbitems=0; ++ newbox->box[0]=NULL; ++ newbox->box[1]=NULL; ++ newbox->box[2]=NULL; ++ newbox->box[3]=NULL; ++ switch(index){ ++ case 0: ++ newbox->xcenter=master->xcenter - master->length/4; ++ newbox->ycenter=master->ycenter - master->length/4; ++ break; ++ case 1: ++ newbox->xcenter=master->xcenter + master->length/4; ++ newbox->ycenter=master->ycenter - master->length/4; ++ break; ++ case 2: ++ newbox->xcenter=master->xcenter - master->length/4; ++ newbox->ycenter=master->ycenter + master->length/4; ++ break; ++ case 3: ++ newbox->xcenter=master->xcenter + master->length/4; ++ newbox->ycenter=master->ycenter + master->length/4; ++ break; ++ default: ++ _error_("Case %i not supported",index); ++ } ++ newbox->length=master->length/2; ++ ++ /*Add to container*/ ++ this->boxcontainer->AddObject(newbox); ++ NbQuadtreeBox++; ++ ++ /*currentbox now points toward next quadtree box*/ ++ return newbox; ++}/*}}}*/ + /*FUNCTION Quadtree::QuadtreeColoring{{{1*/ +-void Quadtree::QuadtreeColoring(double* A,int *xi,int *yi,int n){ ++void Quadtree::QuadtreeColoring(double* A,int xi,int yi){ + +- QuadtreeBox **pb = NULL; +- QuadtreeBox *b = NULL; +- int level; ++ QuadtreeBox **pbox = NULL; ++ QuadtreeBox *box = NULL; ++ int level,levelbin; + +- for(int i=0;iMaxDepth);// = 2^30 + +- /*Initialize level*/ +- level=(1L<MaxDepth);// = 2^30 ++ /*Get inital box (the largest)*/ ++ pbox=&root; + +- /*Get inital box (the largest)*/ +- pb=&root; ++ /*Find the smallest box where this point is located*/ ++ while((box=*pbox) && (box->nbitems<0)){ + +- /*Find the smallest box where the observation is located*/ +- while((b=*pb) && (b->nbitems<0)){ ++ levelbin>>=1; level+=1; _assert_(levelMaxDepth); + +- /*Color matrix onces more*/ +- A[i]+=1; ++ pbox = &box->box[IJ(xi,yi,levelbin)]; ++ } ++ if(box && box->nbitems>0){ ++ /*This box is not empty, add one level*/ ++ level+=1; ++ } + +- /*Go to one box deeper*/ +- level>>=1; +- pb = &b->box[IJ(xi[i],yi[i],level)]; +- } +- } ++ *A=level; + }/*}}}*/ ++ ++/*QuadtreeBox methos*/ ++/*FUNCTION QuadtreeBox::Echo{{{1*/ ++void Quadtree::QuadtreeBox::Echo(void){ ++ ++ printf("QuadtreeBox:\n"); ++ printf(" nbitems = %i\n",this->nbitems); ++ printf(" xcenter = %g\n",this->xcenter); ++ printf(" ycenter = %g\n",this->ycenter); ++ printf(" length = %g\n",this->length); ++ ++}/*}}}*/ Index: /issm/oecreview/Archive/12221-12240/ISSM-12225-12226.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12225-12226.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12225-12226.diff (revision 12325) @@ -0,0 +1,202 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12225) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12226) +@@ -31,14 +31,14 @@ + return; + } + /*}}}*/ +-/*FUNCTION Observations::Observations(double* observations_list,double* x,double* y,int n){{{*/ +-Observations::Observations(double* observations_list,double* x,double* y,int n){ ++/*FUNCTION Observations::Observations(double* observations_list,double* x,double* y,int n,Options* options){{{*/ ++Observations::Observations(double* observations_list,double* x,double* y,int n,Options* options){ + + /*Intermediaries*/ +- int i; ++ int i,maxdepth; + int xi,yi; + double xmin,xmax,ymin,ymax; +- double offset; ++ double offset,minlength; + Observation *observation = NULL; + + /*Get extrema*/ +@@ -51,16 +51,36 @@ + offset=0.05*(xmax-xmin); xmin-=offset; xmax+=offset; + offset=0.05*(ymax-ymin); ymin-=offset; ymax+=offset; + ++ /*Get Minimum box size*/ ++ if(options->GetOption("boxlength")){ ++ options->Get(&minlength,"boxlength"); ++ if(minlength<=0)_error_("boxlength should be a positive number"); ++ maxdepth=int(log(max(xmax-xmin,ymax-ymin)/minlength +1)/log(2)); ++ } ++ else{ ++ maxdepth = 30; ++ minlength=max(xmax-xmin,ymax-ymin)/double((1L<quadtree = new Quadtree(xmin,xmax,ymin,ymax,30); ++ printf("Generating quadtree with a maximum box size %g (depth=%i)...",minlength,maxdepth); ++ this->quadtree = new Quadtree(xmin,xmax,ymin,ymax,maxdepth); + + /*Add observations one by one*/ ++ int level; + for(i=0;iquadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); +- observation = new Observation(x[i],y[i],xi,yi,observations_list[i]); +- this->quadtree->Add(observation); +- this->AddObject(observation); ++ this->quadtree->QuadtreeDepth2(&level,xi,yi); ++ if((int)level >= maxdepth){ ++ } ++ else{ ++ observation = new Observation(x[i],y[i],xi,yi,observations_list[i]); ++ this->quadtree->Add(observation); ++ this->AddObject(observation); ++ } + } ++ printf("done\n"); + } + /*}}}*/ + /*FUNCTION Observations::~Observations(){{{*/ +@@ -104,11 +124,12 @@ + /*FUNCTION Observations::QuadtreeColoring{{{*/ + void Observations::QuadtreeColoring(double* A,double *x,double *y,int n){ + +- int xi,yi; ++ int xi,yi,level; + + for(int i=0;iquadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); +- this->quadtree->QuadtreeColoring(&A[i],xi,yi); ++ this->quadtree->QuadtreeDepth(&level,xi,yi); ++ A[i]=(double)level; + } + + }/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12225) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12226) +@@ -7,6 +7,7 @@ + + class Obsevration; + class Quadtree; ++class Options; + + class Observations: public DataSet{ + +@@ -17,7 +18,7 @@ + + /*constructors, destructors*/ + Observations(); +- Observations(double* observations_list,double* x,double* y,int n); ++ Observations(double* observations_list,double* x,double* y,int n,Options* options); + ~Observations(); + + /*Methods*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12225) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12226) +@@ -39,7 +39,7 @@ + ProcessVariogram(&variogram,options); + + /*Process observation dataset*/ +- observations=new Observations(obs_list,obs_x,obs_y,obs_length); ++ observations=new Observations(obs_list,obs_x,obs_y,obs_length,options); + + /*Allocation output*/ + predictions =(double*)xmalloc(n_interp*sizeof(double)); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12225) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12226) +@@ -52,6 +52,7 @@ + void IntergerCoordinates(int *xi,int *yi,double x,double y); + QuadtreeBox *NewQuadtreeBox(double xcenter,double ycenter,double length); + QuadtreeBox *NewQuadtreeBox(QuadtreeBox* master,int index); +- void QuadtreeColoring(double *A,int xi,int yi); ++ void QuadtreeDepth(int *A,int xi,int yi); ++ void QuadtreeDepth2(int *A,int xi,int yi); + }; + #endif //_QUADTREEK_H +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12225) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12226) +@@ -311,8 +311,8 @@ + /*currentbox now points toward next quadtree box*/ + return newbox; + }/*}}}*/ +-/*FUNCTION Quadtree::QuadtreeColoring{{{1*/ +-void Quadtree::QuadtreeColoring(double* A,int xi,int yi){ ++/*FUNCTION Quadtree::QuadtreeDepth{{{1*/ ++void Quadtree::QuadtreeDepth(int* A,int xi,int yi){ + + QuadtreeBox **pbox = NULL; + QuadtreeBox *box = NULL; +@@ -339,7 +339,60 @@ + + *A=level; + }/*}}}*/ ++/*FUNCTION Quadtree::QuadtreeDepth2{{{1*/ ++void Quadtree::QuadtreeDepth2(int* A,int xi,int yi){ + ++ QuadtreeBox **pbox = NULL; ++ QuadtreeBox *box = NULL; ++ int level,levelbin; ++ ++ /*Initialize levels*/ ++ level = 0; ++ levelbin = (1L<MaxDepth);// = 2^30 ++ ++ /*Get inital box (the largest)*/ ++ pbox=&root; ++ ++ /*Find the smallest box where this point is located*/ ++ while((box=*pbox) && (box->nbitems<0)){ ++ ++ levelbin>>=1; level+=1; ++ ++ pbox = &box->box[IJ(xi,yi,levelbin)]; ++ } ++ if(box && box->nbitems>0){ ++ /*This box is not empty, add one level*/ ++ level+=1; ++ } ++ ++ /*If we were to add the vertex, get level*/ ++ if(box && box->nbitems==4){ ++ int ij; ++ bool flag=true; ++ while(flag){ ++ ++ levelbin>>=1; level+=1; ++ if(level>this->MaxDepth){ ++ level+=1; ++ break; ++ } ++ ++ /*loop over the four observations*/ ++ ij=IJ(box->obs[0]->xi,box->obs[0]->yi,levelbin); ++ for (int k=1;k<4;k++){ ++ if(IJ(box->obs[k]->xi,box->obs[k]->yi,levelbin) != ij){ ++ flag = false; ++ } ++ } ++ if(IJ(xi,yi,levelbin)!=ij){ ++ flag = false; ++ } ++ } ++ } ++ ++ *A=level; ++}/*}}}*/ ++ + /*QuadtreeBox methos*/ + /*FUNCTION QuadtreeBox::Echo{{{1*/ + void Quadtree::QuadtreeBox::Echo(void){ Index: /issm/oecreview/Archive/12221-12240/ISSM-12226-12227.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12226-12227.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12226-12227.diff (revision 12325) @@ -0,0 +1,77 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh (revision 12226) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk/install.sh (revision 12227) +@@ -1,7 +1,7 @@ + #This installs the Android SDK (Software Development Kit) + #which is needed for the compilation of the Java project. + +-step=1; ++step=3; + + #Different steps here. + #1: install sdk, ant and sdk tools +@@ -11,6 +11,7 @@ + + present_dir=`pwd`; + default_droid="Android-4.0" ++sd_card="issm-sdcard" + + if [[ $step == "1" ]]; then + +@@ -61,6 +62,8 @@ + #default settings will suffice. Press 'enter' to take default settings or enter 'no'. + + ./android create avd -f -n $default_droid -t 1 -p $ANDROID_DIR/android-emulators/$default_droid --abi armeabi-v7a ++ echo "Creating an SD Card" ++ ./mksdcard -l $sd_card 2G $ANDROID_DIR/android-emulators/$sd_card.img + fi + + if [[ $step == "3" ]]; then +@@ -69,11 +72,14 @@ + #a terminal in our device. + + cd $present_dir/install-sdk/tools +- ./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/test & ++ ./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/$sd_card.img & + + cd ../platform-tools +- ./adb wait-for-device shell +- ++ ./adb wait-for-device shell mount -o rw,remount -t yaffs2 /dev/block/mtdblock1 /system ++ #./adb wait-for-device shell ++ ./adb push $ISSM_TIER/src/c/issm.exe /data/issm.exe ++ ./adb shell chmod 777 /data/issm.exe ++ ./adb shell /data/issm.exe + fi + + if [[ $step == "4" ]]; then +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12226) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-arm-linux.sh (revision 12227) +@@ -4,6 +4,10 @@ + --prefix=$ISSM_DIR \ + --host="arm-linux" \ + --without-modules \ ++ CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc \ ++ GCC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc \ ++ CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-g++ \ + --with-vendor=arm-linux \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ +- --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ ++ --without-fortran-lib +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 12226) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 12227) +@@ -9,7 +9,7 @@ + AC_PROG_CC([cccl cl icl gcc]) + AC_PROG_CPP + AC_PROG_CXX([cccl cl icl g++]) +-AC_PROG_F77([ifort g77 gfortran]) ++#AC_PROG_F77([ifort g77 gfortran]) + #Libraries and linking + AC_PROG_RANLIB + AC_F77_LIBRARY_LDFLAGS Index: /issm/oecreview/Archive/12221-12240/ISSM-12227-12228.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12227-12228.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12227-12228.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12227) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12228) +@@ -55,7 +55,7 @@ + if(options->GetOption("boxlength")){ + options->Get(&minlength,"boxlength"); + if(minlength<=0)_error_("boxlength should be a positive number"); +- maxdepth=int(log(max(xmax-xmin,ymax-ymin)/minlength +1)/log(2)); ++ maxdepth=int(log(max(xmax-xmin,ymax-ymin)/minlength +1)/log(2.0)); + } + else{ + maxdepth = 30; Index: /issm/oecreview/Archive/12221-12240/ISSM-12228-12229.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12228-12229.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12228-12229.diff (revision 12325) @@ -0,0 +1,414 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12228) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12229) +@@ -35,7 +35,7 @@ + Observations::Observations(double* observations_list,double* x,double* y,int n,Options* options){ + + /*Intermediaries*/ +- int i,maxdepth; ++ int i,maxdepth,level,counter; + int xi,yi; + double xmin,xmax,ymin,ymax; + double offset,minlength; +@@ -62,23 +62,23 @@ + minlength=max(xmax-xmin,ymax-ymin)/double((1L<quadtree = new Quadtree(xmin,xmax,ymin,ymax,maxdepth); + + /*Add observations one by one*/ +- int level; ++ counter = 0; + for(i=0;iquadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); + this->quadtree->QuadtreeDepth2(&level,xi,yi); +- if((int)level >= maxdepth){ +- } +- else{ +- observation = new Observation(x[i],y[i],xi,yi,observations_list[i]); ++ if((int)level <= maxdepth){ ++ observation = new Observation(x[i],y[i],xi,yi,counter++,observations_list[i]); + this->quadtree->Add(observation); + this->AddObject(observation); + } ++ else{ ++ //We need to average with the current observations (not done yet) ++ } + } + printf("done\n"); + } +@@ -92,30 +92,46 @@ + + /*Methods*/ + /*FUNCTION Observations::ObservationList{{{*/ +-void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp){ ++void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp,double range){ + + /*Output and Intermediaries*/ +- int nobs,i; +- double *x = NULL; +- double *y = NULL; +- double *obs = NULL; +- Observation *observation = NULL; ++ int nobs,i,index; ++ double *x = NULL; ++ double *y = NULL; ++ double *obs = NULL; ++ Observation *observation = NULL; ++ int *indices = NULL; + +- /*Get number of observations*/ +- nobs = this->Size(); ++ /*Treat range*/ ++ if(range==0){ ++ range=this->quadtree->root->length; ++ } + +- /*Allocate vectors*/ +- x = (double*)xmalloc(nobs*sizeof(double)); +- y = (double*)xmalloc(nobs*sizeof(double)); +- obs = (double*)xmalloc(nobs*sizeof(double)); ++ /*Find all observations that are in range*/ ++ this->quadtree->RangeSearch(&indices,&nobs,x_interp,y_interp,range); + +- /*Loop over all observations and fill in x, y and obs*/ +- for (i=0;iGetObjectByOffset(i); +- observation->WriteXYObs(&x[i],&y[i],&obs[i]); ++ if(nobs==0){ ++ /*No observation found, double range*/ ++ printf("No observation found within range, doubling range\n"); ++ xfree((void**)&indices); ++ this->ObservationList(&x,&y,&obs,&nobs,x_interp,y_interp,range*2); + } ++ else{ ++ if(nobs>1000) printf("Taking more than 1000 observations\n"); ++ /*Allocate vectors*/ ++ x = (double*)xmalloc(nobs*sizeof(double)); ++ y = (double*)xmalloc(nobs*sizeof(double)); ++ obs = (double*)xmalloc(nobs*sizeof(double)); + ++ /*Loop over all observations and fill in x, y and obs*/ ++ for (i=0;iGetObjectByOffset(indices[i]); ++ observation->WriteXYObs(&x[i],&y[i],&obs[i]); ++ } ++ } ++ + /*Assign output pointer*/ ++ xfree((void**)&indices); + *px=x; + *py=y; + *pobs=obs; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12228) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12229) +@@ -22,7 +22,7 @@ + ~Observations(); + + /*Methods*/ +- void ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp); ++ void ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp,double range); + void QuadtreeColoring(double* A,double *x,double *y,int n); + + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12228) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12229) +@@ -22,6 +22,7 @@ + + /*Intermediaries*/ + int i,j,n_obs; ++ double range; + double numerator,denominator,ratio; + double *x = NULL; + double *y = NULL; +@@ -32,30 +33,37 @@ + double *GinvZ = NULL; + double *gamma0 = NULL; + double *ones = NULL; ++ char *output = NULL; + Variogram *variogram = NULL; + Observations *observations = NULL; + + /*Get Variogram from Options*/ + ProcessVariogram(&variogram,options); ++ options->Get(&range,"searchrange",0.); + + /*Process observation dataset*/ + observations=new Observations(obs_list,obs_x,obs_y,obs_length,options); + + /*Allocation output*/ + predictions =(double*)xmalloc(n_interp*sizeof(double)); +- + for(i=0;iQuadtreeColoring(predictions,x_interp,y_interp,n_interp); +- *ppredictions=predictions; +- return 1; + ++ /*Get output*/ ++ options->Get(&output,"output","quadtree"); ++ ++ if(strcmp(output,"quadtree")==0){ ++ observations->QuadtreeColoring(predictions,x_interp,y_interp,n_interp); ++ *ppredictions=predictions; ++ return 1; ++ } ++ + /*Loop over all interpolations*/ + printf(" interpolation progress: %5.2lf %%",0.0); + for(int idx=0;idxObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx]); ++ observations->ObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx],range); + + /*Allocate intermediary matrix and vectors*/ + Gamma =(double*)xmalloc(n_obs*n_obs*sizeof(double)); +@@ -104,6 +112,7 @@ + /*clean-up and Assign output pointer*/ + delete variogram; + delete observations; ++ xfree((void**)&output); + *ppredictions=predictions; + return 1; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.h (revision 12228) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/BamgQuadtree.h (revision 12229) +@@ -1,6 +1,6 @@ + /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.h)*/ +-#ifndef _QUADTREE_H +-#define _QUADTREE_H ++#ifndef _BAMGQUADTREE_H ++#define _BAMGQUADTREE_H + + #include "./include.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12228) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12229) +@@ -1,6 +1,6 @@ + +-#ifndef _QUADTREEK_H +-#define _QUADTREEK_H ++#ifndef _QUADTREE_H ++#define _QUADTREE_H + + class Observation; + +@@ -31,6 +31,12 @@ + int MyRank() {_error_("not implemented yet"); }; + int ObjectEnum(){_error_("not implemented yet"); }; + Object *copy() {_error_("not implemented yet"); }; ++ ++ /*Methods*/ ++ int IsWithinRange(double x,double y,double range); ++ void RangeSearch(int* indices,int *pnobs,double x,double y,double range); ++ void WriteObservations(int* indices,int *pnobs); ++ + }; + + /*Quadtree private Fields*/ +@@ -38,7 +44,6 @@ + + public: + int MaxDepth; // maximum number of subdivision +- double coordconversion; // Coefficient to convert coordinates to integer + QuadtreeBox *root; // main box + long NbQuadtreeBox; // total number of boxes + long NbObs; // number of points +@@ -54,5 +59,6 @@ + QuadtreeBox *NewQuadtreeBox(QuadtreeBox* master,int index); + void QuadtreeDepth(int *A,int xi,int yi); + void QuadtreeDepth2(int *A,int xi,int yi); ++ void RangeSearch(int **pindices,int *pnobs,double x,double y,double range); + }; +-#endif //_QUADTREEK_H ++#endif //_QUADTREE_H +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h (revision 12228) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h (revision 12229) +@@ -12,11 +12,12 @@ + public: + double x,y; + int xi,yi; ++ int index; + double value; + + /*Observation constructors, destructors*/ + Observation(); +- Observation(double x_in,double y_in,int xi_in,int yi_in,double value_in); ++ Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in); + ~Observation(); + + /*Object virtual functions definitions*/ +@@ -30,4 +31,4 @@ + /*Management*/ + void WriteXYObs(double* px,double* py,double* pobs); + }; +-#endif /* _EXPONENTIALVARIOGRAM_H */ ++#endif /* _OBSERVATION_*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12228) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12229) +@@ -392,7 +392,25 @@ + + *A=level; + }/*}}}*/ ++/*FUNCTION Quadtree::RangeSearch{{{1*/ ++void Quadtree::RangeSearch(int **pindices,int *pnobs,double x,double y,double range){ + ++ /*Intermediaries*/ ++ int nobs; ++ int *indices = NULL; ++ ++ /*Allocate indices (maximum by default*/ ++ indices = (int*)xmalloc(this->NbObs*sizeof(int)); ++ nobs = 0; ++ ++ this->root->RangeSearch(indices,&nobs,x,y,range); ++ ++ /*Clean-up and return*/ ++ *pnobs=nobs; ++ *pindices=indices; ++ ++}/*}}}*/ ++ + /*QuadtreeBox methos*/ + /*FUNCTION QuadtreeBox::Echo{{{1*/ + void Quadtree::QuadtreeBox::Echo(void){ +@@ -404,3 +422,92 @@ + printf(" length = %g\n",this->length); + + }/*}}}*/ ++/*FUNCTION QuadtreeBox::IsWithinRange{{{1*/ ++int Quadtree::QuadtreeBox::IsWithinRange(double x,double y,double range){ ++ ++ /*Return 0 if the 2 boxes do not overlap*/ ++ if(this->xcenter+this->length/2 < x-range) return 0; ++ if(this->xcenter-this->length/2 > x+range) return 0; ++ if(this->ycenter+this->length/2 < y-range) return 0; ++ if(this->ycenter-this->length/2 > y+range) return 0; ++ ++ /*Return 2 if the this box is included in the range*/ ++ if( ++ this->xcenter+this->length/2 <= x+range && ++ this->ycenter+this->length/2 <= y+range && ++ this->xcenter-this->length/2 >= x-range && ++ this->ycenter-this->length/2 >= y-range ++ ) return 2; ++ ++ /*This is a simple overlap*/ ++ return 1; ++ ++}/*}}}*/ ++/*FUNCTION QuadtreeBox::RangeSearch{{{1*/ ++void Quadtree::QuadtreeBox::RangeSearch(int* indices,int *pnobs,double x,double y,double range){ ++ ++ /*Intermediaries*/ ++ int i,nobs; ++ ++ /*Recover current number of observations*/ ++ nobs = *pnobs; ++ ++ switch(this->IsWithinRange(x,y,range)){ ++ case 0: ++ /*If this box is not within range, return*/ ++ break; ++ case 2: ++ /*This box is included in range*/ ++ this->WriteObservations(indices,&nobs); ++ break; ++ case 1: ++ /*This box is partly included*/ ++ if(this->nbitems>0){ ++ /*If this box has only observations, add indices that are within range*/ ++ for(i=0;inbitems;i++){ ++ if(fabs(this->obs[i]->x-x) <= range && fabs(this->obs[i]->y-y) <= range){ ++ indices[nobs++]=this->obs[i]->index; ++ } ++ } ++ } ++ else{ ++ /*This box points toward boxes*/ ++ if(this->box[0]) this->box[0]->RangeSearch(indices,&nobs,x,y,range); ++ if(this->box[1]) this->box[1]->RangeSearch(indices,&nobs,x,y,range); ++ if(this->box[2]) this->box[2]->RangeSearch(indices,&nobs,x,y,range); ++ if(this->box[3]) this->box[3]->RangeSearch(indices,&nobs,x,y,range); ++ } ++ break; ++ default: ++ _error_("Case %i not supported",this->IsWithinRange(x,y,range)); ++ } ++ ++ /*Assign output pointers: */ ++ *pnobs=nobs; ++}/*}}}*/ ++/*FUNCTION QuadtreeBox::WriteObservations{{{1*/ ++void Quadtree::QuadtreeBox::WriteObservations(int* indices,int *pnobs){ ++ ++ /*Intermediaries*/ ++ int i,nobs; ++ ++ /*Recover current number of observations*/ ++ nobs = *pnobs; ++ ++ if(this->nbitems>0){ ++ /*If this box has only observations, add all indices*/ ++ for(i=0;inbitems;i++){ ++ indices[nobs++]=this->obs[i]->index; ++ } ++ } ++ else{ ++ /*This box points toward boxes, */ ++ if(this->box[0]) this->box[0]->WriteObservations(indices,&nobs); ++ if(this->box[1]) this->box[1]->WriteObservations(indices,&nobs); ++ if(this->box[2]) this->box[2]->WriteObservations(indices,&nobs); ++ if(this->box[3]) this->box[3]->WriteObservations(indices,&nobs); ++ } ++ ++ /*Assign output pointers: */ ++ *pnobs=nobs; ++}/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp (revision 12228) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp (revision 12229) +@@ -11,13 +11,14 @@ + return; + } + /*}}}*/ +-/*FUNCTION Observation::Observation(double x,double y,int xi,int yi,double value){{{1*/ +-Observation::Observation(double x_in,double y_in,int xi_in,int yi_in,double value_in){ ++/*FUNCTION Observation::Observation(double x,double y,int xi,int yi,int index,double value){{{1*/ ++Observation::Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in){ + + this->x = x_in; + this->y = y_in; + this->xi = xi_in; + this->yi = yi_in; ++ this->index = index_in; + this->value = value_in; + + } +@@ -35,6 +36,7 @@ + int bit; + + printf("Observation\n"); ++ printf(" index : %i\n",this->index); + printf(" x : %g\n",this->x); + printf(" y : %g\n",this->y); + printf(" xi : "); printbinary(this->xi); printf("\n"); Index: /issm/oecreview/Archive/12221-12240/ISSM-12229-12230.