Index: /issm/oecreview/Archive/20496-20544/Date.tex =================================================================== --- /issm/oecreview/Archive/20496-20544/Date.tex (revision 20545) +++ /issm/oecreview/Archive/20496-20544/Date.tex (revision 20545) @@ -0,0 +1,1 @@ +Apr-25-2016 Index: /issm/oecreview/Archive/20496-20544/ISSM-20496-20497.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20496-20497.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20496-20497.diff (revision 20545) @@ -0,0 +1,27 @@ +Index: ../trunk-jpl/test +=================================================================== +--- ../trunk-jpl/test (revision 20496) ++++ ../trunk-jpl/test (revision 20497) + +Property changes on: ../trunk-jpl/test +___________________________________________________________________ +Modified: svn:mergeinfo + Merged /issm/trunk/test:r18303-19104,19106-20496 +Index: ../trunk-jpl/src +=================================================================== +--- ../trunk-jpl/src (revision 20496) ++++ ../trunk-jpl/src (revision 20497) + +Property changes on: ../trunk-jpl/src +___________________________________________________________________ +Modified: svn:mergeinfo + Merged /issm/trunk/src:r19102-19104,19106-20496 +Index: ../trunk-jpl +=================================================================== +--- ../trunk-jpl (revision 20496) ++++ ../trunk-jpl (revision 20497) + +Property changes on: ../trunk-jpl +___________________________________________________________________ +Modified: svn:mergeinfo + Merged /issm/trunk:r19102-19104,19106-20496 Index: /issm/oecreview/Archive/20496-20544/ISSM-20501-20502.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20501-20502.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20501-20502.diff (revision 20545) @@ -0,0 +1,62 @@ +Index: ../trunk-jpl/src/m/exp/flowlines.m +=================================================================== +--- ../trunk-jpl/src/m/exp/flowlines.m (revision 20501) ++++ ../trunk-jpl/src/m/exp/flowlines.m (revision 20502) +@@ -36,9 +36,9 @@ + end + precision=1; %division of each segment (higer precision increases number of segments) + +-%check seed points +-tria=TriaSearch(index,x,y,x0,y0); +-%tria=tsearch(x,y,index,x0,y0); ++%Create triangulation once for all and check seed points ++trep = triangulation(index,x,y); ++tria = pointLocation(trep,[x0 y0]); + pos=find(isnan(tria)); + x0(pos)=[]; + y0(pos)=[]; +@@ -69,8 +69,7 @@ + + %find current triangle + queue=find(~done); +- tria=TriaSearch(index,x,y,X(queue),Y(queue)); +- %tria=tsearch(x,y,index,X(queue),Y(queue)); ++ tria = pointLocation(trep,[X(queue),Y(queue)]); + + %check that the point is actually inside a triangle of the mesh + listnan=find(isnan(tria)); +@@ -120,8 +119,7 @@ + + %find current triangle + queue=find(~done); +- tria=TriaSearch(index,x,y,X(queue),Y(queue)); +- %tria=tsearch(x,y,index,X(queue),Y(queue)); ++ tria = pointLocation(trep,[X(queue),Y(queue)]); + + %check that the point is actually inside a triangle of the mesh + listnan=find(isnan(tria)); +Index: ../trunk-jpl/src/m/exp/downstreamflowlines.m +=================================================================== +--- ../trunk-jpl/src/m/exp/downstreamflowlines.m (revision 20501) ++++ ../trunk-jpl/src/m/exp/downstreamflowlines.m (revision 20502) +@@ -37,8 +37,9 @@ + precision=1; %division of each segment (higer precision increases number of segments) + end + +-%check seed points +-tria=TriaSearch(index,x,y,x0,y0); ++%Create triangulation once for all and check seed points ++trep = triangulation(index,x,y); ++tria = pointLocation(trep,[x0 y0]); + pos=find(isnan(tria)); + x0(pos)=[]; + y0(pos)=[]; +@@ -69,7 +70,7 @@ + + %find current triangle + queue=find(~done); +- tria=TriaSearch(index,x,y,X(queue),Y(queue)); ++ tria = pointLocation(trep,[X(queue),Y(queue)]); + + %check that the point is actually inside a triangle of the mesh + listnan=find(isnan(tria)); Index: /issm/oecreview/Archive/20496-20544/ISSM-20502-20503.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20502-20503.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20502-20503.diff (revision 20545) @@ -0,0 +1,252 @@ +Index: ../trunk-jpl/src/c/modules/TriaSearchx/TriaSearchx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/TriaSearchx/TriaSearchx.cpp (revision 20502) ++++ ../trunk-jpl/src/c/modules/TriaSearchx/TriaSearchx.cpp (revision 20503) +@@ -1,49 +0,0 @@ +-/*!\file TriaSearchx +- */ +- +-#include "./TriaSearchx.h" +- +-#include "../../shared/shared.h" +-#include "../../toolkits/toolkits.h" +-#include "../../bamg/bamgobjects.h" +- +-using namespace bamg; +-using namespace std; +- +-void TriaSearchx(double** ptria,int* index,int nel, double* x, double* y, int nods,double* x0, double* y0,int numberofnodes){ +- +- /*Output*/ +- double* tria=NULL; +- +- /*allocate: */ +- tria=xNew(numberofnodes); +- +- /*Intermediary*/ +- R2 r; +- I2 I; +- int i; +- Icoor2 dete[3]; +- +- /* read background mesh */ +- Mesh Th(index,x,y,nods,nel); +- Th.CreateSingleVertexToTriangleConnectivity(); +- +- for(i=0;i +-#else +- #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-/*For python modules: needs to come before header files inclusion*/ +-#ifdef _HAVE_PYTHON_ +-#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +-#endif +- +-#include "../bindings.h" +-#include "../../c/main/globals.h" +-#include "../../c/modules/modules.h" +-#include "../../c/shared/shared.h" +- +-#undef __FUNCT__ +-#define __FUNCT__ "TriaSearch" +- +-#ifdef _HAVE_MATLAB_MODULES_ +-/* serial input macros: */ +-#define INDEXHANDLE prhs[0] +-#define XHANDLE prhs[1] +-#define YHANDLE prhs[2] +-#define X0HANDLE prhs[3] +-#define Y0HANDLE prhs[4] +- +-/* serial output macros: */ +-#define TRIA (mxArray**)&plhs[0] +-#endif +- +-#ifdef _HAVE_PYTHON_MODULES_ +-/* serial input macros: */ +-#define INDEXHANDLE PyTuple _GetItem(args,0) +-#define XHANDLE PyTuple _GetItem(args,1) +-#define YHANDLE PyTuple _GetItem(args,2) +-#define X0HANDLE PyTuple _GetItem(args,3) +-#define Y0HANDLE PyTuple _GetItem(args,4) +- +-/* serial output macros: */ +-#define TRIA output,0 +-#endif +- +-/* serial arg counts: */ +-#undef NLHS +-#define NLHS 1 +-#undef NRHS +-#define NRHS 5 +- +-#endif +Index: ../trunk-jpl/src/wrappers/TriaSearch/TriaSearch.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/TriaSearch/TriaSearch.cpp (revision 20502) ++++ ../trunk-jpl/src/wrappers/TriaSearch/TriaSearch.cpp (revision 20503) +@@ -1,68 +0,0 @@ +-/*\file TriaSearch.c +- *\brief: TriaSearch module. See TriaSearchx for more details. +- */ +-#include "./TriaSearch.h" +- +-void TriaSearchUsage(void){/*{{{*/ +- _printf0_("TriaSearch- find triangle holding a point (x0,y0) in a mesh\n"); +- _printf0_("\n"); +- _printf0_(" Usage:\n"); +- _printf0_(" tria=TriaSearch(index,x,y,x0,y0);\n"); +- _printf0_(" index,x,y: mesh triangulatrion\n"); +- _printf0_(" x0,y0: coordinates of the point for which we are trying to find a triangle\n"); +- _printf0_(" x0,y0 can be an array of points\n"); +- _printf0_("\n"); +-}/*}}}*/ +-WRAPPER(TriaSearch){ +- +- int i; +- +- /*input: */ +- int* 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); +- +- /* Run core computations: */ +- TriaSearchx(&tria,index,nel,x,y,nods,x0,y0,numberofnodes); +- +- /* c to matlab: */ +- for(i=0;i(index); +- xDelete(x); +- xDelete(y); +- xDelete(x0); +- xDelete(y0); +- xDelete(tria); +- +- /*end module: */ +- MODULEEND(); +-} +Index: ../trunk-jpl/src/wrappers/matlab/Makefile.am +=================================================================== +--- ../trunk-jpl/src/wrappers/matlab/Makefile.am (revision 20502) ++++ ../trunk-jpl/src/wrappers/matlab/Makefile.am (revision 20503) +@@ -60,7 +60,6 @@ + PointCloudFindNeighbors.la\ + PropagateFlagsFromConnectivity.la\ + StringToEnum.la\ +- TriaSearch.la\ + TriMesh.la\ + TriMeshProcessRifts.la\ + Scotch.la\ +@@ -249,9 +248,6 @@ + Shp2Kml_la_SOURCES = ../Shp2Kml/Shp2Kml.cpp + Shp2Kml_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB) + +-TriaSearch_la_SOURCES = ../TriaSearch/TriaSearch.cpp +-TriaSearch_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB) +- + TriMesh_la_SOURCES = ../TriMesh/TriMesh.cpp + TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB) $(GSLLIB) $(PROJ4LIB) + Index: /issm/oecreview/Archive/20496-20544/ISSM-20503-20504.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20503-20504.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20503-20504.diff (revision 20545) @@ -0,0 +1,43 @@ +Index: ../trunk-jpl/test/NightlyRun/test422.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test422.m (revision 20503) ++++ ../trunk-jpl/test/NightlyRun/test422.m (revision 20504) +@@ -10,7 +10,7 @@ + + %Fields and tolerances to track changes + field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={4e-07,4e-07,2e-06,2e-07,5e-07}; ++field_tolerances={4e-07,4e-07,2e-06,4e-07,5e-07}; + field_values={... + (md.results.StressbalanceSolution.Vx),... + (md.results.StressbalanceSolution.Vy),... +Index: ../trunk-jpl/test/NightlyRun/test211.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.py (revision 20503) ++++ ../trunk-jpl/test/NightlyRun/test211.py (revision 20504) +@@ -27,9 +27,9 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', \ + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] + field_tolerances=[\ +- 2e-08,2e-08,1e-06,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,\ +- 5e-07,5e-07,5e-05,1e-07,1e-08,1e-08,1e-08,1e-08,5e-08,2e-06,\ +- 5e-06,5e-06,5e-05,5e-06,1e-07,5e-07,5e-07,5e-07,5e-06,5e-05] ++ 2e-08,2e-08,2e-06,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,\ ++ 5e-07,5e-07,5e-05,2e-07,1e-08,1e-08,1e-08,1e-08,6e-08,2e-06,\ ++ 5e-06,5e-06,5e-05,5e-06,5e-07,5e-07,5e-07,5e-07,5e-06,5e-05] + field_values=[\ + md.results.TransientSolution[0].Vx,\ + md.results.TransientSolution[0].Vy,\ +Index: ../trunk-jpl/test/NightlyRun/test422.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test422.py (revision 20503) ++++ ../trunk-jpl/test/NightlyRun/test422.py (revision 20504) +@@ -20,7 +20,7 @@ + + #Fields and tolerances to track changes + field_names =['Vx','Vy','Vz','Vel','Pressure'] +-field_tolerances=[4e-07,4e-07,2e-06,2e-07,5e-07] ++field_tolerances=[4e-07,4e-07,2e-06,4e-07,5e-07] + field_values=[\ + md.results.StressbalanceSolution.Vx,\ + md.results.StressbalanceSolution.Vy,\ Index: /issm/oecreview/Archive/20496-20544/ISSM-20504-20505.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20504-20505.