Index: /issm/oecreview/Archive/21724-22754/Date.tex =================================================================== --- /issm/oecreview/Archive/21724-22754/Date.tex (revision 22755) +++ /issm/oecreview/Archive/21724-22754/Date.tex (revision 22755) @@ -0,0 +1,1 @@ +May-10-2018 Index: /issm/oecreview/Archive/21724-22754/ISSM-21724-21725.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21724-21725.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21724-21725.diff (revision 22755) @@ -0,0 +1,19 @@ +Index: ../trunk-jpl/src/m/plot/scaleruler.m +=================================================================== +--- ../trunk-jpl/src/m/plot/scaleruler.m (revision 21724) ++++ ../trunk-jpl/src/m/plot/scaleruler.m (revision 21725) +@@ -25,9 +25,12 @@ + + %If only one tick, just draw a rectangle + if numberofticks==1, +- text(x0+lengthscale/2,y0+2*widthscale,2,[num2str(lengthscale*unitscale/1000) ' km'],... ++ t=text(x0+lengthscale/2,y0+2*widthscale,2,[num2str(lengthscale*unitscale/1000) ' km'],... + 'FontSize',fontsize,'FontWeight',fontweight,'Color',fontcolor,'HorizontalAlignment','center','VerticalAlignment','baseline'); +- patch([x0 x0+lengthscale x0+lengthscale x0],[y0 y0 y0+widthscale y0+widthscale],2*ones(1,4),fontcolor,'Edgecolor',fontcolor); ++ if ~verLessThan('matlab', '8.3') ++ set(t,'Layer','front'); ++ end ++ p=patch([x0 x0+lengthscale x0+lengthscale x0],[y0 y0 y0+widthscale y0+widthscale],2*ones(1,4),fontcolor,'Edgecolor',fontcolor); + else + %initialize some coordinates + unitlength=lengthscale/(numberofticks -1); Index: /issm/oecreview/Archive/21724-22754/ISSM-21730-21731.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21730-21731.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21730-21731.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/configure.ac +=================================================================== +--- ../trunk-jpl/configure.ac (revision 21730) ++++ ../trunk-jpl/configure.ac (revision 21731) +@@ -1,7 +1,7 @@ + # Process this file with autoconf to produce a configure script. + + #AUTOCONF +-AC_INIT([Ice Sheet System Model (ISSM)],[4.12],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure ++AC_INIT([Ice Sheet System Model (ISSM)],[4.13],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure + AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config + AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 + m4_include([m4/issm_options.m4]) Index: /issm/oecreview/Archive/21724-22754/ISSM-21736-21737.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21736-21737.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21736-21737.diff (revision 22755) @@ -0,0 +1,24 @@ +Index: ../trunk-jpl/src/m/plot/plot_unit.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_unit.m (revision 21736) ++++ ../trunk-jpl/src/m/plot/plot_unit.m (revision 21737) +@@ -29,8 +29,17 @@ + patch( 'Faces',[B C D],'Vertices', [x y z],'CData',data(pos),'FaceColor','flat','EdgeColor',edgecolor); + patch( 'Faces',[C A D],'Vertices', [x y z],'CData',data(pos),'FaceColor','flat','EdgeColor',edgecolor); + else +- A=elements(pos,1); B=elements(pos,2); C=elements(pos,3); +- patch( 'Faces', [A B C], 'Vertices', [x y z],'CData', data(pos),'FaceColor','flat','EdgeColor',edgecolor); ++ A=elements(pos,1); B=elements(pos,2); C=elements(pos,3); data=data(pos); ++ patch( 'Faces', [A B C], 'Vertices', [x y z],'CData', data,'FaceColor','flat','EdgeColor',edgecolor); ++ ++ %mask value NaN, plot white faces. ++ if getfieldvalue(options,'maskwhite',0), ++ pos2=find(data==getfieldvalue(options,'maskvalue',NaN)); ++ if ~isempty(pos2), ++ A=elements(pos(pos2),1); B=elements(pos(pos2),2); C=elements(pos(pos2),3); data=data(pos2); ++ patch( 'Faces', [A B C], 'Vertices', [x y z],'FaceColor','w','EdgeColor',edgecolor); ++ end ++ end + end + + if is2d, Index: /issm/oecreview/Archive/21724-22754/ISSM-21737-21738.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21737-21738.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21737-21738.diff (revision 22755) @@ -0,0 +1,223 @@ +Index: ../trunk-jpl/src/m/classes/misfit.m +=================================================================== +--- ../trunk-jpl/src/m/classes/misfit.m (revision 21737) ++++ ../trunk-jpl/src/m/classes/misfit.m (revision 21738) +@@ -17,13 +17,13 @@ + classdef misfit + properties (SetAccess=public) + %misfit +- name = ''; ++ name = ''; + definitionstring = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-10]' + model_string = ''; %string for field that is modeled + observation = NaN; %observed field that we compare the model against + observation_string = ''; %string for observed field. + timeinterpolation = ''; +- local = 1; ++ local = 1; + weights = NaN; %weight coefficients for every vertex + weights_string = ''; %string to identify this particular set of weights + cumulated = NaN; %do we cumulate misfit through time? +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21737) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21738) +@@ -786,6 +786,8 @@ + SealevelEmotionEnum, + SealevelAbsoluteEnum, + SealevelEustaticEnum, ++ SealevelObsEnum, ++ SealevelWeightsEnum, + SealevelriseDeltathicknessEnum, + SealevelriseMaxiterEnum, + SealevelriseReltolEnum, +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21737) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21738) +@@ -766,6 +766,8 @@ + case SealevelEmotionEnum : return "SealevelEmotion"; + case SealevelAbsoluteEnum : return "SealevelAbsolute"; + case SealevelEustaticEnum : return "SealevelEustatic"; ++ case SealevelObsEnum : return "SealevelObs"; ++ case SealevelWeightsEnum : return "SealevelWeights"; + case SealevelriseDeltathicknessEnum : return "SealevelriseDeltathickness"; + case SealevelriseMaxiterEnum : return "SealevelriseMaxiter"; + case SealevelriseReltolEnum : return "SealevelriseReltol"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21737) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21738) +@@ -784,6 +784,8 @@ + else if (strcmp(name,"SealevelEmotion")==0) return SealevelEmotionEnum; + else if (strcmp(name,"SealevelAbsolute")==0) return SealevelAbsoluteEnum; + else if (strcmp(name,"SealevelEustatic")==0) return SealevelEustaticEnum; ++ else if (strcmp(name,"SealevelObs")==0) return SealevelObsEnum; ++ else if (strcmp(name,"SealevelWeights")==0) return SealevelWeightsEnum; + else if (strcmp(name,"SealevelriseDeltathickness")==0) return SealevelriseDeltathicknessEnum; + else if (strcmp(name,"SealevelriseMaxiter")==0) return SealevelriseMaxiterEnum; + else if (strcmp(name,"SealevelriseReltol")==0) return SealevelriseReltolEnum; +@@ -872,12 +874,12 @@ + else if (strcmp(name,"SpcDynamic")==0) return SpcDynamicEnum; + else if (strcmp(name,"SpcStatic")==0) return SpcStaticEnum; + else if (strcmp(name,"SpcTransient")==0) return SpcTransientEnum; +- else if (strcmp(name,"StringArrayParam")==0) return StringArrayParamEnum; +- else if (strcmp(name,"StringParam")==0) return StringParamEnum; + else stage=8; + } + if(stage==8){ +- if (strcmp(name,"Seg")==0) return SegEnum; ++ if (strcmp(name,"StringArrayParam")==0) return StringArrayParamEnum; ++ else if (strcmp(name,"StringParam")==0) return StringParamEnum; ++ else if (strcmp(name,"Seg")==0) return SegEnum; + else if (strcmp(name,"SegInput")==0) return SegInputEnum; + else if (strcmp(name,"Tria")==0) return TriaEnum; + else if (strcmp(name,"TriaInput")==0) return TriaInputEnum; +@@ -995,12 +997,12 @@ + else if (strcmp(name,"P1xP3")==0) return P1xP3Enum; + else if (strcmp(name,"P2xP4")==0) return P2xP4Enum; + else if (strcmp(name,"P1P1")==0) return P1P1Enum; +- else if (strcmp(name,"P1P1GLS")==0) return P1P1GLSEnum; +- else if (strcmp(name,"MINI")==0) return MINIEnum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"MINIcondensed")==0) return MINIcondensedEnum; ++ if (strcmp(name,"P1P1GLS")==0) return P1P1GLSEnum; ++ else if (strcmp(name,"MINI")==0) return MINIEnum; ++ else if (strcmp(name,"MINIcondensed")==0) return MINIcondensedEnum; + else if (strcmp(name,"TaylorHood")==0) return TaylorHoodEnum; + else if (strcmp(name,"LATaylorHood")==0) return LATaylorHoodEnum; + else if (strcmp(name,"XTaylorHood")==0) return XTaylorHoodEnum; +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 21737) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 21738) +@@ -95,7 +95,7 @@ + for(j=0;jAddObject(new Misfit(misfit_name_s[j],StringToEnumx(misfit_definitionstring_s[j]),StringToEnumx(misfit_model_string_s[j]),StringToEnumx(misfit_observation_string_s[j]),misfit_timeinterpolation_s[j],(bool)misfit_local_s[j],StringToEnumx(misfit_weights_string_s[j]))); ++ output_definitions->AddObject(new Misfit(misfit_name_s[j],StringToEnumx(misfit_definitionstring_s[j]),StringToEnumx(misfit_model_string_s[j]),StringToEnumx(misfit_observation_string_s[j]),misfit_timeinterpolation_s[j],misfit_local_s[j],StringToEnumx(misfit_weights_string_s[j]))); + + /*Now, for this particular misfit object, make sure we plug into the elements: the observation, and the weights.*/ + for(int k=0;kSize();k++){ +Index: ../trunk-jpl/src/c/classes/Misfit.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Misfit.h (revision 21737) ++++ ../trunk-jpl/src/c/classes/Misfit.h (revision 21738) +@@ -18,13 +18,15 @@ + #include "../classes/gauss/Gauss.h" + /*}}}*/ + IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); ++void GetVectorFromInputsx( IssmDouble** pvector,FemModel* femmodel,int name,int type); + ++ + class Misfit: public Object, public Definition{ + + public: + + int definitionenum; +- bool local; ++ int local; + int model_enum; + char* name; + int observation_enum; +@@ -43,13 +45,13 @@ + this->observation_enum = UNDEF; + this->weights_enum = UNDEF; + this->timeinterpolation=NULL; +- this->local=true; ++ this->local=1; + this->misfit=0; + this->lock=0; + + } + /*}}}*/ +- Misfit(char* in_name, int in_definitionenum, int in_model_enum, int in_observation_enum, char* in_timeinterpolation, bool in_local, int in_weights_enum){/*{{{*/ ++ Misfit(char* in_name, int in_definitionenum, int in_model_enum, int in_observation_enum, char* in_timeinterpolation, int in_local, int in_weights_enum){/*{{{*/ + + this->definitionenum=in_definitionenum; + +@@ -132,7 +134,7 @@ + femmodel->parameters->FindParam(&time,TimeEnum); + femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + +- if (this->local){ /*local computation: {{{*/ ++ if (this->local==1){ /*area integration using elements: {{{*/ + + int i; + IssmDouble misfit_t=0.; +@@ -167,6 +169,72 @@ + /*What we return is the value of misfit / time: */ + return misfit/(time-starttime); + } /*}}}*/ ++ else if (this->local==2){ /*vertex by vertex computation: {{{*/ ++ ++ IssmDouble* model = NULL; ++ IssmDouble* observation= NULL; ++ IssmDouble* weights= NULL; ++ ++ /*Are we transient?:*/ ++ if (time==0){ ++ IssmDouble misfit_t=0.; ++ ++ /*get global vectors: */ ++ GetVectorFromInputsx(&model,femmodel,model_enum,VertexSIdEnum); ++ GetVectorFromInputsx(&observation,femmodel,observation_enum,VertexSIdEnum); ++ GetVectorFromInputsx(&weights,femmodel,weights_enum,VertexSIdEnum); ++ ++ int count=0; ++ for (int i=0;ivertices->NumberOfVertices();i++){ ++ misfit_t += pow(model[i]-observation[i],2)*weights[i]; ++ if (weights[i]!=0)count++; ++ } ++ misfit=sqrt(misfit_t)/count; ++ ++ /*Free ressources:*/ ++ xDelete(model); ++ xDelete(observation); ++ xDelete(weights); ++ ++ /*return value: */ ++ return misfit; ++ } ++ else{ ++ ++ IssmDouble misfit_t=0.; ++ IssmDouble all_misfit_t=0.; ++ ++ /*If we are locked, return time average: */ ++ if(this->lock)return misfit/(time-starttime); ++ ++ /*get global vectors: */ ++ GetVectorFromInputsx(&model,femmodel,model_enum,VertexSIdEnum); ++ GetVectorFromInputsx(&observation,femmodel,observation_enum,VertexSIdEnum); ++ GetVectorFromInputsx(&weights,femmodel,weights_enum,VertexSIdEnum); ++ ++ int count=0; ++ for (int i=0;ivertices->NumberOfVertices();i++){ ++ misfit_t += pow(model[i]-observation[i],2)*weights[i]; ++ if (weights[i]!