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12229-12230.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12229-12230.diff (revision 12325) @@ -0,0 +1,252 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12229) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12230) +@@ -149,3 +149,44 @@ + } + + }/*}}}*/ ++/*FUNCTION Observations::Variomap{{{*/ ++void Observations::Variomap(double* gamma,double *x,int n){ ++ ++ /*Output and Intermediaries*/ ++ int nobs,i,j,k; ++ double range; ++ Observation *observation1 = NULL; ++ Observation *observation2 = NULL; ++ int *indices = NULL; ++ ++ int *counter= (int*)xmalloc(n*sizeof(int)); ++ for(j=0;jSize();i++){ ++ observation1=(Observation*)this->GetObjectByOffset(i); ++ ++ for(j=0;j=0.); ++ ++ /*Find all observations that are in range*/ ++ this->quadtree->RangeSearch(&indices,&nobs,observation1->x,observation1->y,range); ++ ++ for (k=0;kGetObjectByOffset(indices[k]); ++ gamma[j] += 1./2.*pow(observation1->value - observation2->value,2.); ++ } ++ ++ counter[j] += nobs; ++ xfree((void**)&indices); ++ } ++ } ++ ++ /*Normalize semivariogram*/ ++ for(j=0;jVariomap(predictions,x_interp,n_interp); ++ *ppredictions=predictions; ++ return 1; ++ } + + /*Loop over all interpolations*/ + printf(" interpolation progress: %5.2lf %%",0.0); +@@ -128,7 +133,8 @@ + if (strcmp(model,"gaussian")==0) variogram = new GaussianVariogram(options); + else if(strcmp(model,"exponential")==0) variogram = new ExponentialVariogram(options); + else if(strcmp(model,"spherical")==0) variogram = new SphericalVariogram(options); +- else _error_("variogram %s not supported yet (list of supported variogram: gaussian, exponential and spherical)",model); ++ else if(strcmp(model,"power")==0) variogram = new PowerVariogram(options); ++ else _error_("variogram %s not supported yet (list of supported variogram: gaussian, exponential, spherical and power)",model); + } + else variogram = new GaussianVariogram(options); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12229) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12230) +@@ -618,6 +618,8 @@ + ./objects/Kriging/ExponentialVariogram.cpp\ + ./objects/Kriging/SphericalVariogram.h\ + ./objects/Kriging/SphericalVariogram.cpp\ ++ ./objects/Kriging/PowerVariogram.h\ ++ ./objects/Kriging/PowerVariogram.cpp\ + ./objects/Kriging/Quadtree.h\ + ./objects/Kriging/Quadtree.cpp\ + ./objects/Kriging/Observation.h\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 12229) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 12230) +@@ -177,6 +177,7 @@ + #include "./Kriging/GaussianVariogram.h" + #include "./Kriging/ExponentialVariogram.h" + #include "./Kriging/SphericalVariogram.h" ++#include "./Kriging/PowerVariogram.h" + #include "./Kriging/Quadtree.h" + #include "./Kriging/Observation.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.cpp (revision 12230) +@@ -0,0 +1,75 @@ ++/*!\file PowerVariogram.c ++ * \brief: implementation of the PowerVariogram object ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++ ++/*PowerVariogram constructors and destructor*/ ++/*FUNCTION PowerVariogram::PowerVariogram(){{{1*/ ++PowerVariogram::PowerVariogram(){ ++ this->nugget = 0.2; ++ this->slope = 1.; ++ this->power = 1.; ++ return; ++} ++/*}}}*/ ++/*FUNCTION PowerVariogram::PowerVariogram(Options* options){{{1*/ ++PowerVariogram::PowerVariogram(Options* options){ ++ ++ /*Defaults*/ ++ this->nugget = 0.2; ++ this->slope = 1.; ++ this->power = 1.; ++ ++ /*Overwrite from options*/ ++ if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); ++ if(options->GetOption("slope")) options->Get(&this->slope,"slope"); ++ if(options->GetOption("power")) options->Get(&this->power,"power"); ++ ++ /*Checks*/ ++ if(power<=0 || power>=2) _error_("power must be betwwen 0 and 2 (0 < power < 2)"); ++ if(slope<=0) _error_("slope must be positive"); ++} ++/*}}}*/ ++/*FUNCTION PowerVariogram::~PowerVariogram(){{{1*/ ++PowerVariogram::~PowerVariogram(){ ++ return; ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION PowerVariogram::Echo {{{1*/ ++void PowerVariogram::Echo(void){ ++ printf("PowerVariogram\n"); ++ printf(" nugget: %g\n",this->nugget); ++ printf(" slope : %g\n",this->slope); ++ printf(" power : %g\n",this->power); ++} ++/*}}}*/ ++ ++/*Variogram function*/ ++/*FUNCTION PowerVariogram::SemiVariogram{{{1*/ ++double PowerVariogram::SemiVariogram(double deltax,double deltay){ ++ /*http://en.wikipedia.org/wiki/Variogram*/ ++ double h,gamma; ++ ++ /*Calculate length square*/ ++ h=sqrt(pow(deltax,2.)+pow(deltay,2.)); ++ ++ /*return semi-variogram*/ ++ gamma = this->nugget + this->slope*pow(h,this->power); ++ ++ return gamma; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.h (revision 12230) +@@ -0,0 +1,34 @@ ++/*! \file PowerVariogram.h ++ * \brief: header file for triavertexinput object ++ */ ++ ++#ifndef _POWERVARIOGRAM_H_ ++#define _POWERVARIOGRAM_H_ ++ ++/*Headers:*/ ++#include "./Variogram.h" ++ ++class PowerVariogram: public Variogram{ ++ ++ public: ++ double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin ++ double slope; ++ double power; ++ ++ /*PowerVariogram constructors, destructors*/ ++ PowerVariogram(); ++ PowerVariogram(Options* options); ++ ~PowerVariogram(); ++ ++ /*Object virtual functions definitions*/ ++ void Echo(); ++ void DeepEcho(){_error_("Not implemented yet");}; ++ int Id(){_error_("Not implemented yet");}; ++ int MyRank(){_error_("Not implemented yet");}; ++ int ObjectEnum(){_error_("Not implemented yet");}; ++ Object* copy(){_error_("Not implemented yet");}; ++ ++ /*Variogram functions*/ ++ double SemiVariogram(double deltax,double deltay); ++}; ++#endif /* _POWERVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12229) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12230) +@@ -432,12 +432,10 @@ + if(this->ycenter-this->length/2 > y+range) return 0; + + /*Return 2 if the this box is included in the range*/ +- if( +- this->xcenter+this->length/2 <= x+range && +- this->ycenter+this->length/2 <= y+range && +- this->xcenter-this->length/2 >= x-range && +- this->ycenter-this->length/2 >= y-range +- ) return 2; ++ if(this->xcenter+this->length/2 <= x+range && ++ this->ycenter+this->length/2 <= y+range && ++ this->xcenter-this->length/2 >= x-range && ++ this->ycenter-this->length/2 >= y-range) return 2; + + /*This is a simple overlap*/ + return 1; Index: /issm/oecreview/Archive/12221-12240/ISSM-12230-12231.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12230-12231.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12230-12231.diff (revision 12325) @@ -0,0 +1,237 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12230) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12231) +@@ -112,12 +112,12 @@ + + if(nobs==0){ + /*No observation found, double range*/ +- printf("No observation found within range, doubling range\n"); ++ //printf("No observation found within range, doubling range\n"); + xfree((void**)&indices); + this->ObservationList(&x,&y,&obs,&nobs,x_interp,y_interp,range*2); + } + else{ +- if(nobs>1000) printf("Taking more than 1000 observations\n"); ++ //if(nobs>1000) printf("Taking more than 1000 observations\n"); + /*Allocate vectors*/ + x = (double*)xmalloc(nobs*sizeof(double)); + y = (double*)xmalloc(nobs*sizeof(double)); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12230) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12231) +@@ -15,28 +15,25 @@ + #endif + + #include "../../objects/Kriging/GaussianVariogram.h" ++/*FUNCTION Krigingx{{{*/ + int Krigingx(double** ppredictions,double* obs_x, double* obs_y, double* obs_list, int obs_length,double* x_interp,double* y_interp,int n_interp,Options* options){ + + /*output*/ + double *predictions = NULL; + + /*Intermediaries*/ +- int i,j,n_obs; + double range; +- double numerator,denominator,ratio; +- double *x = NULL; +- double *y = NULL; +- double *obs = NULL; +- double *Gamma = NULL; +- double *GinvG0 = NULL; +- double *Ginv1 = NULL; +- double *GinvZ = NULL; +- double *gamma0 = NULL; +- double *ones = NULL; + char *output = NULL; + Variogram *variogram = NULL; + Observations *observations = NULL; + ++ /*threading: */ ++ KrigingxThreadStruct gate; ++ int num=1; ++#ifdef _MULTITHREADING_ ++ num=_NUMTHREADS_; ++#endif ++ + /*Get Variogram from Options*/ + ProcessVariogram(&variogram,options); + options->Get(&range,"searchrange",0.); +@@ -44,29 +41,88 @@ + /*Process observation dataset*/ + observations=new Observations(obs_list,obs_x,obs_y,obs_length,options); + +- /*Allocation output*/ ++ /*Allocate output*/ + predictions =(double*)xmalloc(n_interp*sizeof(double)); +- for(i=0;iGet(&output,"output","quadtree"); ++ options->Get(&output,"output","prediction"); + + if(strcmp(output,"quadtree")==0){ + observations->QuadtreeColoring(predictions,x_interp,y_interp,n_interp); +- *ppredictions=predictions; +- return 1; + } +- if(strcmp(output,"variomap")==0){ ++ else if(strcmp(output,"variomap")==0){ + observations->Variomap(predictions,x_interp,n_interp); +- *ppredictions=predictions; +- return 1; + } ++ else if(strcmp(output,"prediction")==0){ + +- /*Loop over all interpolations*/ +- printf(" interpolation progress: %5.2lf %%",0.0); +- for(int idx=0;idxgate; ++ my_thread = handle->id; ++ num_threads = handle->num; ++ ++ /*recover parameters :*/ ++ int n_interp = gate->n_interp; ++ double *x_interp = gate->x_interp; ++ double *y_interp = gate->y_interp; ++ double range = gate->range; ++ Variogram *variogram = gate->variogram; ++ Observations *observations = gate->observations; ++ double *predictions = gate->predictions; ++ ++ /*Intermediaries*/ ++ int i,j,n_obs; ++ double numerator,denominator,ratio; ++ double *x = NULL; ++ double *y = NULL; ++ double *obs = NULL; ++ double *Gamma = NULL; ++ double *GinvG0 = NULL; ++ double *Ginv1 = NULL; ++ double *GinvZ = NULL; ++ double *gamma0 = NULL; ++ double *ones = NULL; ++ ++ /*partition loop across threads: */ ++ if(my_thread==0) printf(" interpolation progress: %5.2lf %%",0.0); ++ PartitionRange(&i0,&i1,n_interp,num_threads,my_thread); ++ for(int idx=i0;idxObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx],range); + +@@ -88,9 +144,9 @@ + for(i=0;iSemiVariogram(x[i]-x_interp[idx],y[i]-y_interp[idx]); + + /*Solve the three linear systems*/ +- GslSolve(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0 +- GslSolve(&Ginv1, Gamma,ones,n_obs); // Gamma^-1 ones +- GslSolve(&GinvZ, Gamma,obs,n_obs); // Gamma^-1 Z ++ GslSolve(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0 ++ GslSolve(&Ginv1, Gamma,ones,n_obs); // Gamma^-1 ones ++ GslSolve(&GinvZ, Gamma,obs,n_obs); // Gamma^-1 Z + + /*Prepare predictor*/ + numerator=-1.; denominator=0.; +@@ -112,15 +168,10 @@ + xfree((void**)&Ginv1); + xfree((void**)&GinvZ); + } +- printf("\b\b\b\b\b\b\b\b%5.2lf %%\n",100.0); ++ if(my_thread==0) printf("\b\b\b\b\b\b\b\b%5.2lf %%\n",100.0); + +- /*clean-up and Assign output pointer*/ +- delete variogram; +- delete observations; +- xfree((void**)&output); +- *ppredictions=predictions; +- return 1; +-} ++ return NULL; ++}/*}}}*/ + + void ProcessVariogram(Variogram **pvariogram,Options* options){/*{{{*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12230) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.h (revision 12231) +@@ -8,8 +8,23 @@ + #include "../../objects/objects.h" + #include "../../toolkits/toolkits.h" + ++class Observations; ++class Variogram; ++ + int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options); + void ProcessVariogram(Variogram **pvariogram,Options* options); + void GslSolve(double** pX,double* A,double* B,int n); + ++/*threading: */ ++typedef struct{ ++ int n_interp; ++ double *x_interp; ++ double *y_interp; ++ double range; ++ Variogram *variogram; ++ Observations *observations; ++ double *predictions; ++}KrigingxThreadStruct; ++ ++void* Krigingxt(void*); + #endif /* _KRIGINGX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Shp2Kmlx/Shp2Kmlx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Shp2Kmlx/Shp2Kmlx.h (revision 12230) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Shp2Kmlx/Shp2Kmlx.h (revision 12231) +@@ -21,9 +21,7 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-int Shp2Kmlx(char* filshp,char* filkml, +- int sgn); +-int Shp2Kmlx(char* filshp,char* filkml, +- int sgn,double cm,double sp); ++int Shp2Kmlx(char* filshp,char* filkml, int sgn); ++int Shp2Kmlx(char* filshp,char* filkml, int sgn,double cm,double sp); + + #endif /* _SHP2KMLX_H */ Index: /issm/oecreview/Archive/12221-12240/ISSM-12231-12232.diff =================================================================== --- /issm/oecreview/Archive/12221-12240/ISSM-12231-12232.diff (revision 12325) +++ /issm/oecreview/Archive/12221-12240/ISSM-12231-12232.diff (revision 12325) @@ -0,0 +1,80 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12231) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12232) +@@ -63,10 +63,13 @@ + gate.range = range; + gate.variogram = variogram; + gate.observations = observations; +- gate.predictions = predictions; ++ gate.predictions = predictions; ++ gate.percent = (double*)xcalloc(num,sizeof(double)); + + /*launch the thread manager with Krigingxt as a core: */ + LaunchThread(Krigingxt,(void*)&gate,num); ++ printf("\r interpolation progress: 100.00%%\n"); ++ xfree((void**)&gate.percent); + } + else{ + _error_("output '%s' not supported yet",output); +@@ -103,10 +106,11 @@ + Variogram *variogram = gate->variogram; + Observations *observations = gate->observations; + double *predictions = gate->predictions; ++ double *percent = gate->percent; + + /*Intermediaries*/ + int i,j,n_obs; +- double numerator,denominator,ratio; ++ double numerator,denominator,ratio,localpercent; + double *x = NULL; + double *y = NULL; + double *obs = NULL; +@@ -118,18 +122,22 @@ + double *ones = NULL; + + /*partition loop across threads: */ +- if(my_thread==0) printf(" interpolation progress: %5.2lf %%",0.0); + PartitionRange(&i0,&i1,n_interp,num_threads,my_thread); + for(int idx=i0;idxObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx],range); + + /*Allocate intermediary matrix and vectors*/ +- Gamma =(double*)xmalloc(n_obs*n_obs*sizeof(double)); +- gamma0 =(double*)xmalloc(n_obs*sizeof(double)); +- ones =(double*)xmalloc(n_obs*sizeof(double)); ++ Gamma = (double*)xmalloc(n_obs*n_obs*sizeof(double)); ++ gamma0 = (double*)xmalloc(n_obs*sizeof(double)); ++ ones = (double*)xmalloc(n_obs*sizeof(double)); + + /*First: Create semivariogram matrix for observations*/ + for(i=0;i0) { + if (n&i) Index: /issm/oecreview/Archive/12241-12260/ISSM-12248-12249.diff =================================================================== --- /issm/oecreview/Archive/12241-12260/ISSM-12248-12249.diff (revision 12325) +++ /issm/oecreview/Archive/12241-12260/ISSM-12248-12249.diff (revision 12325) @@ -0,0 +1,43 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh (revision 12248) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh (revision 12249) +@@ -1,7 +1,7 @@ + #!/bin/bash + #Step 1: unzip and install + #Step 2: After Plapack implodes +-STEP=2 ++STEP=1 + + if [ $STEP -eq 1 ]; then + #Some cleanup +@@ -40,7 +40,7 @@ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 +- echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc31/) ==" ++ echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/documentation/faq/petsc32/) ==" + echo "== Then run STEP=2 ==" + fi + if [ $STEP -eq 2 ]; then +@@ -68,5 +68,20 @@ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 ++ cat > src/script.queue << EOF ++#PBS -S /bin/bash ++#PBS -q debug ++#PBS -l select=1:ncpus=1:model=har ++#PBS -l walltime=200 ++#PBS -W group_list=s1010 ++#PBS -m e ++. /usr/share/modules/init/bash ++module load comp-intel/11.1.046 ++module load mpi/mpt.1.25 ++module load math/intel_mkl_64_10.0.011 ++export PATH="$PATH:." ++export MPI_GROUP_MAX=64 ++mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py ++EOF + echo "== Follow PETSc's instructions" + fi Index: /issm/oecreview/Archive/12241-12260/ISSM-12249-12250.diff =================================================================== --- /issm/oecreview/Archive/12241-12260/ISSM-12249-12250.diff (revision 12325) +++ /issm/oecreview/Archive/12241-12260/ISSM-12249-12250.diff (revision 12325) @@ -0,0 +1,87 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12249) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12250) +@@ -16,10 +16,11 @@ + + #include "../../objects/Kriging/GaussianVariogram.h" + /*FUNCTION Krigingx{{{*/ +-int Krigingx(double** ppredictions,double* obs_x, double* obs_y, double* obs_list, int obs_length,double* x_interp,double* y_interp,int n_interp,Options* options){ ++int Krigingx(double** ppredictions,double **perror,double* obs_x, double* obs_y, double* obs_list, int obs_length,double* x_interp,double* y_interp,int n_interp,Options* options){ + + /*output*/ + double *predictions = NULL; ++ double *error = NULL; + + /*Intermediaries*/ + double range; +@@ -42,8 +43,8 @@ + observations=new Observations(obs_list,obs_x,obs_y,obs_length,options); + + /*Allocate output*/ +- predictions =(double*)xmalloc(n_interp*sizeof(double)); +- for(int i=0;iGet(&output,"output","prediction"); +@@ -64,6 +65,7 @@ + gate.variogram = variogram; + gate.observations = observations; + gate.predictions = predictions; ++ gate.error = error; + gate.percent = (double*)xcalloc(num,sizeof(double)); + + /*launch the thread manager with Krigingxt as a core: */ +@@ -79,7 +81,8 @@ + delete variogram; + delete observations; + xfree((void**)&output); +- *ppredictions=predictions; ++ *ppredictions = predictions; ++ *perror = error; + return 1; + }/*}}}*/ + /*FUNCTION Krigingxt{{{*/ +@@ -106,6 +109,7 @@ + Variogram *variogram = gate->variogram; + Observations *observations = gate->observations; + double *predictions = gate->predictions; ++ double *error = gate->error; + double *percent = gate->percent; + + /*Intermediaries*/ +@@ -162,8 +166,10 @@ + for(i=0;iNLHS){ + KrigingUsage(); _error_("Kriging usage error"); + } + +@@ -32,10 +33,11 @@ + FetchData(&options,NRHS,nrhs,prhs); + + /*Call x layer*/ +- Krigingx(&predictions,x,y,observations,n_obs,x_interp,y_interp,M_interp*N_interp,options); ++ Krigingx(&predictions,&error,x,y,observations,n_obs,x_interp,y_interp,M_interp*N_interp,options); + + /*Generate output Matlab Structures*/ +- WriteData(PREDICTIONS,predictions,M_interp,N_interp); ++ if(nlhs>=1) WriteData(PREDICTIONS,predictions,M_interp,N_interp); ++ if(nlhs==2) WriteData(ERROR,error,M_interp,N_interp); + + /*Free ressources: */ + xfree((void**)&x); +@@ -44,6 +46,7 @@ + xfree((void**)&x_interp); + xfree((void**)&y_interp); + xfree((void**)&predictions); ++ xfree((void**)&error); + + /*end module: */ + MODULEEND(); Index: /issm/oecreview/Archive/12241-12260/ISSM-12259-12260.diff =================================================================== --- /issm/oecreview/Archive/12241-12260/ISSM-12259-12260.diff (revision 12325) +++ /issm/oecreview/Archive/12241-12260/ISSM-12259-12260.diff (revision 12325) @@ -0,0 +1,41 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/octave/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/octave/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/octave/install.sh (revision 12260) +@@ -0,0 +1,30 @@ ++#!/bin/bash ++ ++#Some cleanup ++version=3.6.1 ++rm -rf src install octave-$version octave-$version.tar.gz ++mkdir install src ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/octave-$version.tar.gz" "octave-$version.tar.gz" ++ ++#Untar ++tar -zxvf octave-$version.tar.gz ++ ++#Move octave into install directory ++mv octave-$version/* src ++rm -rf octave-$version ++ ++#install ++cd src ++ ++exit ++make ++ ++#Compile ++cd ../install ++mkdir lib ++cd lib ++cp ../../src/*.a . ++ln -s octave_LINUX.a octave.a ++ln -s octave_LINUX.a liboctave.a + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/octave/install.