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20504-20505.diff (revision 20545) @@ -0,0 +1,25 @@ +Index: ../trunk-jpl/src/m/classes/model.m +=================================================================== +--- ../trunk-jpl/src/m/classes/model.m (revision 20504) ++++ ../trunk-jpl/src/m/classes/model.m (revision 20505) +@@ -207,7 +207,6 @@ + elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref), + md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers); + end; +- if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end; + + %results + if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end; +Index: ../trunk-jpl/src/m/classes/model.py +=================================================================== +--- ../trunk-jpl/src/m/classes/model.py (revision 20504) ++++ ../trunk-jpl/src/m/classes/model.py (revision 20505) +@@ -686,8 +686,6 @@ + if not numpy.isnan(md.smb.mass_balance).all(): + md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers) + +- if not numpy.isnan(md.balancethickness.thickening_rate).all(): md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers) +- + #results + if not numpy.isnan(md.initialization.vx).all(): md.initialization.vx=DepthAverage(md,md.initialization.vx) + if not numpy.isnan(md.initialization.vy).all(): md.initialization.vy=DepthAverage(md,md.initialization.vy) Index: /issm/oecreview/Archive/20496-20544/ISSM-20505-20506.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20505-20506.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20505-20506.diff (revision 20545) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 20505) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 20506) +@@ -136,7 +136,7 @@ + source $ISSM_DIR/etc/environment.sh + + #If external package is rebuilt, we also need to recompile +- ISSM_COMPILATION = "yes" ++ ISSM_COMPILATION="yes" + else + echo "======================================================"; + echo " Skipping $PACKAGENAME "; Index: /issm/oecreview/Archive/20496-20544/ISSM-20508-20509.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20508-20509.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20508-20509.diff (revision 20545) @@ -0,0 +1,32 @@ +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 20508) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 20509) +@@ -114,9 +114,8 @@ + + cd $ISSM_DIR/externalpackages/$PACKAGENAME + +- #install if requested or if install does not exist +- if [ "$ISSM_EXTERNALPACKAGES" == "install" ] || [ ! -d install ] || [ ! "$(ls -A install)" ]; +- then ++ #install if requested or if previous install has not been successful ++ if [ "$ISSM_EXTERNALPACKAGES" == "install" ] || [ ! -f SUCCESS ]; then + echo "======================================================"; + echo " Installing $PACKAGENAME "; + echo "======================================================"; +@@ -125,13 +124,13 @@ + echo "======================================================"; + echo " ERROR: installation of $PACKAGENAME failed "; + echo "======================================================"; +- #erase install directory, so that next time, we still try and compile this! +- rm -rf install + echo "" >> $EXTERNAL_TEST_FILE + echo 'External packages did not install right. Check it.' >> $EXTERNAL_TEST_FILE + echo '' >> $EXTERNAL_TEST_FILE ++ exit 1 + else + echo "" >> $EXTERNAL_TEST_FILE ++ touch SUCCESS + fi + source $ISSM_DIR/etc/environment.sh + Index: /issm/oecreview/Archive/20496-20544/ISSM-20511-20512.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20511-20512.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20511-20512.diff (revision 20545) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/m/exp/flowlines.m +=================================================================== +--- ../trunk-jpl/src/m/exp/flowlines.m (revision 20511) ++++ ../trunk-jpl/src/m/exp/flowlines.m (revision 20512) +@@ -87,7 +87,7 @@ + end + + %velocity of the current triangle and norm it +- ut=u(tria); vt=v(tria); normv=sqrt(ut.^2+vt.^2); ++ ut=u(tria); vt=v(tria); normv=max(eps,sqrt(ut.^2+vt.^2)); + ut=ut./normv;vt=vt./normv; + + %check counter +@@ -137,7 +137,7 @@ + end + + %velocity of the current triangle and norm it +- ut=-u(tria); vt=-v(tria); normv=sqrt(ut.^2+vt.^2); ++ ut=-u(tria); vt=-v(tria); normv=max(eps,sqrt(ut.^2+vt.^2)); + ut=ut./normv;vt=vt./normv; + + %check counter Index: /issm/oecreview/Archive/20496-20544/ISSM-20512-20513.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20512-20513.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20512-20513.diff (revision 20545) @@ -0,0 +1,88 @@ +Index: ../trunk-jpl/src/m/plot/plot_unit.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_unit.js (revision 20512) ++++ ../trunk-jpl/src/m/plot/plot_unit.js (revision 20513) +@@ -95,7 +95,7 @@ + } + else{ //triangular elements + caxis = options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]); +- if (options.exist('log')) caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log')),Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log'))]; ++ if (options.getfieldvalue('log',10)!='off') caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log')),Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log'))]; + datamin = caxis[0]; + datamax = caxis[1]; + datadelta = datamax - datamin; +@@ -203,7 +203,7 @@ + else { + caxis = [ArrayMin(data[0]),ArrayMax(data[0].slice(0,-1))]; + } +- if (options.exist('log')) caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log')),Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log'))]; ++ if (options.getfieldvalue('log',10)!='off') caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log')),Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log'))]; + + for(var i = 0; i < data.length; i++){ + datamin = caxis[0]; +Index: ../trunk-jpl/src/m/plot/applyoptions.js +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.js (revision 20512) ++++ ../trunk-jpl/src/m/plot/applyoptions.js (revision 20513) +@@ -29,7 +29,6 @@ + //Variable options initialization {{{ + + var caxis = options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]); +- //if (options.exist('log')) options.changefieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]); + var canvassize = options.getfieldvalue('canvassize',480); + var cheight; + var cwidth; +@@ -48,7 +47,7 @@ + var caxisdelta = caxis[1] - caxis[0]; + var clabelitem; + var precision=options.getfieldvalue('colorbarprecision',3); +- if (options.exist('log')) { ++ if (options.getfieldvalue('log',10)!='off') { + for (var i = cdivisions; i >= 0; i--) { + if (caxisdelta*i/cdivisions==caxis[0]) { + labels[i] = (caxis[0]).toPrecision(precision); +@@ -229,11 +228,11 @@ + + var cmap = options.getfieldvalue('cmap','jet'); + var colorbar = colorbars[cmap]; +- if (options.exist('log')) { ++ if (options.getfieldvalue('log',10)!='off') { + for (var i = 0; i < colorbar.length; i++) { + color = colorbar[colorbar.length-i-1]; + color = [Math.round(color[0]*255),Math.round(color[1]*255),Math.round(color[2]*255)]; +- tgradient.addColorStop(1.0-Math.exp(Math.log((colorbar.length-i)/colorbar.length)/Math.log(options.getfieldvalue('log',Math.E))*i/colorbar.length),'rgba('+color.toString()+',1.0)'); ++ tgradient.addColorStop(1.0-Math.exp(Math.log((colorbar.length-i)/colorbar.length)/Math.log(options.getfieldvalue('log',10))*i/colorbar.length),'rgba('+color.toString()+',1.0)'); + } + } else { + for (var i = 0; i < colorbar.length; i++) { +Index: ../trunk-jpl/src/m/plot/processdata.js +=================================================================== +--- ../trunk-jpl/src/m/plot/processdata.js (revision 20512) ++++ ../trunk-jpl/src/m/plot/processdata.js (revision 20513) +@@ -142,7 +142,7 @@ + } + + //log? +- if (options.exist('log')){ ++ if (options.getfieldvalue('log',10)!='off'){ + var bounds=options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]); + for(var i=0;ibounds[1])data[i]=bounds[1]; +@@ -201,7 +201,7 @@ + datatype=5; + + //log? +- if (options.exist('log')){ ++ if (options.getfieldvalue('log',10)!='off'){ + var bounds=options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]); + for(var i=0;ibounds[1])data[i]=bounds[1]; +@@ -191,7 +191,7 @@ + throw Error("Log option cannot be applied on negative values. Use caxis option (Rignot''s settings: [1.5 max(data)])"); + } + for(var i=0;iNumberofNodes(finiteelement); + + /*Get nodal functions derivatives in reference triangle*/ +- IssmDouble* dbasis_ref=xNew(2*numnodes); ++ IssmDouble dbasis_ref[2*NUMNODESMAX]; + GetNodalFunctionsDerivativesReference(dbasis_ref,gauss,finiteelement); + + /*Get Jacobian invert: */ +@@ -211,9 +211,6 @@ + dbasis[numnodes*1+i] = Jinv[1][0]*dbasis_ref[0*numnodes+i]+Jinv[1][1]*dbasis_ref[1*numnodes+i]; + } + +- /*Clean up*/ +- xDelete(dbasis_ref); +- + } + /*}}}*/ + void TriaRef::GetNodalFunctionsDerivativesReference(IssmDouble* dbasis,Gauss* gauss_in,int finiteelement){/*{{{*/ +Index: ../trunk-jpl/src/c/classes/Elements/PentaRef.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/PentaRef.cpp (revision 20514) ++++ ../trunk-jpl/src/c/classes/Elements/PentaRef.cpp (revision 20515) +@@ -442,7 +442,7 @@ + int numnodes = this->NumberofNodes(finiteelement); + + /*Get nodal functions derivatives in reference triangle*/ +- IssmDouble* dbasis_ref=xNew(3*numnodes); ++ IssmDouble dbasis_ref[3*NUMNODESMAX]; + GetNodalFunctionsDerivativesReference(dbasis_ref,gauss,finiteelement); + + /*Get Jacobian invert: */ +@@ -460,9 +460,6 @@ + dbasis[numnodes*1+i]=Jinv[1][0]*dbasis_ref[0*numnodes+i]+Jinv[1][1]*dbasis_ref[1*numnodes+i]+Jinv[1][2]*dbasis_ref[2*numnodes+i]; + dbasis[numnodes*2+i]=Jinv[2][0]*dbasis_ref[0*numnodes+i]+Jinv[2][1]*dbasis_ref[1*numnodes+i]+Jinv[2][2]*dbasis_ref[2*numnodes+i]; + } +- +- /*Clean up*/ +- xDelete(dbasis_ref); + } + /*}}}*/ + void PentaRef::GetNodalFunctionsDerivativesReference(IssmDouble* dbasis,Gauss* gauss_in,int finiteelement){/*{{{*/ +Index: ../trunk-jpl/src/c/classes/Elements/SegRef.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/SegRef.cpp (revision 20514) ++++ ../trunk-jpl/src/c/classes/Elements/SegRef.cpp (revision 20515) +@@ -145,7 +145,7 @@ + int numnodes = this->NumberofNodes(finiteelement); + + /*Get nodal functions derivatives in reference triangle*/ +- IssmDouble* dbasis_ref=xNew(numnodes); ++ IssmDouble dbasis_ref[1*NUMNODESMAX]; + GetNodalFunctionsDerivativesReference(dbasis_ref,gauss,finiteelement); + + /*Get Jacobian invert: */ +@@ -157,10 +157,6 @@ + for(int i=0;i(dbasis_ref); +- + } + /*}}}*/ + void SegRef::GetNodalFunctionsDerivativesReference(IssmDouble* dbasis,GaussSeg* gauss,int finiteelement){/*{{{*/ +Index: ../trunk-jpl/src/c/classes/Elements/TetraRef.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/TetraRef.cpp (revision 20514) ++++ ../trunk-jpl/src/c/classes/Elements/TetraRef.cpp (revision 20515) +@@ -224,7 +224,7 @@ + int numnodes = this->NumberofNodes(finiteelement); + + /*Get nodal functions derivatives in reference triangle*/ +- IssmDouble* dbasis_ref=xNew(3*numnodes); ++ IssmDouble dbasis_ref[3*NUMNODESMAX]; + GetNodalFunctionsDerivativesReference(dbasis_ref,gauss,finiteelement); + + /*Get Jacobian invert: */ +@@ -242,9 +242,6 @@ + dbasis[numnodes*1+i]=Jinv[1][0]*dbasis_ref[0*numnodes+i]+Jinv[1][1]*dbasis_ref[1*numnodes+i]+Jinv[1][2]*dbasis_ref[2*numnodes+i]; + dbasis[numnodes*2+i]=Jinv[2][0]*dbasis_ref[0*numnodes+i]+Jinv[2][1]*dbasis_ref[1*numnodes+i]+Jinv[2][2]*dbasis_ref[2*numnodes+i]; + } +- +- /*Clean up*/ +- xDelete(dbasis_ref); + } + /*}}}*/ + void TetraRef::GetNodalFunctionsDerivativesReference(IssmDouble* dbasis,GaussTetra* gauss,int finiteelement){/*{{{*/ Index: /issm/oecreview/Archive/20496-20544/ISSM-20515-20516.