=0)count++; ++ } ++ ++ /*Add this time's contribution to curent misfit: */ ++ misfit=sqrt(misfit_t)/count; ++ misfit+=dt*misfit_t; ++ ++ /*Do we lock? i.e. are we at final_time? :*/ ++ if(time==finaltime)this->lock=1; ++ ++ /*Free ressources:*/ ++ xDelete(model); ++ xDelete(observation); ++ xDelete(weights); ++ ++ /*What we return is the value of misfit / time: */ ++ return misfit/(time-starttime); ++ } ++ ++ } /*}}}*/ + else{ /*global computation: {{{ */ + + IssmDouble model, observation; Index: /issm/oecreview/Archive/21724-22754/ISSM-21738-21739.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21738-21739.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21738-21739.diff (revision 22755) @@ -0,0 +1,335 @@ +Index: ../trunk-jpl/src/m/classes/frictionhydro.py +=================================================================== +--- ../trunk-jpl/src/m/classes/frictionhydro.py (nonexistent) ++++ ../trunk-jpl/src/m/classes/frictionhydro.py (revision 21739) +@@ -0,0 +1,93 @@ ++import numpy as np ++from project3d import project3d ++from fielddisplay import fielddisplay ++from checkfield import checkfield ++from WriteData import WriteData ++ ++ ++class frictionhydro(object): ++ """ ++ FRICTIONWEERTMAN class definition ++ ++ Usage: ++ friction=frictionhydro(); ++ """ ++ def __init__(self): # {{{ ++ self.coupling = 0 ++ self.q = float('NaN') ++ self.C = float('NaN') ++ self.As = float('NaN') ++ self.effective_pressure = float('NaN') ++ #set defaults ++ self.setdefaultparameters() ++ #}}} ++ ++ #what is this: ++ #function self = frictionhydro(varargin) % {{{ ++ # switch nargin ++ # case 0 ++ # self=setdefaultparameters(self); ++ # otherwise ++ # error('constructor not supported'); ++ # end ++ #end % }}} ++ ++ def checkconsistency(self,md,solution,analyses): #{{{ ++ ++ #Early return ++ if 'StressbalanceAnalysis' in analyses and 'ThermalAnalysis' in analyses: ++ return md ++ ++ md = checkfield(md,'fieldname','friction.coupling','numel',[1],'values',[0,1,2]) ++ md = checkfield(md,'fieldname','friction.q','NaN',1,'Inf',1,'size',[md.mesh.numberofelements,1]) ++ md = checkfield(md,'fieldname','friction.C','NaN',1,'Inf',1,'size',[md.mesh.numberofelements,1]) ++ md = checkfield(md,'fieldname','friction.As','NaN',1,'Inf',1,'size',[md.mesh.numberofelements,1]) ++ if self.coupling==1: ++ md = checkfield(md,'fieldname','friction.effective_pressure','NaN',1,'Inf',1,'timeseries',1) ++ elif self.coupling==2: ++ raise ValueError('coupling not supported yet') ++ elif self.coupling > 2: ++ raise ValueError('md.friction.coupling larger than 2, not supported yet') ++ # }}} ++ ++ def extrude(self,md): # {{{ ++ self.q=project3d(md,'vector',self.q,'type','element') ++ self.C=project3d(md,'vector',self.C,'type','element') ++ self.As=project3d(md,'vector',self.As,'type','element') ++ if self.coupling==1: ++ self.effective_pressure=project3d(md,'vector',self.effective_pressure,'type','node','layer',1) ++ elif self.coupling==2: ++ raise ValueError('coupling not supported yet') ++ elif self.coupling > 2: ++ raise ValueError('md.friction.coupling larger than 2, not supported yet') ++ return self ++ # }}} ++ ++ ++ def __repr__(self): # {{{ ++ string='Effective Pressure based friction law described in Gagliardini 2007' ++ string="%s\n%s"%(string,fielddisplay(self,'coupling','Coupling flag: 0 for default, 1 for forcing(provide md.friction.effective_pressure) and 2 for coupled(not implemented yet)')) ++ string="%s\n%s"%(string,fielddisplay(self,'q','friction law exponent q>=1')) ++ string="%s\n%s"%(string,fielddisplay(self,'C','friction law max value [SI]')) ++ string="%s\n%s"%(string,fielddisplay(self,'As','Sliding Parameter without cavitation [m Pa^-n s^-1]')) ++ string="%s\n%s"%(string,fielddisplay(self,'effective_pressure','Effective Pressure for the forcing if not coupled [Pa]')) ++ ++ return string ++ #}}} ++ ++ ++ def marshall(self,prefix,md,fid): #{{{ ++ WriteData(fid,prefix,'name','md.friction.law','data',3,'format','Integer') ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','coupling','format','Integer') ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','q','format','DoubleMat','mattype',2) ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','C','format','DoubleMat','mattype',2) ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','As','format','DoubleMat','mattype',2) ++ if self.coupling==1: ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','effective_pressure','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) ++ elif self.coupling==2: ++ raise ValueError('coupling not supported yet') ++ elif self.coupling > 2: ++ raise ValueError('md.friction.coupling larger than 2, not supported yet') ++ #}}} ++ ++ +Index: ../trunk-jpl/src/m/classes/friction.py +=================================================================== +--- ../trunk-jpl/src/m/classes/friction.py (revision 21738) ++++ ../trunk-jpl/src/m/classes/friction.py (revision 21739) +@@ -1,3 +1,4 @@ ++import numpy as np + from fielddisplay import fielddisplay + from project3d import project3d + from checkfield import checkfield +@@ -15,17 +16,20 @@ + self.coefficient = float('NaN') + self.p = float('NaN') + self.q = float('NaN') +- ++ self.coupling = 0 ++ self.effective_pressure = float('NaN') + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(self): # {{{ +- string="Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s-1) * u_b,\n(effective stress Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p)" ++ string="Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s-1) * u_b,\n(effective stress Neff=rho_ice*g*thickness+rho_water*g*base, r=q/p and s=1/p)" + + string="%s\n%s"%(string,fielddisplay(self,"coefficient","friction coefficient [SI]")) + string="%s\n%s"%(string,fielddisplay(self,"p","p exponent")) + string="%s\n%s"%(string,fielddisplay(self,"q","q exponent")) ++ string="%s\n%s"%(string,fielddisplay(self,'coupling','Coupling flag: 0 for default, 1 for forcing(provide md.friction.effective_pressure) and 2 for coupled(not implemented yet)')) ++ string="%s\n%s"%(string,fielddisplay(self,'effective_pressure','Effective Pressure for the forcing if not coupled [Pa]')) + return string + #}}} + def extrude(self,md): # {{{ +@@ -32,6 +36,13 @@ + self.coefficient=project3d(md,'vector',self.coefficient,'type','node','layer',1) + self.p=project3d(md,'vector',self.p,'type','element') + self.q=project3d(md,'vector',self.q,'type','element') ++ #if self.coupling==0: #doesnt work with empty loop, so just skip it? ++ if self.coupling==1: ++ self.effective_pressure=project3d(md,'vector',self.effective_pressure,'type','node','layer',1) ++ elif self.coupling==2: ++ raise ValueError('coupling not supported yet') ++ elif self.coupling > 2: ++ raise ValueError('md.friction.coupling larger than 2, not supported yet') + return self + #}}} + def setdefaultparameters(self): # {{{ +@@ -46,7 +57,13 @@ + md = checkfield(md,'fieldname','friction.coefficient','timeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','friction.q','NaN',1,'Inf',1,'size',[md.mesh.numberofelements]) + md = checkfield(md,'fieldname','friction.p','NaN',1,'Inf',1,'size',[md.mesh.numberofelements]) +- ++ md = checkfield(md,'fieldname','friction.coupling','numel',[1],'values',[0,1,2]) ++ if self.coupling==1: ++ md = checkfield(md,'fieldname','friction.effective_pressure','NaN',1,'Inf',1,'timeseries',1) ++ elif self.coupling==2: ++ raise ValueError('coupling not supported yet') ++ elif self.coupling > 2: ++ raise ValueError('md.friction.coupling larger than 2, not supported yet') + return md + # }}} + def marshall(self,prefix,md,fid): # {{{ +@@ -54,4 +71,11 @@ + WriteData(fid,prefix,'object',self,'fieldname','coefficient','format','DoubleMat','mattype',1) + WriteData(fid,prefix,'object',self,'fieldname','p','format','DoubleMat','mattype',2) + WriteData(fid,prefix,'object',self,'fieldname','q','format','DoubleMat','mattype',2) ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','coupling','format','Integer') ++ if self.coupling==1: ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','effective_pressure','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) ++ elif self.coupling==2: ++ raise ValueError('coupling not supported yet') ++ elif self.coupling > 2: ++ raise ValueError('md.friction.coupling larger than 2, not supported yet') + # }}} +Index: ../trunk-jpl/src/m/classes/frictionhydro.m +=================================================================== +--- ../trunk-jpl/src/m/classes/frictionhydro.m (revision 21738) ++++ ../trunk-jpl/src/m/classes/frictionhydro.m (revision 21739) +@@ -5,7 +5,7 @@ + + classdef frictionhydro + properties (SetAccess=public) +- Coupling = 0; ++ coupling = 0; + q = NaN; + C = NaN; + As = NaN; +@@ -27,12 +27,19 @@ + + %Early return + if ~ismember('StressbalanceAnalysis',analyses) & ~ismember('ThermalAnalysis',analyses), return; end +- md = checkfield(md,'fieldname','friction.Coupling','numel',[1],'values',[0 1]); ++ md = checkfield(md,'fieldname','friction.coupling','numel',[1],'values',[0 1 2]); + md = checkfield(md,'fieldname','friction.q','NaN',1,'Inf',1,'size',[md.mesh.numberofelements 1]); + md = checkfield(md,'fieldname','friction.C','NaN',1,'Inf',1,'size',[md.mesh.numberofelements 1]); + md = checkfield(md,'fieldname','friction.As','NaN',1,'Inf',1,'size',[md.mesh.numberofelements 1]); +- if self.Coupling==0, +- md = checkfield(md,'fieldname','friction.effective_pressure','NaN',1,'Inf',1,'timeseries',1); ++ switch self.coupling ++ case 0 ++ case 1 ++ md = checkfield(md,'fieldname','friction.effective_pressure','NaN',1,'Inf',1,'timeseries',1); ++ case 2 ++ error('not implemented yet'); ++ otherwise ++ error('not supported yet'); ++ end + end + end % }}} + function self = extrude(self,md) % {{{ +@@ -39,13 +46,19 @@ + self.q=project3d(md,'vector',self.q,'type','element'); + self.C=project3d(md,'vector',self.C,'type','element'); + self.As=project3d(md,'vector',self.As,'type','element'); +- if self.Coupling==0, +- self.effective_pressure=project3d(md,'vector',self.effective_pressure,'type','node','layer',1); ++ switch self.coupling ++ case 0 ++ case 1 ++ self.effective_pressure=project3d(md,'vector',self.effective_pressure,'type','node','layer',1); ++ case 2 ++ error('not implemented yet'); ++ otherwise ++ error('not supported yet'); + end + end % }}} + function disp(self) % {{{ + disp(sprintf('Effective Pressure based friction law described in Gagliardini 2007')); +- fielddisplay(self,'Coupling','Coupling flag, 1 for coupling and 0 for forcing'); ++ fielddisplay(self,'coupling','Coupling flag: 0 for default, 1 for forcing(provide md.friction.effective_pressure) and 2 for coupled(not implemented yet)'); + fielddisplay(self,'q','friction law exponent q>=1'); + fielddisplay(self,'C','friction law max value [SI]'); + fielddisplay(self,'As','Sliding Parameter without cavitation [m Pa^-n s^-1]'); +@@ -53,12 +66,18 @@ + end % }}} + function marshall(self,prefix,md,fid) % {{{ + WriteData(fid,prefix,'name','md.friction.law','data',3,'format','Integer'); +- WriteData(fid,prefix,'class','friction','object',self,'fieldname','Coupling','format','Integer'); ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','coupling','format','Integer'); + WriteData(fid,prefix,'class','friction','object',self,'fieldname','q','format','DoubleMat','mattype',2); + WriteData(fid,prefix,'class','friction','object',self,'fieldname','C','format','DoubleMat','mattype',2); + WriteData(fid,prefix,'class','friction','object',self,'fieldname','As','format','DoubleMat','mattype',2); +- if