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12241-12260/ISSM-DocReview-12241-12260.tex =================================================================== --- /issm/oecreview/Archive/12241-12260/ISSM-DocReview-12241-12260.tex (revision 12325) +++ /issm/oecreview/Archive/12241-12260/ISSM-DocReview-12241-12260.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12241-12260/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12241-12260/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12241-12260/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12241-12260 Index: /issm/oecreview/Archive/12241-12260/Makefile =================================================================== --- /issm/oecreview/Archive/12241-12260/Makefile (revision 12325) +++ /issm/oecreview/Archive/12241-12260/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12241-12260 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12241-12260/log.tex =================================================================== --- /issm/oecreview/Archive/12241-12260/log.tex (revision 12325) +++ /issm/oecreview/Archive/12241-12260/log.tex (revision 12325) @@ -0,0 +1,22 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12241-12242.diff: \\ Function name: \\A /issm/trunk-jpl/src/android/test102 A /issm/trunk-jpl/src/android/test102/test102.bin A /issm/trunk-jpl/src/android/test102/test102.petsc A /issm/trunk-jpl/src/android/test102/test102.queue \\ Export determination: 6. \\Rationale: Temporary android test102 +D /issm/trunk-jpl/src/android/test102/test102.queue A /issm/trunk-jpl/src/android/test102/test102.sh (from /issm/trunk-jpl/src/android/test102/test102.queue:12241) Moved queue to shell \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12242-12243.diff: \\ Function name: \\D /issm/trunk-jpl/src/android/test102/test102.queue A /issm/trunk-jpl/src/android/test102/test102.sh (from /issm/trunk-jpl/src/android/test102/test102.queue:12241) \\ Export determination: 6. \\Rationale: Moved queue to shell +M /issm/trunk-jpl/externalpackages/python A /issm/trunk-jpl/externalpackages/python/install-macosx-snowleopard.sh install script for 32-bit python, needed on OSX 10.6 for numpy/scipy/matplotlib \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12243-12244.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/python A /issm/trunk-jpl/externalpackages/python/install-macosx-snowleopard.sh \\ Export determination: 6. \\Rationale: install script for 32-bit python, needed on OSX 10.6 for numpy/scipy/matplotlib +A /issm/trunk-jpl/externalpackages/python/install-macosx-lion.sh (from /issm/trunk-jpl/externalpackages/python/install-macosx.sh:12242) D /issm/trunk-jpl/externalpackages/python/install-macosx.sh renamed install script to reflect OS version \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12244-12245.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/python/install-macosx-lion.sh (from /issm/trunk-jpl/externalpackages/python/install-macosx.sh:12242) D /issm/trunk-jpl/externalpackages/python/install-macosx.sh \\ Export determination: 6. \\Rationale: renamed install script to reflect OS version +M /issm/trunk-jpl/externalpackages/scipy/README A /issm/trunk-jpl/externalpackages/scipy/install-macosx-lion.sh (from /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh:12243) A /issm/trunk-jpl/externalpackages/scipy/install-macosx-snowleopard.sh D /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh osx version-specific install scripts for scipy/numpy \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12245-12246.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/scipy/README A /issm/trunk-jpl/externalpackages/scipy/install-macosx-lion.sh (from /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh:12243) A /issm/trunk-jpl/externalpackages/scipy/install-macosx-snowleopard.sh D /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh \\ Export determination: 6. \\Rationale: osx version-specific install scripts for scipy/numpy +M /issm/trunk-jpl/externalpackages/matplotlib A /issm/trunk-jpl/externalpackages/matplotlib/install-osx.sh matplotlib osx install script which automatically fetches and builds dependencies (zlib, png, freetype) \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12246-12247.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/matplotlib A /issm/trunk-jpl/externalpackages/matplotlib/install-osx.sh \\ Export determination: 6. \\Rationale: matplotlib osx install script which automatically fetches and builds dependencies (zlib, png, freetype) +A /issm/trunk-jpl/externalpackages/gsl/install-pleiades.sh Added gsl compilation for pleiades \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12247-12248.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/gsl/install-pleiades.sh \\ Export determination: 6. \\Rationale: Added gsl compilation for pleiades +M /issm/trunk-jpl/src/c/shared/Elements/elements.h fixed bad initialization of 1L \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12248-12249.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/shared/Elements/elements.h \\ Export determination: 6. \\Rationale: fixed bad initialization of 1L +M /issm/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh minor \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12249-12250.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/petsc/install-3.2-pleiades.sh \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.h Added Error calculation \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12250-12251.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.h \\ Export determination: 6. \\Rationale: Added Error calculation +M /issm/trunk-jpl/src/modules/Kriging/Kriging.cpp M /issm/trunk-jpl/src/modules/Kriging/Kriging.h Added Error calculation \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12251-12252.diff: \\ Function name: \\M /issm/trunk-jpl/src/modules/Kriging/Kriging.cpp M /issm/trunk-jpl/src/modules/Kriging/Kriging.h \\ Export determination: 6. \\Rationale: Added Error calculation \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-12259-12260.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/octave A /issm/trunk-jpl/externalpackages/octave/install.sh \\ Export determination: 6. \\Rationale: octave package \\\\ Index: /issm/oecreview/Archive/12241-12260/r1.tex =================================================================== --- /issm/oecreview/Archive/12241-12260/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12241-12260/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12241 Index: /issm/oecreview/Archive/12241-12260/r2.tex =================================================================== --- /issm/oecreview/Archive/12241-12260/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12241-12260/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12260 Index: /issm/oecreview/Archive/12261-12280/Date.tex =================================================================== --- /issm/oecreview/Archive/12261-12280/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12261-12280/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12261-12280/ISSM-12261-12262.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12261-12262.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12261-12262.diff (revision 12325) @@ -0,0 +1,60 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh (revision 12261) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh (revision 12262) +@@ -1,8 +1,8 @@ + #!/bin/bash + #Synchronize EnumToStringx.cpp and StringToEnumx.cpp and matlab Enums + +-#Get all lines of EnumDefinitions2.h which hold Enum | remove all comas | add line number in the first column > put everything in file temp +-cat EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-zA-Z]Enum," | grep -v include | sed -e "s/,//g" | awk '{ printf "%s %s\n", NR, $0 }' > temp ++#Get all lines of EnumDefinitions2.h which hold Enum | remove all comas > put everything in file temp ++cat EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-zA-Z]Enum," | grep -v include | sed -e "s/,//g" > temp + + #Removed existing files + rm $ISSM_DIR/src/m/enum/*.m +@@ -12,7 +12,7 @@ + #Get number of enums + NUMENUMS=$(wc -l temp | awk '{printf("%s",$1);}'); + +-#Build EnumToStringx.cpp {{{1 ++#Build EnumToStringx.cpp {{{ + #Header + cat < $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp + /* +@@ -34,7 +34,7 @@ + + END + #core +-cat temp | awk '{print "\t\t" "case " $2" : return \"" substr($2,1,length($2)-4) "\";"}' >> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp ++cat temp | awk '{print "\t\t" "case " $1" : return \"" substr($1,1,length($1)-4) "\";"}' >> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp + #Footer + cat <> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp + default : return "unknown"; +@@ -82,7 +82,7 @@ + for (( i=1 ; i<=100 ; i++ )); do + echo " if(stage==$i){" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + awk -v i1=$i1 -v i2=$i2 '{if(NR>=i1 && NR<=i2) print $0 }' temp | +- awk '{print "\t" ((NR==1)?" if":" else if") " (strcmp(name,\"" substr($2,1,length($2)-4) "\")==0) return " $2 ";"}' >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp ++ awk '{print "\t" ((NR==1)?" if":" else if") " (strcmp(name,\"" substr($1,1,length($1)-4) "\")==0) return " $1 ";"}' >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + echo " else stage=$(($i+1));" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + echo " }" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + +@@ -103,7 +103,7 @@ + for (( i=1 ; i<=$NUMENUMS ; i++ )); do + + #Get name and enum of the line i +- NAMEENUM=$(cat temp | grep "^[ ]*$i " | awk '{printf("%s",$2);}'); ++ NAMEENUM=$(cat temp | grep "^[ ]*$i " | awk '{printf("%s",$1);}'); + NAME=$(echo $NAMEENUM | sed -e "s/Enum//g") + ENUM=$i; + #offset Enum by one (Enum begins with 0 and not 1!) +@@ -155,7 +155,7 @@ + % macro=MaximumNumberOfEnums() + + macro=$(cat EnumDefinitions.h | grep -e "[0-9]Enum" -e "[a-zA-Z]Enum" | grep -v include \ +- | awk '{ printf "%s %s\n", NR, $0 }' \ ++ | awk '{ printf "%s %s\n", NR-1, $0 }' \ + | grep "MaximumNumberOfEnums" | awk '{print $1}'); + END + #}}} Index: /issm/oecreview/Archive/12261-12280/ISSM-12262-12263.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12262-12263.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12262-12263.diff (revision 12325) @@ -0,0 +1,16 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 12263) +@@ -0,0 +1,11 @@ ++function macro=MaximumNumberOfEnums() ++%MAXIMUMNUMBEROFENUMS - Enum of MaximumNumberOfEnums ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=MaximumNumberOfEnums() ++ ++macro=436; Index: /issm/oecreview/Archive/12261-12280/ISSM-12263-12264.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12263-12264.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12263-12264.diff (revision 12325) @@ -0,0 +1,50 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh (revision 12263) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh (revision 12264) +@@ -2,7 +2,7 @@ + #Synchronize EnumToStringx.cpp and StringToEnumx.cpp and matlab Enums + + #Get all lines of EnumDefinitions2.h which hold Enum | remove all comas > put everything in file temp +-cat EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-zA-Z]Enum," | grep -v include | sed -e "s/,//g" > temp ++cat EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-zA-Z]Enum," | grep -v include | sed -e "s/,/ /g" | awk '{print $1}' > temp + + #Removed existing files + rm $ISSM_DIR/src/m/enum/*.m +@@ -100,28 +100,27 @@ + #}}} + + # go through the lines of temp +-for (( i=1 ; i<=$NUMENUMS ; i++ )); do ++ENUM=0; ++for NAMEENUM in $(cat temp); do + + #Get name and enum of the line i +- NAMEENUM=$(cat temp | grep "^[ ]*$i " | awk '{printf("%s",$1);}'); + NAME=$(echo $NAMEENUM | sed -e "s/Enum//g") +- ENUM=$i; + #offset Enum by one (Enum begins with 0 and not 1!) +- let ENUM=$ENUM-1 ++ let ENUM=$ENUM+1 + + #print info {{{ +- if [ $i -lt 10 ] ++ if [ $ENUM -lt 10 ] + then + printf "\r " +- printf "\r $i/$NUMENUMS Adding "$NAME"..." ++ printf "\r $ENUM/$NUMENUMS Adding "$NAME"..." + else +- if [ $i -lt 100 ] ++ if [ $ENUM -lt 100 ] + then + printf "\r " +- printf "\r $i/$NUMENUMS Adding "$NAME"..." ++ printf "\r $ENUM/$NUMENUMS Adding "$NAME"..." + else + printf "\r " +- printf "\r$i/$NUMENUMS Adding "$NAME"..." ++ printf "\r$ENUM/$NUMENUMS Adding "$NAME"..." + fi + fi + #}}} Index: /issm/oecreview/Archive/12261-12280/ISSM-12264-12265.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12264-12265.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12264-12265.diff (revision 12325) @@ -0,0 +1,114 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.h (revision 12264) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.h (revision 12265) +@@ -40,25 +40,26 @@ + IoModel(FILE* iomodel_handle); + + /*Input/Output*/ +- void Constant(bool *poutput,int constant_enum); +- void Constant(int *poutput,int constant_enum); +- void Constant(double *poutput,int constant_enum); +- void Constant(char **poutput,int constant_enum); +- Param *CopyConstantObject(int constant_enum); +- double *Data(int dataenum); +- void DeleteData(int num,...); +- void FetchConstants(void); +- void FetchData(bool* pboolean,int data_enum); +- void FetchData(int* pinteger,int data_enum); +- void FetchData(double* pscalar,int data_enum); +- void FetchData(char** pstring,int data_enum); +- void FetchData(int** pmatrix,int* pM,int* pN,int data_enum); +- void FetchData(double** pscalarmatrix,int* pM,int* pN,int data_enum); +- void FetchData(char*** pstringarray,int* pnumstrings,int data_enum); +- void FetchData(double*** pmatrixarray,int** pmdims,int** pndims, int* pnumrecords,int data_enum); +- void FetchData(int num,...); +- void FetchDataToInput(Elements* elements,int vector_enum,int default_vector_enum=NoneEnum,double default_value=0); +- FILE* SetFilePointerToData(int* pcode,int* pvector_type, int data_enum); ++ void CheckEnumSync(void); ++ void Constant(bool *poutput,int constant_enum); ++ void Constant(int *poutput,int constant_enum); ++ void Constant(double *poutput,int constant_enum); ++ void Constant(char **poutput,int constant_enum); ++ Param *CopyConstantObject(int constant_enum); ++ double *Data(int dataenum); ++ void DeleteData(int num,...); ++ void FetchConstants(void); ++ void FetchData(bool* pboolean,int data_enum); ++ void FetchData(int* pinteger,int data_enum); ++ void FetchData(double* pscalar,int data_enum); ++ void FetchData(char** pstring,int data_enum); ++ void FetchData(int** pmatrix,int* pM,int* pN,int data_enum); ++ void FetchData(double** pscalarmatrix,int* pM,int* pN,int data_enum); ++ void FetchData(char*** pstringarray,int* pnumstrings,int data_enum); ++ void FetchData(double*** pmatrixarray,int** pmdims,int** pndims, int* pnumrecords,int data_enum); ++ void FetchData(int num,...); ++ void FetchDataToInput(Elements* elements,int vector_enum,int default_vector_enum=NoneEnum,double default_value=0); ++ FILE* SetFilePointerToData(int* pcode,int* pvector_type, int data_enum); + }; + + #endif /* _IOMODEL_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp (revision 12264) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp (revision 12265) +@@ -44,6 +44,9 @@ + /*First, keep track of the file handle: */ + this->fid=iomodel_handle; + ++ /*Check that Enums are Synchronized*/ ++ this->CheckEnumSync(); ++ + /*Initialize and read constants:*/ + this->constants=new Parameters(); + this->FetchConstants(); /*this routine goes through the input file, and fetches bools, ints, doubles and strings only, nothing memory intensive*/ +@@ -88,6 +91,35 @@ + } + /*}}}*/ + ++/*FUNCTION IoModel::CheckEnumSync{{{1*/ ++void IoModel::CheckEnumSync(void){ ++ ++ extern int my_rank; ++ int record_enum = 0; ++ ++ ++ /*Check that some fields have been allocated*/ ++ _assert_(this->fid || my_rank); ++ ++ ++ /*Go find in the binary file, the position of the data we want to fetch: */ ++ if(my_rank==0){ //cpu 0 ++ ++ /*First set FILE* position to the beginning of the file: */ ++ fseek(this->fid,0,SEEK_SET); ++ ++ /*Get first Enum*/ ++ if(fread(&record_enum,sizeof(int),1,this->fid)==0){ ++ _error_("Marshalled file is empty"); ++ } ++ else{ ++ if(record_enum!=MaximumNumberOfEnums){ ++ _error_("Enums in marshalled file are not compatible with compiled code, make sure you are using the same version of ISSM"); ++ } ++ } ++ } ++} ++/*}}}*/ + /*FUNCTION IoModel::Constant(bool* poutput,int constant_enum){{{1*/ + void IoModel::Constant(bool* poutput,int constant_enum){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/marshall.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/marshall.m (revision 12264) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/marshall.m (revision 12265) +@@ -15,6 +15,9 @@ + error(['marshall error message: could not open ' [md.miscellaneous.name '.bin'],' file for binary writing']); + end + ++%First, right MaximumNumberOfEnum to make sure that the Enums are synchronized ++WriteData(fid,'enum',MaximumNumberOfEnums(),'data',true,'format','Boolean'); ++ + %Go through all model fields: check that it is a class and call checkconsistency + fields=properties('model'); + for i=1:length(fields), Index: /issm/oecreview/Archive/12261-12280/ISSM-12265-12266.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12265-12266.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12265-12266.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 12265) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 12266) +@@ -151,6 +151,7 @@ + PetscProfilingCurrentMemEnum, + PetscProfilingCurrentFlopsEnum, + PetscProfilingSolutionTimeEnum, ++ MaxIterationConvergenceFlagEnum, + SteadystateMaxiterEnum, + SteadystateNumRequestedOutputsEnum, + SteadystateReltolEnum, Index: /issm/oecreview/Archive/12261-12280/ISSM-12266-12267.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12266-12267.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12266-12267.diff (revision 12325) @@ -0,0 +1,16 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaxIterationConvergenceFlagEnum.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaxIterationConvergenceFlagEnum.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaxIterationConvergenceFlagEnum.m (revision 12267) +@@ -0,0 +1,11 @@ ++function macro=MaxIterationConvergenceFlagEnum() ++%MAXITERATIONCONVERGENCEFLAGENUM - Enum of MaxIterationConvergenceFlag ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=MaxIterationConvergenceFlagEnum() ++ ++macro=StringToEnum('MaxIterationConvergenceFlag'); Index: /issm/oecreview/Archive/12261-12280/ISSM-12267-12268.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12267-12268.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12267-12268.diff (revision 12325) @@ -0,0 +1,10 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 12267) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 12268) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=436; ++macro=437; Index: /issm/oecreview/Archive/12261-12280/ISSM-12268-12269.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12268-12269.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12268-12269.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 12268) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 12269) +@@ -155,6 +155,7 @@ + case PetscProfilingCurrentMemEnum : return "PetscProfilingCurrentMem"; + case PetscProfilingCurrentFlopsEnum : return "PetscProfilingCurrentFlops"; + case PetscProfilingSolutionTimeEnum : return "PetscProfilingSolutionTime"; ++ case MaxIterationConvergenceFlagEnum : return "MaxIterationConvergenceFlag"; + case SteadystateMaxiterEnum : return "SteadystateMaxiter"; + case SteadystateNumRequestedOutputsEnum : return "SteadystateNumRequestedOutputs"; + case SteadystateReltolEnum : return "SteadystateReltol"; Index: /issm/oecreview/Archive/12261-12280/ISSM-12269-12270.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12269-12270.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12269-12270.diff (revision 12325) @@ -0,0 +1,40 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 12269) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 12270) +@@ -159,6 +159,7 @@ + else if (strcmp(name,"PetscProfilingCurrentMem")==0) return PetscProfilingCurrentMemEnum; + else if (strcmp(name,"PetscProfilingCurrentFlops")==0) return PetscProfilingCurrentFlopsEnum; + else if (strcmp(name,"PetscProfilingSolutionTime")==0) return PetscProfilingSolutionTimeEnum; ++ else if (strcmp(name,"MaxIterationConvergenceFlag")==0) return MaxIterationConvergenceFlagEnum; + else if (strcmp(name,"SteadystateMaxiter")==0) return SteadystateMaxiterEnum; + else if (strcmp(name,"SteadystateNumRequestedOutputs")==0) return SteadystateNumRequestedOutputsEnum; + else if (strcmp(name,"SteadystateReltol")==0) return SteadystateReltolEnum; +@@ -258,11 +259,11 @@ + else if (strcmp(name,"IntParam")==0) return IntParamEnum; + else if (strcmp(name,"IntVecParam")==0) return IntVecParamEnum; + else if (strcmp(name,"MacAyeal2dIceFront")==0) return MacAyeal2dIceFrontEnum; +- else if (strcmp(name,"MacAyeal3dIceFront")==0) return MacAyeal3dIceFrontEnum; + else stage=3; + } + if(stage==3){ +- if (strcmp(name,"Matice")==0) return MaticeEnum; ++ if (strcmp(name,"MacAyeal3dIceFront")==0) return MacAyeal3dIceFrontEnum; ++ else if (strcmp(name,"Matice")==0) return MaticeEnum; + else if (strcmp(name,"Matpar")==0) return MatparEnum; + else if (strcmp(name,"Node")==0) return NodeEnum; + else if (strcmp(name,"Numericalflux")==0) return NumericalfluxEnum; +@@ -381,11 +382,11 @@ + else if (strcmp(name,"IceVolume")==0) return IceVolumeEnum; + else if (strcmp(name,"P0")==0) return P0Enum; + else if (strcmp(name,"P1")==0) return P1Enum; +- else if (strcmp(name,"P1DG")==0) return P1DGEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"SaveResults")==0) return SaveResultsEnum; ++ if (strcmp(name,"P1DG")==0) return P1DGEnum; ++ else if (strcmp(name,"SaveResults")==0) return SaveResultsEnum; + else if (strcmp(name,"BoolElementResult")==0) return BoolElementResultEnum; + else if (strcmp(name,"BoolExternalResult")==0) return BoolExternalResultEnum; + else if (strcmp(name,"DoubleElementResult")==0) return DoubleElementResultEnum; Index: /issm/oecreview/Archive/12261-12280/ISSM-12270-12271.