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20515-20516.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20515-20516.diff (revision 20545) @@ -0,0 +1,53 @@ +Index: ../trunk-jpl/src/m/plot/manualcb.m +=================================================================== +--- ../trunk-jpl/src/m/plot/manualcb.m (revision 20515) ++++ ../trunk-jpl/src/m/plot/manualcb.m (revision 20516) +@@ -61,25 +61,39 @@ + end + ytick = (ztick-zmin)/(zmax-zmin); + else +- ztick = getfieldvalue(options,'tick',round(logspace(log(zmin)/log(10),log(zmax)/log(10),8))); ++ %old method ++ ztick = getfieldvalue(options,'tick',round( logspace(log10(zmin),log10(zmax),8) )); + ytick = linspace(0,1,numel(ztick)); ++ ++ %New method ++ test=logspace(-10,10,21); ++ pos=find(test>=zmin & test<=zmax); ++ ztick= test(pos); ++ ytick= (log(ztick) - log(zmin))/(log(zmax) - log(zmin)); + end + + %Display colorbar + hold on + numcolors=size(cmap,1); +-if strcmpi(getfieldvalue(options,'orientation','vertical'),'vertical'), +- image_rgb = ind2rgb(repmat((1:numcolors)',1,2),cmap); +-else +- image_rgb = ind2rgb(repmat((1:numcolors)',1,2)',cmap); +-end + if 1, + %disappears somtimes +- imagesc([0 1],[0 1],repmat(image_rgb,[1 10 1])); ++ if strcmpi(getfieldvalue(options,'orientation','vertical'),'vertical'), ++ image_rgb = ind2rgb(repmat((1:numcolors)',1,10),cmap); ++ else ++ image_rgb = ind2rgb(repmat((1:numcolors),10,1),cmap); ++ end ++ ++ imagesc([0 1],[0 1],image_rgb); + else + %Creates triangles when exported as pdf +- for i=1:numcolors, +- patch([0,0,1,1],[(i-1)/numcolors,i/numcolors,i/numcolors,(i-1)/numcolors],'none','FaceColor',cmap(i,:),'Clipping','off','EdgeColor','none') ++ if strcmpi(getfieldvalue(options,'orientation','vertical'),'vertical'), ++ for i=1:numcolors, ++ patch([0,0,1,1],[(i-1)/numcolors,i/numcolors,i/numcolors,(i-1)/numcolors],0,'FaceColor',cmap(i,:),'Clipping','off','EdgeColor','none') ++ end ++ else ++ for i=1:numcolors, ++ patch([(i-1)/numcolors,i/numcolors,i/numcolors,(i-1)/numcolors],[0,0,1,1],0,'FaceColor',cmap(i,:),'Clipping','off','EdgeColor','none') ++ end + end + end + patch([0,0,1,1],[0,1,1,0],'k','FaceColor','none','Clipping','off') Index: /issm/oecreview/Archive/20496-20544/ISSM-20516-20517.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20516-20517.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20516-20517.diff (revision 20545) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp (revision 20516) ++++ ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp (revision 20517) +@@ -77,10 +77,6 @@ + /*Finite element Analysis*/ + void LevelsetAnalysis::Core(FemModel* femmodel){/*{{{*/ + +- #if !defined(_DEVELOPMENT_) +- _error_("Not implemented yet"); +- #endif +- + /*parameters: */ + int stabilization; + bool save_results; Index: /issm/oecreview/Archive/20496-20544/ISSM-20517-20518.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20517-20518.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20517-20518.diff (revision 20545) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/m/classes/calving.m +=================================================================== +--- ../trunk-jpl/src/m/classes/calving.m (revision 20517) ++++ ../trunk-jpl/src/m/classes/calving.m (revision 20518) +@@ -38,8 +38,8 @@ + %Early return + if (solution~=TransientSolutionEnum() | md.transient.ismovingfront==0), return; end + +- md = checkfield(md,'fieldname','calving.calvingrate(1:md.mesh.numberofvertices,:)','>=',0,'timeseries',1,'NaN',1,'Inf',1); +- md = checkfield(md,'fieldname','calving.meltingrate(1:md.mesh.numberofvertices,:)','>=',0,'timeseries',1,'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','calving.calvingrate','>=',0,'timeseries',1,'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','calving.meltingrate','>=',0,'timeseries',1,'NaN',1,'Inf',1); + end % }}} + function disp(self) % {{{ + disp(sprintf(' Calving parameters:')); Index: /issm/oecreview/Archive/20496-20544/ISSM-20518-20519.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20518-20519.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20518-20519.diff (revision 20545) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/miscellaneous/transientrestart.m +=================================================================== +--- ../trunk-jpl/src/m/miscellaneous/transientrestart.m (revision 20518) ++++ ../trunk-jpl/src/m/miscellaneous/transientrestart.m (revision 20519) +@@ -17,7 +17,7 @@ + end + + %Change time +-md.timestepping.start_time = results.time/md.constants.yts; ++md.timestepping.start_time = results.time; + + %Change initialization fields + if isfield(results,'Vx'), md.initialization.vx=results.Vx; end Index: /issm/oecreview/Archive/20496-20544/ISSM-20519-20520.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20519-20520.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20519-20520.diff (revision 20545) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/m/coordsystems/gdaltransform.m +=================================================================== +--- ../trunk-jpl/src/m/coordsystems/gdaltransform.m (revision 20519) ++++ ../trunk-jpl/src/m/coordsystems/gdaltransform.m (revision 20520) +@@ -22,6 +22,9 @@ + fclose(fid); + + [s,r]=system(['gdaltransform -s_srs ',proj_in,' -t_srs ',proj_out,' < ' temproot '/.rand1234.txt > ' temproot '/.rand1235.txt']); ++ if s~=0 | ~isempty(deblank(r)), ++ error(r); ++ end + A=textread([temproot '/.rand1235.txt']); + xout=A(:,1); + yout=A(:,2); Index: /issm/oecreview/Archive/20496-20544/ISSM-20520-20521.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20520-20521.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20520-20521.diff (revision 20545) @@ -0,0 +1,17 @@ +Index: ../trunk-jpl/test/NightlyRun/test124.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test124.m (revision 20520) ++++ ../trunk-jpl/test/NightlyRun/test124.m (revision 20521) +@@ -20,9 +20,9 @@ + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2',... + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; + field_tolerances={... +- 2e-09,3.0e-9,3.0e-9,1e-10,1e-13,1e-12,1e-12,... +- 1e-09,3e-10,8e-10,1e-10,1e-10,1e-10,1e-10,... +- 1e-09,3e-10,8e-10,1e-10,1e-10,1e-10,1e-10}; ++ 2e-09,3e-9,3.0e-9,1e-10,1e-13,1e-12,1e-12,... ++ 2e-09,3e-9,8e-10,1e-10,1e-10,1e-10,1e-10,... ++ 2e-09,3e-9,8e-10,1e-10,1e-10,1e-10,1e-10}; + field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... Index: /issm/oecreview/Archive/20496-20544/ISSM-20521-20522.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20521-20522.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20521-20522.diff (revision 20545) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/src/m/classes/clusters/lonestar.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/lonestar.m (revision 20521) ++++ ../trunk-jpl/src/m/classes/clusters/lonestar.m (revision 20522) +@@ -122,10 +122,17 @@ + for i=1:numel(cluster.modules), + fprintf(fid,['module load ' cluster.modules{i} '\n']); + end ++ ++ %fprintf(fid,'export KMP_AFFINITY="granularity=fine,compact,verbose" \n\n'); ++ + if length(find(cluster.email=='@'))>0 +- fprintf(fid,'#SBATCH --mail-user=%s \n',cluster.email); +- fprintf(fid,'#SBATCH --mail-type=end \n\n'); ++ %fprintf(fid,'#SBATCH --mail-user=%s \n',cluster.email); ++ %fprintf(fid,'#SBATCH --mail-type=end \n\n'); ++ ++ fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Began on Lonestar 5.'' \\ \n'); ++ fprintf(fid,'%s <<< ''Job Started'' " \n\n',cluster.email); + end ++ + fprintf(fid,'export PATH="$PATH:."\n\n'); + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME + fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME +@@ -134,6 +141,12 @@ + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end ++ ++ if length(find(cluster.email=='@'))>0 ++ fprintf(fid,'\n'); ++ fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Ended on Lonestar 5.'' \\ \n'); ++ fprintf(fid,'%s <<< ''Job Started'' " \n\n',cluster.email); ++ end + fclose(fid); + + %in interactive mode, create a run file, and errlog and outlog file Index: /issm/oecreview/Archive/20496-20544/ISSM-20522-20523.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20522-20523.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20522-20523.diff (revision 20545) @@ -0,0 +1,48 @@ +Index: ../trunk-jpl/src/m/coordsystems/gdaltransform.m +=================================================================== +--- ../trunk-jpl/src/m/coordsystems/gdaltransform.m (revision 20522) ++++ ../trunk-jpl/src/m/coordsystems/gdaltransform.m (revision 20523) +@@ -5,26 +5,33 @@ + % [x,y] = gdaltransform(x1,y1,epsg_in, epsg_out); + % + % Example: +-% [x,y] = gdaltransform(md.mesh.lat,md.mesh.long,'EPSG:3184','EPSG:3411'); ++% [x,y] = gdaltransform(md.mesh.long,md.mesh.lat,'EPSG:4326','EPSG:3031') + % + % For reference: +-% EPSG: 4326 (lat,long) +-% EPSG: 3411 (greenland, +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.449 +units=m +no_defs) +-% EPSG: 3031 (antarctica, +proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs) ++% EPSG: 4326 (lat,long) ++% EPSG: 3411 (Greenland, UPS 45W, 70N) ++% EPSG: 3031 (Antarctica, UPS 0E, 71S) ++% ++% ll2xy default projection Antarctica: ++% +proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs ++% ll2xy default projection Greenland: ++% +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs ++% Bamber's Greeland projection ++% +proj=stere +lat_0=90 +lat_ts=71 +lon_0=-39 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs ++% ++% To get proj.4 string from EPSG, use gdalsrsinfo. Example: gdalsrsinfo "EPSG:4326" | grep "PROJ.4" + + %give ourselves a unique temporary directory: + temproot=tempname; mkdir(temproot); + + fid=fopen([temproot '/.rand1234.txt'],'w'); +- for i=1:length(x), +- fprintf(fid,'%g %g\n',x(i),y(i)); +- end ++ fprintf(fid,'%8g %8g\n',[x(:) y(:)]'); + fclose(fid); + + [s,r]=system(['gdaltransform -s_srs ',proj_in,' -t_srs ',proj_out,' < ' temproot '/.rand1234.txt > ' temproot '/.rand1235.txt']); + if s~=0 | ~isempty(deblank(r)), + error(r); + end +- A=textread([temproot '/.rand1235.txt']); +- xout=A(:,1); +- yout=A(:,2); ++ A=load([temproot '/.rand1235.txt']); ++ xout=A(:,1); xout=reshape(xout,size(x)); ++ yout=A(:,2); yout=reshape(yout,size(y)); Index: /issm/oecreview/Archive/20496-20544/ISSM-20523-20524.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20523-20524.