self.Coupling==0, +- WriteData(fid,prefix,'class','friction','object',self,'fieldname','effective_pressure','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ switch self.coupling ++ case 0 ++ case 1 ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','effective_pressure','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ case 2 ++ error('not implemented yet'); ++ otherwise ++ error('not supported yet'); + end + end % }}} + end +Index: ../trunk-jpl/src/m/classes/friction.m +=================================================================== +--- ../trunk-jpl/src/m/classes/friction.m (revision 21738) ++++ ../trunk-jpl/src/m/classes/friction.m (revision 21739) +@@ -8,6 +8,8 @@ + coefficient = NaN; + p = NaN; + q = NaN; ++ coupling = 0; %Silje ++ effective_pressure = NaN; %Silje + end + methods + function self = extrude(self,md) % {{{ +@@ -14,6 +16,15 @@ + self.coefficient=project3d(md,'vector',self.coefficient,'type','node','layer',1); + self.p=project3d(md,'vector',self.p,'type','element'); + self.q=project3d(md,'vector',self.q,'type','element'); ++ switch self.coupling ++ case 0 ++ case 1 ++ self.effective_pressure=project3d(md,'vector',self.effective_pressure,'type','node','layer',1); ++ case 2 ++ error('not implemented yet'); ++ otherwise ++ error('not supported yet'); ++ end + end % }}} + function self = friction(varargin) % {{{ + switch nargin +@@ -35,6 +46,16 @@ + md = checkfield(md,'fieldname','friction.coefficient','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','friction.q','NaN',1,'Inf',1,'size',[md.mesh.numberofelements 1]); + md = checkfield(md,'fieldname','friction.p','NaN',1,'Inf',1,'size',[md.mesh.numberofelements 1]); ++ md = checkfield(md,'fieldname','friction.coupling','numel',[1],'values',[0 1 2]);%Silje ++ switch self.coupling ++ case 0 ++ case 1 ++ md = checkfield(md,'fieldname','friction.effective_pressure','NaN',1,'Inf',1,'timeseries',1); ++ case 2 ++ error('not implemented yet'); ++ otherwise ++ error('not supported yet'); ++ end + end % }}} + function disp(self) % {{{ + disp(sprintf('Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s-1) * u_b\n(effective stress Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p)')); +@@ -41,6 +62,8 @@ + fielddisplay(self,'coefficient','friction coefficient [SI]'); + fielddisplay(self,'p','p exponent'); + fielddisplay(self,'q','q exponent'); ++ fielddisplay(self,'effective_pressure','Effective Pressure for the forcing if not coupled [Pa]');%Silje ++ fielddisplay(self,'coupling','Coupling flag: 0 for default, 1 for forcing(provide md.friction.effective_pressure) and 2 for coupled(not implemented yet)');%Silje + end % }}} + function marshall(self,prefix,md,fid) % {{{ + yts=md.constants.yts; +@@ -49,8 +72,16 @@ + WriteData(fid,prefix,'object',self,'fieldname','coefficient','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'fieldname','p','format','DoubleMat','mattype',2); + WriteData(fid,prefix,'object',self,'fieldname','q','format','DoubleMat','mattype',2); +- +- ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','coupling','format','Integer'); %Silje ++ switch self.coupling ++ case 0 ++ case 1 ++ WriteData(fid,prefix,'class','friction','object',self,'fieldname','effective_pressure','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ case 2 ++ error('not implemented yet'); ++ otherwise ++ error('not supported yet'); ++ end + end % }}} + function savemodeljs(self,fid,modelname) % {{{ + +@@ -57,6 +88,8 @@ + writejs1Darray(fid,[modelname '.friction.coefficient'],self.coefficient); + writejs1Darray(fid,[modelname '.friction.p'],self.p); + writejs1Darray(fid,[modelname '.friction.q'],self.q); ++ writejs1Darray(fid,[modelname '.friction.coupling'],self.coupling);%Silje ++ writejs1Darray(fid,[modelname '.friction.effective_pressure'],self.effective_pressure);%Silje + + end % }}} + end Index: /issm/oecreview/Archive/21724-22754/ISSM-21739-21740.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21739-21740.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21739-21740.diff (revision 22755) @@ -0,0 +1,397 @@ +Index: ../trunk-jpl/src/c/classes/Loads/Friction.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Loads/Friction.cpp (revision 21739) ++++ ../trunk-jpl/src/c/classes/Loads/Friction.cpp (revision 21740) +@@ -69,6 +69,7 @@ + IssmDouble Chi,Gamma; + IssmDouble vx,vy,vz,vmag; + IssmDouble alpha_complement; ++ IssmDouble base,sealevel,thickness; + + /*Recover parameters: */ + element->GetInputValue(&q_exp,FrictionQEnum); +@@ -76,14 +77,28 @@ + + element->GetInputValue(&As,gauss,FrictionAsEnum); + element->GetInputValue(&n,gauss,MaterialsRheologyNEnum); ++ element->GetInputValue(&thickness, gauss,ThicknessEnum); ++ element->GetInputValue(&base, gauss,BaseEnum); ++ element->GetInputValue(&sealevel, gauss,SealevelEnum); ++ ++ IssmDouble rho_water = element->GetMaterialParameter(MaterialsRhoSeawaterEnum); ++ IssmDouble rho_ice = element->GetMaterialParameter(MaterialsRhoIceEnum); ++ IssmDouble gravity = element->GetMaterialParameter(ConstantsGEnum); + element->parameters->FindParam(&CoupledFlag,FrictionCouplingEnum); + +- if (CoupledFlag==1){ +- element->GetInputValue(&Neff,gauss,EffectivePressureEnum); ++ switch(CoupledFlag){ ++ case 0: ++ Neff=gravity*(rho_ice*thickness+rho_water*(base-sealevel)); ++ break; ++ case 1: ++ element->GetInputValue(&Neff,gauss,FrictionEffectivePressureEnum); ++ break; ++ case 2: ++ element->GetInputValue(&Neff,gauss,EffectivePressureEnum); ++ break; ++ default: ++ _error_("not supported"); + } +- else{ +- element->GetInputValue(&Neff,gauss,FrictionEffectivePressureEnum); +- } + + if(Neff<0)Neff=0; + +@@ -158,17 +173,18 @@ + }/*}}}*/ + void Friction::GetAlphaViscousComplement(IssmDouble* palpha_complement, Gauss* gauss){/*{{{*/ + +- /* FrictionGetAlpha2 computes alpha2= drag^2 * Neff ^r * vel ^s, with Neff=rho_ice*g*thickness+rho_ice*g*bed, r=q/p and s=1/p. ++ /* FrictionGetAlpha2 computes alpha2= drag^2 * Neff ^r * vel ^s, with Neff=rho_ice*g*thickness+rho_ice*g*base, r=q/p and s=1/p. + * FrictionGetAlphaComplement is used in control methods on drag, and it computes: + * alpha_complement= Neff ^r * vel ^s*/ + + /*diverse: */ ++ int CoupledFlag; + IssmDouble r,s; + IssmDouble vx,vy,vz,vmag; + IssmDouble drag_p,drag_q; + IssmDouble Neff; + IssmDouble drag_coefficient; +- IssmDouble bed,thickness,sealevel; ++ IssmDouble base,thickness,sealevel; + IssmDouble alpha_complement; + + /*Recover parameters: */ +@@ -175,19 +191,31 @@ + element->GetInputValue(&drag_p,FrictionPEnum); + element->GetInputValue(&drag_q,FrictionQEnum); + element->GetInputValue(&thickness, gauss,ThicknessEnum); +- element->GetInputValue(&bed, gauss,BaseEnum); ++ element->GetInputValue(&base, gauss,BaseEnum); + element->GetInputValue(&sealevel, gauss,SealevelEnum); + element->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum); + IssmDouble rho_water = element->GetMaterialParameter(MaterialsRhoSeawaterEnum); + IssmDouble rho_ice = element->GetMaterialParameter(MaterialsRhoIceEnum); + IssmDouble gravity = element->GetMaterialParameter(ConstantsGEnum); +- ++ element->parameters->FindParam(&CoupledFlag,FrictionCouplingEnum); + //compute r and q coefficients: */ + r=drag_q/drag_p; + s=1./drag_p; + +- //From bed and thickness, compute effective pressure when drag is viscous: +- Neff=gravity*(rho_ice*thickness+rho_water*(bed-sealevel)); ++ //From base and thickness, compute effective pressure when drag is viscous, or get Neff from forcing or coupled to hydrologymodel: ++ switch(CoupledFlag){ ++ case 0: ++ Neff=gravity*(rho_ice*thickness+rho_water*(base-sealevel)); ++ break; ++ case 1: ++ element->GetInputValue(&Neff,gauss,FrictionEffectivePressureEnum); ++ break; ++ case 2: ++ element->GetInputValue(&Neff,gauss,EffectivePressureEnum); ++ break; ++ default: ++ _error_("not supported"); ++ } + if(Neff<0)Neff=0; + + //We need the velocity magnitude to evaluate the basal stress: +@@ -263,7 +291,7 @@ + IssmDouble r,s; + IssmDouble drag_p, drag_q; + IssmDouble Neff; +- IssmDouble thickness,base,bed,floatation_thickness,sealevel; ++ IssmDouble thickness,base,floatation_thickness,sealevel; + IssmDouble vx,vy,vz,vmag; + IssmDouble drag_coefficient,drag_coefficient_coulomb; + IssmDouble alpha2,alpha2_coulomb; +@@ -274,7 +302,6 @@ + element->GetInputValue(&thickness, gauss,ThicknessEnum); + element->GetInputValue(&base, gauss,BaseEnum); + element->GetInputValue(&sealevel, gauss,SealevelEnum); +- element->GetInputValue(&bed, gauss,BedEnum); + element->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum); + element->GetInputValue(&drag_coefficient_coulomb, gauss,FrictionCoefficientcoulombEnum); + IssmDouble rho_water = element->GetMaterialParameter(MaterialsRhoSeawaterEnum); +@@ -314,7 +341,7 @@ + else alpha2=drag_coefficient*drag_coefficient*pow(Neff,r)*pow(vmag,(s-1.)); + + floatation_thickness=0; +- if(bed<0) floatation_thickness=-rho_water/rho_ice*bed; ++ if(base<0) floatation_thickness=-rho_water/rho_ice*base; + if(vmag==0.) alpha2_coulomb=0.; + else alpha2_coulomb=drag_coefficient_coulomb*drag_coefficient_coulomb*rho_water*gravity*(thickness-floatation_thickness)/vmag; + +@@ -348,6 +375,7 @@ + + IssmDouble vx,vy,vz,vmag; + IssmDouble alpha2; ++ IssmDouble base,thickness,sealevel; + + /*Recover parameters: */ + element->GetInputValue(&q_exp,FrictionQEnum); +@@ -354,15 +382,28 @@ + element->GetInputValue(&C_param,FrictionCEnum); + element->GetInputValue(&As,gauss,FrictionAsEnum); + element->GetInputValue(&n,gauss,MaterialsRheologyNEnum); ++ element->GetInputValue(&thickness, gauss,ThicknessEnum); ++ element->GetInputValue(&base, gauss,BaseEnum); ++ element->GetInputValue(&sealevel, gauss,SealevelEnum); ++ IssmDouble rho_water = element->GetMaterialParameter(MaterialsRhoSeawaterEnum); ++ IssmDouble rho_ice = element->GetMaterialParameter(MaterialsRhoIceEnum); ++ IssmDouble gravity = element->GetMaterialParameter(ConstantsGEnum); ++ element->parameters->FindParam(&CoupledFlag,FrictionCouplingEnum); + +- element->parameters->FindParam(&CoupledFlag,FrictionCouplingEnum); +- if (CoupledFlag==1){ +- element->GetInputValue(&Neff,gauss,EffectivePressureEnum); ++ switch(CoupledFlag){ ++ case 0: ++ Neff=gravity*(rho_ice*thickness+rho_water*(base-sealevel)); ++ break; ++ case 1: ++ element->GetInputValue(&Neff,gauss,FrictionEffectivePressureEnum); ++ break; ++ case 2: ++ element->GetInputValue(&Neff,gauss,EffectivePressureEnum); ++ break; ++ default: ++ _error_("not supported"); + } +- else{ +- element->GetInputValue(&Neff,gauss,FrictionEffectivePressureEnum); +- } +- ++ + if(Neff<0)Neff=0; + + switch(dim){ +@@ -406,18 +447,18 @@ + }/*}}}*/ + void Friction::GetAlpha2Sommers(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + +- /* FrictionGetAlpha2 computes alpha2= drag^2 * Neff, with Neff=rho_ice*g*thickness+rho_ice*g*(head-bed)*/ ++ /* FrictionGetAlpha2 computes alpha2= drag^2 * Neff, with Neff=rho_ice*g*thickness+rho_ice*g*(head-base)*/ + + /*diverse: */ + IssmDouble pressure_ice,pressure_water; + IssmDouble Neff; + IssmDouble drag_coefficient; +- IssmDouble bed,thickness,head,sealevel; ++ IssmDouble base,thickness,head,sealevel; + IssmDouble alpha2; + + /*Recover parameters: */ + element->GetInputValue(&thickness, gauss,ThicknessEnum); +- element->GetInputValue(&bed, gauss,BaseEnum); ++ element->GetInputValue(&base, gauss,BaseEnum); + element->GetInputValue(&head, gauss,HydrologyHeadEnum); + element->GetInputValue(&sealevel, gauss,SealevelEnum); + element->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum); +@@ -425,9 +466,9 @@ + IssmDouble rho_ice = element->GetMaterialParameter(MaterialsRhoIceEnum); + IssmDouble gravity = element->GetMaterialParameter(ConstantsGEnum); + +- //From bed and thickness, compute effective pressure when drag is viscous: ++ //From base and thickness, compute effective pressure when drag is viscous: + pressure_ice = rho_ice*gravity*thickness; +- pressure_water = rho_water*gravity*(head-bed+sealevel); ++ pressure_water = rho_water*gravity*(head-base+sealevel); + Neff=pressure_ice-pressure_water; + if(Neff<0.) Neff=0.; + +@@ -510,9 +551,10 @@ + void Friction::GetAlpha2Viscous(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + + /*This routine calculates the basal friction coefficient +- alpha2= drag^2 * Neff ^r * | vel | ^(s-1), with Neff=rho_ice*g*thickness+rho_ice*g*bed, r=q/p and s=1/p**/ ++ alpha2= drag^2 * Neff ^r * | vel | ^(s-1), with Neff=rho_ice*g*thickness+rho_ice*g*base, r=q/p and s=1/p**/ + + /*diverse: */ ++ int CoupledFlag; + IssmDouble r,s; + IssmDouble drag_p, drag_q; + IssmDouble Neff; +@@ -531,13 +573,25 @@ + IssmDouble rho_water = element->GetMaterialParameter(MaterialsRhoSeawaterEnum); + IssmDouble rho_ice = element->GetMaterialParameter(MaterialsRhoIceEnum); + IssmDouble gravity = element->GetMaterialParameter(ConstantsGEnum); +- ++ element->parameters->FindParam(&CoupledFlag,FrictionCouplingEnum); + //compute r and q coefficients: */ + r=drag_q/drag_p; + s=1./drag_p; + +- //From base and thickness, compute effective pressure when drag is viscous: +- Neff=gravity*(rho_ice*thickness+rho_water*(base-sealevel)); ++ //From base and thickness, compute effective pressure when drag is viscous, or get Neff from forcing: ++ switch(CoupledFlag){ ++ case 0: ++ Neff=gravity*(rho_ice*thickness+rho_water*(base-sealevel)); ++ break; ++ case 1: ++ element->GetInputValue(&Neff,gauss,FrictionEffectivePressureEnum); ++ break; ++ case 2: ++ element->GetInputValue(&Neff,gauss,EffectivePressureEnum); ++ break; ++ default: ++ _error_("not supported"); ++ } + if(Neff<0)Neff=0; + + switch(dim){ +@@ -571,13 +625,13 @@ + void Friction::GetAlpha2WaterLayer(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + + /*This routine calculates the basal friction coefficient +- alpha2= drag^2 * Neff ^r * | vel | ^(s-1), with Neff=rho_ice*g*thickness+rho_ice*g*bed, r=q/p and s=1/p**/ ++ alpha2= drag^2 * Neff ^r * | vel | ^(s-1), with Neff=rho_ice*g*thickness+rho_ice*g*base, r=q/p and s=1/p**/ + + /*diverse: */ + IssmDouble r,s; + IssmDouble drag_p, drag_q; + IssmDouble Neff,F; +- IssmDouble thickness,bed,sealevel; ++ IssmDouble thickness,base,sealevel; + IssmDouble vx,vy,vz,vmag; + IssmDouble drag_coefficient,water_layer; + IssmDouble alpha2; +@@ -587,7 +641,7 @@ + element->GetInputValue(&drag_p,FrictionPEnum); + element->GetInputValue(&drag_q,FrictionQEnum); + element->GetInputValue(&thickness, gauss,ThicknessEnum); +- element->GetInputValue(&bed, gauss,BaseEnum); ++ element->GetInputValue(&base, gauss,BaseEnum); + element->GetInputValue(&sealevel, gauss,SealevelEnum); + element->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum); + element->GetInputValue(&water_layer, gauss,FrictionWaterLayerEnum); +@@ -599,9 +653,9 @@ + r=drag_q/drag_p; + s=1./drag_p; + +- //From bed and thickness, compute effective pressure when drag is viscous: +- if(bed>0) bed=0; +- if(water_layer==0) Neff=gravity*rho_ice*thickness+gravity*rho_water*(bed-sealevel); ++ //From base and thickness, compute effective pressure when drag is viscous: ++ if(base>0) base=0; ++ if(water_layer==0) Neff=gravity*rho_ice*thickness+gravity*rho_water*(base-sealevel); + else if(water_layer>0) Neff=gravity*rho_ice*thickness*F; + else _error_("negative water layer thickness"); + if(Neff<0) Neff=0; +Index: ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 21739) ++++ ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 21740) +@@ -780,9 +780,13 @@ + /*Friction law variables*/ + switch(frictionlaw){ + case 1: ++ iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); + iomodel->FetchDataToInput(elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(elements,"md.friction.p",FrictionPEnum); + iomodel->FetchDataToInput(elements,"md.friction.q",FrictionQEnum); ++ if(FrictionCoupling==1){ ++ iomodel->FetchDataToInput(elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum); ++ } + break; + case 2: + iomodel->FetchDataToInput(elements,"md.friction.C",FrictionCEnum); +@@ -793,7 +797,7 @@ + iomodel->FetchDataToInput(elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(elements,"md.friction.As",FrictionAsEnum); + iomodel->FetchDataToInput(elements,"md.friction.q",FrictionQEnum); +- if(FrictionCoupling==0){ ++ if(FrictionCoupling==1){ + iomodel->FetchDataToInput(elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum); + } + break; +@@ -892,7 +896,7 @@ + int frictionlaw; + iomodel->FindConstant(&frictionlaw,"md.friction.law"); + if(frictionlaw==4 || frictionlaw==6) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); +- if(frictionlaw==3) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); ++ if(frictionlaw==3 || frictionlaw==1) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + if(frictionlaw==5) parameters->AddObject(iomodel->CopyConstantObject("md.friction.f",FrictionFEnum)); + if(frictionlaw==9) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); + +Index: ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 21739) ++++ ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 21740) +@@ -156,9 +156,13 @@ + /*Friction law variables*/ + switch(frictionlaw){ + case 1: ++ iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); + iomodel->FetchDataToInput(elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(elements,"md.friction.p",FrictionPEnum); + iomodel->FetchDataToInput(elements,"md.friction.q",FrictionQEnum); ++ if (FrictionCoupling==1){ ++ iomodel->FetchDataToInput(elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum); ++ } + break; + case 2: + iomodel->FetchDataToInput(elements,"md.friction.C",FrictionCEnum); +@@ -169,8 +173,8 @@ + iomodel->FetchDataToInput(elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(elements,"md.friction.As",FrictionAsEnum); + iomodel->FetchDataToInput(elements,"md.friction.q",FrictionQEnum); +- if (FrictionCoupling==0){ +- iomodel->FetchDataToInput(elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum); ++ if (FrictionCoupling==1){ ++ iomodel->FetchDataToInput(elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum); + } + break; + case 4: +@@ -219,7 +223,8 @@ + int frictionlaw; + iomodel->FindConstant(&frictionlaw,"md.friction.law"); + if(frictionlaw==4 || frictionlaw==6) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); +- if(frictionlaw==3) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); ++ if(frictionlaw==3 || frictionlaw==1) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); ++ + }/*}}}*/ + + /*Finite Element Analysis*/ +Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21739) ++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21740) +@@ -173,9 +173,13 @@ + /*Friction law variables*/ + switch(frictionlaw){ + case 1: ++ iomodel->FindConstant(&FrictionCoupling,"md.friction.coupling"); + iomodel->FetchDataToInput(elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(elements,"md.friction.p",FrictionPEnum); + iomodel->FetchDataToInput(elements,"md.friction.q",FrictionQEnum); ++ if (FrictionCoupling==1){ ++ iomodel->FetchDataToInput(elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum); ++ } + break; + case 2: + iomodel->FetchDataToInput(elements,"md.friction.C",FrictionCEnum); +@@ -186,7 +190,7 @@ + iomodel->FetchDataToInput(elements,"md.friction.C",FrictionCEnum); + iomodel->FetchDataToInput(elements,"md.friction.As",FrictionAsEnum); + iomodel->FetchDataToInput(elements,"md.friction.q",FrictionQEnum); +- if (FrictionCoupling==0){ ++ if (FrictionCoupling==1){ + iomodel->FetchDataToInput(elements,"md.friction.effective_pressure",FrictionEffectivePressureEnum); + } + break; +@@ -244,7 +248,7 @@ + int frictionlaw; + iomodel->FindConstant(&frictionlaw,"md.friction.law"); + if(frictionlaw==4 || frictionlaw==6) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); +- if(frictionlaw==3) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); ++ if(frictionlaw==3 || frictionlaw==1) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + if(frictionlaw==9) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); + }/*}}}*/ + Index: /issm/oecreview/Archive/21724-22754/ISSM-21740-21741.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21740-21741.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21740-21741.diff (revision 22755) @@ -0,0 +1,27 @@ +Index: ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp (revision 21740) ++++ ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp (revision 21741) +@@ -89,16 +89,16 @@ + /*compute elastic green function for a range of angles*/ + iomodel->FetchData(°acc,"md.slr.degacc"); + M=reCast(180./degacc+1.); +- G_elastic=xNew(M); +- U_elastic=xNew(M); +- H_elastic=xNew(M); ++ G_elastic=xNew(M,"t"); ++ U_elastic=xNew(M,"t"); ++ H_elastic=xNew(M,"t"); + + /*compute combined legendre + love number (elastic green function:*/ + m=DetermineLocalSize(M,IssmComm::GetComm()); + GetOwnershipBoundariesFromRange(&lower_row,&upper_row,m,IssmComm::GetComm()); +- G_elastic_local=xNew(m); +- U_elastic_local=xNew(m); +- H_elastic_local=xNew(m); ++ G_elastic_local=xNew(m,"t"); ++ U_elastic_local=xNew(m,"t"); ++ H_elastic_local=xNew(m,"t"); + + for(int i=lower_row;iFetchData(°acc,"md.slr.degacc"); + M=reCast(180./degacc+1.); ++ ++ // AD performance is sensitive to calls to ensurecontiguous. ++ // // Providing "t" will cause ensurecontiguous to be called. ++ #ifdef _HAVE_AD_ + G_elastic=xNew(M,"t"); + U_elastic=xNew(M,"t"); + H_elastic=xNew(M,"t"); ++ #else ++ G_elastic=xNew(M); ++ U_elastic=xNew(M); ++ H_elastic=xNew(M); ++ #endif ++ + + /*compute combined legendre + love number (elastic green function:*/ + m=DetermineLocalSize(M,IssmComm::GetComm()); + GetOwnershipBoundariesFromRange(&lower_row,&upper_row,m,IssmComm::GetComm()); ++ // AD performance is sensitive to calls to ensurecontiguous. ++ // // Providing "t" will cause ensurecontiguous to be called. ++ #ifdef _HAVE_AD_ + G_elastic_local=xNew(m,"t"); + U_elastic_local=xNew(m,"t"); + H_elastic_local=xNew(m,"t"); ++ #else ++ G_elastic_local=xNew(m); ++ U_elastic_local=xNew(m); ++ H_elastic_local=xNew(m); ++ #endif + + for(int i=lower_row;i(string); +- char* string2 = gatedefinitionstrings[j]; xDelete(string2); +- IssmDouble* gate = gatesegments[j]; xDelete(gate); ++ char* string = gatenames[j]; xDelete(string); ++ IssmDouble* gate = gatesegments[j]; xDelete(gate); + } + xDelete(gatenames); + xDelete(gatesegments); +@@ -94,6 +93,14 @@ + + for(j=0;jnumberofvertices) || (misfit_observation_M_s[j]==iomodel->numberofvertices+1))obs_vector_type=1; ++ if ((misfit_observation_M_s[j]==iomodel->numberofelements) || (misfit_observation_M_s[j]==iomodel->numberofelements+1))obs_vector_type=2; ++ int weight_vector_type=0; ++ if ((misfit_weights_M_s[j]==iomodel->numberofvertices) || (misfit_weights_M_s[j]==iomodel->numberofvertices+1))weight_vector_type=1; ++ if ((misfit_weights_M_s[j]==iomodel->numberofelements) || (misfit_weights_M_s[j]==iomodel->numberofelements+1))weight_vector_type=2; ++ ++ + /*First create a misfit object for that specific string (misfit_model_string_s[j]):*/ + output_definitions->AddObject(new Misfit(misfit_name_s[j],StringToEnumx(misfit_definitionstring_s[j]),StringToEnumx(misfit_model_string_s[j]),StringToEnumx(misfit_observation_string_s[j]),misfit_timeinterpolation_s[j],misfit_local_s[j],StringToEnumx(misfit_weights_string_s[j]))); + +@@ -100,8 +107,8 @@ + /*Now, for this particular misfit object, make sure we plug into the elements: the observation, and the weights.