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12270-12271.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12270-12271.diff (revision 12325) @@ -0,0 +1,57 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_nonlinear.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_nonlinear.cpp (revision 12270) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_nonlinear.cpp (revision 12271) +@@ -84,12 +84,22 @@ + + /*Increase count: */ + count++; +- if(converged==true)break; ++ if(converged==true){ ++ bool max_iteration_state=false; ++ int tempStep=1; ++ double tempTime=1.0; ++ femmodel->results->AddObject(new BoolExternalResult(femmodel->results->Size()+1, MaxIterationConvergenceFlagEnum, max_iteration_state, tempStep, tempTime)); ++ break; ++ } + if(count>=max_nonlinear_iterations){ +- _printf_(true," maximum number of iterations (%i) exceeded\n",max_nonlinear_iterations); ++ _printf_(true," maximum number of nonlinear iterations (%i) exceeded\n",max_nonlinear_iterations); + converged=true; +- InputUpdateFromConstantx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,converged,ConvergedEnum); +- InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); ++ InputUpdateFromConstantx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,converged,ConvergedEnum); ++ InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); ++ bool max_iteration_state=true; ++ int tempStep=1; ++ double tempTime=1.0; ++ femmodel->results->AddObject(new BoolExternalResult(femmodel->results->Size()+1, MaxIterationConvergenceFlagEnum, max_iteration_state, tempStep, tempTime)); + break; + } + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_newton.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_newton.cpp (revision 12270) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_newton.cpp (revision 12271) +@@ -66,9 +66,19 @@ + /*Check convergence*/ + convergence(&converged,Kff,pf,uf,old_uf,femmodel->parameters); + xdelete(&Kff); xdelete(&pf); +- if(converged==true) break; ++ if(converged==true){ ++ bool max_iteration_state=false; ++ int tempStep=1; ++ double tempTime=1.0; ++ femmodel->results->AddObject(new BoolExternalResult(femmodel->results->Size()+1, MaxIterationConvergenceFlagEnum, max_iteration_state, tempStep, tempTime)); ++ break; ++ } + if(count>=max_nonlinear_iterations){ +- _printf_(true," maximum number of iterations (%i) exceeded\n",max_nonlinear_iterations); ++ _printf_(true," maximum number of Newton iterations (%i) exceeded\n",max_nonlinear_iterations); ++ bool max_iteration_state=true; ++ int tempStep=1; ++ double tempTime=1.0; ++ femmodel->results->AddObject(new BoolExternalResult(femmodel->results->Size()+1, MaxIterationConvergenceFlagEnum, max_iteration_state, tempStep, tempTime)); + break; + } + Index: /issm/oecreview/Archive/12261-12280/ISSM-12271-12272.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12271-12272.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12271-12272.diff (revision 12325) @@ -0,0 +1,60 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.h (revision 12271) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.h (revision 12272) +@@ -42,6 +42,7 @@ + void AddToGlobal(Vector* pf); + void InsertIntoGlobal(Vector* pf); + void Echo(void); ++ void CheckConsistency(void); + void Init(ElementVector* pe); + void SetValue(double scalar); + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp (revision 12271) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp (revision 12272) +@@ -165,6 +165,9 @@ + int i; + double* localvalues=NULL; + ++ /*In debugging mode, check consistency (no NaN, and values not too big)*/ ++ this->CheckConsistency(); ++ + if(this->fsize){ + /*first, retrieve values that are in the f-set from the g-set values vector: */ + localvalues=(double*)xmalloc(this->fsize*sizeof(double)); +@@ -201,6 +204,17 @@ + + } + /*}}}*/ ++/*FUNCTION ElementVector::CheckConsistency{{{1*/ ++void ElementVector::CheckConsistency(void){ ++ /*Check element matrix values, only in debugging mode*/ ++#ifdef _ISSM_DEBUG_ ++ for (int i=0;inrows;i++){ ++ if (isnan(this->values[i])) _error_("NaN found in Element Vector"); ++ if (fabs( this->values[i])>1.e+50) _error_("Element Vector values exceeds 1.e+50"); ++ } ++#endif ++} ++/*}}}*/ + /*FUNCTION ElementVector::Echo{{{1*/ + void ElementVector::Echo(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 12271) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 12272) +@@ -628,7 +628,10 @@ + surface_mass_balance_input->GetInputValue(&surface_mass_balance_g,gauss); + basal_melting_input->GetInputValue(&basal_melting_g,gauss); + thickness_input->GetInputValue(&thickness_g,gauss); +- if(basal_melting_correction_input) basal_melting_correction_input->GetInputValue(&basal_melting_correction_g,gauss); ++ if(basal_melting_correction_input) ++ basal_melting_correction_input->GetInputValue(&basal_melting_correction_g,gauss); ++ else ++ basal_melting_correction_g=0.; + + for(i=0;ivalues[i]+=Jdettria*gauss->weight*(thickness_g+dt*(surface_mass_balance_g-basal_melting_g-basal_melting_correction_g))*L[i]; + } Index: /issm/oecreview/Archive/12261-12280/ISSM-12272-12273.diff =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-12272-12273.diff (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-12272-12273.diff (revision 12325) @@ -0,0 +1,133 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12272) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12273) +@@ -77,7 +77,8 @@ + this->AddObject(observation); + } + else{ +- //We need to average with the current observations (not done yet) ++ /*We need to average with the current observations*/ ++ this->quadtree->AddAndAverage(x[i],y[i],observations_list[i]); + } + } + printf("done\n"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12272) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12273) +@@ -52,6 +52,7 @@ + Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth_in); + ~Quadtree(); + void Add(Observation *observation); ++ void AddAndAverage(double x,double y,double value); + void DeepEcho(void); + void Echo(void); + void IntergerCoordinates(int *xi,int *yi,double x,double y); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h (revision 12272) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.h (revision 12273) +@@ -13,6 +13,7 @@ + double x,y; + int xi,yi; + int index; ++ double weight; + double value; + + /*Observation constructors, destructors*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12272) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12273) +@@ -197,6 +197,58 @@ + NbObs++; + + }/*}}}*/ ++/*FUNCTION Quadtree::AddAndAverage{{{1*/ ++void Quadtree::AddAndAverage(double x,double y,double value){ ++ ++ QuadtreeBox **pbox = NULL; ++ QuadtreeBox *box = NULL; ++ int xi,yi; ++ int level,levelbin; ++ int index; ++ double length,length2; ++ ++ /*Get integer coodinates*/ ++ this->IntergerCoordinates(&xi,&yi,x,y); ++ ++ /*Initialize levels*/ ++ level = 0; ++ levelbin = (1L<MaxDepth);// = 2^30 ++ ++ /*Get inital box (the largest)*/ ++ pbox=&root; ++ ++ /*Find the smallest box where this point is located*/ ++ while((box=*pbox) && (box->nbitems<0)){ ++ ++ levelbin>>=1; level+=1; ++ ++ pbox = &box->box[IJ(xi,yi,levelbin)]; ++ } ++ ++ /*Add obervation in this box (should be full)*/ ++ if(box && box->nbitems==4){ ++ index = 0; ++ length = pow(box->obs[0]->x - x,2.) + pow(box->obs[0]->y - y,2.); ++ for(int i=1;i<4;i++){ ++ length2 = pow(box->obs[i]->x - x,2.) + pow(box->obs[i]->y - y,2.); ++ if(length2obs[index]->x = (box->obs[index]->weight*box->obs[index]->x + x)/(box->obs[index]->weight+1); ++ box->obs[index]->y = (box->obs[index]->weight*box->obs[index]->y + y)/(box->obs[index]->weight+1); ++ box->obs[index]->xi= int((box->obs[index]->weight*double(box->obs[index]->xi) + double(xi))/(box->obs[index]->weight+1)); ++ box->obs[index]->yi= int((box->obs[index]->weight*double(box->obs[index]->yi) + double(yi))/(box->obs[index]->weight+1)); ++ box->obs[index]->value = (box->obs[index]->weight*box->obs[index]->value + value)/(box->obs[index]->weight+1); ++ box->obs[index]->weight += 1; ++ } ++ else{ ++ _error_("Box is not full"); ++ } ++}/*}}}*/ + /*FUNCTION Quadtree::Echo{{{1*/ + void Quadtree::Echo(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp (revision 12272) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Observation.cpp (revision 12273) +@@ -14,12 +14,13 @@ + /*FUNCTION Observation::Observation(double x,double y,int xi,int yi,int index,double value){{{1*/ + Observation::Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in){ + +- this->x = x_in; +- this->y = y_in; +- this->xi = xi_in; +- this->yi = yi_in; +- this->index = index_in; +- this->value = value_in; ++ this->x = x_in; ++ this->y = y_in; ++ this->xi = xi_in; ++ this->yi = yi_in; ++ this->index = index_in; ++ this->value = value_in; ++ this->weight = 1.; + + } + /*}}}*/ +@@ -41,6 +42,7 @@ + printf(" y : %g\n",this->y); + printf(" xi : "); printbinary(this->xi); printf("\n"); + printf(" yi : "); printbinary(this->yi); printf("\n"); ++ printf(" weight: %g\n",this->weight); + printf(" value : %g\n",this->value); + } + /*}}}*/ Index: /issm/oecreview/Archive/12261-12280/ISSM-DocReview-12261-12280.tex =================================================================== --- /issm/oecreview/Archive/12261-12280/ISSM-DocReview-12261-12280.tex (revision 12325) +++ /issm/oecreview/Archive/12261-12280/ISSM-DocReview-12261-12280.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12261-12280/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12261-12280/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12261-12280/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12261-12280 Index: /issm/oecreview/Archive/12261-12280/Makefile =================================================================== --- /issm/oecreview/Archive/12261-12280/Makefile (revision 12325) +++ /issm/oecreview/Archive/12261-12280/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12261-12280 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12261-12280/log.tex =================================================================== --- /issm/oecreview/Archive/12261-12280/log.tex (revision 12325) +++ /issm/oecreview/Archive/12261-12280/log.tex (revision 12325) @@ -0,0 +1,25 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12261-12262.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh \\ Export determination: 6. \\Rationale: Added MaximumNumberOfEnums matlab file to check Enum Sync +M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh Simplified Synchronize \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12262-12263.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh \\ Export determination: 6. \\Rationale: Simplified Synchronize +A /issm/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m Added MaximumNumberOfEnums.m \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12263-12264.diff: \\ Function name: \\A /issm/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m \\ Export determination: 6. \\Rationale: Added MaximumNumberOfEnums.m +M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh Fixed issue with matlab files \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12264-12265.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh \\ Export determination: 6. \\Rationale: Fixed issue with matlab files +M /issm/trunk-jpl/src/c/objects/IoModel.cpp M /issm/trunk-jpl/src/c/objects/IoModel.h M /issm/trunk-jpl/src/m/model/marshall.m Added check that Enums are synchronized between matlab's interface and compiled code \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12265-12266.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/IoModel.cpp M /issm/trunk-jpl/src/c/objects/IoModel.h M /issm/trunk-jpl/src/m/model/marshall.m \\ Export determination: 6. \\Rationale: Added check that Enums are synchronized between matlab's interface and compiled code +M /issm/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h Added convergence flag for reaching maximum iteration number \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12266-12267.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h \\ Export determination: 6. \\Rationale: Added convergence flag for reaching maximum iteration number +A /issm/trunk-jpl/src/m/enum/MaxIterationConvergenceFlagEnum.m Added convergence flag for reaching maximum number of iterations \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12267-12268.diff: \\ Function name: \\A /issm/trunk-jpl/src/m/enum/MaxIterationConvergenceFlagEnum.m \\ Export determination: 6. \\Rationale: Added convergence flag for reaching maximum number of iterations +M /issm/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m Added convergence flag for reaching maximum number of iterations \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12268-12269.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/enum/MaximumNumberOfEnums.m \\ Export determination: 6. \\Rationale: Added convergence flag for reaching maximum number of iterations +M /issm/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp Added convergence flag for reaching maximum number of iterations \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12269-12270.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp \\ Export determination: 6. \\Rationale: Added convergence flag for reaching maximum number of iterations +M /issm/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp Added convergence flag for reaching maximum number of iterations \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12270-12271.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp \\ Export determination: 6. \\Rationale: Added convergence flag for reaching maximum number of iterations +M /issm/trunk-jpl/src/c/solvers/solver\_newton.cpp M /issm/trunk-jpl/src/c/solvers/solver\_nonlinear.cpp First attempt at adding convergence flag: (i.e. whether loop exited due to convergence criteria or maximum number of iterations). Not sure if Addobject( new BoolExternalResults \_ ) is correct or will it end up duplicating this field in the results in multiple solves within a solution sequence? I have not checked-in thermal\_nonlinear.cpp or stokescoupling\_nonlinear.cpp since I am not using these yet...Will be testing, but feel free to change \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12271-12272.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/solvers/solver\_newton.cpp M /issm/trunk-jpl/src/c/solvers/solver\_nonlinear.cpp \\ Export determination: 6. \\Rationale: First attempt at adding convergence flag: (i.e. whether loop exited due to convergence criteria or maximum number of iterations). Not sure if Addobject( new BoolExternalResults \_ ) is correct or will it end up duplicating this field in the results in multiple solves within a solution sequence? I have not checked-in thermal\_nonlinear.cpp or stokescoupling\_nonlinear.cpp since I am not using these yet...Will be testing, but feel free to change +M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.h Fixed BIG error in prognostic: melting rate correction was never defined \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-12272-12273.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.h \\ Export determination: 6. \\Rationale: Fixed BIG error in prognostic: melting rate correction was never defined +M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Observation.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Observation.h M /issm/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Quadtree.h Added observation averaging \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-12273-12274.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Observation.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Observation.h M /issm/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Quadtree.h \\ Export determination: 6. \\Rationale: Added observation averaging \\\\ Index: /issm/oecreview/Archive/12261-12280/r1.tex =================================================================== --- /issm/oecreview/Archive/12261-12280/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12261-12280/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12261 Index: /issm/oecreview/Archive/12261-12280/r2.tex =================================================================== --- /issm/oecreview/Archive/12261-12280/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12261-12280/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12280 Index: /issm/oecreview/Archive/12281-12300/Date.tex =================================================================== --- /issm/oecreview/Archive/12281-12300/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12281-12300/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12281-12300/ISSM-12281-12282.diff =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-12281-12282.diff (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-12281-12282.diff (revision 12325) @@ -0,0 +1,68 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12281) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12282) +@@ -109,26 +109,33 @@ + } + + /*Find all observations that are in range*/ +- this->quadtree->RangeSearch(&indices,&nobs,x_interp,y_interp,range); +- +- if(nobs==0){ +- /*No observation found, double range*/ +- //printf("No observation found within range, doubling range\n"); ++ nobs=0; ++ while(nobs==0){ + xfree((void**)&indices); +- this->ObservationList(&x,&y,&obs,&nobs,x_interp,y_interp,range*2); ++ this->quadtree->RangeSearch(&indices,&nobs,x_interp,y_interp,range); ++ if(!nobs){ ++ /*No observation found, double range*/ ++ range=2*range; ++ } + } +- else{ +- //if(nobs>1000) printf("Taking more than 1000 observations\n"); +- /*Allocate vectors*/ +- x = (double*)xmalloc(nobs*sizeof(double)); +- y = (double*)xmalloc(nobs*sizeof(double)); +- obs = (double*)xmalloc(nobs*sizeof(double)); ++ /*Check that we do not have more than 50 observations*/ ++ //while(nobs>50){ ++ // range=range/2; ++ // xfree((void**)&indices); ++ // this->quadtree->RangeSearch(&indices,&nobs,x_interp,y_interp,range); ++ //} + +- /*Loop over all observations and fill in x, y and obs*/ +- for (i=0;iGetObjectByOffset(indices[i]); +- observation->WriteXYObs(&x[i],&y[i],&obs[i]); +- } ++ if(!nobs) _error_("Unexpected error: no observation within current range and more than 50 observations if doubling range"); ++ ++ /*Allocate vectors*/ ++ x = (double*)xmalloc(nobs*sizeof(double)); ++ y = (double*)xmalloc(nobs*sizeof(double)); ++ obs = (double*)xmalloc(nobs*sizeof(double)); ++ ++ /*Loop over all observations and fill in x, y and obs*/ ++ for (i=0;iGetObjectByOffset(indices[i]); ++ observation->WriteXYObs(&x[i],&y[i],&obs[i]); + } + + /*Assign output pointer*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12281) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12282) +@@ -68,7 +68,7 @@ + + /*return semi-variogram*/ + a = 1./3.; +- gamma = (sill-nugget)*(1-exp(-h2/(a*pow(range,2.)))) + nugget; ++ gamma = (sill-nugget)*(1.-exp(-h2/(a*range*range))) + nugget; + return gamma; + } + /*}}}*/ Index: /issm/oecreview/Archive/12281-12300/ISSM-12286-12287.diff =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-12286-12287.diff (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-12286-12287.diff (revision 12325) @@ -0,0 +1,34 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gslib/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gslib/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gslib/install.sh (revision 12287) +@@ -0,0 +1,23 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf install ++mkdir install ++ ++#Download from ISSM server ++#$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gslib90_ls.tar.gz' 'gslib90_ls.tar.gz' ++ ++#Untar ++tar -zxvf gslib90_ls.tar.gz ++ ++#Move gslib into install directory ++mv gslib90/* install ++rm -rf gslib90 ++ ++#Change compiler to gfortran ++cd install ++cat Makefile | sed -e "s/FC=g95/FC=gfortran/g" > Makefile.bak ++mv Makefile.bak Makefile ++cat gslib/Makefile | sed -e "s/FC=g95/FC=gfortran/g" > Makefile.bak ++mv Makefile.bak gslib/Makefile ++make + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gslib/install.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12281-12300/ISSM-12287-12288.diff =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-12287-12288.diff (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-12287-12288.