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20523-20524.diff (revision 20545) @@ -0,0 +1,24 @@ +Index: ../trunk-jpl/src/m/classes/clusters/lonestar.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/lonestar.m (revision 20523) ++++ ../trunk-jpl/src/m/classes/clusters/lonestar.m (revision 20524) +@@ -129,8 +129,7 @@ + %fprintf(fid,'#SBATCH --mail-user=%s \n',cluster.email); + %fprintf(fid,'#SBATCH --mail-type=end \n\n'); + +- fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Began on Lonestar 5.'' \\ \n'); +- fprintf(fid,'%s <<< ''Job Started'' " \n\n',cluster.email); ++ fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Began on Lonestar 5.'' %s <<< ''Job Started'' " \n\n',cluster.email); + end + + fprintf(fid,'export PATH="$PATH:."\n\n'); +@@ -144,8 +143,7 @@ + + if length(find(cluster.email=='@'))>0 + fprintf(fid,'\n'); +- fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Ended on Lonestar 5.'' \\ \n'); +- fprintf(fid,'%s <<< ''Job Started'' " \n\n',cluster.email); ++ fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Ended on Lonestar 5.'' %s <<< ''Job Started'' " \n\n',cluster.email); + end + fclose(fid); + Index: /issm/oecreview/Archive/20496-20544/ISSM-20524-20525.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20524-20525.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20524-20525.diff (revision 20545) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test404.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test404.m (revision 20524) ++++ ../trunk-jpl/test/NightlyRun/test404.m (revision 20525) +@@ -9,7 +9,7 @@ + + %Fields and tolerances to track changes + field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={6e-07,6e-07,2e-06,1e-06,3e-07}; ++field_tolerances={6e-07,6e-07,2e-06,1e-06,5e-07}; + field_values={... + (md.results.StressbalanceSolution.Vx),... + (md.results.StressbalanceSolution.Vy),... +Index: ../trunk-jpl/test/NightlyRun/test404.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test404.py (revision 20524) ++++ ../trunk-jpl/test/NightlyRun/test404.py (revision 20525) +@@ -19,7 +19,7 @@ + + #Fields and tolerances to track changes + field_names =['Vx','Vy','Vz','Vel','Pressure'] +-field_tolerances=[6e-07,6e-07,2e-06,1e-06,3e-07] ++field_tolerances=[6e-07,6e-07,2e-06,1e-06,5e-07] + field_values=[\ + md.results.StressbalanceSolution.Vx,\ + md.results.StressbalanceSolution.Vy,\ Index: /issm/oecreview/Archive/20496-20544/ISSM-20525-20526.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20525-20526.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20525-20526.diff (revision 20545) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/classes/independent.py +=================================================================== +--- ../trunk-jpl/src/m/classes/independent.py (revision 20525) ++++ ../trunk-jpl/src/m/classes/independent.py (revision 20526) +@@ -51,7 +51,7 @@ + if self.nods==0: + raise TypeError("independent checkconsistency error: nods should be set to the size of the independent variable") + +- if self.fov_forward_indices: ++ if len(self.fov_forward_indices) > 0: + if not strcmpi(driver,'fov_forward'): + raise TypeError("cannot declare an independent with fov_forward_indices when the driver is not fov_forward!") + if self.nods==0: Index: /issm/oecreview/Archive/20496-20544/ISSM-20526-20527.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20526-20527.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20526-20527.diff (revision 20545) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test3020.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3020.py (revision 20526) ++++ ../trunk-jpl/test/NightlyRun/test3020.py (revision 20527) +@@ -61,8 +61,8 @@ + md=SetIceShelfBC(md) + + md=solve(md,TransientSolutionEnum()) +-V0=md.results.TransientSolution[2].IceVolume +-MaxV0=md.results.TransientSolution[2].MaxVel ++V0=md.results.TransientSolution[-1].IceVolume ++MaxV0=md.results.TransientSolution[-1].MaxVel + + #backward + md=copy.deepcopy(md2) +@@ -73,8 +73,8 @@ + md=SetIceShelfBC(md) + + md=solve(md,TransientSolutionEnum()) +-V2=md.results.TransientSolution[2].IceVolume +-MaxV2=md.results.TransientSolution[2].MaxVel ++V2=md.results.TransientSolution[-1].IceVolume ++MaxV2=md.results.TransientSolution[-1].MaxVel + + #compute resulting derivative + dVdh_an=(V2-V0)/deltaH Index: /issm/oecreview/Archive/20496-20544/ISSM-20527-20528.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20527-20528.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20527-20528.diff (revision 20545) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/m/classes/independent.py +=================================================================== +--- ../trunk-jpl/src/m/classes/independent.py (revision 20527) ++++ ../trunk-jpl/src/m/classes/independent.py (revision 20528) +@@ -1,6 +1,7 @@ + import numpy + from pairoptions import pairoptions + from fielddisplay import fielddisplay ++from checkfield import checkfield + from MatlabFuncs import * + from EnumDefinitions import * + Index: /issm/oecreview/Archive/20496-20544/ISSM-20528-20529.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20528-20529.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20528-20529.diff (revision 20545) @@ -0,0 +1,16 @@ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 20528) ++++ ../trunk-jpl/src/c/Makefile.am (revision 20529) +@@ -592,8 +592,11 @@ + if !WINDOWS + if !STANDALONE_LIBRARIES + libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) ++if FORTRAN ++libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB) + endif + endif ++endif + + if WRAPPERS + libISSMModules_la_SOURCES = $(modules_sources) Index: /issm/oecreview/Archive/20496-20544/ISSM-20529-20530.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20529-20530.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20529-20530.diff (revision 20545) @@ -0,0 +1,35 @@ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 20529) ++++ ../trunk-jpl/src/c/Makefile.am (revision 20530) +@@ -646,7 +646,6 @@ + + libISSMOverload_la_CFLAGS = -D_C_ -fPIC $(COPTFLAGS) $(CFLAGS) + #}}} +- + #Executable {{{ + if ANDROID + if ANDROIDEXE +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 20529) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 20530) +@@ -7,6 +7,9 @@ + rm -rf $ISSM_DIR/nightlylog + mkdir $ISSM_DIR/nightlylog + ++#Server URI ++SERVER='https://ross.ics.uci.edu:8080' ++ + #Get configuration + #Source config file{{{ + if [ $# -ne 1 ]; +@@ -43,7 +46,7 @@ + + #Get changes from jenkins itself (svn requires credentials) + rm -rf changes +- wget http://ross.ics.uci.edu:8080/job/$JOB_NAME/$BUILD_NUMBER/changes > /dev/null 2>&1 ++ wget $SERVER/job/$JOB_NAME/$BUILD_NUMBER/changes > /dev/null 2>&1 + + #Process html page and get the list of files that has changed (tricky...) + cat changes | grep 'alt="The file was modified"' |sed -e 's/alt="The file was modified"/\ Index: /issm/oecreview/Archive/20496-20544/ISSM-20530-20531.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20530-20531.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20530-20531.diff (revision 20545) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/classes/clusters/lonestar.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/lonestar.m (revision 20530) ++++ ../trunk-jpl/src/m/classes/clusters/lonestar.m (revision 20531) +@@ -143,7 +143,7 @@ + + if length(find(cluster.email=='@'))>0 + fprintf(fid,'\n'); +- fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Ended on Lonestar 5.'' %s <<< ''Job Started'' " \n\n',cluster.email); ++ fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Ended on Lonestar 5.'' %s <<< ''Job Ended'' " \n\n',cluster.email); + end + fclose(fid); + Index: /issm/oecreview/Archive/20496-20544/ISSM-20531-20532.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20531-20532.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20531-20532.diff (revision 20545) @@ -0,0 +1,209 @@ +Index: ../trunk-jpl/examples/IceflowModels/EISMINT.par +=================================================================== +--- ../trunk-jpl/examples/IceflowModels/EISMINT.par (revision 20531) ++++ ../trunk-jpl/examples/IceflowModels/EISMINT.par (revision 20532) +@@ -28,7 +28,7 @@ + smb_max=0.5; %m/yr + sb=10^-2/1000.; %m/yr/m + rel=450.*1000.; %m +-md.surfaceforcings.mass_balance=min(smb_max,sb*(rel-radius)); ++md.smb.mass_balance=min(smb_max,sb*(rel-radius)); + + disp(' creating velocities'); + constant=0.3; +Index: ../trunk-jpl/examples/IceBridge/Greenland_noOIB.par +=================================================================== +--- ../trunk-jpl/examples/IceBridge/Greenland_noOIB.par (revision 20531) ++++ ../trunk-jpl/examples/IceBridge/Greenland_noOIB.par (revision 20532) +@@ -39,8 +39,8 @@ + md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; + + disp(' Interpolating surface mass balance'); +-md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +-md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; ++md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); ++md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; + + disp(' Construct basal friction parameters'); + md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +Index: ../trunk-jpl/examples/IceBridge/Greenland_cheatsheet.par +=================================================================== +--- ../trunk-jpl/examples/IceBridge/Greenland_cheatsheet.par (revision 20531) ++++ ../trunk-jpl/examples/IceBridge/Greenland_cheatsheet.par (revision 20532) +@@ -65,8 +65,8 @@ + md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; + + disp(' Interpolating surface mass balance'); +-md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +-md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; ++md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); ++md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; + + disp(' Construct basal friction parameters'); + md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +Index: ../trunk-jpl/examples/IceBridge/Greenland.par +=================================================================== +--- ../trunk-jpl/examples/IceBridge/Greenland.par (revision 20531) ++++ ../trunk-jpl/examples/IceBridge/Greenland.par (revision 20532) +@@ -61,8 +61,8 @@ + md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; + + disp(' Interpolating surface mass balance'); +-md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +-md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; ++md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); ++md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; + + disp(' Construct basal friction parameters'); + md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +Index: ../trunk-jpl/examples/IceBridge/runme.m +=================================================================== +--- ../trunk-jpl/examples/IceBridge/runme.m (revision 20531) ++++ ../trunk-jpl/examples/IceBridge/runme.m (revision 20532) +@@ -45,7 +45,7 @@ + md = loadmodel('./Models/Greenland.Mesh_generation'); + + md = setmask(md,'',''); +- md = parameterize(md,'./Greenland_cheatsheet.par'); ++ md = parameterize(md,'./Greenland.par'); + %md = parameterize(md,'./Greenland_noOIB.par'); + md = setflowequation(md,'SSA','all'); + +@@ -107,7 +107,7 @@ + smb = ncread(ncdata,'smb'); + smb = InterpFromGridToMesh(x1,y1,smb',md.mesh.x,md.mesh.y,0)*1000/md.materials.rho_ice; + smb = [smb smb smb-1.0]; +- md.surfaceforcings.mass_balance = [smb;1 10 20]; ++ md.smb.mass_balance = [smb;1 10 20]; + + %Set transient options, run for 20 years, saving every year + md.timestepping.time_step=0.2; %This must be reduced for finer resolutions +@@ -116,7 +116,7 @@ + + %Additional options + md.inversion.iscontrol=0; +- md.transient.requested_outputs={'IceVolume','TotalSmb','SurfaceforcingsMassBalance'}; ++ md.transient.requested_outputs={'IceVolume','TotalSmb','SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true,'convergence',true); + + %Go solve +@@ -133,7 +133,7 @@ + %Planview plots + plotmodel(md,'data',md.results.TransientSolution(end).Vel,'caxis',[1e-1 6000],... + 'log', 10, 'title', 'Velocity (m/y)','gridded',1, ... +- 'data', md.results.TransientSolution(end).SurfaceforcingsMassBalance, ... ++ 'data', md.results.TransientSolution(end).SmbMassBalance, ... + 'title', 'Surface mass balance (m/y)','gridded',1, ... + 'data',md.results.TransientSolution(end).Thickness,... + 'title','Thickness (m)','gridded',1, ... +@@ -145,7 +145,7 @@ + + %Plot surface mass balance + surfmb=[]; for i=1:100; surfmb=[surfmb ... +- md.results.TransientSolution(i).SurfaceforcingsMassBalance]; end ++ md.results.TransientSolution(i).SmbMassBalance]; end + subplot(3,1,1); plot([0.2:0.2:20],mean(surfmb)); title('Mean Surface mass balance'); + + %Plot velocity +Index: ../trunk-jpl/examples/Greenland/runme.m +=================================================================== +--- ../trunk-jpl/examples/Greenland/runme.m (revision 20531) ++++ ../trunk-jpl/examples/Greenland/runme.m (revision 20532) +@@ -1,5 +1,5 @@ + clear all; +-steps=[1 2 3 4 5]; ++steps=[1]; + + %Location of SeaRISE dataset + ncdata='../Data/Greenland_5km_dev1.2.nc'; +@@ -145,7 +145,7 @@ + %Set surface mass balance + lat = ncread(ncbox,'lat'); + lon = ncread(ncbox,'lon'); +- smbbox = ncread(ncbox,'SMB'); ++ smbbox = ncread(ncbox,'MassFlux'); + [x1 y1]=ll2xy(lat,lon,+1,45,70); + + years_of_simulation = 1840:2012; +Index: ../trunk-jpl/examples/ISMIP/CheatyRunme.m +=================================================================== +--- ../trunk-jpl/examples/ISMIP/CheatyRunme.m (revision 20531) ++++ ../trunk-jpl/examples/ISMIP/CheatyRunme.m (revision 20532) +@@ -2,7 +2,7 @@ + %step 7 is specific to ISMIPA + %step 8 is specific to ISMIPF + +-steps=[1:7]; ++steps=[1]; + + % parameter file to be used, choose between CheatyIsmipA.par or CheatyIsmipF.par + ParamFile='CheatyIsmipF.par' +Index: ../trunk-jpl/examples/UncertaintyQuantification/runme.m +=================================================================== +--- ../trunk-jpl/examples/UncertaintyQuantification/runme.m (revision 20531) ++++ ../trunk-jpl/examples/UncertaintyQuantification/runme.m (revision 20532) +@@ -1,5 +1,5 @@ + %PIG Uncertainty Quantification Application +-steps=[1:3]; ++steps=[1]; + + if any(steps==1) + disp(' Step 1: plot flux gates'); +@@ -139,10 +139,19 @@ + md.qmu.params.tabular_graphics_data=true; + + md.stressbalance.restol=10^-5; %tighten tolerances for UQ analyses ++ ++ %Turn off verbosity ++ md.verbose=verbose(0); + + %solve + md.qmu.isdakota=1; md.inversion.iscontrol=0; + md.cluster=generic('name',oshostname,'np',4); ++ ++ %Dakota runs in parallel with a master/slave configuration. ++ % At least 2 cpu's are needed to run the UQ ++ md.qmu.params.evaluation_scheduling='master'; ++ md.qmu.params.processors_per_evaluation=md.cluster.np-1; ++ + md=solve(md,StressbalanceSolutionEnum,'overwrite','y'); + + save ./Models/PIG.Sampling md; +@@ -216,6 +225,12 @@ + md.qmu.isdakota=1; + md.inversion.iscontrol=0; + md.cluster=generic('name',oshostname,'np',2); ++ ++ %Dakota runs in parallel with a master/slave configuration. ++ % At least 2 cpu's are needed to run the UQ ++ md.qmu.params.evaluation_scheduling='master'; ++ md.qmu.params.processors_per_evaluation=md.cluster.np-1 ++ + md.verbose=verbose('qmu',true); + md=solve(md,StressbalanceSolutionEnum,'overwrite','y'); + +Index: ../trunk-jpl/examples/Jakobshavn/runme.m +=================================================================== +--- ../trunk-jpl/examples/Jakobshavn/runme.m (revision 20531) ++++ ../trunk-jpl/examples/Jakobshavn/runme.m (revision 20532) +@@ -1,4 +1,4 @@ +-steps=[4]; ++steps=[1]; + + if any(steps==1) + disp(' Step 1: Mesh creation'); +Index: ../trunk-jpl/examples/Jakobshavn/Jks.par +=================================================================== +--- ../trunk-jpl/examples/Jakobshavn/Jks.par (revision 20531) ++++ ../trunk-jpl/examples/Jakobshavn/Jks.par (revision 20532) +@@ -37,8 +37,8 @@ + md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; %convert to Kelvin + + disp(' Interpolating surface mass balance'); +-md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +-md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; ++md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); ++md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; + + disp(' Construct basal friction parameters'); + md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); Index: /issm/oecreview/Archive/20496-20544/ISSM-20532-20533.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20532-20533.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20532-20533.diff (revision 20545) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/m/classes/clusters/pfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 20532) ++++ ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 20533) +@@ -91,7 +91,16 @@ + md = checkmessage(md,'cpuspernode should be between 1 and 20 for ''ivy'' processors'); + end + end +- ++ elseif strcmpi(cluster.processor,'bro'), ++ if cluster.hyperthreading, ++ if ((cluster.cpuspernode>56 ) | (cluster.cpuspernode<1)), ++ md = checkmessage(md,'cpuspernode should be between 1 and 56 for ''bro'' processors in hyperthreading mode'); ++ end ++ else ++ if ((cluster.cpuspernode>28 ) | (cluster.cpuspernode<1)), ++ md = checkmessage(md,'cpuspernode should be between 1 and 28 for ''bro'' processors'); ++ end ++ end + elseif strcmpi(cluster.processor,'has'), + if cluster.hyperthreading, + if ((cluster.cpuspernode>48 ) | (cluster.cpuspernode<1)), Index: /issm/oecreview/Archive/20496-20544/ISSM-20533-20534.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20533-20534.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20533-20534.diff (revision 20545) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.m +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.m (revision 20533) ++++ ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.m (revision 20534) +@@ -39,7 +39,7 @@ + end + pos=find(md.mesh.vertexonboundary & ~vertexonicefront); + if isempty(pos), +- warning('SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually') ++ disp('SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet applied') + end + md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1); + md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1); Index: /issm/oecreview/Archive/20496-20544/ISSM-20534-20535.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20534-20535.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20534-20535.diff (revision 20545) @@ -0,0 +1,344 @@ +Index: ../trunk-jpl/src/m/exp/downstreamflowlines.m +=================================================================== +--- ../trunk-jpl/src/m/exp/downstreamflowlines.m (revision 20534) ++++ ../trunk-jpl/src/m/exp/downstreamflowlines.m (revision 20535) +@@ -1,111 +0,0 @@ +-function flowpath=downstreamflowlines(index,x,y,u,v,x0,y0,varargin) +-%DOWNSTREAMFLOWLINES - compute flowlines from a given set of seed points +-% +-% Usage: +-% flowpath=downstreamflowlines(index,x,y,u,v,x0,y0) +-% +-% the velocity field is given by the couple (u,v) and the coordinates +-% of the seed points are (x0,y0). One can use one or several seed +-% points +-% +-% Example: +-% flowpath=downstreamflowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.vx,md.initialization.vy,x0,y0) +- +-%check input size +-if nargin>9 | nargin<7, +- help flowlines +- error('flowlines error message: bad usage'); +-end +- +-%check input +-if (length(x)~=length(y) | length(x)~=length(u) | length(x)~=length(v)), +- error('flowlines error message: x,y,u and v must have the same length'); +-end +-if length(x)<3, +- error('flowlines error message: at least one element is required'); +-end +-if length(x0)~=length(y0), +- error('flowlines error message: x0 and y0 do not have the same length'); +-end +- +-%get maxiter and precision +-if nargin==9 +- maxiter=varargin{1};%maximum number of iterations +- precision=varargin{2}; %division of each segment (higer precision increases number of segments) +-else +- maxiter=200; %maximum number of iterations +- precision=1; %division of each segment (higer precision increases number of segments) +-end +- +-%Create triangulation once for all and check seed points +-trep = triangulation(index,x,y); +-tria = pointLocation(trep,[x0 y0]); +-pos=find(isnan(tria)); +-x0(pos)=[]; +-y0(pos)=[]; +- +-%initialize other variables +-N=length(x0); +-X=x0; Y=y0; +-flowpath=struct('x',cell(N,1),'y',cell(N,1),'name','','density',1); +-for i=1:N, +- flowpath(i).x=x0(i); +- flowpath(i).y=y0(i); +-end +-done=zeros(N,1); +- +-%get avegared length of each element +-length_tria=1/3*(sqrt( (x(index(:,1))-x(index(:,2))).^2+(y(index(:,1))-y(index(:,2))).^2 )+... +- sqrt((x(index(:,1))-x(index(:,3))).^2+(y(index(:,1))-y(index(:,3))).^2 )+... +- sqrt((x(index(:,2))-x(index(:,3))).^2+(y(index(:,2))-y(index(:,3))).^2 )); +- +-%take velocity for each element +-u=u(index)*[1;1;1]/3; +-v=v(index)*[1;1;1]/3; +- +-%initialization: +-counter=1; +- +-while any(~done) +- +- %find current triangle +- queue=find(~done); +- tria = pointLocation(trep,[X(queue),Y(queue)]); +- +- %check that the point is actually inside a triangle of the mesh +- listnan=find(isnan(tria)); +- for i=1:length(listnan) +- %remove the last point +- flowpath(queue(listnan(i))).x(end)=[]; +- flowpath(queue(listnan(i))).y(end)=[]; +- done(queue(listnan(i)))=1; +- end +- tria(listnan)=[]; +- queue(listnan)=[]; +- +- if isempty(tria), +- break; +- end +- +- %velocity of the current triangle and norm it +- ut=u(tria); vt=v(tria); normv=sqrt(ut.^2+vt.