*/ + for(int k=0;kSize();k++){ + Element* element=xDynamicCast(elements->GetObjectByOffset(k)); +- element->InputCreate(misfit_observation_s[j], iomodel,misfit_observation_M_s[j],misfit_observation_N_s[j],1,StringToEnumx(misfit_observation_string_s[j]),7); +- element->InputCreate(misfit_weights_s[j], iomodel,misfit_weights_M_s[j],misfit_weights_N_s[j],1,StringToEnumx(misfit_weights_string_s[j]),7); ++ element->InputCreate(misfit_observation_s[j], iomodel,misfit_observation_M_s[j],misfit_observation_N_s[j],obs_vector_type,StringToEnumx(misfit_observation_string_s[j]),7); ++ element->InputCreate(misfit_weights_s[j], iomodel,misfit_weights_M_s[j],misfit_weights_N_s[j],weight_vector_type,StringToEnumx(misfit_weights_string_s[j]),7); + } + + } +@@ -211,7 +218,7 @@ + + /*masscon variables: */ + char** masscon_name_s = NULL; +- int* masscon_definitionenum_s = NULL; ++ char** masscon_definitionstring_s = NULL; + char** masscon_namex_s = NULL; + char** masscon_namey_s = NULL; + IssmDouble* masscon_alpha_s = NULL; +@@ -220,7 +227,7 @@ + + /*Fetch names and multiplicators, etc ... (see src/m/classes/masscon_axpby.m): */ + iomodel->FetchMultipleData(&masscon_name_s,&num, "md.massconaxpby.name"); +- iomodel->FetchMultipleData(&masscon_definitionenum_s,&num,"md.massconaxpby.definitionenum"); ++ iomodel->FetchMultipleData(&masscon_definitionstring_s,&num,"md.massconaxpby.definitionstring"); + iomodel->FetchMultipleData(&masscon_namex_s,&num, "md.massconaxpby.namex"); + iomodel->FetchMultipleData(&masscon_namey_s,&num, "md.massconaxpby.namey"); + iomodel->FetchMultipleData(&masscon_alpha_s,&num, "md.massconaxpby.alpha"); +@@ -228,7 +235,7 @@ + for(j=0;jAddObject(new Massconaxpby(masscon_name_s[j],masscon_definitionenum_s[j],masscon_namex_s[j],masscon_namey_s[j],masscon_alpha_s[j],masscon_beta_s[j])); ++ output_definitions->AddObject(new Massconaxpby(masscon_name_s[j],StringToEnumx(masscon_definitionstring_s[j]),masscon_namex_s[j],masscon_namey_s[j],masscon_alpha_s[j],masscon_beta_s[j])); + + } + +@@ -235,14 +242,15 @@ + /*Free ressources:*/ + for(j=0;j(string); + string = masscon_name_s[j]; xDelete(string); + string = masscon_namex_s[j]; xDelete(string); + string = masscon_namey_s[j]; xDelete(string); + } ++ xDelete(masscon_definitionstring_s); + xDelete(masscon_name_s); + xDelete(masscon_namex_s); + xDelete(masscon_namey_s); +- xDelete(masscon_definitionenum_s); + xDelete(masscon_alpha_s); + xDelete(masscon_beta_s); + /*}}}*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21744-21745.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21744-21745.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21744-21745.diff (revision 22755) @@ -0,0 +1,33 @@ +Index: ../trunk-jpl/src/m/classes/massconaxpby.m +=================================================================== +--- ../trunk-jpl/src/m/classes/massconaxpby.m (revision 21744) ++++ ../trunk-jpl/src/m/classes/massconaxpby.m (revision 21745) +@@ -2,7 +2,7 @@ + % + % Usage: + % massconaxpby=massconaxpby(); +-% massconsumaxpby=massconaxpby('name','MassCon58+35','namex','MassCon58','alpha',.5,'namey','MassCon35','beta',.5); ++% massconaxpby=massconaxpby('name','MassCon58+35','namex','MassCon58','alpha',.5,'namey','MassCon35','beta',.5); + % + % where name is the name of the massconaxpby object, namex is the name of the first masscon, namey the name of the second masscon and alpha,beta the + % multiplicators. The meaning of axpby here is: resulting masscon is the linear combination (alpha *x + beta * y) +@@ -76,13 +76,12 @@ + end % }}} + function md = marshall(self,prefix,md,fid) % {{{ + +- WriteData(fid,prefix,'object',self,'fieldname','name','format','String'); +- WriteData(fid,prefix,'object',self,'fieldname','definitionstring','format','Integer'); +- WriteData(fid,prefix,'object',self,'fieldname','namex','format','String'); +- WriteData(fid,prefix,'object',self,'fieldname','namey','format','String'); +- WriteData(fid,prefix,'object',self,'fieldname','alpha','format','Double'); +- WriteData(fid,prefix,'object',self,'fieldname','beta','format','Double'); +- ++ WriteData(fid,prefix,'data',self.name,'name','md.massconaxpby.name','format','String'); ++ WriteData(fid,prefix,'data',self.definitionstring,'name','md.massconaxpby.definitionstring','format','String'); ++ WriteData(fid,prefix,'data',self.namex,'name','md.massconaxpby.namex','format','String'); ++ WriteData(fid,prefix,'data',self.namey,'name','md.massconaxpby.namey','format','String'); ++ WriteData(fid,prefix,'data',self.alpha,'name','md.massconaxpby.alpha','format','Double'); ++ WriteData(fid,prefix,'data',self.beta,'name','md.massconaxpby.beta','format','Double'); + end % }}} + end + end Index: /issm/oecreview/Archive/21724-22754/ISSM-21745-21746.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21745-21746.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21745-21746.diff (revision 22755) @@ -0,0 +1,42 @@ +Index: ../trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp (revision 21745) ++++ ../trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp (revision 21746) +@@ -53,3 +53,26 @@ + /*Assign output pointers:*/ + *pvector=vector; + } ++ ++void GetVectorFromInputsx(IssmDouble** pvector,int* pvector_size, FemModel* femmodel,int name){ ++ ++ int interpolation_type; ++ /*this one is special: we don't specify the type, but let the nature of the inputs dictace. ++ * P0 -> ElementSIdEnum, P1 ->VertexSIdEnum: */ ++ ++ /*We go find the input of the first element, and query its interpolation type: */ ++ Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(0)); ++ Input* input=element->GetInput(name); ++ if (!input) _error_("could not find input: " << name); ++ ++ interpolation_type=input->GetInputInterpolationType(); ++ if(interpolation_type==P0Enum){ ++ *pvector_size=femmodel->elements->NumberOfElements(); ++ GetVectorFromInputsx(pvector,femmodel,name, ElementSIdEnum); ++ } ++ else if(interpolation_type==P1Enum){ ++ *pvector_size=femmodel->vertices->NumberOfVertices(); ++ GetVectorFromInputsx(pvector,femmodel,name, VertexSIdEnum); ++ } ++ else _error_("interpolation type : " << interpolation_type << " not supported yet!"); ++} +Index: ../trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h (revision 21745) ++++ ../trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h (revision 21746) +@@ -9,5 +9,6 @@ + /* local prototypes: */ + void GetVectorFromInputsx( Vector** pvector,FemModel* femmodel,int name,int type); + void GetVectorFromInputsx( IssmDouble** pvector,FemModel* femmodel,int name,int type); ++void GetVectorFromInputsx(IssmDouble** pvector,int* pvector_size, FemModel* femmodel,int name); + + #endif /* _GETVECTORFROMINPUTSXX_H */ Index: /issm/oecreview/Archive/21724-22754/ISSM-21746-21747.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21746-21747.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21746-21747.diff (revision 22755) @@ -0,0 +1,67 @@ +Index: ../trunk-jpl/src/c/classes/Misfit.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Misfit.h (revision 21746) ++++ ../trunk-jpl/src/c/classes/Misfit.h (revision 21747) +@@ -18,9 +18,8 @@ + #include "../classes/gauss/Gauss.h" + /*}}}*/ + IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); +-void GetVectorFromInputsx( IssmDouble** pvector,FemModel* femmodel,int name,int type); ++void GetVectorFromInputsx( IssmDouble** pvector, int* pvector_size, FemModel* femmodel,int name); + +- + class Misfit: public Object, public Definition{ + + public: +@@ -174,6 +173,7 @@ + IssmDouble* model = NULL; + IssmDouble* observation= NULL; + IssmDouble* weights= NULL; ++ int msize,osize,wsize; + + /*Are we transient?:*/ + if (time==0){ +@@ -180,16 +180,16 @@ + IssmDouble misfit_t=0.; + + /*get global vectors: */ +- GetVectorFromInputsx(&model,femmodel,model_enum,VertexSIdEnum); +- GetVectorFromInputsx(&observation,femmodel,observation_enum,VertexSIdEnum); +- GetVectorFromInputsx(&weights,femmodel,weights_enum,VertexSIdEnum); ++ GetVectorFromInputsx(&model,&msize,femmodel,model_enum); ++ GetVectorFromInputsx(&observation,&osize,femmodel,observation_enum);_assert_(msize==osize); ++ GetVectorFromInputsx(&weights,&wsize,femmodel,weights_enum); _assert_(wsize==msize); + + int count=0; +- for (int i=0;ivertices->NumberOfVertices();i++){ ++ for (int i=0;i(model); +@@ -208,15 +208,16 @@ + if(this->lock)return misfit/(time-starttime); + + /*get global vectors: */ +- GetVectorFromInputsx(&model,femmodel,model_enum,VertexSIdEnum); +- GetVectorFromInputsx(&observation,femmodel,observation_enum,VertexSIdEnum); +- GetVectorFromInputsx(&weights,femmodel,weights_enum,VertexSIdEnum); +- ++ GetVectorFromInputsx(&model,&msize,femmodel,model_enum); ++ GetVectorFromInputsx(&observation,&osize,femmodel,observation_enum);_assert_(msize==osize); ++ GetVectorFromInputsx(&weights,&wsize,femmodel,weights_enum); _assert_(wsize==msize); ++ + int count=0; +- for (int i=0;ivertices->NumberOfVertices();i++){ ++ for (int i=0;i* vector,int* doflist){_error_("not implemented yet");}; ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + IssmDouble InfinityNorm(void){_error_("not implemented yet");}; + IssmDouble Max(void){_error_("not implemented yet");}; + IssmDouble MaxAbs(void){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Inputs/DoubleInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/DoubleInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/DoubleInput.h (revision 21748) +@@ -62,6 +62,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,IssmDouble time){_error_("not implemented yet");}; + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index){_error_("not implemented yet");}; + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime){_error_("not implemented yet");}; ++ int GetInputInterpolationType(){return P0Enum; }; + void GetVectorFromInputs(Vector* vector,int* doflist); + IssmDouble InfinityNorm(void){_error_("not implemented yet");}; + IssmDouble Max(void); +Index: ../trunk-jpl/src/c/classes/Inputs/SegInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/SegInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/SegInput.h (revision 21748) +@@ -65,6 +65,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index){_error_("not implemented yet");}; + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime){_error_("not implemented yet");}; + void GetVectorFromInputs(Vector* vector,int* doflist){_error_("not implemented yet");}; ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + IssmDouble InfinityNorm(void){_error_("not implemented yet");}; + IssmDouble Max(void){_error_("not implemented yet");}; + IssmDouble MaxAbs(void){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Inputs/TetraInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TetraInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/TetraInput.h (revision 21748) +@@ -65,6 +65,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,int index){_error_("not implemented yet");}; + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime); + void GetVectorFromInputs(Vector* vector,int* doflist); ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + IssmDouble InfinityNorm(void); + IssmDouble Max(void); + IssmDouble MaxAbs(void); +Index: ../trunk-jpl/src/c/classes/Inputs/Input.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/Input.