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gslib/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gslib/install.sh (revision 12287) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gslib/install.sh (revision 12288) +@@ -5,7 +5,7 @@ + mkdir install + + #Download from ISSM server +-#$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gslib90_ls.tar.gz' 'gslib90_ls.tar.gz' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gslib90_ls.tar.gz' 'gslib90_ls.tar.gz' + + #Untar + tar -zxvf gslib90_ls.tar.gz Index: /issm/oecreview/Archive/12281-12300/ISSM-12288-12289.diff =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-12288-12289.diff (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-12288-12289.diff (revision 12325) @@ -0,0 +1,351 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12289) +@@ -161,11 +161,10 @@ + void Observations::Variomap(double* gamma,double *x,int n){ + + /*Output and Intermediaries*/ +- int nobs,i,j,k; +- double range; ++ int i,j,k; ++ double distance; + Observation *observation1 = NULL; + Observation *observation2 = NULL; +- int *indices = NULL; + + int *counter= (int*)xmalloc(n*sizeof(int)); + for(j=0;jSize();i++){ + observation1=(Observation*)this->GetObjectByOffset(i); + +- for(j=0;j=0.); ++ for(j=i+1;jSize();j++){ ++ observation2=(Observation*)this->GetObjectByOffset(j); + +- /*Find all observations that are in range*/ +- this->quadtree->RangeSearch(&indices,&nobs,observation1->x,observation1->y,range); ++ distance=sqrt(pow(observation1->x - observation2->x,2.) + pow(observation1->y - observation2->y,2.)); ++ if(distance>x[n-1]) continue; + +- for (k=0;kGetObjectByOffset(indices[k]); +- gamma[j] += 1./2.*pow(observation1->value - observation2->value,2.); +- } ++ int index = int(distance/(x[1]-x[0])); ++ if(index>n-1) index = n-1; ++ if(index<0) index = 0; + +- counter[j] += nobs; +- xfree((void**)&indices); ++ gamma[index] += 1./2.*pow(observation1->value - observation2->value,2.); ++ counter[index] += 1; + } + } + + /*Normalize semivariogram*/ +- for(j=0;j beg + 1) { +- int piv = arr[beg], l = beg + 1, r = end; +- while (l < r) +- { +- if (arr[l] <= piv) +- l++; +- else +- swap(&arr[l], &arr[--r]); +- } +- swap(&arr[--l], &arr[beg]); +- sort(arr, beg, l); +- sort(arr, r, end); +- } +-} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Sorting/binary_search.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Sorting/binary_search.cpp (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Sorting/binary_search.cpp (revision 12289) +@@ -10,11 +10,11 @@ + + #include + +-int binary_search(int* poffset,int target, int* sorted_integers,int num_integers){ ++int binary_search(int* poffset,int target,int* sorted_integers,int num_integers){ + + /*output: */ + int offset; //offset, if found +- int found=0; //found=0 if target is not found, 1 otherwise. ++ int found=0; //found=0 if target is not found, 1 otherwise. + + /*intermediary: */ + int* beg=NULL; +@@ -63,4 +63,3 @@ + /*Return result: */ + return found; + } +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Sorting/sorting.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Sorting/sorting.h (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Sorting/sorting.h (revision 12289) +@@ -5,8 +5,6 @@ + #ifndef _SORTING_H_ + #define _SORTING_H_ + +-int binary_search(int* poffset,int target, int* sorted_integers,int num_integers); ++int binary_search(int* poffset,int target,int* sorted_integers,int num_integers); + +- + #endif //ifndef _SORTING_H_ +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12289) +@@ -137,8 +137,14 @@ + + /*Get list of observations for current point*/ + observations->ObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx],range); ++ if(n_obs==0){ ++ predictions[idx] = -999.; ++ error[idx] = -999.; ++ continue; ++ } + + /*Allocate intermediary matrix and vectors*/ ++ + Gamma = (double*)xmalloc(n_obs*n_obs*sizeof(double)); + gamma0 = (double*)xmalloc(n_obs*sizeof(double)); + ones = (double*)xmalloc(n_obs*sizeof(double)); +@@ -146,14 +152,16 @@ + /*First: Create semivariogram matrix for observations*/ + for(i=0;iSemiVariogram(x[i]-x[j],y[i]-y[j]); ++ //Gamma[i*n_obs+j] = variogram->SemiVariogram(x[i]-x[j],y[i]-y[j]); ++ Gamma[i*n_obs+j] = variogram->Covariance(x[i]-x[j],y[i]-y[j]); + Gamma[j*n_obs+i] = Gamma[i*n_obs+j]; + } + } + for(i=0;iSemiVariogram(x[i]-x_interp[idx],y[i]-y_interp[idx]); ++ //for(i=0;iSemiVariogram(x[i]-x_interp[idx],y[i]-y_interp[idx]); ++ for(i=0;iCovariance(x[i]-x_interp[idx],y[i]-y_interp[idx]); + + /*Solve the three linear systems*/ + GslSolve(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp (revision 12289) +@@ -58,6 +58,24 @@ + /*}}}*/ + + /*Variogram function*/ ++/*FUNCTION ExponentialVariogram::Covariance{{{1*/ ++double ExponentialVariogram::Covariance(double deltax,double deltay){ ++ /*The covariance can be deduced from the variogram from the following ++ * relationship: ++ * 2 gamma = C(x,x) + C(y,y) -2 C(x,y) ++ * so ++ * C(h) = sill - gamma */ ++ double h,a,cova; ++ ++ /*Calculate length*/ ++ h=sqrt(pow(deltax,2.)+pow(deltay,2.)); ++ ++ /*return covariance*/ ++ a = 1./3.; ++ cova = (sill-nugget)*exp(-h/(a*range)); ++ return cova; ++} ++/*}}}*/ + /*FUNCTION ExponentialVariogram::SemiVariogram{{{1*/ + double ExponentialVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12289) +@@ -58,6 +58,27 @@ + /*}}}*/ + + /*Variogram function*/ ++/*FUNCTION GaussianVariogram::Covariance{{{1*/ ++double GaussianVariogram::Covariance(double deltax,double deltay){ ++ /*The covariance can be deduced from the variogram from the following ++ * relationship: ++ * 2 gamma = C(x,x) + C(y,y) -2 C(x,y) ++ * so ++ * C(h) = sill - gamma */ ++ double h2,a,cova; ++ ++ /*Calculate length square*/ ++ h2=pow(deltax,2.)+pow(deltay,2.); ++ ++ /*return covariance*/ ++ a = 1./3.; ++ cova = (sill-nugget)*exp(-h2/(a*range*range)); ++ ++ //if(h2<0.0000001) cova = sill; ++ ++ return cova; ++} ++/*}}}*/ + /*FUNCTION GaussianVariogram::SemiVariogram{{{1*/ + double GaussianVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ +@@ -69,6 +90,9 @@ + /*return semi-variogram*/ + a = 1./3.; + gamma = (sill-nugget)*(1.-exp(-h2/(a*range*range))) + nugget; ++ ++ //if(h2>1000*1000) printf("gamma = %g h= %g\n",gamma,sqrt(h2)); ++ printf("h = %g gamma = %g\n",sqrt(h2),gamma); + return gamma; + } + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp (revision 12289) +@@ -58,6 +58,27 @@ + /*}}}*/ + + /*Variogram function*/ ++/*FUNCTION SphericalVariogram::Covariance{{{1*/ ++double SphericalVariogram::Covariance(double deltax,double deltay){ ++ /*The covariance can be deduced from the variogram from the following ++ * relationship: ++ * 2 gamma = C(x,x) + C(y,y) -2 C(x,y) ++ * so ++ * C(h) = sill - gamma */ ++ double h,cova; ++ ++ /*Calculate length square*/ ++ h=sqrt(pow(deltax,2.)+pow(deltay,2.)); ++ ++ /*return covariance*/ ++ if(h<=range) ++ cova = (sill-nugget)*(1 - (3*h)/(2*range) + pow(h,3.)/(2*pow(range,3.)) ); ++ else ++ cova = 0.; ++ ++ return cova; ++} ++/*}}}*/ + /*FUNCTION SphericalVariogram::SemiVariogram{{{1*/ + double SphericalVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h (revision 12289) +@@ -30,5 +30,6 @@ + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); ++ double Covariance(double deltax,double deltay); + }; + #endif /* _EXPONENTIALVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.cpp (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.cpp (revision 12289) +@@ -59,6 +59,24 @@ + /*}}}*/ + + /*Variogram function*/ ++/*FUNCTION PowerVariogram::Covariance{{{1*/ ++double PowerVariogram::Covariance(double deltax,double deltay){ ++ /*The covariance can be deduced from the variogram from the following ++ * relationship: ++ * 2 gamma = C(x,x) + C(y,y) -2 C(x,y) ++ * so ++ * C(h) = sill - gamma */ ++ double h,cova; ++ ++ /*Calculate length square*/ ++ h=sqrt(pow(deltax,2.)+pow(deltay,2.)); ++ ++ /*return covariance*/ ++ cova = 9999. - this->slope*pow(h,this->power); ++ ++ return cova; ++} ++/*}}}*/ + /*FUNCTION PowerVariogram::SemiVariogram{{{1*/ + double PowerVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ +@@ -70,6 +88,7 @@ + /*return semi-variogram*/ + gamma = this->nugget + this->slope*pow(h,this->power); + ++ //if(h>1000) printf("gamma = %g h=%g\n",gamma,h); + return gamma; + } + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h (revision 12289) +@@ -30,5 +30,6 @@ + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); ++ double Covariance(double deltax,double deltay); + }; + #endif /* _GAUSSIANVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h (revision 12289) +@@ -30,5 +30,6 @@ + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); ++ double Covariance(double deltax,double deltay); + }; + #endif /* _SPHERICALVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.h (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/PowerVariogram.h (revision 12289) +@@ -30,5 +30,6 @@ + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); ++ double Covariance(double deltax,double deltay); + }; + #endif /* _POWERVARIOGRAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h (revision 12288) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Variogram.h (revision 12289) +@@ -12,6 +12,7 @@ + public: + virtual ~Variogram(){}; + virtual double SemiVariogram(double deltax,double deltay)=0; ++ virtual double Covariance(double deltax,double deltay)=0; + + }; + #endif Index: /issm/oecreview/Archive/12281-12300/ISSM-12289-12290.diff =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-12289-12290.diff (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-12289-12290.diff (revision 12325) @@ -0,0 +1,135 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m (revision 12290) +@@ -0,0 +1,130 @@ ++x=[]; ++y=[]; ++thickness=[]; ++for i=1:5, ++ switch(i) ++ case 1, filename='2002_Antarctica_P3chile'; ++ case 2, filename='2004_Antarctica_P3chile'; ++ case 3, filename='2009_Antarctica_DC8'; ++ case 4, filename='2009_Antarctica_TO'; ++ case 5, filename='2010_Antarctica_DC8'; ++ otherwise, error('not supported'); ++ end ++ disp(['Loading ' filename '...']); ++ A=load(filename); ++ [tempx tempy]=ll2xy(A.lat(:),A.lon(:),-1,0,71); ++ x=[x;tempx]; ++ y=[y;tempy]; ++ thickness=[thickness;A.thickness]; ++end ++[xl yl]=basinzoom(pairoptions('basin','Pine Island Glacier')); ++x=x(1:100:end); ++y=y(1:100:end); ++data=thickness(1:100:end); ++ ++%Output Matrix ++xmin = xl(1); ++ymin = yl(1); ++nx = 101; ++ny = 101; ++deltax = 5000; ++deltay = 5000; ++ ++%Variogram ++nugget=10; ++sill =164; ++range =25763; ++ ++%Kriging options ++mindata = 1; ++maxdata = 50; ++maxsearchradius = 50000; ++ ++%Some intermediaries (Convert to gslib's parameters); ++c = (sill-nugget); ++a = sqrt(3)*range; ++ ++ ++%Write data file ++fid=fopen('cluster.dat','w'); ++fprintf(fid,'%s\n','Data file'); ++fprintf(fid,'%i\n',3); ++fprintf(fid,'%s\n','Xlocation'); ++fprintf(fid,'%s\n','Ylocation'); ++fprintf(fid,'%s\n','Data'); ++fprintf(fid,'%g %g %g\n',[x y data]'); ++fclose(fid); ++ ++if 0, %GAMV ++ %Write parameter file ++ fid=fopen('gamv.par','w'); ++ fprintf(fid,'\t\t\t\t%s\n','Parameters for GAMV'); ++ fprintf(fid,'\t\t\t\t%s\n','*******************'); ++ fprintf(fid,'\n'); ++ fprintf(fid,'%s\n','START OF PARAMETERS:'); ++ fprintf(fid,'%-30s %s\n','./cluster.dat' ,'\file with data'); ++ fprintf(fid,'%-30s %s\n','1 2 0' ,'\columns for X, Y, Z coordinates'); ++ fprintf(fid,'%-30s %s\n','1 3 ' ,'\number of variables, column number'); ++ fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); ++ fprintf(fid,'%-30s %s\n','gamv.out' ,'\file for variogram output'); ++ fprintf(fid,'%-30s %s\n','20' ,'\number of lags'); ++ fprintf(fid,'%-30s %s\n','5.0' ,'\lag separation distance'); ++ fprintf(fid,'%-30s %s\n','3.0' ,'\lag tolerance'); ++ fprintf(fid,'%-30s %s\n','3' ,'\number of directions'); ++ fprintf(fid,'%-30s %s\n','0.0 90.0 50.0 0.0 90.0 50.0','\azm, atol, bandh, dip, dtol, bandv'); ++ fprintf(fid,'%-30s %s\n','0.0 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); ++ fprintf(fid,'%-30s %s\n','90. 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); ++ fprintf(fid,'%-30s %s\n','0' ,'\standardize sill? (0=no, 1=yes)'); ++ fprintf(fid,'%-30s %s\n','2' ,'\number of variograms'); ++ fprintf(fid,'%-30s %s\n','1 1 1' ,'\tail var., head vars., variogram type'); ++ fprintf(fid,'%-30s %s\n','1 1 3' ,'\tail var., head vars., variogram type'); ++ fclose(fid); ++ ++ %Call gamv ++ system([issmdir() '/externalpackages/gslib/install/gamv gamv.par']); ++ ++else, %Kriging KB2D ++ %Write parameter file ++ fid=fopen('kb2d.par','w'); ++ fprintf(fid,'\t\t\t\t%s\n','Parameters for KB2D'); ++ fprintf(fid,'\t\t\t\t%s\n','*******************'); ++ fprintf(fid,'\n'); ++ fprintf(fid,'%s\n','START OF PARAMETERS:'); ++ fprintf(fid,'%-30s %s\n','./cluster.dat' ,'\file with data'); ++ fprintf(fid,'%-30s %s\n','1 2 3' ,'\columns for X, Y and variable'); ++ fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); ++ fprintf(fid,'%-30s %s\n','0' ,'\debugging level: 0,1,2,3'); ++ fprintf(fid,'%-30s %s\n','kb2d.dbg' ,'\file for debuggging output'); ++ fprintf(fid,'%-30s %s\n','kb2d.out' ,'\file for kriged output'); ++ fprintf(fid,'%-30s %s\n',num2str([nx xmin deltax],'%i %10g %6g') ,'\nx, xmn, xsiz'); ++ fprintf(fid,'%-30s %s\n',num2str([ny ymin deltay],'%i %10g %6g') ,'\nx, xmn, xsiz'); ++ fprintf(fid,'%-30s %s\n','1 1' ,'\x and y block discretization'); ++ fprintf(fid,'%-30s %s\n',num2str([mindata maxdata],'%6g') ,'\min and max data for kriging'); ++ fprintf(fid,'%-30s %s\n',num2str(maxsearchradius,'%6g') ,'\max search radius'); ++ fprintf(fid,'%-30s %s\n','1 2.302' ,'\0=SK, 1=OK, (mean if SK)'); ++ fprintf(fid,'%-30s %s\n',['1 ' num2str(nugget)] ,'\nst, nugget effect'); ++ fprintf(fid,'%-30s %s\n',['3 ' num2str([c 0.0 a a],'%10g')],'\it, c, azm, a_max, a_min'); ++ fclose(fid); ++ ++ tic;system([issmdir() '/externalpackages/gslib/install/kb2d kb2d.par']);toc; ++ ++ %Read output ++ fid=fopen('kb2d.out','r'); ++ while (~feof(fid)), ++ A=fscanf(fid,'%s',1); ++ if strcmp(A,'KB2D'); ++ A=fscanf(fid,'%s',1); %Read output ++ params=fscanf(fid,'%i %i %i %i %g %g %g %g %g %g %1',[11 1]); ++ elseif strcmp(A,' Estimate'), ++ continue; ++ elseif strcmp(A,'Estimation'), ++ A=fscanf(fid,'%s',1); %Read Variance ++ A=fscanf(fid,'%g %g',[params(1) params(2)*params(3)]); ++ B=A(1,:); B=reshape(B,[params(2),params(3)]); ++ E=A(2,:); E=reshape(E,[params(2),params(3)]); ++ else ++ %do nothing ++ end ++ end ++ fclose(fid); ++end Index: /issm/oecreview/Archive/12281-12300/ISSM-12290-12291.diff =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-12290-12291.diff (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-12290-12291.diff (revision 12325) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m (revision 12290) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m (revision 12291) +@@ -120,8 +120,8 @@ + elseif strcmp(A,'Estimation'), + A=fscanf(fid,'%s',1); %Read Variance + A=fscanf(fid,'%g %g',[params(1) params(2)*params(3)]); +- B=A(1,:); B=reshape(B,[params(2),params(3)]); +- E=A(2,:); E=reshape(E,[params(2),params(3)]); ++ B=A(1,:); B=reshape(B,[params(3),params(2)])'; ++ E=A(2,:); E=reshape(E,[params(3),params(2)])'; + else + %do nothing + end Index: /issm/oecreview/Archive/12281-12300/ISSM-12291-12292.diff =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-12291-12292.diff (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-12291-12292.diff (revision 12325) @@ -0,0 +1,379 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.h (revision 12292) +@@ -21,6 +21,8 @@ + Option* GetOption(const char* name); + void Get(double* pvalue,const char* name); + void Get(double* pvalue,const char* name,double default_value); ++ void Get(int* pvalue,const char* name); ++ void Get(int* pvalue,const char* name,int default_value); + void Get(bool* pvalue,const char* name); + void Get(bool* pvalue,const char* name,bool default_value); + void Get(char** pvalue,const char* name); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12292) +@@ -93,49 +93,73 @@ + + /*Methods*/ + /*FUNCTION Observations::ObservationList{{{*/ +-void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp,double range){ ++void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp,double radius,int maxdata){ + + /*Output and Intermediaries*/ +- int nobs,i,index; ++ bool stop; ++ int nobs,i,j,k,n,counter; ++ double h2,radius2; ++ int *indices = NULL; ++ double *dists = NULL; + double *x = NULL; + double *y = NULL; + double *obs = NULL; + Observation *observation = NULL; +- int *indices = NULL; + +- /*Treat range*/ +- if(range==0){ +- range=this->quadtree->root->length; +- } ++ /*Compute radius square*/ ++ if(radius==0) radius=this->quadtree->root->length; ++ radius2 = radius*radius; + +- /*Find all observations that are in range*/ +- nobs=0; +- while(nobs==0){ +- xfree((void**)&indices); +- this->quadtree->RangeSearch(&indices,&nobs,x_interp,y_interp,range); +- if(!nobs){ +- /*No observation found, double range*/ +- range=2*range; ++ /*Find all observations that are in radius*/ ++ indices = (int*)xmalloc(this->Size()*sizeof(int)); ++ dists = (double*)xmalloc(this->Size()*sizeof(double)); ++ nobs = 0; ++ ++ for (i=0;iSize();i++){ ++ observation=(Observation*)this->GetObjectByOffset(i); ++ h2 = (observation->x-x_interp)*(observation->x-x_interp) + (observation->y-y_interp)*(observation->y-y_interp); ++ ++ if(nobs==maxdata && h2>radius2) continue; ++ if(nobs<=maxdata){ ++ indices[nobs] = i; ++ dists[nobs] = h2; ++ nobs++; + } +- } +- /*Check that we do not have more than 50 observations*/ +- //while(nobs>50){ +- // range=range/2; +- // xfree((void**)&indices); +- // this->quadtree->RangeSearch(&indices,&nobs,x_interp,y_interp,range); +- //} ++ if(nobs==1) continue; + +- if(!nobs) _error_("Unexpected error: no observation within current range and more than 50 observations if doubling range"); ++ /*Sort all dists up to now*/ ++ n=nobs-1; ++ stop = false; ++ for(k=0;kGetObjectByOffset(indices[i]); +- observation->WriteXYObs(&x[i],&y[i],&obs[i]); ++ /*Loop over all observations and fill in x, y and obs*/ ++ for (i=0;iGetObjectByOffset(indices[i]); ++ observation->WriteXYObs(&x[i],&y[i],&obs[i]); ++ } + } + + /*Assign output pointer*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.h (revision 12292) +@@ -22,7 +22,7 @@ + ~Observations(); + + /*Methods*/ +- void ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp,double range); ++ void ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp,double radius,int maxdata); + void QuadtreeColoring(double* A,double *x,double *y,int n); + void Variomap(double* gamma,double *x,int n); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp (revision 12292) +@@ -66,6 +66,44 @@ + return 1; + } + /*}}}*/ ++/*FUNCTION Options::Get(int* pvalue, char* name){{{1*/ ++void Options::Get(int* pvalue,const char* name){ ++ ++ vector::iterator object; ++ Option* option=NULL; ++ ++ /*Get option*/ ++ option=GetOption(name); ++ ++ /*If the pointer is not NULL, the option has been found*/ ++ if(option){ ++ option->Get(pvalue); ++ } ++ /*Else, the Option does not exist, no default provided*/ ++ else{ ++ _error_("option of name \"%s\" not found, and no default value has been provided",name); ++ } ++} ++/*}}}*/ ++/*FUNCTION Options::Get(int* pvalue, char* name,int default_value){{{1*/ ++void Options::Get(int* pvalue,const char* name,int default_value){ ++ ++ vector::iterator object; ++ Option* option=NULL; ++ ++ /*Get option*/ ++ option=GetOption(name); ++ ++ /*If the pointer is not NULL, the option has been found*/ ++ if(option){ ++ option->Get(pvalue); ++ } ++ /*Else, the Option does not exist, a default is provided here*/ ++ else{ ++ *pvalue=default_value; ++ } ++} ++/*}}}*/ + /*FUNCTION Options::Get(double* pvalue, char* name){{{1*/ + void Options::Get(double* pvalue,const char* name){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Threads/LaunchThread.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Threads/LaunchThread.cpp (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Threads/LaunchThread.cpp (revision 12292) +@@ -66,5 +66,4 @@ + + function((void*)&handle); + #endif +- + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp (revision 12292) +@@ -23,7 +23,8 @@ + double *error = NULL; + + /*Intermediaries*/ +- double range; ++ int mindata,maxdata; ++ double radius; + char *output = NULL; + Variogram *variogram = NULL; + Observations *observations = NULL; +@@ -37,7 +38,9 @@ + + /*Get Variogram from Options*/ + ProcessVariogram(&variogram,options); +- options->Get(&range,"searchrange",0.); ++ options->Get(&radius,"searchradius",0.); ++ options->Get(&mindata,"mindata",1); ++ options->Get(&maxdata,"maxdata",50); + + /*Process observation dataset*/ + observations=new Observations(obs_list,obs_x,obs_y,obs_length,options); +@@ -61,7 +64,9 @@ + gate.n_interp = n_interp; + gate.x_interp = x_interp; + gate.y_interp = y_interp; +- gate.range = range; ++ gate.radius = radius; ++ gate.mindata = mindata; ++ gate.maxdata = maxdata; + gate.variogram = variogram; + gate.observations = observations; + gate.predictions = predictions; +@@ -105,7 +110,9 @@ + int n_interp = gate->n_interp; + double *x_interp = gate->x_interp; + double *y_interp = gate->y_interp; +- double range = gate->range; ++ double radius = gate->radius; ++ int mindata = gate->mindata; ++ int maxdata = gate->maxdata; + Variogram *variogram = gate->variogram; + Observations *observations = gate->observations; + double *predictions = gate->predictions; +@@ -136,10 +143,10 @@ + printf("\r interpolation progress: %5.2lf%%",localpercent); + + /*Get list of observations for current point*/ +- observations->ObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx],range); +- if(n_obs==0){ +- predictions[idx] = -999.; +- error[idx] = -999.; ++ observations->ObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx],radius,maxdata); ++ if(n_obsNumEl()!=1){ ++ _error_("option \"%s\" has %i elements and cannot return a single int",this->name,this->NumEl()); ++ } ++ ++ /*Assign output pointer*/ ++ *pvalue=(int)this->values[0]; ++} ++/*}}}*/ + /*FUNCTION OptionDouble::Get(double* pvalue) {{{1*/ + void OptionDouble::Get(double* pvalue){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionDouble.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionDouble.h (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionDouble.h (revision 12292) +@@ -38,6 +38,7 @@ + int NumEl(); + int NDims(); + int* Size(); ++ void Get(int* pvalue); + void Get(double* pvalue); + void Get(bool* pvalue){ _error_("An OptionDouble object cannot return a bool");}; + void Get(char** pvalue){ _error_("An OptionDouble object cannot return a string");}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionLogical.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionLogical.h (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionLogical.h (revision 12292) +@@ -38,6 +38,7 @@ + int NumEl(); + int NDims(); + int* Size(); ++ void Get(int* pvalue){_error_("An OptionLogical object cannot return a int");}; + void Get(double* pvalue){_error_("An OptionLogical object cannot return a double");}; + void Get(bool* pvalue); + void Get(char** pvalue){ _error_("An OptionLogical object cannot return a string");}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionChar.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionChar.h (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionChar.h (revision 12292) +@@ -38,6 +38,7 @@ + int NumEl(); + int NDims(); + int* Size(); ++ void Get(int* pvalue){_error_("An OptionChar object cannot return a int");}; + void Get(double* pvalue){_error_("An OptionChar object cannot return a double");}; + void Get(bool* pvalue){ _error_("An OptionChar object cannot return a bool");}; + void Get(char** pvalue); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/Option.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/Option.h (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/Option.h (revision 12292) +@@ -41,6 +41,7 @@ + virtual int NumEl()=0; + virtual int NDims()=0; + virtual int* Size()=0; ++ virtual void Get(int* pvalue)=0; + virtual void Get(double* pvalue)=0; + virtual void Get(bool* pvalue)=0; + virtual void Get(char** pvalue)=0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionCell.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionCell.h (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Options/OptionCell.h (revision 12292) +@@ -38,6 +38,7 @@ + int NumEl(); + int NDims(); + int* Size(); ++ void Get(int* pvalue){_error_("An OptionCell object cannot return a int");}; + void Get(double* pvalue){_error_("An OptionCell object cannot return a double");}; + void Get(bool* pvalue){ _error_("An OptionCell object cannot return a bool");}; + void Get(char** pvalue){ _error_("An OptionCell object cannot return a string");}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12291) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12292) +@@ -74,7 +74,7 @@ + a = 1./3.; + cova = (sill-nugget)*exp(-h2/(a*range*range)); + +- //if(h2<0.0000001) cova = sill; ++ if(h2<0.0000001) cova = sill; + + return cova; + } Index: /issm/oecreview/Archive/12281-12300/ISSM-12297-12298.diff =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-12297-12298.diff (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-12297-12298.diff (revision 12325) @@ -0,0 +1,233 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12297) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Observations.cpp (revision 12298) +@@ -35,10 +35,11 @@ + Observations::Observations(double* observations_list,double* x,double* y,int n,Options* options){ + + /*Intermediaries*/ +- int i,maxdepth,level,counter; ++ int i,j,maxdepth,level,counter,index; + int xi,yi; + double xmin,xmax,ymin,ymax; +- double offset,minlength; ++ double offset,minlength,minspacing,mintrimming,maxtrimming; ++ int *indices = NULL; + Observation *observation = NULL; + + /*Get extrema*/ +@@ -51,6 +52,12 @@ + offset=0.05*(xmax-xmin); xmin-=offset; xmax+=offset; + offset=0.05*(ymax-ymin); ymin-=offset; ymax+=offset; + ++ /*Get trimming limits*/ ++ options->Get(&mintrimming,"mintrimming",-1.e+21); ++ options->Get(&maxtrimming,"maxtrimming",+1.e+21); ++ options->Get(&minspacing,"minspacing",0.01); ++ if(minspacing<=0) _error_("minspacing must > 0"); ++ + /*Get Minimum box size*/ + if(options->GetOption("boxlength")){ + options->Get(&minlength,"boxlength"); +@@ -69,6 +76,18 @@ + /*Add observations one by one*/ + counter = 0; + for(i=0;imaxtrimming) continue; ++ if(observations_list[i]quadtree->ClosestObs(&index,x[i],y[i]); ++ if(index>=0){ ++ observation=(Observation*)this->GetObjectByOffset(index); ++ if(pow(observation->x-x[i],2)+pow(observation->y-y[i],2) < minspacing) continue; ++ } ++ + this->quadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); + this->quadtree->QuadtreeDepth2(&level,xi,yi); + if((int)level <= maxdepth){ +@@ -82,6 +101,8 @@ + } + } + printf("done\n"); ++ printf("Initial number of observations: %i\n",n); ++ printf(" Final number of observations: %i\n",this->quadtree->NbObs); + } + /*}}}*/ + /*FUNCTION Observations::~Observations(){{{*/ +@@ -97,9 +118,10 @@ + + /*Output and Intermediaries*/ + bool stop; +- int nobs,i,j,k,n,counter; ++ int nobs,tempnobs,i,j,k,n,counter; + double h2,radius2; + int *indices = NULL; ++ int *tempindices = NULL; + double *dists = NULL; + double *x = NULL; + double *y = NULL; +@@ -111,17 +133,19 @@ + radius2 = radius*radius; + + /*Find all observations that are in radius*/ +- indices = (int*)xmalloc(this->Size()*sizeof(int)); +- dists = (double*)xmalloc(this->Size()*sizeof(double)); +- nobs = 0; +- +- for (i=0;iSize();i++){ +- observation=(Observation*)this->GetObjectByOffset(i); ++ this->quadtree->RangeSearch(&tempindices,&tempnobs,x_interp,y_interp,radius); ++ if(tempnobs){ ++ indices = (int*)xmalloc(tempnobs*sizeof(int)); ++ dists = (double*)xmalloc(tempnobs*sizeof(double)); ++ } ++ nobs = 0; ++ for (i=0;iGetObjectByOffset(tempindices[i]); + h2 = (observation->x-x_interp)*(observation->x-x_interp) + (observation->y-y_interp)*(observation->y-y_interp); + + if(nobs==maxdata && h2>radius2) continue; + if(nobs<=maxdata){ +- indices[nobs] = i; ++ indices[nobs] = tempindices[i]; + dists[nobs] = h2; + nobs++; + } +@@ -140,7 +164,7 @@ + counter++; + } + dists[k] = h2; +- indices[k] = i; ++ indices[k] = tempindices[i]; + stop = true; + break; + } +@@ -148,6 +172,7 @@ + } + } + xfree((void**)&dists); ++ xfree((void**)&tempindices); + + if(nobs){ + /*Allocate vectors*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12297) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.h (revision 12298) +@@ -33,9 +33,9 @@ + Object *copy() {_error_("not implemented yet"); }; + + /*Methods*/ +- int IsWithinRange(double x,double y,double range); +- void RangeSearch(int* indices,int *pnobs,double x,double y,double range); +- void WriteObservations(int* indices,int *pnobs); ++ int IsWithinRange(double x,double y,double range); ++ void RangeSearch(int *indices,int *pnobs,double x,double y,double range); ++ void WriteObservations(int *indices,int *pnobs); + + }; + +@@ -53,6 +53,7 @@ + ~Quadtree(); + void Add(Observation *observation); + void AddAndAverage(double x,double y,double value); ++ void ClosestObs(int *pindex,double x,double y); + void DeepEcho(void); + void Echo(void); + void IntergerCoordinates(int *xi,int *yi,double x,double y); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12297) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp (revision 12298) +@@ -249,6 +249,49 @@ + _error_("Box is not full"); + } + }/*}}}*/ ++/*FUNCTION Quadtree::ClosestObs{{{1*/ ++void Quadtree::ClosestObs(int *pindex,double x,double y){ ++ ++ QuadtreeBox **pbox = NULL; ++ QuadtreeBox *box = NULL; ++ int xi,yi; ++ int level,levelbin; ++ int index = -1; ++ double length,length2; ++ ++ /*Get integer coodinates*/ ++ this->IntergerCoordinates(&xi,&yi,x,y); ++ ++ /*Initialize levels*/ ++ level = 0; ++ levelbin = (1L<MaxDepth);// = 2^30 ++ ++ /*Get inital box (the largest)*/ ++ pbox=&root; ++ ++ /*Find the smallest box where this point is located*/ ++ while((box=*pbox) && (box->nbitems<0)){ ++ ++ levelbin>>=1; level+=1; ++ ++ pbox = &box->box[IJ(xi,yi,levelbin)]; ++ } ++ ++ /*Add obervation in this box (should be full)*/ ++ if(box && box->nbitems>0){ ++ index = box->obs[0]->index; ++ length = pow(box->obs[0]->x - x,2.) + pow(box->obs[0]->y - y,2.); ++ for(int i=1;inbitems;i++){ ++ length2 = pow(box->obs[i]->x - x,2.) + pow(box->obs[i]->y - y,2.); ++ if(length2obs[i]->index; ++ length = length2; ++ } ++ } ++ } ++ ++ *pindex=index; ++}/*}}}*/ + /*FUNCTION Quadtree::Echo{{{1*/ + void Quadtree::Echo(void){ + +@@ -452,10 +495,10 @@ + int *indices = NULL; + + /*Allocate indices (maximum by default*/ +- indices = (int*)xmalloc(this->NbObs*sizeof(int)); ++ if(this->NbObs) indices = (int*)xmalloc(this->NbObs*sizeof(int)); + nobs = 0; + +- this->root->RangeSearch(indices,&nobs,x,y,range); ++ if(this->root) this->root->RangeSearch(indices,&nobs,x,y,range); + + /*Clean-up and return*/ + *pnobs=nobs; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.cpp (revision 12297) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/modules/Kriging/Kriging.cpp (revision 12298) +@@ -54,6 +54,20 @@ + + void KrigingUsage(void){ + _printf_(true,"\n"); +- _printf_(true," usage: predictions=%s(x,y,observations,x_interp,y_interp);\n",__FUNCT__); ++ _printf_(true," usage: predictions=%s(x,y,observations,x_interp,y_interp,'options');\n",__FUNCT__); ++ _printf_(true," available options:\n"); ++ _printf_(true," -'model': Available variogram models 'gaussian' (default),'spherical','power','exponential'\n"); ++ _printf_(true," -'nugget': nugget effect (default 0.2)\n"); ++ _printf_(true," -'range': for gaussian, spherical and exponential models (default sqrt(3))\n"); ++ _printf_(true," -'sill': for gaussian, spherical and exponential models (default 1)\n"); ++ _printf_(true," -'slope': for power model (default 1)\n"); ++ _printf_(true," -'power': for power model (default 1)\n"); ++ _printf_(true," -'searchradius': search radius for each prediction (default is observations span)\n"); ++ _printf_(true," -'boxlength': minimum length of quadtree boxes (useful to decrease the number of observations)\n"); ++ _printf_(true," -'maxdata': minimum number of observations for a prediction (default is 50)\n"); ++ _printf_(true," -'mindata': maximum number of observations for a prediction (default is 1)\n"); ++ _printf_(true," -'maxtrimming': maximum trimming value (default is -1.e+21)\n"); ++ _printf_(true," -'mintrimming': minimum trimming value (default is +1.e+21)\n"); ++ _printf_(true," -'minspacing': minimum distance between observation (default is 0.01)\n"); + _printf_(true,"\n"); + } Index: /issm/oecreview/Archive/12281-12300/ISSM-DocReview-12281-12300.tex =================================================================== --- /issm/oecreview/Archive/12281-12300/ISSM-DocReview-12281-12300.tex (revision 12325) +++ /issm/oecreview/Archive/12281-12300/ISSM-DocReview-12281-12300.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12281-12300/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12281-12300/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12281-12300/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12281-12300 Index: /issm/oecreview/Archive/12281-12300/Makefile =================================================================== --- /issm/oecreview/Archive/12281-12300/Makefile (revision 12325) +++ /issm/oecreview/Archive/12281-12300/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12281-12300 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12281-12300/log.tex =================================================================== --- /issm/oecreview/Archive/12281-12300/log.tex (revision 12325) +++ /issm/oecreview/Archive/12281-12300/log.tex (revision 12325) @@ -0,0 +1,17 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12281-12282.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/marshall.m \\ Export determination: 6. \\Rationale: typo +M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp minor: better deal with nobs=0 \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12282-12283.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp \\ Export determination: 6. \\Rationale: minor: better deal with nobs=0 \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12286-12287.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/gslib A /issm/trunk-jpl/externalpackages/gslib/install.sh \\ Export determination: 6. \\Rationale: Added gslib \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12287-12288.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/gslib A /issm/trunk-jpl/externalpackages/gslib/install.sh \\ Export determination: 6. \\Rationale: Added gslib +M /issm/trunk-jpl/externalpackages/gslib/install.sh minor \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12288-12289.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/gslib/install.sh \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp M /issm/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h M /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp M /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h M /issm/trunk-jpl/src/c/objects/Kriging/PowerVariogram.cpp M /issm/trunk-jpl/src/c/objects/Kriging/PowerVariogram.h M /issm/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp M /issm/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h M /issm/trunk-jpl/src/c/objects/Kriging/Variogram.h D /issm/trunk-jpl/src/c/shared/Sorting/Quicksort.c M /issm/trunk-jpl/src/c/shared/Sorting/binary\_search.cpp M /issm/trunk-jpl/src/c/shared/Sorting/sorting.h Added Covariance for Kriging calculation (similar to gslib) \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12289-12290.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.cpp M /issm/trunk-jpl/src/c/objects/Kriging/ExponentialVariogram.h M /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp M /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.h M /issm/trunk-jpl/src/c/objects/Kriging/PowerVariogram.cpp M /issm/trunk-jpl/src/c/objects/Kriging/PowerVariogram.h M /issm/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.cpp M /issm/trunk-jpl/src/c/objects/Kriging/SphericalVariogram.h M /issm/trunk-jpl/src/c/objects/Kriging/Variogram.h D /issm/trunk-jpl/src/c/shared/Sorting/Quicksort.c M /issm/trunk-jpl/src/c/shared/Sorting/binary\_search.cpp M /issm/trunk-jpl/src/c/shared/Sorting/sorting.h \\ Export determination: 6. \\Rationale: Added Covariance for Kriging calculation (similar to gslib) +A /issm/trunk-jpl/src/m/utils/DataProcessing/gslib.m Added gslib routine to call gslib from matlab \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12290-12291.diff: \\ Function name: \\A /issm/trunk-jpl/src/m/utils/DataProcessing/gslib.m \\ Export determination: 6. \\Rationale: Added gslib routine to call gslib from matlab +M /issm/trunk-jpl/src/m/utils/DataProcessing/gslib.m minor \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12291-12292.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/DataProcessing/gslib.m \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/Container/Observations.h M /issm/trunk-jpl/src/c/Container/Options.cpp M /issm/trunk-jpl/src/c/Container/Options.h M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.h M /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp M /issm/trunk-jpl/src/c/objects/Options/Option.h M /issm/trunk-jpl/src/c/objects/Options/OptionCell.h M /issm/trunk-jpl/src/c/objects/Options/OptionChar.h M /issm/trunk-jpl/src/c/objects/Options/OptionDouble.cpp M /issm/trunk-jpl/src/c/objects/Options/OptionDouble.h M /issm/trunk-jpl/src/c/objects/Options/OptionLogical.h M /issm/trunk-jpl/src/c/objects/Options/OptionStruct.h M /issm/trunk-jpl/src/c/shared/Threads/LaunchThread.cpp Added mindata and maxdata options to Kriging \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12292-12293.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/Container/Observations.h M /issm/trunk-jpl/src/c/Container/Options.cpp M /issm/trunk-jpl/src/c/Container/Options.h M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.cpp M /issm/trunk-jpl/src/c/modules/Krigingx/Krigingx.h M /issm/trunk-jpl/src/c/objects/Kriging/GaussianVariogram.cpp M /issm/trunk-jpl/src/c/objects/Options/Option.h M /issm/trunk-jpl/src/c/objects/Options/OptionCell.h M /issm/trunk-jpl/src/c/objects/Options/OptionChar.h M /issm/trunk-jpl/src/c/objects/Options/OptionDouble.cpp M /issm/trunk-jpl/src/c/objects/Options/OptionDouble.h M /issm/trunk-jpl/src/c/objects/Options/OptionLogical.h M /issm/trunk-jpl/src/c/objects/Options/OptionStruct.h M /issm/trunk-jpl/src/c/shared/Threads/LaunchThread.cpp \\ Export determination: 6. \\Rationale: Added mindata and maxdata options to Kriging \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12297-12298.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Quadtree.h M /issm/trunk-jpl/src/modules/Kriging/Kriging.cpp \\ Export determination: 6. \\Rationale: Added many options to Kriging now equivalent to gslib \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12298-12299.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Observations.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Quadtree.cpp M /issm/trunk-jpl/src/c/objects/Kriging/Quadtree.h M /issm/trunk-jpl/src/modules/Kriging/Kriging.cpp \\ Export determination: 6. \\Rationale: Added many options to Kriging now equivalent to gslib \\\\ Index: /issm/oecreview/Archive/12281-12300/r1.tex =================================================================== --- /issm/oecreview/Archive/12281-12300/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12281-12300/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12281 Index: /issm/oecreview/Archive/12281-12300/r2.tex =================================================================== --- /issm/oecreview/Archive/12281-12300/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12281-12300/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12300 Index: /issm/oecreview/Archive/12301-12308/Date.tex =================================================================== --- /issm/oecreview/Archive/12301-12308/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12301-12308/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12301-12308/ISSM-12301-12302.diff =================================================================== --- /issm/oecreview/Archive/12301-12308/ISSM-12301-12302.diff (revision 12325) +++ /issm/oecreview/Archive/12301-12308/ISSM-12301-12302.diff (revision 12325) @@ -0,0 +1,159 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/varmap.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/varmap.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/varmap.m (revision 12302) +@@ -0,0 +1,55 @@ ++function output = varmap(x,y,data,varargin); ++%VARMAP - use gslib for Kriging ++% ++% Usage: ++% output = varmap(x,y,data,varargin) ++ ++options=pairoptions(varargin{:}); ++ ++nxlag = getfieldvalue(options,'nxlag', 20); ++nylag = getfieldvalue(options,'nylag', 20); ++dxlag = getfieldvalue(options,'dxlag', 1000); ++dylag = getfieldvalue(options,'dylag', 1000); ++ ++%Write data file ++fid=fopen('cluster.dat','w'); ++fprintf(fid,'%s\n','Data file'); ++fprintf(fid,'%i\n',3); ++fprintf(fid,'%s\n','Xlocation'); ++fprintf(fid,'%s\n','Ylocation'); ++fprintf(fid,'%s\n','Data'); ++fprintf(fid,'%g %g %g\n',[x y data]'); ++fclose(fid); ++ ++%Write parameter file ++fid=fopen('varmap.par','w'); ++fprintf(fid,'\t\t\t\t%s\n','Parameters for GAMV'); ++fprintf(fid,'\t\t\t\t%s\n','*******************'); ++fprintf(fid,'\n'); ++fprintf(fid,'%s\n','START OF PARAMETERS:'); ++fprintf(fid,'%-30s %s\n','./cluster.dat' ,'\file with data'); ++fprintf(fid,'%-30s %s\n','1 3 ' ,'\number of variables, column number'); ++fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); ++fprintf(fid,'%-30s %s\n','0 ' ,'\1=regular grid, 0=scattered values'); ++fprintf(fid,'%-30s %s\n','50 50 1' ,'\if =1: nx, ny, nz'); ++fprintf(fid,'%-30s %s\n','1.0 1.0 1.0' ,'\ xsiz, ysiz, zsiz if igrid=1'); ++fprintf(fid,'%-30s %s\n','1 2 0' ,'\if =0: columns for x, y and z coordinates'); ++fprintf(fid,'%-30s %s\n','varmap.out' ,'\file for variogram output'); ++fprintf(fid,'%-30s %s\n',num2str([nxlag nylag 0],'%i '),'\nxlag, nylag, nzlag'); ++fprintf(fid,'%-30s %s\n',num2str([dxlag dylag 1],'%g %g %i'),'\dxlag, dylag, dzlag'); ++fprintf(fid,'%-30s %s\n','5' ,'\minimum number of pairs'); ++fprintf(fid,'%-30s %s\n','0' ,'\standardize sill? (0=no, 1=yes)'); ++fprintf(fid,'%-30s %s\n','1' ,'\number of variograms'); ++fprintf(fid,'%-30s %s\n','1 1 1' ,'\tail, head, variogram type'); ++fclose(fid); ++ ++%Call varmap ++system([issmdir() '/externalpackages/gslib/install/varmap varmap.par']); ++delete('varmap.par'); ++ ++%Read output ++fid=fopen('varmap.out','r'); ++A = textscan(fid,'%f %f %f %f %f %f','headerlines',8); ++fclose(fid); ++delete('varmap.out') ++output = reshape(A{1},[2*nxlag+1 2*nylag+1]); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gamv.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gamv.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gamv.m (revision 12302) +@@ -0,0 +1,42 @@ ++function output = gamv(x,y,data,varargin); ++%GAMV - use gslib for Kriging ++% ++% Usage: ++% output = gamv(x,y,data,varargin) ++ ++%Write data file ++fid=fopen('cluster.dat','w'); ++fprintf(fid,'%s\n','Data file'); ++fprintf(fid,'%i\n',3); ++fprintf(fid,'%s\n','Xlocation'); ++fprintf(fid,'%s\n','Ylocation'); ++fprintf(fid,'%s\n','Data'); ++fprintf(fid,'%g %g %g\n',[x y data]'); ++fclose(fid); ++ ++%Write parameter file ++fid=fopen('gamv.par','w'); ++fprintf(fid,'\t\t\t\t%s\n','Parameters for GAMV'); ++fprintf(fid,'\t\t\t\t%s\n','*******************'); ++fprintf(fid,'\n'); ++fprintf(fid,'%s\n','START OF PARAMETERS:'); ++fprintf(fid,'%-30s %s\n','./cluster.dat' ,'\file with data'); ++fprintf(fid,'%-30s %s\n','1 2 0' ,'\columns for X, Y, Z coordinates'); ++fprintf(fid,'%-30s %s\n','1 3 ' ,'\number of variables, column number'); ++fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); ++fprintf(fid,'%-30s %s\n','gamv.out' ,'\file for variogram output'); ++fprintf(fid,'%-30s %s\n','20' ,'\number of lags'); ++fprintf(fid,'%-30s %s\n','5.0' ,'\lag separation distance'); ++fprintf(fid,'%-30s %s\n','3.0' ,'\lag tolerance'); ++fprintf(fid,'%-30s %s\n','3' ,'\number of directions'); ++fprintf(fid,'%-30s %s\n','0.0 90.0 50.0 0.0 90.0 50.0','\azm, atol, bandh, dip, dtol, bandv'); ++fprintf(fid,'%-30s %s\n','0.0 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); ++fprintf(fid,'%-30s %s\n','90. 