^2); +- ut=ut./normv;vt=vt./normv; +- +- %check counter +- if counter>maxiter +- disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going forward']) +- break +- end +- counter=counter+1; +- +- %remove stagnant point +- done(queue(find(ut==0 & vt==0)))=1; +- +- %build next point +- for i=1:length(queue) +- X(queue(i))=flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision; +- Y(queue(i))=flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision; +- flowpath(queue(i)).x=[flowpath(queue(i)).x;flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision]; +- flowpath(queue(i)).y=[flowpath(queue(i)).y;flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision]; +- end +-end +Index: ../trunk-jpl/src/m/exp/flowlines.m +=================================================================== +--- ../trunk-jpl/src/m/exp/flowlines.m (revision 20534) ++++ ../trunk-jpl/src/m/exp/flowlines.m (revision 20535) +@@ -2,7 +2,7 @@ + %FLOWLINES - compute flowlines from a given set of seed points + % + % Usage: +-% flowpath=flowlines(index,x,y,u,v,x0,y0) ++% flowpath=flowlines(index,x,y,u,v,x0,y0,varargin) + % + % the velocity field is given by the couple (u,v) and the coordinates + % of the seed points are (x0,y0). One can use one or several seed +@@ -10,6 +10,12 @@ + % + % Example: + % flowpath=flowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.vx,md.initialization.vy,x0,y0) ++% ++% Options: ++% - 'maxiter': how many steps upstream and downstream of the seed points (default: 200) ++% - 'precision': division of each segment (higer precision increases number of segments, default: 1) ++% - 'downstream':flow line upstream of the seed points (default: 1) ++% - 'upstream': flow line upstream of the seed points (default: 1) + + %check input size + if nargin>8 | nargin<7, +@@ -28,13 +34,10 @@ + error('flowlines error message: x0 and y0 do not have the same length'); + end + +-%get maxiter and precision +-if nargin==8 +- maxiter=varargin{1}; +-else +- maxiter=200; %maximum number of iterations +-end +-precision=1; %division of each segment (higer precision increases number of segments) ++%process options ++options = pairoptions(varargin{:}); ++maxiter = getfieldvalue(options,'maxiter',200); ++precision = getfieldvalue(options,'precision',1); + + %Create triangulation once for all and check seed points + trep = triangulation(index,x,y); +@@ -62,104 +65,108 @@ + u=u(index)*[1;1;1]/3; + v=v(index)*[1;1;1]/3; + +-%initialization: +-counter=1; ++if downstream, ++ %initialization: ++ counter=1; + +-while any(~done) ++ while any(~done) + +- %find current triangle +- queue=find(~done); +- tria = pointLocation(trep,[X(queue),Y(queue)]); ++ %find current triangle ++ queue=find(~done); ++ tria = pointLocation(trep,[X(queue),Y(queue)]); + +- %check that the point is actually inside a triangle of the mesh +- listnan=find(isnan(tria)); +- for i=1:length(listnan) +- %remove the last point +- flowpath(queue(listnan(i))).x(end)=[]; +- flowpath(queue(listnan(i))).y(end)=[]; +- done(queue(listnan(i)))=1; +- end +- tria(listnan)=[]; +- queue(listnan)=[]; ++ %check that the point is actually inside a triangle of the mesh ++ listnan=find(isnan(tria)); ++ for i=1:length(listnan) ++ %remove the last point ++ flowpath(queue(listnan(i))).x(end)=[]; ++ flowpath(queue(listnan(i))).y(end)=[]; ++ done(queue(listnan(i)))=1; ++ end ++ tria(listnan)=[]; ++ queue(listnan)=[]; + +- if isempty(tria), +- break; +- end ++ if isempty(tria), ++ break; ++ end + +- %velocity of the current triangle and norm it +- ut=u(tria); vt=v(tria); normv=max(eps,sqrt(ut.^2+vt.^2)); +- ut=ut./normv;vt=vt./normv; ++ %velocity of the current triangle and norm it ++ ut=u(tria); vt=v(tria); normv=max(eps,sqrt(ut.^2+vt.^2)); ++ ut=ut./normv;vt=vt./normv; + +- %check counter +- if counter>maxiter +- disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going forward']) +- break +- end +- counter=counter+1; ++ %check counter ++ if counter>maxiter ++ disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going forward']) ++ break ++ end ++ counter=counter+1; + +- %remove stagnant point +- done(queue(find(ut==0 & vt==0)))=1; ++ %remove stagnant point ++ done(queue(find(ut==0 & vt==0)))=1; + +- %build next point +- for i=1:length(queue) +- X(queue(i))=flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision; +- Y(queue(i))=flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision; +- flowpath(queue(i)).x=[flowpath(queue(i)).x;flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision]; +- flowpath(queue(i)).y=[flowpath(queue(i)).y;flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision]; ++ %build next point ++ for i=1:length(queue) ++ X(queue(i))=flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision; ++ Y(queue(i))=flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision; ++ flowpath(queue(i)).x=[flowpath(queue(i)).x;flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision]; ++ flowpath(queue(i)).y=[flowpath(queue(i)).y;flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision]; ++ end + end + end + + %same process but reverse (vel=-vel) to have a vcomplete flow line +-queue=[]; +-counter=1; +-X=x0; Y=y0; +-done=zeros(N,1); ++if upstream, ++ queue=[]; ++ counter=1; ++ X=x0; Y=y0; ++ done=zeros(N,1); + +-while any(~done) ++ while any(~done) + +- %find current triangle +- queue=find(~done); +- tria = pointLocation(trep,[X(queue),Y(queue)]); ++ %find current triangle ++ queue=find(~done); ++ tria = pointLocation(trep,[X(queue),Y(queue)]); + +- %check that the point is actually inside a triangle of the mesh +- listnan=find(isnan(tria)); +- for i=1:length(listnan) +- %remove the last point +- flowpath(queue(listnan(i))).x(1)=[]; +- flowpath(queue(listnan(i))).y(1)=[]; +- done(queue(listnan(i)))=1; +- end +- tria(listnan)=[]; +- queue(listnan)=[]; ++ %check that the point is actually inside a triangle of the mesh ++ listnan=find(isnan(tria)); ++ for i=1:length(listnan) ++ %remove the last point ++ flowpath(queue(listnan(i))).x(1)=[]; ++ flowpath(queue(listnan(i))).y(1)=[]; ++ done(queue(listnan(i)))=1; ++ end ++ tria(listnan)=[]; ++ queue(listnan)=[]; + +- if isempty(tria), +- break; +- end ++ if isempty(tria), ++ break; ++ end + +- %velocity of the current triangle and norm it +- ut=-u(tria); vt=-v(tria); normv=max(eps,sqrt(ut.^2+vt.^2)); +- ut=ut./normv;vt=vt./normv; ++ %velocity of the current triangle and norm it ++ ut=-u(tria); vt=-v(tria); normv=max(eps,sqrt(ut.^2+vt.^2)); ++ ut=ut./normv;vt=vt./normv; + +- %check counter +- if counter>maxiter +- disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going backward']) +- break +- end +- counter=counter+1; ++ %check counter ++ if counter>maxiter ++ disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going backward']) ++ break ++ end ++ counter=counter+1; + +- %remove stagnant point +- done(queue(find(ut==0 & vt==0)))=1; ++ %remove stagnant point ++ done(queue(find(ut==0 & vt==0)))=1; + +- %build next point +- for i=1:length(queue) +- X(queue(i))=flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision; +- Y(queue(i))=flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision; +- flowpath(queue(i)).x=[flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision; flowpath(queue(i)).x]; +- flowpath(queue(i)).y=[flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision; flowpath(queue(i)).y]; ++ %build next point ++ for i=1:length(queue) ++ X(queue(i))=flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision; ++ Y(queue(i))=flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision; ++ flowpath(queue(i)).x=[flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision; flowpath(queue(i)).x]; ++ flowpath(queue(i)).y=[flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision; flowpath(queue(i)).y]; ++ end + end + end + +-%EXP compatibility ++%EXP compatibility (add name) + for i=1:length(queue) + flowpath(queue(i)).name=['flowline' num2str(i)]; + end Index: /issm/oecreview/Archive/20496-20544/ISSM-20535-20536.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20535-20536.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20535-20536.diff (revision 20545) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/src/m/classes/clusters/generic_static.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/generic_static.m (revision 20535) ++++ ../trunk-jpl/src/m/classes/clusters/generic_static.m (revision 20536) +@@ -50,10 +50,20 @@ + %}}} + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + ++ %write queuing script ++ %what is the executable being called? ++ executable='issm.exe'; ++ if isdakota, ++ version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3)); ++ if (version>=6), ++ executable='issm_dakota.exe'; ++ end ++ end ++ + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!%s\n',cluster.shell); +- fprintf(fid,[cluster.codepath '/mpiexec -np %i %s/issm.exe %s %s %s \n'],cluster.np,cluster.codepath,EnumToString(solution),'./',modelname); ++ fprintf(fid,[cluster.codepath '/mpiexec -np %i %s/%s %s %s %s \n'],cluster.np,cluster.codepath,executable,EnumToString(solution),'./',modelname); + fclose(fid); + + %in interactive mode, create a run file, and errlog and outlog file Index: /issm/oecreview/Archive/20496-20544/ISSM-20536-20537.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20536-20537.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20536-20537.diff (revision 20545) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/src/m/exp/flowlines.m +=================================================================== +--- ../trunk-jpl/src/m/exp/flowlines.m (revision 20536) ++++ ../trunk-jpl/src/m/exp/flowlines.m (revision 20537) +@@ -9,7 +9,7 @@ + % points + % + % Example: +-% flowpath=flowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.vx,md.initialization.vy,x0,y0) ++% flowpath=flowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.initialization.vx,md.initialization.vy,x0,y0) + % + % Options: + % - 'maxiter': how many steps upstream and downstream of the seed points (default: 200) +@@ -17,12 +17,6 @@ + % - 'downstream':flow line upstream of the seed points (default: 1) + % - 'upstream': flow line upstream of the seed points (default: 1) + +-%check input size +-if nargin>8 | nargin<7, +- help flowlines +- error('flowlines error message: bad usage'); +-end +- + %check input + if (length(x)~=length(y) | length(x)~=length(u) | length(x)~=length(v)), + error('flowlines error message: x,y,u and v must have the same length'); Index: /issm/oecreview/Archive/20496-20544/ISSM-20537-20538.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20537-20538.