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/Input.h (revision 21748) +@@ -36,6 +36,7 @@ + virtual void GetInputValue(IssmDouble* pvalue,Gauss* gauss)=0; + virtual void GetInputValue(IssmDouble* pvalue,Gauss* gauss,IssmDouble time)=0; + virtual void GetInputValue(IssmDouble* pvalue,Gauss* gauss,int index)=0; ++ virtual int GetInputInterpolationType()=0; + virtual void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime)=0; + virtual int InstanceEnum()=0; + +Index: ../trunk-jpl/src/c/classes/Inputs/ControlInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/ControlInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/ControlInput.h (revision 21748) +@@ -66,6 +66,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss); + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,IssmDouble time){_error_("not implemented yet");}; + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index){_error_("not implemented yet");}; ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + int GetResultArraySize(void){return 1;}; + int GetResultInterpolation(void); + int GetResultNumberOfNodes(void); +Index: ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h (revision 21748) +@@ -63,6 +63,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,IssmDouble time){_error_("not implemented yet");}; + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index); + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime){_error_("not implemented yet");}; ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + int GetResultArraySize(void){_error_("not implemented yet");}; + int GetResultInterpolation(void){_error_("not implemented yet");}; + int GetResultNumberOfNodes(void){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Inputs/IntInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/IntInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/IntInput.h (revision 21748) +@@ -63,6 +63,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,IssmDouble time){_error_("not implemented yet");}; + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index){_error_("not implemented yet");}; + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime){_error_("not implemented yet");}; ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + void GetVectorFromInputs(Vector* vector,int* doflist); + IssmDouble InfinityNorm(void){_error_("InfinityNorm not implemented for integers");}; + IssmDouble Max(void){_error_("Max not implemented for integers");}; +Index: ../trunk-jpl/src/c/classes/Inputs/BoolInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/BoolInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/BoolInput.h (revision 21748) +@@ -60,6 +60,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,IssmDouble time){_error_("not implemented yet");}; + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index){_error_("not implemented yet");}; + void GetVectorFromInputs(Vector* vector,int* doflist); ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + IssmDouble InfinityNorm(void){_error_("InfinityNorm not implemented for booleans");}; + IssmDouble Max(void){_error_("Max not implemented for booleans");}; + IssmDouble MaxAbs(void){_error_("Max not implemented for booleans");}; +Index: ../trunk-jpl/src/c/classes/Inputs/TriaInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TriaInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/TriaInput.h (revision 21748) +@@ -64,6 +64,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,IssmDouble time){_error_("not implemented yet");}; + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,int index){_error_("not implemented yet");}; + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime); ++ int GetInputInterpolationType(){return interpolation_type;}; + void GetVectorFromInputs(Vector* vector,int* doflist); + IssmDouble InfinityNorm(void); + IssmDouble Max(void); +Index: ../trunk-jpl/src/c/classes/Inputs/PentaInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/PentaInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/PentaInput.h (revision 21748) +@@ -62,6 +62,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index){_error_("not implemented yet");}; + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime){_error_("not implemented yet");}; + void GetVectorFromInputs(Vector* vector,int* doflist); ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + IssmDouble InfinityNorm(void); + IssmDouble Max(void); + IssmDouble MaxAbs(void); +Index: ../trunk-jpl/src/c/classes/Inputs/TransientInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TransientInput.h (revision 21747) ++++ ../trunk-jpl/src/c/classes/Inputs/TransientInput.h (revision 21748) +@@ -68,6 +68,7 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss,IssmDouble time); + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index){_error_("not implemented yet");}; + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime); ++ int GetInputInterpolationType(){_error_("not implemented yet!");}; + Input* GetTimeInput(IssmDouble time); + void GetTimeValues(IssmDouble* values,IssmDouble time){_error_("not implemented yet");}; + void GetVectorFromInputs(Vector* vector,int* doflist); Index: /issm/oecreview/Archive/21724-22754/ISSM-21748-21749.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21748-21749.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21748-21749.diff (revision 22755) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21748) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21749) +@@ -240,6 +240,9 @@ + ParseToolkitsOptionsx(parameters,toolkitsoptionsfid); + + #ifdef _HAVE_ADOLC_ ++ if(VerboseMProcessor()) _printf0_(" starting autodiff parameters \n"); + CreateParametersAutodiff(parameters,iomodel); ++ if(VerboseMProcessor()) _printf0_(" ending autodiff parameters \n"); ++ + #endif + } Index: /issm/oecreview/Archive/21724-22754/ISSM-21749-21750.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21749-21750.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21749-21750.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 21749) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 21750) +@@ -1171,7 +1171,7 @@ + xDelete(rawmatrix); + + /*read time now*/ +- IssmPDouble* timematrix=xNew(N); ++ IssmPDouble* timematrix=xNew(N); + if(my_rank==0) if(fread(timematrix,N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read time in compressed matrix"); + ISSM_MPI_Bcast(timematrix,N,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + Index: /issm/oecreview/Archive/21724-22754/ISSM-21750-21751.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21750-21751.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21750-21751.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/configure.ac +=================================================================== +--- ../trunk-jpl/configure.ac (revision 21750) ++++ ../trunk-jpl/configure.ac (revision 21751) +@@ -19,6 +19,7 @@ + AC_PROG_CPP + AC_PROG_CXX([icpc cl icl g++]) + AC_PROG_F77([ifort g77 gfortran]) ++AC_PROG_FC([gfortran]) + + #AUTOMAKE + #Initialize automake and declare foreign so that we don't need a ChangeLog, INSTALL, etc Index: /issm/oecreview/Archive/21724-22754/ISSM-21751-21752.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21751-21752.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21751-21752.diff (revision 22755) @@ -0,0 +1,206 @@ +Index: ../trunk-jpl/src/m/classes/slr.m +=================================================================== +--- ../trunk-jpl/src/m/classes/slr.m (revision 21751) ++++ ../trunk-jpl/src/m/classes/slr.m (revision 21752) +@@ -23,6 +23,7 @@ + elastic = 0; + rotation = 0; + ocean_area_scaling = 0; ++ steric_rate = 0; %rate of ocean expansion from steric effects. + degacc = 0; + requested_outputs = {}; + transitions = {}; +@@ -67,7 +68,11 @@ + + %numerical discretization accuracy + self.degacc=.01; +- ++ ++ %steric: ++ self.steric_rate=0; ++ ++ + %output default: + self.requested_outputs={'default'}; + +@@ -92,6 +97,7 @@ + md = checkfield(md,'fieldname','slr.reltol','size',[1 1]); + md = checkfield(md,'fieldname','slr.abstol','size',[1 1]); + md = checkfield(md,'fieldname','slr.maxiter','size',[1 1],'>=',1); ++ md = checkfield(md,'fieldname','slr.steric_rate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); + md = checkfield(md,'fieldname','slr.degacc','size',[1 1],'>=',1e-10); + md = checkfield(md,'fieldname','slr.requested_outputs','stringrow',1); + +@@ -133,6 +139,7 @@ + fielddisplay(self,'elastic','elastic earth graviational potential perturbation'); + fielddisplay(self,'rotation','earth rotational potential perturbation'); + fielddisplay(self,'ocean_area_scaling','correction for model representation of ocean area [default: No correction]'); ++ fielddisplay(self,'steric_rate','rate of steric ocean expansion (in mm/yr)'); + fielddisplay(self,'degacc','accuracy (default .01 deg) for numerical discretization of the Green''s functions'); + fielddisplay(self,'transitions','indices into parts of the mesh that will be icecaps'); + fielddisplay(self,'requested_outputs','additional outputs requested'); +@@ -158,6 +165,7 @@ + WriteData(fid,prefix,'object',self,'fieldname','elastic','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','rotation','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','ocean_area_scaling','format','Boolean'); ++ WriteData(fid,prefix,'object',self,'fieldname','steric_rate','format','DoubleMat','mattype',1,'scale',1e-3/md.constants.yts); + WriteData(fid,prefix,'object',self,'fieldname','degacc','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','transitions','format','MatArray'); + +@@ -191,6 +199,7 @@ + writejsdouble(fid,[modelname '.slr.elastic'],self.elastic); + writejsdouble(fid,[modelname '.slr.rotation'],self.rotation); + writejsdouble(fid,[modelname '.slr.ocean_area_scaling'],self.ocean_area_scaling); ++ writejs1Darray(fid,[modelname '.slr.steric_rate'],self.steric_rate); + writejsdouble(fid,[modelname '.slr.degacc'],self.degacc); + writejscellstring(fid,[modelname '.slr.requested_outputs'],self.requested_outputs); + writejscellarray(fid,[modelname '.slr.transitions'],self.transitions); +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21751) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21752) +@@ -802,6 +802,7 @@ + SealevelrisePolarMoiEnum, + SealevelriseAngularVelocityEnum, + SealevelriseOceanAreaScalingEnum, ++ SealevelriseStericRateEnum, + SealevelriseGElasticEnum, + SealevelriseUElasticEnum, + SealevelriseHElasticEnum, +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21751) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21752) +@@ -782,6 +782,7 @@ + case SealevelrisePolarMoiEnum : return "SealevelrisePolarMoi"; + case SealevelriseAngularVelocityEnum : return "SealevelriseAngularVelocity"; + case SealevelriseOceanAreaScalingEnum : return "SealevelriseOceanAreaScaling"; ++ case SealevelriseStericRateEnum : return "SealevelriseStericRate"; + case SealevelriseGElasticEnum : return "SealevelriseGElastic"; + case SealevelriseUElasticEnum : return "SealevelriseUElastic"; + case SealevelriseHElasticEnum : return "SealevelriseHElastic"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21751) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21752) +@@ -800,6 +800,7 @@ + else if (strcmp(name,"SealevelrisePolarMoi")==0) return SealevelrisePolarMoiEnum; + else if (strcmp(name,"SealevelriseAngularVelocity")==0) return SealevelriseAngularVelocityEnum; + else if (strcmp(name,"SealevelriseOceanAreaScaling")==0) return SealevelriseOceanAreaScalingEnum; ++ else if (strcmp(name,"SealevelriseStericRate")==0) return SealevelriseStericRateEnum; + else if (strcmp(name,"SealevelriseGElastic")==0) return SealevelriseGElasticEnum; + else if (strcmp(name,"SealevelriseUElastic")==0) return SealevelriseUElasticEnum; + else if (strcmp(name,"SealevelriseHElastic")==0) return SealevelriseHElasticEnum; +@@ -873,11 +874,11 @@ + else if (strcmp(name,"SegmentRiftfront")==0) return SegmentRiftfrontEnum; + else if (strcmp(name,"SpcDynamic")==0) return