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); ++fprintf(fid,'%-30s %s\n','0' ,'\standardize sill? (0=no, 1=yes)'); ++fprintf(fid,'%-30s %s\n','2' ,'\number of variograms'); ++fprintf(fid,'%-30s %s\n','1 1 1' ,'\tail var., head vars., variogram type'); ++fprintf(fid,'%-30s %s\n','1 1 3' ,'\tail var., head vars., variogram type'); ++fclose(fid); ++ ++%Call gamv ++system([issmdir() '/externalpackages/gslib/install/gamv gamv.par']); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m (revision 12301) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gslib.m (revision 12302) +@@ -1,26 +1,8 @@ +-x=[]; +-y=[]; +-thickness=[]; +-for i=1:5, +- switch(i) +- case 1, filename='2002_Antarctica_P3chile'; +- case 2, filename='2004_Antarctica_P3chile'; +- case 3, filename='2009_Antarctica_DC8'; +- case 4, filename='2009_Antarctica_TO'; +- case 5, filename='2010_Antarctica_DC8'; +- otherwise, error('not supported'); +- end +- disp(['Loading ' filename '...']); +- A=load(filename); +- [tempx tempy]=ll2xy(A.lat(:),A.lon(:),-1,0,71); +- x=[x;tempx]; +- y=[y;tempy]; +- thickness=[thickness;A.thickness]; +-end +-[xl yl]=basinzoom(pairoptions('basin','Pine Island Glacier')); +-x=x(1:100:end); +-y=y(1:100:end); +-data=thickness(1:100:end); ++function output = gslib(x,y,data,varargin); ++%GSLIB - use gslib for Kriging ++% ++% Usage: ++% output = gslib(x,y,data,varargin) + + %Output Matrix + xmin = xl(1); +@@ -44,7 +26,6 @@ + c = (sill-nugget); + a = sqrt(3)*range; + +- + %Write data file + fid=fopen('cluster.dat','w'); + fprintf(fid,'%s\n','Data file'); +@@ -107,6 +88,7 @@ + fclose(fid); + + tic;system([issmdir() '/externalpackages/gslib/install/kb2d kb2d.par']);toc; ++ delete('kb2d.par'); + + %Read output + fid=fopen('kb2d.out','r'); Index: /issm/oecreview/Archive/12301-12308/ISSM-12302-12303.diff =================================================================== --- /issm/oecreview/Archive/12301-12308/ISSM-12302-12303.diff (revision 12325) +++ /issm/oecreview/Archive/12301-12308/ISSM-12302-12303.diff (revision 12325) @@ -0,0 +1,56 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gamv.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gamv.m (revision 12302) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing/gamv.m (revision 12303) +@@ -4,6 +4,11 @@ + % Usage: + % output = gamv(x,y,data,varargin) + ++options=pairoptions(varargin{:}); ++ ++nlag = getfieldvalue(options,'nlag', 20); ++dlag = getfieldvalue(options,'dlag', 1000); ++ + %Write data file + fid=fopen('cluster.dat','w'); + fprintf(fid,'%s\n','Data file'); +@@ -25,9 +30,9 @@ + fprintf(fid,'%-30s %s\n','1 3 ' ,'\number of variables, column number'); + fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); + fprintf(fid,'%-30s %s\n','gamv.out' ,'\file for variogram output'); +-fprintf(fid,'%-30s %s\n','20' ,'\number of lags'); +-fprintf(fid,'%-30s %s\n','5.0' ,'\lag separation distance'); +-fprintf(fid,'%-30s %s\n','3.0' ,'\lag tolerance'); ++fprintf(fid,'%-30s %s\n',num2str(nlag,'%i') ,'\number of lags'); ++fprintf(fid,'%-30s %s\n',num2str(dlag,'%g') ,'\lag separation distance'); ++fprintf(fid,'%-30s %s\n',num2str(dlag/2,'%g') ,'\lag tolerance'); + fprintf(fid,'%-30s %s\n','3' ,'\number of directions'); + fprintf(fid,'%-30s %s\n','0.0 90.0 50.0 0.0 90.0 50.0','\azm, atol, bandh, dip, dtol, bandv'); + fprintf(fid,'%-30s %s\n','0.0 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); +@@ -40,3 +45,26 @@ + + %Call gamv + system([issmdir() '/externalpackages/gslib/install/gamv gamv.par']); ++delete('gamv.par'); ++ ++%Read output ++output = struct('Semivariogram',[],'Covariance',[]); ++counter1 = 1; ++counter2 = 1; ++fid=fopen('gamv.out','r'); ++while (~feof(fid)), ++ A=fscanf(fid,'%s',1); ++ if strcmp(A,'Covariance'); ++ A=fscanf(fid,'%s',4); %Read tail:Data head:Data direction 2 ++ output(counter1).Covariance=fscanf(fid,'%i %g %g %i %g %g',[6 nlag+2])'; ++ counter1=counter1+1; ++ elseif strcmp(A,'Semivariogram'), ++ A=fscanf(fid,'%s',4); %Read tail:Data head:Data direction 2 ++ output(counter2).Semivariogram=fscanf(fid,'%i %g %g %i %g %g',[6 nlag+2])'; ++ counter2=counter2+1; ++ else ++ %do nothing ++ end ++end ++fclose(fid); ++delete('gamv.out') Index: /issm/oecreview/Archive/12301-12308/ISSM-12303-12304.diff =================================================================== --- /issm/oecreview/Archive/12301-12308/ISSM-12303-12304.diff (revision 12325) +++ /issm/oecreview/Archive/12301-12308/ISSM-12303-12304.diff (revision 12325) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12303) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 12304) +@@ -952,7 +952,7 @@ + dnl check that --with-fortran-lib may have been provided + HAVE_FORTRAN=no + if test -n "$FORTRAN_LIB" ; then +- if test x$FORTRAN_LIB = xno; then ++ if test "x$FORTRAN_LIB" = "xno"; then + HAVE_FORTRAN=NO + else + HAVE_FORTRAN=yes Index: /issm/oecreview/Archive/12301-12308/ISSM-12304-12305.diff =================================================================== --- /issm/oecreview/Archive/12301-12308/ISSM-12304-12305.diff (revision 12325) +++ /issm/oecreview/Archive/12301-12308/ISSM-12304-12305.diff (revision 12325) @@ -0,0 +1,20 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp (revision 12304) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp (revision 12305) +@@ -114,7 +114,14 @@ + } + else{ + if(record_enum!=MaximumNumberOfEnums){ +- _error_("Enums in marshalled file are not compatible with compiled code, make sure you are using the same version of ISSM"); ++ printf("\n"); ++ printf(" Enums in marshalled file are not compatible with compiled code\n"); ++ printf(" * If you are running ISSM a remote cluster:\n"); ++ printf(" make sure that you are using the same version of ISSM on both machines\n"); ++ printf(" * If you are running ISSM on your local machine:\n"); ++ printf(" make sure that the all the code is compiled (modules and executables)\n"); ++ printf("\n"); ++ _error_("Enums not consistent (See error message above)"); + } + } + } Index: /issm/oecreview/Archive/12301-12308/ISSM-12305-12306.diff =================================================================== --- /issm/oecreview/Archive/12301-12308/ISSM-12305-12306.diff (revision 12325) +++ /issm/oecreview/Archive/12301-12308/ISSM-12305-12306.diff (revision 12325) @@ -0,0 +1,28 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp (revision 12305) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/IoModel.cpp (revision 12306) +@@ -115,11 +115,18 @@ + else{ + if(record_enum!=MaximumNumberOfEnums){ + printf("\n"); +- printf(" Enums in marshalled file are not compatible with compiled code\n"); +- printf(" * If you are running ISSM a remote cluster:\n"); +- printf(" make sure that you are using the same version of ISSM on both machines\n"); +- printf(" * If you are running ISSM on your local machine:\n"); +- printf(" make sure that the all the code is compiled (modules and executables)\n"); ++ printf("=========================================================================\n"); ++ printf(" Enums in marshalled file are not compatible with compiled code \n"); ++ printf(" \n"); ++ printf(" * If you are running ISSM on a remote cluster: \n"); ++ printf(" make sure that you are using the same version of ISSM on your local \n"); ++ printf(" machine and remote cluster (you might need to run svn update) \n"); ++ printf(" * If you are running ISSM on your local machine: \n"); ++ printf(" make sure that all the code is compiled (modules and executables) \n"); ++ printf(" * If you are a developer and just added a new Enum: \n"); ++ printf(" you might need to run ./Synchronize.sh in src/c/EnumDefinitions \n"); ++ printf(" and recompile \n"); ++ printf("=========================================================================\n"); + printf("\n"); + _error_("Enums not consistent (See error message above)"); + } Index: /issm/oecreview/Archive/12301-12308/ISSM-12306-12307.diff =================================================================== --- /issm/oecreview/Archive/12301-12308/ISSM-12306-12307.diff (revision 12325) +++ /issm/oecreview/Archive/12301-12308/ISSM-12306-12307.diff (revision 12325) @@ -0,0 +1,87 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m (revision 12306) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot/applyoptions.m (revision 12307) +@@ -291,7 +291,7 @@ + textcolori=textcolor{i}; + textpositioni=textposition{i}; + textrotationi=textrotation{i}; +- h=text(textpositioni(1),textpositioni(2),textstringi,'FontSize',textsizei,'FontWeight',textweighti,'Color',textcolori,'Rotation',textrotationi); ++ h=text(textpositioni(1),textpositioni(2),10,textstringi,'FontSize',textsizei,'FontWeight',textweighti,'Color',textcolori,'Rotation',textrotationi); + set(h,'Clipping','on'); %prevent text from appearing outside of the box + end + end +@@ -348,6 +348,7 @@ + end + if exist(options,'axispos'), + Axis=getfieldvalue(options,'axispos'); ++ hold on + set(gca,'pos',Axis); + end + +@@ -413,26 +414,28 @@ + axis equal off + %box off + if strcmpi(md.mesh.hemisphere,'n') | strcmpi(md.mesh.hemisphere,'north'), +- A=expread([ issmdir() '/projects/Exp/GreenlandBoxFront.exp']); ++ A=expread([ jplsvn() '/projects/Exp/GreenlandBoxFront.exp']); + [A.x A.y]=ll2xy(A.x,A.y,+1,45,70); ++ A.x = A.x(1:30:end); ++ A.y = A.y(1:30:end); + elseif strcmpi(md.mesh.hemisphere,'s') | strcmpi(md.mesh.hemisphere,'south'), +- A=expread([ issmdir() '/projects/Exp/Antarctica.exp']); ++ A=expread([ jplsvn() '/projects/Exp/Antarctica.exp']); + else + error('applyoptions error message: hemisphere not defined'); + end +- Ax=[min(A.x) max(A.x)]; +- Ay=[min(A.y) max(A.y)]; ++ offset=3*10^4; ++ Ax=[min(A.x)-offset max(A.x)+offset]; ++ Ay=[min(A.y)-offset max(A.y)+offset]; + %if we are zooming on a basin, don't take the mesh for the boundaries! + if exist(options,'basin'), + [mdx mdy]=basinzoom(options); + else +- offset=3*10^4; + mdx=[min(md.mesh.x)-offset max(md.mesh.x)+offset]; + mdy=[min(md.mesh.y)-offset max(md.mesh.y)+offset]; + end + line(A.x,A.y,ones(size(A.x)),'color','b'); + patch([Ax(1) Ax(2) Ax(2) Ax(1) Ax(1)],[Ay(1) Ay(1) Ay(2) Ay(2) Ay(1)],[1 1 1],'EdgeColor',[0 0 0],'LineWidth',1,'FaceLighting','none') +- patch( [mdx(1) mdx(2) mdx(2) mdx(1)],[mdy(1) mdy(1) mdy(2) mdy(2)],ones(4,1),'EdgeColor',[0 0 0],'FaceColor','r','FaceAlpha',0.5) ++ patch([mdx(1) mdx(2) mdx(2) mdx(1)],[mdy(1) mdy(1) mdy(2) mdy(2)],ones(4,1),'EdgeColor',[0 0 0],'FaceColor','r','FaceAlpha',0.5) + colorbar('off'); + %back to main gca + set(gcf,'CurrentAxes',maingca) +@@ -440,15 +443,22 @@ + + %flag edges of a partition + if exist(options,'partitionedges') +-[xsegments ysegments]=flagedges(md.mesh.elements,md.mesh.x,md.mesh.y,md.qmu.partition); +-xsegments=xsegments*getfieldvalue(options,'unit',1); +-ysegments=ysegments*getfieldvalue(options,'unit',1); +-color=getfieldvalue(options,'partitionedgescolor','r-'); +-linewidth=getfieldvalue(options,'linewidth',1); +-hold on; +-for i=1:length(xsegments), +- plot(xsegments(i,:),ysegments(i,:),color,'LineWidth',linewidth); ++ [xsegments ysegments]=flagedges(md.mesh.elements,md.mesh.x,md.mesh.y,md.qmu.partition); ++ xsegments=xsegments*getfieldvalue(options,'unit',1); ++ ysegments=ysegments*getfieldvalue(options,'unit',1); ++ color=getfieldvalue(options,'partitionedgescolor','r-'); ++ linewidth=getfieldvalue(options,'linewidth',1); ++ hold on; ++ for i=1:length(xsegments), ++ plot(xsegments(i,:),ysegments(i,:),color,'LineWidth',linewidth); ++ end + end ++ ++%Scatter ++if exist(options,'scatter') ++ data=getfieldvalue(options,'scatter'); ++ hold on ++ plot_scatter(data(:,1),data(:,2),getfieldvalue(options,'scattersize',3),data(:,3)); + end + + %backgroundcolor Index: /issm/oecreview/Archive/12301-12308/ISSM-12307-12308.diff =================================================================== --- /issm/oecreview/Archive/12301-12308/ISSM-12307-12308.diff (revision 12325) +++ /issm/oecreview/Archive/12301-12308/ISSM-12307-12308.diff (revision 12325) @@ -0,0 +1,208 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/discover/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/discover/Makefile.in.patch (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/discover/Makefile.in.patch (revision 12308) +@@ -0,0 +1,10 @@ ++3c3,5 ++< CC = cc ++--- ++> CC = icc ++> OBJ_EXT=o ++> LIB_EXT=a ++6c8 ++< OPTFLAGS = -O2 ++--- ++> OPTFLAGS = -DLINUX -fPIC +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/install-4.0-discover.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/install-4.0-discover.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/install-4.0-discover.sh (revision 12308) +@@ -0,0 +1,23 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf install metis-4.0 ++mkdir install ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' ++ ++#Untar ++tar -zxvf metis-4.0.tar.gz ++ ++#Move metis into install directory ++mv metis-4.0/* install ++rm -rf metis-4.0 ++ ++#Apply patches ++cd install ++patch -p1 < ../metis-4.0.patch ++patch Makefile.in ../configs/4.0/discover/Makefile.in.patch ++ ++#Compile ++make + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/install-4.0-discover.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-discover.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-discover.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-discover.sh (revision 12308) +@@ -0,0 +1,103 @@ ++#!/bin/bash ++ ++echo "Currently, this script must be pasted line by line into the terminal" ++ ++#Get number of cpus ++NUMCPUS=$1; ++ ++#Some cleanup ++rm -rf Dakota ++rm -rf src ++rm -rf install ++mkdir src install ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' ++ ++#Untar ++tar -zxvf Dakota_4_3.src.tar.gz ++ ++#Move Dakota to src directory ++mv Dakota/* src ++rm -rf Dakota ++ ++#Apply patches ++patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch ++patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch ++patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch ++patch src/src/NonDSampling.C ./NonDSampling.C.patch ++patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch ++patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? ++#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch ++ ++#Configure dakota ++cd src ++ ++./configure \ ++ --prefix="$ISSM_DIR/externalpackages/dakota/install/" \ ++ --without-graphics \ ++ --with-pic \ ++ --disable-mpi \ ++ --with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ ++ --with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" ++ ++cd .. ++ ++#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages ++#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC ++#flag to the compilation. ++cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/NCSUOpt/Makefile ++ ++cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/pebbl/src/Makefile ++ ++cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-nappspack/Makefile ++ ++cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-cddlib/Makefile ++ ++cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-shared/Makefile ++ ++cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-shared/Makefile ++ ++cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-conveyor/Makefile ++ ++cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-appspack/Makefile ++ ++cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/colin/src/Makefile ++ ++cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/coliny/src/Makefile ++ ++cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/tpl/3po/Makefile ++ ++cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/tpl/3po/Makefile ++ ++cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/packages/ampl/Makefile ++ ++#Compile and install dakota ++cd src ++if [ -z $NUMCPUS ]; ++then ++ make ++ make install ++else ++ make -j $NUMCPUS ++ make -j $NUMCPUS install ++fi ++cd .. ++ ++#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! ++cd install/lib ++mv libamplsolver.a libamplsolver.a.bak ++ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-discover.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-discover.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-discover.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-discover.sh (revision 12308) +@@ -0,0 +1,34 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf install petsc-3.2-p3 src ++mkdir install src ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' ++ ++#Untar and move petsc to install directory ++tar -zxvf petsc-3.2-p3.tar.gz ++mv petsc-3.2-p3/* src/ ++rm -rf petsc-3.2-p3 ++ ++#configure ++cd src ++./config/configure.py \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ ++ --PETSC_ARCH="$ISSM_ARCH" \ ++ --with-batch=1 \ ++ --with-debugging=0 \ ++ --with-shared-libraries=0 \ ++ --known-mpi-shared-libraries=1 \ ++ --with-mpi-dir=/usr/local/intel/mpi/3.2.2.006/lib64 \ ++ --with-blas-lapack-dir=/usr/local/intel/mkl/10.1.2.024/lib/64/ \ ++ --download-mumps=yes \ ++ --download-scalapack=yes \ ++ --download-blacs=yes \ ++ --download-plapack=yes \ ++ --download-parmetis=yes \ ++ --with-pic=1 ++ ++echo "== Follow PETSc's instructions" + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-3.2-discover.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12301-12308/ISSM-DocReview-12301-12308.tex =================================================================== --- /issm/oecreview/Archive/12301-12308/ISSM-DocReview-12301-12308.tex (revision 12325) +++ /issm/oecreview/Archive/12301-12308/ISSM-DocReview-12301-12308.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12301-12308/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12301-12308/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12301-12308/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12301-12308 Index: /issm/oecreview/Archive/12301-12308/Makefile =================================================================== --- /issm/oecreview/Archive/12301-12308/Makefile (revision 12325) +++ /issm/oecreview/Archive/12301-12308/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12301-12308 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12301-12308/log.tex =================================================================== --- /issm/oecreview/Archive/12301-12308/log.tex (revision 12325) +++ /issm/oecreview/Archive/12301-12308/log.tex (revision 12325) @@ -0,0 +1,13 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12301-12302.diff: \\ Function name: \\A /issm/trunk-jpl/src/m/utils/DataProcessing/gamv.m M /issm/trunk-jpl/src/m/utils/DataProcessing/gslib.m A /issm/trunk-jpl/src/m/utils/DataProcessing/varmap.m \\ Export determination: 6. \\Rationale: Added varmap.m gamv.m \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12302-12303.diff: \\ Function name: \\A /issm/trunk-jpl/src/m/utils/DataProcessing/gamv.m M /issm/trunk-jpl/src/m/utils/DataProcessing/gslib.m A /issm/trunk-jpl/src/m/utils/DataProcessing/varmap.m \\ Export determination: 6. \\Rationale: Added varmap.m gamv.m +M /issm/trunk-jpl/src/m/utils/DataProcessing/gamv.m Better input output \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12303-12304.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/DataProcessing/gamv.m \\ Export determination: 6. \\Rationale: Better input output +M /issm/trunk-jpl/m4/issm\_options.m4 Fixing fortran lib test \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12304-12305.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: Fixing fortran lib test +M /issm/trunk-jpl/src/c/objects/IoModel.cpp Better error message \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12305-12306.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/IoModel.cpp \\ Export determination: 6. \\Rationale: Better error message +M /issm/trunk-jpl/src/c/objects/IoModel.cpp Clearer error message \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12306-12307.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/IoModel.cpp \\ Export determination: 6. \\Rationale: Clearer error message +M /issm/trunk-jpl/src/m/model/plot/applyoptions.m Added plot\_scatter as an option to plotmodel and fixed showregion \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12307-12308.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/plot/applyoptions.m \\ Export determination: 6. \\Rationale: Added plot\_scatter as an option to plotmodel and fixed showregion +A /issm/trunk-jpl/externalpackages/dakota/install-discover.sh A /issm/trunk-jpl/externalpackages/metis/configs/4.0/discover A /issm/trunk-jpl/externalpackages/metis/configs/4.0/discover/Makefile.in.patch A /issm/trunk-jpl/externalpackages/metis/install-4.0-discover.sh A /issm/trunk-jpl/externalpackages/petsc/install-3.2-discover.sh add discover scripts \\\\ Index: /issm/oecreview/Archive/12301-12308/r1.tex =================================================================== --- /issm/oecreview/Archive/12301-12308/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12301-12308/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12301 Index: /issm/oecreview/Archive/12301-12308/r2.tex =================================================================== --- /issm/oecreview/Archive/12301-12308/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12301-12308/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12308 Index: /issm/oecreview/Archive/12309-12320/Date.tex =================================================================== --- /issm/oecreview/Archive/12309-12320/Date.tex (revision 12325) +++ /issm/oecreview/Archive/12309-12320/Date.tex (revision 12325) @@ -0,0 +1,1 @@ +Jun-1-2012 Index: /issm/oecreview/Archive/12309-12320/ISSM-12309-12310.