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20537-20538.diff (revision 20545) @@ -0,0 +1,19 @@ +Index: ../trunk-jpl/src/m/exp/flowlines.m +=================================================================== +--- ../trunk-jpl/src/m/exp/flowlines.m (revision 20537) ++++ ../trunk-jpl/src/m/exp/flowlines.m (revision 20538) +@@ -29,9 +29,11 @@ + end + + %process options +-options = pairoptions(varargin{:}); +-maxiter = getfieldvalue(options,'maxiter',200); +-precision = getfieldvalue(options,'precision',1); ++options = pairoptions(varargin{:}); ++maxiter = getfieldvalue(options,'maxiter',200); ++precision = getfieldvalue(options,'precision',1); ++downstream = getfieldvalue(options,'downstream',1); ++upstream = getfieldvalue(options,'upstream',1); + + %Create triangulation once for all and check seed points + trep = triangulation(index,x,y); Index: /issm/oecreview/Archive/20496-20544/ISSM-20538-20539.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20538-20539.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20538-20539.diff (revision 20545) @@ -0,0 +1,19 @@ +Index: ../trunk-jpl/src/m/mesh/patchglobe.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/patchglobe.m (revision 20538) ++++ ../trunk-jpl/src/m/mesh/patchglobe.m (revision 20539) +@@ -6,6 +6,14 @@ + %recover basic options: + bandwidth=getfieldvalue(options,'bandwidth',100000); + ++ %some checks on the mesh: ++ if (isempty(mh.x) | isempty(mh.y) | isempty(mh.z) | isempty(mh.lat) | isempty(mh.long) | isempty(mh.r) ) ++ error('patchglobe error message: 3D planet mesh has one of the following empty: ''x'',''y'',''z'',''lat'',''long'' or ''r'''); ++ end ++ if (isempty(mh2d.x) | isempty(mh2d.y) | isempty(mh2d.lat) | isempty(mh2d.long)) ++ error('patchglobe error message: 3D planet mesh has one of the following empty: ''x'',''y'',''lat'' or ''long'''); ++ end ++ + %give ourselves a unique temporary directory: + temproot=tempname; mkdir(temproot); + Index: /issm/oecreview/Archive/20496-20544/ISSM-20539-20540.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20539-20540.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20539-20540.diff (revision 20545) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/m/classes/miscellaneous.m +=================================================================== +--- ../trunk-jpl/src/m/classes/miscellaneous.m (revision 20539) ++++ ../trunk-jpl/src/m/classes/miscellaneous.m (revision 20540) +@@ -38,11 +38,15 @@ + WriteData(fid,'object',self,'fieldname','name','format','String'); + end % }}} + function savemodeljs(self,fid,modelname) % {{{ +- ++ + writejsstring(fid,[modelname '.miscellaneous.notes'],self.notes); + writejsstring(fid,[modelname '.miscellaneous.name'],self.name); + if strcmpi(class(self.dummy),'double'), +- writejs1Darray(fid,[modelname '.miscellaneous.dummy'],self.dummy); ++ if size(self.dummy,2)==1, ++ writejs1Darray(fid,[modelname '.miscellaneous.dummy'],self.dummy); ++ else ++ writejs2Darray(fid,[modelname '.miscellaneous.dummy'],self.dummy); ++ end + end + + end % }}} Index: /issm/oecreview/Archive/20496-20544/ISSM-20540-20541.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20540-20541.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20540-20541.diff (revision 20545) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/m/plot/applyoptions.js +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.js (revision 20540) ++++ ../trunk-jpl/src/m/plot/applyoptions.js (revision 20541) +@@ -47,14 +47,11 @@ + var caxisdelta = caxis[1] - caxis[0]; + var clabelitem; + var precision=options.getfieldvalue('colorbarprecision',3); ++ + if (options.getfieldvalue('log',10)!='off') { + for (var i = cdivisions; i >= 0; i--) { +- if (caxisdelta*i/cdivisions==caxis[0]) { +- labels[i] = (caxis[0]).toPrecision(precision); +- } +- else { +- labels[i] = (Math.exp(Math.log(caxisdelta)*(cdivisions-i)/cdivisions)+caxis[0]).toPrecision(precision); +- } ++ var scale = Math.log(caxis[1])-Math.log(caxis[0]); ++ labels[i] = (Math.exp(Math.log(caxis[0])+scale*(cdivisions-i)/cdivisions)).toPrecision(precision); + } + } else { + for (var i = cdivisions; i >= 0; i--) { Index: /issm/oecreview/Archive/20496-20544/ISSM-20541-20542.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20541-20542.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20541-20542.diff (revision 20545) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/src/m/plot/plot_overlay.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_overlay.js (revision 20541) ++++ ../trunk-jpl/src/m/plot/plot_overlay.js (revision 20542) +@@ -126,8 +126,14 @@ + vertices[vertices.length] = vertex[1]; + vertices[vertices.length] = vertex[2]; + +- texcoords[texcoords.length] = (x[i] - modelxlim[0]) / xrange; +- texcoords[texcoords.length] = (y[i] - modelylim[0]) / yrange; ++ if (md.mesh.classname() == 'mesh3dsurface') { ++ texcoords[texcoords.length] = degrees(Math.atan2(y[i], x[i])) / 360 + 0.5; ++ texcoords[texcoords.length] = degrees(Math.asin(z[i] / magnitude)) / 180 + 0.5; ++ } ++ else { ++ texcoords[texcoords.length] = (x[i] - modelxlim[0]) / xrange; ++ texcoords[texcoords.length] = (y[i] - modelylim[0]) / yrange; ++ } + } + + //linearize the elements array: Index: /issm/oecreview/Archive/20496-20544/ISSM-20542-20543.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20542-20543.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20542-20543.diff (revision 20545) @@ -0,0 +1,44 @@ +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 20542) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 20543) +@@ -62,10 +62,10 @@ + echo "Determining installation type" + if [ ! -z "$(cat $ISSM_DIR/TEMP | grep externalpackages)" ] ; then + echo " -- checking for changed externalpackages... yes"; +- ISSM_EXTERNALPACKAGES="install" ++ ISSM_EXTERNALPACKAGES="yes" + else + echo " -- checking for changed externalpackages... no"; +- ISSM_EXTERNALPACKAGES="none" ++ ISSM_EXTERNALPACKAGES="no" + fi + + #Do we need to reconfigure +@@ -91,7 +91,7 @@ + echo " -- checking for changed externalpackages... yes"; + echo " -- checking for reconfiguration... yes"; + echo " -- checking for recompilation... yes"; +- ISSM_EXTERNALPACKAGES="install" ++ ISSM_EXTERNALPACKAGES="yes" + ISSM_RECONFIGURE="yes" + ISSM_COMPILATION="yes" + fi +@@ -99,7 +99,7 @@ + echo "Recording current svn version: $SVN_REVISION_1" + echo $SVN_REVISION_1 > $ISSM_DIR/svn_revision_old + #}}} +-#install/none external packages (ISSM_EXTERNALPACKAGES){{{ ++#Install external packages (ISSM_EXTERNALPACKAGES){{{ + + #Jenkins xml files for individual packages + EXTERNAL_TEST_FILE="$ISSM_DIR/nightlylog/results/external.xml" +@@ -118,7 +118,7 @@ + cd $ISSM_DIR/externalpackages/$PACKAGENAME + + #install if requested or if previous install has not been successful +- if [ "$ISSM_EXTERNALPACKAGES" == "install" ] || [ ! -f SUCCESS ]; then ++ if [ "$ISSM_EXTERNALPACKAGES" == "yes" ] || [ ! -f SUCCESS ]; then + echo "======================================================"; + echo " Installing $PACKAGENAME "; + echo "======================================================"; Index: /issm/oecreview/Archive/20496-20544/ISSM-20543-20544.diff =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-20543-20544.diff (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-20543-20544.diff (revision 20545) @@ -0,0 +1,28 @@ +Index: ../trunk-jpl/src/m/classes/clusters/generic_static.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/generic_static.m (revision 20543) ++++ ../trunk-jpl/src/m/classes/clusters/generic_static.m (revision 20544) +@@ -50,6 +50,14 @@ + %}}} + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + ++ %Check that issm.exe exists in the right path ++ if ~exist([cluster.codepath '/issm.exe'],'file'), ++ error(['File ' cluster.codepath '/issm.exe does not exist']); ++ end ++ ++ %Now process codepath and replace empty spaces with \ to avoid errors in queuing script ++ codepath2=strrep(cluster.codepath,' ','\ '); ++ + %write queuing script + %what is the executable being called? + executable='issm.exe'; +@@ -63,7 +71,7 @@ + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!%s\n',cluster.shell); +- fprintf(fid,[cluster.codepath '/mpiexec -np %i %s/%s %s %s %s \n'],cluster.np,cluster.codepath,executable,EnumToString(solution),'./',modelname); ++ fprintf(fid,['%s/mpiexec -np %i %s/%s %s %s %s \n'],codepath2,cluster.np,codepath2,executable,EnumToString(solution),'./',modelname); + fclose(fid); + + %in interactive mode, create a run file, and errlog and outlog file Index: /issm/oecreview/Archive/20496-20544/ISSM-DocReview-20496-20544.tex =================================================================== --- /issm/oecreview/Archive/20496-20544/ISSM-DocReview-20496-20544.tex (revision 20545) +++ /issm/oecreview/Archive/20496-20544/ISSM-DocReview-20496-20544.tex (revision 20545) @@ -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} + +\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/20496-20544/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/20496-20544/LogNumber.tex (revision 20545) +++ /issm/oecreview/Archive/20496-20544/LogNumber.tex (revision 20545) @@ -0,0 +1,1 @@ +20496-20544 Index: /issm/oecreview/Archive/20496-20544/Makefile =================================================================== --- /issm/oecreview/Archive/20496-20544/Makefile (revision 20545) +++ /issm/oecreview/Archive/20496-20544/Makefile (revision 20545) @@ -0,0 +1,8 @@ +TARGET=ISSM-DocReview-20496-20544 + +all: + pdflatex -interaction=errorstopmode -file-line-error -halt-on-error $(TARGET).tex + rm -rf *.log *.aux + +clean: + rm -rf *.log *.aux Index: /issm/oecreview/Archive/20496-20544/log.tex =================================================================== --- /issm/oecreview/Archive/20496-20544/log.tex (revision 20545) +++ /issm/oecreview/Archive/20496-20544/log.tex (revision 20545) @@ -0,0 +1,301 @@ +\noindent \textbf{Change \#1} with diff file ISSM-20496-20497.diff: \\ +Function name: \\ +M /issm/trunk-jpl/configure.ac\\ +Export determination: 6. \\ +Rationale: CHG: updating revision number\\ +\vspace{3em} + +\noindent \textbf{Change \#2} with diff file ISSM-20497-20498.diff: \\ +Function name: \\ +M /issm/trunk-jpl M /issm/trunk-jpl/src M /issm/trunk-jpl/test\\ +Export determination: 6. \\ +Rationale: merged trunk and trunk-jpl\\ +\vspace{3em} + +\noindent \textbf{Change \#3} with diff file ISSM-20501-20502.diff: \\ +Function name: \\ +M /issm/trunk-jpl M /issm/trunk-jpl/src M /issm/trunk-jpl/test\\ +Export determination: 6. \\ +Rationale: Block revision 20500 from being merged into trunk-jpl\\ +\vspace{3em} + +\noindent \textbf{Change \#4} with diff file ISSM-20502-20503.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/exp/downstreamflowlines.m M /issm/trunk-jpl/src/m/exp/flowlines.m\\ +Export determination: 6. \\ +Rationale: CHG: speedint up flowlines\\ +\vspace{3em} + +\noindent \textbf{Change \#5} with diff file ISSM-20503-20504.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/Makefile.am D /issm/trunk-jpl/src/c/modules/TriaSearchx M /issm/trunk-jpl/src/c/modules/modules.h D /issm/trunk-jpl/src/wrappers/TriaSearch M /issm/trunk-jpl/src/wrappers/matlab/Makefile.am\\ +Export determination: 6. \\ +Rationale: DEL: not needed anymore\\ +\vspace{3em} + +\noindent \textbf{Change \#6} with diff file ISSM-20504-20505.