SpcDynamicEnum; + else if (strcmp(name,"SpcStatic")==0) return SpcStaticEnum; +- else if (strcmp(name,"SpcTransient")==0) return SpcTransientEnum; + else stage=8; + } + if(stage==8){ +- if (strcmp(name,"StringArrayParam")==0) return StringArrayParamEnum; ++ if (strcmp(name,"SpcTransient")==0) return SpcTransientEnum; ++ else if (strcmp(name,"StringArrayParam")==0) return StringArrayParamEnum; + else if (strcmp(name,"StringParam")==0) return StringParamEnum; + else if (strcmp(name,"Seg")==0) return SegEnum; + else if (strcmp(name,"SegInput")==0) return SegInputEnum; +@@ -996,11 +997,11 @@ + else if (strcmp(name,"P1xP2")==0) return P1xP2Enum; + else if (strcmp(name,"P1xP3")==0) return P1xP3Enum; + else if (strcmp(name,"P2xP4")==0) return P2xP4Enum; +- else if (strcmp(name,"P1P1")==0) return P1P1Enum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"P1P1GLS")==0) return P1P1GLSEnum; ++ if (strcmp(name,"P1P1")==0) return P1P1Enum; ++ else if (strcmp(name,"P1P1GLS")==0) return P1P1GLSEnum; + else if (strcmp(name,"MINI")==0) return MINIEnum; + else if (strcmp(name,"MINIcondensed")==0) return MINIcondensedEnum; + else if (strcmp(name,"TaylorHood")==0) return TaylorHoodEnum; +Index: ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp (revision 21751) ++++ ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp (revision 21752) +@@ -35,6 +35,7 @@ + iomodel->FetchDataToInput(elements,"md.mask.land_levelset",MaskLandLevelsetEnum); + iomodel->FetchDataToInput(elements,"md.slr.deltathickness",SealevelriseDeltathicknessEnum); + iomodel->FetchDataToInput(elements,"md.slr.sealevel",SealevelEnum,0); ++ iomodel->FetchDataToInput(elements,"md.slr.steric_rate",SealevelriseStericRateEnum); + + }/*}}}*/ + void SealevelriseAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ +Index: ../trunk-jpl/src/c/cores/sealevelrise_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/sealevelrise_core.cpp (revision 21751) ++++ ../trunk-jpl/src/c/cores/sealevelrise_core.cpp (revision 21752) +@@ -14,6 +14,7 @@ + Vector *Sg = NULL; + Vector *Sg_absolute = NULL; + Vector *Sg_eustatic = NULL; ++ Vector *steric_rate_g = NULL; + Vector *U_radial = NULL; + Vector *U_north = NULL; + Vector *U_east = NULL; +@@ -32,6 +33,7 @@ + IssmDouble *xx = NULL; + IssmDouble *yy = NULL; + IssmDouble *zz = NULL; ++ IssmDouble dt; + + /*Recover some parameters: */ + femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); +@@ -39,7 +41,7 @@ + femmodel->parameters->FindParam(&save_results,SaveResultsEnum); + femmodel->parameters->FindParam(&isslr,TransientIsslrEnum); + femmodel->parameters->FindParam(&iscoupler,TransientIscouplerEnum); +- ++ + /*first, recover lat,long and radius vectors from vertices: */ + VertexCoordinatesx(&latitude,&longitude,&radius,femmodel->vertices,spherical); + +@@ -79,11 +81,9 @@ + Sg_eustatic=sealevelrise_core_eustatic(femmodel); //generalized eustatic (Farrel and Clark, Eq 4, 1st, 3rd and 4rd terms on the RHS. + + Sg=sealevelrise_core_noneustatic(femmodel,Sg_eustatic); //ocean loading tems (2nd and 5th terms on the RHS of Farrel and Clark) +- +- /*get results into elements:*/ +- //InputUpdateFromSolutionx(femmodel,Sg); // from Eric +- InputUpdateFromVectorx(femmodel,Sg,SealevelEnum,VertexSIdEnum); + ++ ++ + /*compute other geodetic signatures, such as absolute sea level chagne, components of 3-D crustal motion: */ + /*Initialize:*/ + U_radial = new Vector(gsize); +@@ -94,6 +94,11 @@ + /*call the geodetic main modlule:*/ + femmodel->SealevelriseGeodetic(U_radial,U_north,U_east,Sg,latitude,longitude,radius,xx,yy,zz); + ++ /*Now deal with steric ocean expansion by just shifting Sg by a spatial rate pattern : */ ++ femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); ++ GetVectorFromInputsx(&steric_rate_g,femmodel,SealevelriseStericRateEnum,VertexPIdEnum); ++ Sg->AXPY(steric_rate_g,dt); ++ + /*compute: absolute sea level change = relative sea level change + vertical motion*/ + Sg->Copy(Sg_absolute); Sg_absolute->AXPY(U_radial,1); + +@@ -101,7 +106,8 @@ + InputUpdateFromVectorx(femmodel,U_radial,SealevelUmotionEnum,VertexSIdEnum); // radial displacement + InputUpdateFromVectorx(femmodel,U_north,SealevelNmotionEnum,VertexSIdEnum); // north motion + InputUpdateFromVectorx(femmodel,U_east,SealevelEmotionEnum,VertexSIdEnum); // east motion +- InputUpdateFromVectorx(femmodel,Sg_absolute,SealevelAbsoluteEnum,VertexSIdEnum); ++ InputUpdateFromVectorx(femmodel,Sg_absolute,SealevelAbsoluteEnum,VertexSIdEnum); //absolute sea level ++ InputUpdateFromVectorx(femmodel,Sg,SealevelEnum,VertexSIdEnum); //relative sea level + + if(save_results){ + if(VerboseSolution()) _printf0_(" saving results\n"); +@@ -118,6 +124,7 @@ + delete U_north; + delete U_east; + delete Sg_absolute; ++ delete steric_rate_g; + if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} + } + Index: /issm/oecreview/Archive/21724-22754/ISSM-21752-21753.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21752-21753.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21752-21753.diff (revision 22755) @@ -0,0 +1,24 @@ +Index: ../trunk-jpl/test/NightlyRun/test2002.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2002.m (revision 21752) ++++ ../trunk-jpl/test/NightlyRun/test2002.m (revision 21753) +@@ -8,6 +8,7 @@ + %slr loading: {{{ + md.slr.deltathickness=zeros(md.mesh.numberofelements,1); + md.slr.sealevel=zeros(md.mesh.numberofvertices,1); ++md.slr.steric_rate=zeros(md.mesh.numberofvertices,1); + %antarctica + late=sum(md.mesh.lat(md.mesh.elements),2)/3; + longe=sum(md.mesh.long(md.mesh.elements),2)/3; +Index: ../trunk-jpl/test/NightlyRun/test2003.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2003.m (revision 21752) ++++ ../trunk-jpl/test/NightlyRun/test2003.m (revision 21753) +@@ -8,6 +8,7 @@ + %slr loading: {{{ + md.slr.deltathickness=zeros(md.mesh.numberofelements,1); + md.slr.sealevel=zeros(md.mesh.numberofvertices,1); ++md.slr.steric_rate=zeros(md.mesh.numberofvertices,1); + %antarctica + late=sum(md.mesh.lat(md.mesh.elements),2)/3; + longe=sum(md.mesh.long(md.mesh.elements),2)/3; Index: /issm/oecreview/Archive/21724-22754/ISSM-21762-21763.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21762-21763.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21762-21763.diff (revision 22755) @@ -0,0 +1,23 @@ +Index: ../trunk-jpl/src/m/plot/plot_unit.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_unit.py (revision 21762) ++++ ../trunk-jpl/src/m/plot/plot_unit.py (revision 21763) +@@ -93,8 +93,6 @@ + triangles=mpl.tri.Triangulation(x,y,elements) + tri=ax.tripcolor(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha,edgecolors=edgecolor) + else: +- +- + #first deal with colormap + loccmap = plt.cm.ScalarMappable(cmap=cmap) + loccmap.set_array([min(data),max(data)]) +@@ -151,7 +149,8 @@ + triangles=mpl.tri.Triangulation(x,y,elements,EltMask) + else: + triangles=mpl.tri.Triangulation(x,y,elements) +- tri=ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha) ++ #tri=ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha) ++ tri=ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha,extend='both') + if edgecolor != 'None': + ax.triplot(x,y,elements,color=edgecolor) + else: Index: /issm/oecreview/Archive/21724-22754/ISSM-21763-21764.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21763-21764.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21763-21764.diff (revision 22755) @@ -0,0 +1,244 @@ +Index: ../trunk-jpl/src/m/classes/clusters/localpfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/localpfe.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/clusters/localpfe.m (revision 21764) +@@ -0,0 +1,239 @@ ++%localpfe cluster class definition ++% ++% Usage: ++% cluster=localpfe('name','astrid','np',3); ++% cluster=localpfe('name',oshostname(),'np',3,'login','username'); ++ ++classdef localpfe ++ properties (SetAccess=public) ++ % {{{ ++ name = ''; ++ login = ''; ++ np = 1; ++ port = 0; ++ interactive = 1; ++ codepath = [IssmConfig('ISSM_PREFIX') '/bin']; ++ etcpath = [issmdir() '/etc']; ++ executionpath = [issmdir() '/execution']; ++ valgrind = [issmdir() '/externalpackages/valgrind/install/bin/valgrind']; ++ valgrindlib = [issmdir() '/externalpackages/valgrind/install/lib/libmpidebug.so']; ++ valgrindsup = [issmdir() '/externalpackages/valgrind/issm.supp']; ++ verbose = 1; ++ shell = '/bin/sh'; ++ %}}} ++ end ++ methods ++ function cluster=localpfe(varargin) % {{{ ++ ++ %Change the defaults if ispc ++ if ispc, ++ cluster.codepath = [issmdir() '\bin']; ++ cluster.etcpath = [issmdir() '\etc']; ++ cluster.executionpath = [issmdir() '\execution']; ++ end ++ ++ %use provided options to change fields ++ options=pairoptions(varargin{:}); ++ ++ %get name ++ cluster.name=getfieldvalue(options,'name',oshostname()); ++ ++ %initialize cluster using user settings if provided ++ if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end ++ ++ %OK get other fields ++ cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); ++ end ++ %}}} ++ function disp(cluster) % {{{ ++ % display the object ++ disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); ++ disp(sprintf(' name: %s',cluster.name)); ++ disp(sprintf(' login: %s',cluster.login)); ++ disp(sprintf(' np: %i',cluster.np)); ++ disp(sprintf(' port: %i',cluster.port)); ++ disp(sprintf(' codepath: %s',cluster.codepath)); ++ disp(sprintf(' executionpath: %s',cluster.executionpath)); ++ disp(sprintf(' etcpath: %s',cluster.etcpath)); ++ disp(sprintf(' valgrind: %s',cluster.valgrind)); ++ disp(sprintf(' valgrindlib: %s',cluster.valgrindlib)); ++ disp(sprintf(' valgrindsup: %s',cluster.valgrindsup)); ++ disp(sprintf(' verbose: %s',cluster.verbose)); ++ disp(sprintf(' shell: %s',cluster.shell)); ++ end ++ %}}} ++ function md = checkconsistency(cluster,md,solution,analyses) % {{{ ++ if cluster.np<1 ++ md = checkmessage(md,['number of processors should be at least 1']); ++ end ++ if isnan(cluster.np), ++ md = checkmessage(md,'number of processors should not be NaN!'); ++ end ++ end ++ %}}} ++ 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 ++ ++ fid=fopen([modelname '.queue'],'w'); ++ fprintf(fid,'#!%s\n',cluster.shell); ++ fprintf(fid,'mpiexec -np %i %s/%s %s %s %s \n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,modelname); ++ fclose(fid); ++ ++ ++ %in interactive mode, create a run file, and errlog and outlog file ++ if cluster.interactive, ++ fid=fopen([modelname '.errlog'],'w'); fclose(fid); ++ fid=fopen([modelname '.outlog'],'w'); fclose(fid); ++ end ++ end ++ %}}} ++ function BuildQueueScriptMultipleModels(cluster,dirname,modelname,solution,dirnames,modelnames,nps) % {{{ ++ ++ %some checks: ++ if isempty(modelname), error('BuildQueueScriptMultipleModels error message: need a non empty model name!');end ++ ++ %what is the executable being called? ++ executable='issm_slr.exe'; ++ ++ if ispc(), error('BuildQueueScriptMultipleModels not support yet on windows machines');end; ++ ++ %write queuing script ++ fid=fopen([modelname '.queue'],'w'); ++ ++ fprintf(fid,'#!%s\n',cluster.shell); ++ ++ %number of cpus: ++ mpistring=sprintf('mpiexec -np %i ',cluster.np); ++ ++ %executable: ++ mpistring=[mpistring sprintf('%s/%s ',cluster.codepath,executable)]; ++ ++ %solution name: ++ mpistring=[mpistring sprintf('%s ',solution)]; ++ ++ %execution directory and model name: ++ mpistring=[mpistring sprintf('%s/%s %s',cluster.executionpath,dirname,modelname)]; ++ ++ %inform main executable of how many icecaps, glaciers and earth models are being run: ++ mpistring=[mpistring sprintf(' %i ',length(dirnames))]; ++ ++ %icecaps, glaciers and earth location, names and number of processors associated: ++ for i=1:length(dirnames), ++ mpistring=[mpistring sprintf(' %s/%s %s %i ',cluster.executionpath,dirnames{i},modelnames{i},nps{i})]; ++ end ++ ++ %log files: ++ if ~cluster.interactive, ++ mpistring=[mpistring sprintf('2> %s.errlog> %s.outlog',modelname,modelname)]; ++ end ++ ++ %write this long string to disk: ++ fprintf(fid,mpistring); ++ fclose(fid); ++ ++ %in interactive mode, create a run file, and errlog and outlog file ++ if cluster.interactive, ++ fid=fopen([modelname '.errlog'],'w'); fclose(fid); ++ fid=fopen([modelname '.outlog'],'w'); fclose(fid); ++ end ++ end ++ %}}} ++ function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{ ++ ++ %write queuing script ++ if ~ispc(), ++ ++ fid=fopen([modelname '.queue'],'w'); ++ fprintf(fid,'#!