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12309-12310.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12309-12310.diff (revision 12325) @@ -0,0 +1,26 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/README.rtf +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/README.rtf (revision 12309) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/README.rtf (revision 12310) +@@ -23,7 +23,7 @@ + \par + ------------------------------------------------------------------------------\par + \par +-Website: ttp://issm.jpl.nasa.gov/ for additional information.\par ++Website: http://issm.jpl.nasa.gov/ for additional information.\par + \par + ------------------------------------------------------------------------------\par + \par +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/README +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/README (revision 12309) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/README (revision 12310) +@@ -21,7 +21,7 @@ + + ------------------------------------------------------------------------------ + +-Website: ttp://issm.jpl.nasa.gov/ for additional information. ++Website: http://issm.jpl.nasa.gov/ for additional information. + + ------------------------------------------------------------------------------ + Index: /issm/oecreview/Archive/12309-12320/ISSM-12310-12311.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12310-12311.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12310-12311.diff (revision 12325) @@ -0,0 +1,35 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-discover.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-discover.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-discover.sh (revision 12311) +@@ -0,0 +1,24 @@ ++#!/bin/csh ++ ++#PETSc 3.2 ++#MPI /usr/local/intel/mpi/3.2.2.006/lib64/ ++ ++./configure \ ++ --prefix=$ISSM_DIR \ ++ --with-modules=no \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include="/usr/local/intel/mpi/3.2.2.006/include64/" \ ++ --with-mpi-lib="-L/usr/local/intel/mpi/3.2.2.006/lib64/ -lmpi -lmpi_ilp64 -lmpiif" \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --with-mkl-dir=/usr/local/intel/mkl/10.1.2.024/ \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-graphics-lib=/usr/lib64/libX11.so \ ++ --with-cxxoptflags="-O3 -xS" \ ++ --with-vendor=intel-linux + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-discover.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12309-12320/ISSM-12311-12312.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12311-12312.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12311-12312.diff (revision 12325) @@ -0,0 +1,92 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-discover.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-discover.sh (revision 12311) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-discover.sh (revision 12312) +@@ -1,15 +1,13 @@ + #!/bin/bash + +-echo "Currently, this script must be pasted line by line into the terminal" +- + #Get number of cpus + NUMCPUS=$1; + + #Some cleanup + rm -rf Dakota +-rm -rf src +-rm -rf install +-mkdir src install ++rm -rf src ++rm -rf install ++mkdir src install + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' +@@ -32,15 +30,13 @@ + + #Configure dakota + cd src +- +-./configure \ +- --prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +- --without-graphics \ +- --with-pic \ +- --disable-mpi \ +- --with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +- --with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +- ++./configure \ ++--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ ++--without-graphics \ ++--with-pic \ ++--disable-mpi \ ++--with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ ++--with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" + cd .. + + #Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +@@ -56,19 +52,19 @@ + mv temp ./src/methods/hopspack/src-nappspack/Makefile + + cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +-mv temp ./src/methods/hopspack/src-cddlib/Makefile ++mv temp ./src/methods/hopspack/src-cddlib/Makefile + + cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +-mv temp ./src/methods/hopspack/src-shared/Makefile ++mv temp ./src/methods/hopspack/src-shared/Makefile + + cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +-mv temp ./src/methods/hopspack/src-shared/Makefile ++mv temp ./src/methods/hopspack/src-shared/Makefile + + cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +-mv temp ./src/methods/hopspack/src-conveyor/Makefile ++mv temp ./src/methods/hopspack/src-conveyor/Makefile + + cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +-mv temp ./src/methods/hopspack/src-appspack/Makefile ++mv temp ./src/methods/hopspack/src-appspack/Makefile + + cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp + mv temp ./src/methods/acro/packages/colin/src/Makefile +@@ -77,16 +73,16 @@ + mv temp ./src/methods/acro/packages/coliny/src/Makefile + + cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +-mv temp ./src/methods/acro/packages/tpl/3po/Makefile ++mv temp ./src/methods/acro/packages/tpl/3po/Makefile + + cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +-mv temp ./src/methods/acro/packages/tpl/3po/Makefile ++mv temp ./src/methods/acro/packages/tpl/3po/Makefile + + cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +-mv temp ./src/packages/ampl/Makefile ++mv temp ./src/packages/ampl/Makefile + + #Compile and install dakota +-cd src ++cd src + if [ -z $NUMCPUS ]; + then + make Index: /issm/oecreview/Archive/12309-12320/ISSM-12312-12313.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12312-12313.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12312-12313.diff (revision 12325) @@ -0,0 +1,74 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12312) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 12313) +@@ -3,13 +3,16 @@ + EXEEXT=$(ISSMEXT) + + #Library declaration {{{1 +-lib_LIBRARIES = libISSMCore.a libISSMModules.a libISSMOverload.a ++lib_LIBRARIES = libISSMCore.a libISSMOverload.a + if PYTHON + lib_LIBRARIES += libISSMPython.a + endif + if MATLAB + lib_LIBRARIES += libISSMMatlab.a + endif ++if MODULES ++lib_LIBRARIES += libISSMModules.a ++endif + #}}} + + #sources +@@ -966,6 +969,7 @@ + libISSMModules_a_SOURCES += $(kriging_sources) + libISSMModules_a_SOURCES += $(kml_sources) + libISSMModules_a_CXXFLAGS = $(ALLCXXFLAGS) ++endif + + if PYTHON + libISSMPython_a_SOURCES = $(python_sources) +@@ -976,7 +980,7 @@ + libISSMMatlab_a_SOURCES = $(matlab_sources) + libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS) + endif +-endif ++ + #}}} + #Overload library, to overload any non-standard symbols. {{{1 + libISSMOverload_a_SOURCES = ./shared/String/stricmp.c +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/todo +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/todo (revision 12312) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/todo (revision 12313) +@@ -28,3 +28,12 @@ + + amatrix will be used in adolc. pmatrix will be used in Petsc routines. Matrix will + have routines to map one into the other. ++ ++ ++Ad: ++Eric: ++Create ISSM namespace. ++Make Matrix Assembly one homogeneous block. ++Make Validation suite for Jean for his prognostic capabilities. ++Jean: ++typedef all double to ISSM_DOUBLE +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-gsl.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-gsl.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-gsl.sh (revision 12313) +@@ -0,0 +1,7 @@ ++#!/bin/sh ++ ++./configure \ ++ --prefix=$ISSM_DIR \ ++ --without-modules\ ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-gsl.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12309-12320/ISSM-12313-12314.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12313-12314.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12313-12314.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.cpp (revision 12313) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Contour.cpp (revision 12314) +@@ -8,6 +8,7 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + ++#include + #include "./objects.h" + #include "../include/include.h" + #include "../io/io.h" Index: /issm/oecreview/Archive/12309-12320/ISSM-12314-12315.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12314-12315.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12314-12315.diff (revision 12325) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.cpp (revision 12314) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/DataSet.cpp (revision 12315) +@@ -10,6 +10,7 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + ++#include + #include + #include + #include Index: /issm/oecreview/Archive/12309-12320/ISSM-12315-12316.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12315-12316.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12315-12316.diff (revision 12325) @@ -0,0 +1,41 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-gsl.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-gsl.sh (revision 12315) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-gsl.sh (revision 12316) +@@ -1,7 +0,0 @@ +-#!/bin/sh +- +-./configure \ +- --prefix=$ISSM_DIR \ +- --without-modules\ +- --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install +- +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-ad.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-ad.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-ad.sh (revision 12316) +@@ -0,0 +1,18 @@ ++#!/bin/sh ++ ++./configure \ ++ --prefix=$ISSM_DIR \ ++ --without-modules\ ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ ++ --without-thermal \ ++ --without-control \ ++ --without-hydrology \ ++ --without-diagnostic \ ++ --without-balanced \ ++ --without-responses \ ++ --without-slope \ ++ --without-rifts \ ++ --without-steadystate \ ++ --without-transient \ ++ --without-3d \ ++ --without-groundingline + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-ad.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12309-12320/ISSM-12316-12317.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12316-12317.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12316-12317.diff (revision 12325) @@ -0,0 +1,48 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-ad.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-ad.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-ad.sh (revision 12317) +@@ -0,0 +1,18 @@ ++#!/bin/sh ++ ++./configure \ ++ --prefix=$ISSM_DIR \ ++ --without-modules\ ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ ++ --without-thermal \ ++ --without-control \ ++ --without-hydrology \ ++ --without-diagnostic \ ++ --without-balanced \ ++ --without-responses \ ++ --without-slope \ ++ --without-rifts \ ++ --without-steadystate \ ++ --without-transient \ ++ --without-3d \ ++ --without-groundingline + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-ad.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-gsl.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-gsl.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-gsl.sh (revision 12317) +@@ -0,0 +1,8 @@ ++#!/bin/sh ++ ++./configure \ ++ --prefix=$ISSM_DIR \ ++ --without-modules\ ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install ++ #--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install ++ #--without-fortran-lib + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-gsl.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/12309-12320/ISSM-12317-12318.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12317-12318.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12317-12318.diff (revision 12325) @@ -0,0 +1,11 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/todo +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/todo (revision 12317) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/todo (revision 12318) +@@ -37,3 +37,6 @@ + Make Validation suite for Jean for his prognostic capabilities. + Jean: + typedef all double to ISSM_DOUBLE ++ ++Create an alloc layer with template functions for new and delete. ++Check that the new code is modular --without-kml, options are up to date. Index: /issm/oecreview/Archive/12309-12320/ISSM-12318-12319.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12318-12319.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12318-12319.diff (revision 12325) @@ -0,0 +1,77 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/ProcessArguments.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/ProcessArguments.cpp (revision 12318) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/ProcessArguments.cpp (revision 12319) +@@ -3,6 +3,8 @@ + */ + + #include ++#include ++ + #include "../shared/shared.h" + #include "../include/include.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp (revision 12318) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp (revision 12319) +@@ -12,6 +12,7 @@ + + #include + #include ++#include + + #include "./DataSet.h" + #include "../shared/shared.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 12318) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 12319) +@@ -8,6 +8,8 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + ++#include ++ + #include "../../objects/objects.h" + #include "../../Container/Parameters.h" + #include "../../EnumDefinitions/EnumDefinitions.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 12318) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 12319) +@@ -7,6 +7,8 @@ + * Please read README for more information + */ + ++#include ++ + #include "../../shared/shared.h" + #include "../../include/include.h" + #include "./StringToEnumx.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 12318) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 12319) +@@ -7,6 +7,8 @@ + * Please read README for more information + */ + ++#include ++ + #include "../../shared/shared.h" + #include "../../include/include.h" + #include "./EnumToStringx.h" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12318) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12319) +@@ -10,6 +10,8 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + ++#include ++ + #include "./ParsePetscOptionsx.h" + #include "../../io/io.h" + #include "../../shared/shared.h" Index: /issm/oecreview/Archive/12309-12320/ISSM-12319-12320.diff =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-12319-12320.diff (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-12319-12320.diff (revision 12325) @@ -0,0 +1,30 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/xNewDelete.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/xNewDelete.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/xNewDelete.h (revision 12320) +@@ -0,0 +1,25 @@ ++/* \file xNewDelete.h ++ * \brief: header file for templated new/delete checking for non-null pointers ++ */ ++ ++#ifndef _XNEWDELETE_H_ ++#define _XNEWDELETE_H_ ++ ++#include ++ ++template ++T* xNew(unsigned int size) { ++ T* aT_p=new T[size]; ++ assert(aT_p); ++ return aT_p; ++}; ++ ++template ++void xDelete(T*& aT_p) { ++ if (aT_p) ++ delete []aT_p; ++ aT_p=0; ++}; ++ ++#endif ++ Index: /issm/oecreview/Archive/12309-12320/ISSM-DocReview-12309-12320.tex =================================================================== --- /issm/oecreview/Archive/12309-12320/ISSM-DocReview-12309-12320.tex (revision 12325) +++ /issm/oecreview/Archive/12309-12320/ISSM-DocReview-12309-12320.tex (revision 12325) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/12309-12320/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/12309-12320/LogNumber.tex (revision 12325) +++ /issm/oecreview/Archive/12309-12320/LogNumber.tex (revision 12325) @@ -0,0 +1,1 @@ +12309-12320 Index: /issm/oecreview/Archive/12309-12320/Makefile =================================================================== --- /issm/oecreview/Archive/12309-12320/Makefile (revision 12325) +++ /issm/oecreview/Archive/12309-12320/Makefile (revision 12325) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-12309-12320 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/12309-12320/log.tex =================================================================== --- /issm/oecreview/Archive/12309-12320/log.tex (revision 12325) +++ /issm/oecreview/Archive/12309-12320/log.tex (revision 12325) @@ -0,0 +1,22 @@ +\noindent \textbf{Change \#1} with diff file ISSM-12309-12310.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/plot/applyoptions.m M /issm/trunk-jpl/src/m/model/plot/plot\_overlay.m A /issm/trunk-jpl/src/m/model/plot/subplotmodel.m \\ Export determination: 6. \\Rationale: Added tightsubplot, very useful to have closer plots +M /issm/trunk-jpl/README M /issm/trunk-jpl/README.rtf fix a typo and see if I can commit \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-12310-12311.diff: \\ Function name: \\M /issm/trunk-jpl/README M /issm/trunk-jpl/README.rtf \\ Export determination: 6. \\Rationale: fix a typo and see if I can commit +A /issm/trunk-jpl/configs/config-discover.sh discover config file \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-12311-12312.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-discover.sh \\ Export determination: 6. \\Rationale: discover config file +M /issm/trunk-jpl/externalpackages/dakota/install-discover.sh fixed cut and paste problem \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-12312-12313.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/dakota/install-discover.sh \\ Export determination: 6. \\Rationale: fixed cut and paste problem +A /issm/trunk-jpl/configs/config-linux64-gsl.sh M /issm/trunk-jpl/src/ad/todo M /issm/trunk-jpl/src/c/Makefile.am Compile without matlab, without python, and just gsl \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-12313-12314.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-linux64-gsl.sh M /issm/trunk-jpl/src/ad/todo M /issm/trunk-jpl/src/c/Makefile.am \\ Export determination: 6. \\Rationale: Compile without matlab, without python, and just gsl +M /issm/trunk-jpl/src/c/objects/Contour.cpp Missing header \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-12314-12315.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Contour.cpp \\ Export determination: 6. \\Rationale: Missing header +M /issm/trunk-jpl/src/c/Container/DataSet.cpp Missing header file \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-12315-12316.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/DataSet.cpp \\ Export determination: 6. \\Rationale: Missing header file +A /issm/trunk-jpl/configs/config-linux64-ad.sh (from /issm/trunk-jpl/configs/config-linux64-gsl.sh:12313) D /issm/trunk-jpl/configs/config-linux64-gsl.sh linux64 ad \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-12316-12317.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-linux64-ad.sh (from /issm/trunk-jpl/configs/config-linux64-gsl.sh:12313) D /issm/trunk-jpl/configs/config-linux64-gsl.sh \\ Export determination: 6. \\Rationale: linux64 ad +A /issm/trunk-jpl/configs/config-macosx64-ad.sh A /issm/trunk-jpl/configs/config-macosx64-gsl.sh ad configs \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-12317-12318.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-macosx64-ad.sh A /issm/trunk-jpl/configs/config-macosx64-gsl.sh \\ Export determination: 6. \\Rationale: ad configs +M /issm/trunk-jpl/src/ad/todo Updated list of ad things to do \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-12318-12319.diff: \\ Function name: \\M /issm/trunk-jpl/src/ad/todo \\ Export determination: 6. \\Rationale: Updated list of ad things to do +M /issm/trunk-jpl/src/c/Container/Options.cpp M /issm/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp M /issm/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp M /issm/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp M /issm/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp M /issm/trunk-jpl/src/c/solutions/ProcessArguments.cpp missing includes (gcc 4.5.1 complains about it) \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-12319-12320.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Options.cpp M /issm/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp M /issm/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp M /issm/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp M /issm/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp M /issm/trunk-jpl/src/c/solutions/ProcessArguments.cpp \\ Export determination: 6. \\Rationale: missing includes (gcc 4.5.1 complains about it) +A /issm/trunk-jpl/src/c/shared/Alloc/xNewDelete.h replacement for xmalloc etc. \\\\ Index: /issm/oecreview/Archive/12309-12320/r1.tex =================================================================== --- /issm/oecreview/Archive/12309-12320/r1.tex (revision 12325) +++ /issm/oecreview/Archive/12309-12320/r1.tex (revision 12325) @@ -0,0 +1,1 @@ +12309 Index: /issm/oecreview/Archive/12309-12320/r2.tex =================================================================== --- /issm/oecreview/Archive/12309-12320/r2.tex (revision 12325) +++ /issm/oecreview/Archive/12309-12320/r2.tex (revision 12325) @@ -0,0 +1,1 @@ +12320