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test211.py M /issm/trunk-jpl/test/NightlyRun/test422.m M /issm/trunk-jpl/test/NightlyRun/test422.py\\ +Export determination: 6. \\ +Rationale: CHG: relaxed toleraces\\ +\vspace{3em} + +\noindent \textbf{Change \#7} with diff file ISSM-20505-20506.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/model.m M /issm/trunk-jpl/src/m/classes/model.py\\ +Export determination: 6. \\ +Rationale: BUG: balancethickness works only in 2D, so do not attempt to collapse it from 3D\\ +\vspace{3em} + +\noindent \textbf{Change \#8} with diff file ISSM-20506-20507.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/jenkins.sh\\ +Export determination: 6. \\ +Rationale: BUG: too many spaces\\ +\vspace{3em} + +\noindent \textbf{Change \#9} with diff file ISSM-20508-20509.diff: \\ +Function name: \\ +A /issm/trunk-jpl/jenkins/macosx\_pine-island\_dakota\_static\\ +Export determination: 6. \\ +Rationale: ADD: New Jenkins configuration script for static Dakota binaries.\\ +\vspace{3em} + +\noindent \textbf{Change \#10} with diff file ISSM-20509-20510.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/jenkins.sh\\ +Export determination: 6. \\ +Rationale: CHG: better way of dealing with externalpackages\\ +\vspace{3em} + +\noindent \textbf{Change \#11} with diff file ISSM-20511-20512.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/plot/applyoptions.js M /issm/trunk-jpl/src/m/plot/plot\_unit.js M /issm/trunk-jpl/src/m/plot/processdata.js\\ +Export determination: 6. \\ +Rationale: CHG (javascript): Updating unit plots to handle log scaling. processdata now handle node transients with log scaling.\\ +\vspace{3em} + +\noindent \textbf{Change \#12} with diff file ISSM-20512-20513.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/exp/flowlines.m\\ +Export determination: 6. \\ +Rationale: BUG: take care of case vx=vy=0\\ +\vspace{3em} + +\noindent \textbf{Change \#13} with diff file ISSM-20513-20514.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/plot/applyoptions.js M /issm/trunk-jpl/src/m/plot/plot\_unit.js M /issm/trunk-jpl/src/m/plot/processdata.js\\ +Export determination: 6. \\ +Rationale: CHG (javascript): log option can now be disabled with 'off' value.\\ +\vspace{3em} + +\noindent \textbf{Change \#14} with diff file ISSM-20514-20515.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/plot/plot\_unit.js M /issm/trunk-jpl/src/m/plot/processdata.js\\ +Export determination: 6. \\ +Rationale: CHG (javascript): Resolving options error with incorrect/missing default values.\\ +\vspace{3em} + +\noindent \textbf{Change \#15} with diff file ISSM-20515-20516.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/Elements/PentaRef.cpp M /issm/trunk-jpl/src/c/classes/Elements/SegRef.cpp M /issm/trunk-jpl/src/c/classes/Elements/TetraRef.cpp M /issm/trunk-jpl/src/c/classes/Elements/TriaRef.cpp\\ +Export determination: 6. \\ +Rationale: CHG: from Alex Scott, no need to use dynamic allocation for dbasis, static allocation seems to be much faster\\ +\vspace{3em} + +\noindent \textbf{Change \#16} with diff file ISSM-20516-20517.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/plot/manualcb.m\\ +Export determination: 6. \\ +Rationale: CHG: fixing colorbar\\ +\vspace{3em} + +\noindent \textbf{Change \#17} with diff file ISSM-20517-20518.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: no need to prevent people from using LSF now\\ +\vspace{3em} + +\noindent \textbf{Change \#18} with diff file ISSM-20518-20519.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/calving.m\\ +Export determination: 6. \\ +Rationale: CHG: forcings should only check the first lines\\ +\vspace{3em} + +\noindent \textbf{Change \#19} with diff file ISSM-20519-20520.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/miscellaneous/transientrestart.m\\ +Export determination: 6. \\ +Rationale: BUG: output time is already in years\\ +\vspace{3em} + +\noindent \textbf{Change \#20} with diff file ISSM-20520-20521.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/coordsystems/gdaltransform.m\\ +Export determination: 6. \\ +Rationale: CHG: added error message in case transformation did not work\\ +\vspace{3em} + +\noindent \textbf{Change \#21} with diff file ISSM-20521-20522.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test124.m\\ +Export determination: 6. \\ +Rationale: CHG: relaxing tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#22} with diff file ISSM-20522-20523.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/clusters/lonestar.m\\ +Export determination: 6. \\ +Rationale: CHG: add email workaround\\ +\vspace{3em} + +\noindent \textbf{Change \#23} with diff file ISSM-20523-20524.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/coordsystems/gdaltransform.m\\ +Export determination: 6. \\ +Rationale: CHG: faster conversion and more complete documentation\\ +\vspace{3em} + +\noindent \textbf{Change \#24} with diff file ISSM-20524-20525.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/clusters/lonestar.m\\ +Export determination: 6. \\ +Rationale: CHG: add email workaround\\ +\vspace{3em} + +\noindent \textbf{Change \#25} with diff file ISSM-20525-20526.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test404.m M /issm/trunk-jpl/test/NightlyRun/test404.py\\ +Export determination: 6. \\ +Rationale: CHG: relaxing tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#26} with diff file ISSM-20526-20527.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/independent.py\\ +Export determination: 6. \\ +Rationale: BUG: fixig AD error on python test\\ +\vspace{3em} + +\noindent \textbf{Change \#27} with diff file ISSM-20527-20528.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test3020.py\\ +Export determination: 6. \\ +Rationale: minor\\ +\vspace{3em} + +\noindent \textbf{Change \#28} with diff file ISSM-20528-20529.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/independent.py\\ +Export determination: 6. \\ +Rationale: BUG: need to import checkfield\\ +\vspace{3em} + +\noindent \textbf{Change \#29} with diff file ISSM-20529-20530.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/Makefile.am\\ +Export determination: 6. \\ +Rationale: CHG: Attempt to fix AD issue relating to missing gfortran symbol in libISSMCore.\\ +\vspace{3em} + +\noindent \textbf{Change \#30} with diff file ISSM-20530-20531.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/jenkins.sh M /issm/trunk-jpl/src/c/Makefile.am\\ +Export determination: 6. \\ +Rationale: CHG: Changed address of wget.\\ +\vspace{3em} + +\noindent \textbf{Change \#31} with diff file ISSM-20531-20532.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/clusters/lonestar.m\\ +Export determination: 6. \\ +Rationale: CHG: minor update to email when job ends\\ +\vspace{3em} + +\noindent \textbf{Change \#32} with diff file ISSM-20532-20533.diff: \\ +Function name: \\ +M /issm/trunk-jpl/examples/Greenland/runme.m M /issm/trunk-jpl/examples/ISMIP/CheatyRunme.m M /issm/trunk-jpl/examples/IceBridge/Greenland.par M /issm/trunk-jpl/examples/IceBridge/Greenland\_cheatsheet.par M /issm/trunk-jpl/examples/IceBridge/Greenland\_noOIB.par M /issm/trunk-jpl/examples/IceBridge/runme.m M /issm/trunk-jpl/examples/IceflowModels/EISMINT.par M /issm/trunk-jpl/examples/Jakobshavn/Jks.par M /issm/trunk-jpl/examples/Jakobshavn/runme.m M /issm/trunk-jpl/examples/UncertaintyQuantification/runme.m\\ +Export determination: 6. \\ +Rationale: CHG: update examples for new code\\ +\vspace{3em} + +\noindent \textbf{Change \#33} with diff file ISSM-20533-20534.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/clusters/pfe.m\\ +Export determination: 6. \\ +Rationale: NEW: added new broadband nodes for pleiades\\ +\vspace{3em} + +\noindent \textbf{Change \#34} with diff file ISSM-20534-20535.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.m\\ +Export determination: 6. \\ +Rationale: CHG: changed warning to simple display\\ +\vspace{3em} + +\noindent \textbf{Change \#35} with diff file ISSM-20535-20536.diff: \\ +Function name: \\ +D /issm/trunk-jpl/src/m/exp/downstreamflowlines.m M /issm/trunk-jpl/src/m/exp/flowlines.m\\ +Export determination: 6. \\ +Rationale: CHG: added more options to flowlines, that can now be used to replace downstreamflowlines.m\\ +\vspace{3em} + +\noindent \textbf{Change \#36} with diff file ISSM-20536-20537.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/clusters/generic\_static.m\\ +Export determination: 6. \\ +Rationale: CHG: add dakota 6 exec to generic\_static\\ +\vspace{3em} + +\noindent \textbf{Change \#37} with diff file ISSM-20537-20538.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/exp/flowlines.m\\ +Export determination: 6. \\ +Rationale: CHG: fixing nargin\\ +\vspace{3em} + +\noindent \textbf{Change \#38} with diff file ISSM-20538-20539.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/exp/flowlines.m\\ +Export determination: 6. \\ +Rationale: CHG: fixing downstream option\\ +\vspace{3em} + +\noindent \textbf{Change \#39} with diff file ISSM-20539-20540.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/mesh/patchglobe.m\\ +Export determination: 6. \\ +Rationale: CHG: added checks.\\ +\vspace{3em} + +\noindent \textbf{Change \#40} with diff file ISSM-20540-20541.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/miscellaneous.m\\ +Export determination: 6. \\ +Rationale: CHG: minor.\\ +\vspace{3em} + +\noindent \textbf{Change \#41} with diff file ISSM-20541-20542.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/plot/applyoptions.js\\ +Export determination: 6. \\ +Rationale: CHG (javascript): Improving log scaling lables.\\ +\vspace{3em} + +\noindent \textbf{Change \#42} with diff file ISSM-20542-20543.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/plot/plot\_overlay.js\\ +Export determination: 6. \\ +Rationale: CHG (javascript): adding overlay support for mesh3dsurface.\\ +\vspace{3em} + +\noindent \textbf{Change \#43} with diff file ISSM-20543-20544.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/jenkins.sh\\ +Export determination: 6. \\ +Rationale: CHG: fixing externalpackages\\ +\vspace{3em} + Index: /issm/oecreview/Archive/20496-20544/r1.tex =================================================================== --- /issm/oecreview/Archive/20496-20544/r1.tex (revision 20545) +++ /issm/oecreview/Archive/20496-20544/r1.tex (revision 20545) @@ -0,0 +1,1 @@ +20496 Index: /issm/oecreview/Archive/20496-20544/r2.tex =================================================================== --- /issm/oecreview/Archive/20496-20544/r2.tex (revision 20545) +++ /issm/oecreview/Archive/20496-20544/r2.tex (revision 20545) @@ -0,0 +1,1 @@ +20544