/bin/sh\n'); ++ if ~isvalgrind, ++ if cluster.interactive ++ fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname); ++ else ++ fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname); ++ end ++ elseif isgprof, ++ fprintf(fid,'\n gprof %s/kriging.exe gmon.out > %s.performance',cluster.codepath,modelname); ++ else ++ %Add --gen-suppressions=all to get suppression lines ++ fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib); ++ fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',... ++ cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname); ++ end ++ if ~io_gather, %concatenate the output files: ++ fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname); ++ end ++ fclose(fid); ++ ++ else % Windows ++ ++ fid=fopen([modelname '.bat'],'w'); ++ fprintf(fid,'@echo off\n'); ++ if cluster.interactive ++ fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname); ++ else ++ fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',... ++ cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname,modelname,modelname); ++ end ++ fclose(fid); ++ end ++ ++ %in interactive mode, create a run file, and errlog and outlog file ++ if cluster.interactive, ++ fid=fopen([modelname '.errlog'],'w'); fclose(fid); ++ fid=fopen([modelname '.outlog'],'w'); fclose(fid); ++ end ++ end ++ %}}} ++ function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ ++ if ~ispc, ++ ++ %compress the files into one zip. ++ compressstring=['tar -zcf ' dirname '.tar.gz ']; ++ for i=1:numel(filelist), ++ compressstring = [compressstring ' ' filelist{i}]; ++ end ++ if cluster.interactive, ++ compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog ']; ++ end ++ system(compressstring); ++ ++ if cluster.verbose, disp('uploading input file and queueing script'); end ++ issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']}); ++ end ++ end %}}} ++ function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ ++ ++ %figure out what shell extension we will use: ++ if isempty(strfind(cluster.shell,'csh')), ++ shellext='sh'; ++ else ++ shellext='csh'; ++ end ++ ++ if cluster.verbose, disp('launching solution sequence on remote cluster'); end ++ ++ launchcommand=['cd ' cluster.executionpath ' && rm -rf *.lock && rm -rf ADOLC* && tar -zxf ' dirname '.tar.gz && rm -rf *.tar.gz']; ++ issmssh(cluster.name,cluster.login,cluster.port,launchcommand); ++ ++ end %}}} ++ function Download(cluster,dirname,filelist)% {{{ ++ ++ if ispc(), ++ %do nothing ++ return; ++ end ++ ++ %copy files from cluster to current directory ++ issmscpin(cluster.name,cluster.login,cluster.port,cluster.executionpath,filelist); ++ end %}}} ++ end ++end Index: /issm/oecreview/Archive/21724-22754/ISSM-21764-21765.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21764-21765.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21764-21765.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/classes/clusters/localpfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/localpfe.m (revision 21764) ++++ ../trunk-jpl/src/m/classes/clusters/localpfe.m (revision 21765) +@@ -71,7 +71,7 @@ + end + end + %}}} +- function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ ++ function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + + %write queuing script + %what is the executable being called? Index: /issm/oecreview/Archive/21724-22754/ISSM-21765-21766.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21765-21766.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21765-21766.diff (revision 22755) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/m/solve/waitonlock.m +=================================================================== +--- ../trunk-jpl/src/m/solve/waitonlock.m (revision 21765) ++++ ../trunk-jpl/src/m/solve/waitonlock.m (revision 21766) +@@ -19,6 +19,9 @@ + if isa(cluster,'pfe') && cluster.interactive>0 + lockfilename = [executionpath '/Interactive' num2str(cluster.interactive) '/' md.miscellaneous.name '.lock']; + logfilename = [executionpath '/Interactive' num2str(cluster.interactive) '/' md.miscellaneous.name '.outlog']; ++elseif isa(cluster,'localpfe'), ++ lockfilename = [executionpath '/' md.miscellaneous.name '.lock']; ++ logfilename = [executionpath '/' md.miscellaneous.name '.outlog']; + else + lockfilename = [executionpath '/' md.private.runtimename '/' md.miscellaneous.name '.lock']; + logfilename = [executionpath '/' md.private.runtimename '/' md.miscellaneous.name '.outlog']; Index: /issm/oecreview/Archive/21724-22754/ISSM-21766-21767.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21766-21767.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21766-21767.diff (revision 22755) @@ -0,0 +1,119 @@ +Index: ../trunk-jpl/src/m/classes/clusters/discover.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/discover.m (revision 21766) ++++ ../trunk-jpl/src/m/classes/clusters/discover.m (revision 21767) +@@ -89,7 +89,7 @@ + + end + %}}} +- function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,ioceancoupling) % {{{ ++ function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + + if(isgprof), disp('gprof not supported by cluster, ignoring...'); end + +@@ -115,7 +115,7 @@ + fprintf(fid,'#SBATCH -n %i \n',cluster.numnodes*cluster.cpuspernode); + fprintf(fid,'#SBATCH -N %i \n',cluster.numnodes); + fprintf(fid,'#SBATCH -t %02i:%02i:00 \n',floor(cluster.time/3600),floor(mod(cluster.time,3600)/60)); +- fprintf(fid,'#SBATCH -A s1010 \n\n'); ++ fprintf(fid,'#SBATCH -A s1690 \n\n'); + for i=1:numel(cluster.modules), + fprintf(fid,['module load ' cluster.modules{i} '\n']); + end +@@ -126,6 +126,7 @@ + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); + fprintf(fid,'module load comp/intel-15.0.0.090\n'); + fprintf(fid,'module load mpi/impi-4.0.3.008\n'); ++ fprintf(fid,'module load other/cmake-3.8.2\n'); + fprintf(fid,'export PATH="$PATH:."\n\n'); + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME + fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 21766) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 21767) +@@ -1319,11 +1319,7 @@ + + dnl scalapack headers and libraries + if test "x$HAVE_SCALAPACK" == "xyes"; then +- if test x$VENDOR = xintel-discover; then +- SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lmkl_scalapack_lp64" +- else +- SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lscalapack" +- fi ++ SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lscalapack" + AC_DEFINE([_HAVE_SCALAPACK_],[1],[with Scalapack in ISSM src]) + AC_SUBST([SCALAPACKLIB]) + fi +@@ -1348,25 +1344,18 @@ + dnl blas-lapack headers and libraries + if test "x$HAVE_BLASLAPACK" == "xyes"; then + BLASLAPACKINCL="" +- if test x$VENDOR = xintel-discover; then +- dnl works for intel 11 +- dnl BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lmkl_lapack -lmkl -lguide -lpthread " +- dnl dnl works for intel 13 +- BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lmkl_lapack95_lp64 -lmkl_rt " +- else +- dnl: branch on whether we are running on windows or linux. +- case "${host_os}" in +- *cygwin*) +- BLASLAPACKLIB="-L`cygpath -m $BLASLAPACK_ROOT` -Wl,libf2cblas.lib -Wl,libf2clapack.lib" +- ;; +- *linux*) +- BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " +- ;; +- *darwin*) +- BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " +- ;; +- esac +- fi ++ dnl: branch on whether we are running on windows or linux. ++ case "${host_os}" in ++ *cygwin*) ++ BLASLAPACKLIB="-L`cygpath -m $BLASLAPACK_ROOT` -Wl,libf2cblas.lib -Wl,libf2clapack.lib" ++ ;; ++ *linux*) ++ BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " ++ ;; ++ *darwin*) ++ BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " ++ ;; ++ esac + AC_DEFINE([_HAVE_BLASLAPACK_],[1],[with blas lapack in ISSM src]) + AC_SUBST([BLASLAPACKLIB]) + AC_SUBST([BLASLAPACKINCL]) +@@ -1471,11 +1460,7 @@ + dnl blacs headers and libraries + if test "x$HAVE_BLACS" == "xyes"; then + BLACSINCL="" +- if test x$VENDOR = xintel-discover; then +- BLACSLIB=-L"$BLACS_ROOT/ -lmkl_blacs_intelmpi_lp64" +- else +- BLACSLIB=-L"$BLACS_ROOT/ -lblacs" +- fi ++ BLACSLIB=-L"$BLACS_ROOT/ -lblacs" + AC_DEFINE([_HAVE_BLACS_],[1],[with Blacs in ISSM src]) + AC_SUBST([BLACSINCL]) + AC_SUBST([BLACSLIB]) +Index: ../trunk-jpl/externalpackages/petsc/install-3.6-discover.sh +=================================================================== +--- ../trunk-jpl/externalpackages/petsc/install-3.6-discover.sh (revision 21766) ++++ ../trunk-jpl/externalpackages/petsc/install-3.6-discover.sh (revision 21767) +@@ -41,7 +41,7 @@ + #SBATCH -J petscinstall # Job Name + #SBATCH -N 1 + #SBATCH -n 1 +-#SBATCH -A s1010 ++#SBATCH -A s1690 + #SBATCH -t 00:01:00 # Run time (hh:mm:ss) - 1.5 hours + #SBATCH --qos=debug + #SBATCH -o petscinstall.outlog +@@ -50,6 +50,7 @@ + . /usr/share/modules/init/bash + module load comp/intel-15.0.0.090 + module load mpi/impi-4.0.3.008 ++module load other/cmake-3.8.2 + + export PATH="$PATH:." + export MPI_GROUP_MAX=64 Index: /issm/oecreview/Archive/21724-22754/ISSM-21767-21768.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21767-21768.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21767-21768.diff (revision 22755) @@ -0,0 +1,3168 @@ +Index: ../trunk-jpl/src/m/plot/webgl.js +=================================================================== +--- ../trunk-jpl/src/m/plot/webgl.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/webgl.js (revision 21768) +@@ -5,12 +5,10 @@ + canvas = document.getElementById(options.getfieldvalue('canvasid')); + //var canvas = document.getElementById(options.getfieldvalue('canvasid')); + if (!canvas.initialized) { +- typedArraySliceSupport(); + if (!isEmptyOrUndefined(canvas.draw) && canvas.draw.handler !== 0) { window.cancelAnimationFrame(canvas.draw.handler); } + if (!isEmptyOrUndefined(canvas.animation) && canvas.animation.handler !== 0) { clearInterval(canvas.animation.handler); } + initWebGL(canvas, options); + initializeMarker(canvas); +- canvas.nodes = []; + draw(canvas); + canvas.initialized = true; + } +@@ -18,8 +16,8 @@ + } + function initWebGL(canvas, options) { //{{{ + //Initialize canvas.gl on page load, reusing gl context on additional runs +- var gl; +- if (!canvas.gl) { ++ var gl = canvas.gl; ++ if (isEmptyOrUndefined(gl)) { + gl = GL.create({canvas: canvas}); + gl.enable(gl.DEPTH_TEST); // Enable depth testing + gl.depthFunc(gl.LEQUAL); // Near things obscure far things +@@ -30,34 +28,35 @@ + gl.textures = {}; + + // Add event listeners for canvas +- var displayview = options.getfieldvalue('displayview', 'off') == 'on'; +- var displayzoom = options.getfieldvalue('displayzoom', 'off') == 'on'; +- var mc = new Hammer.Manager(canvas); +- +- mc.add( new Hammer.Tap({event: 'singletap' }) ); ++ var displayview = options.getfieldvalue('displayview', 'off') === 'on'; ++ var displayzoom = options.getfieldvalue('displayzoom', 'off') === 'on'; ++ var mc = new Hammer(canvas); + mc.add(new Hammer.Pan({threshold: 0, pointers: 0})); + mc.add(new Hammer.Pinch({threshold: 0})).recognizeWith(mc.get('pan')); +- mc.on('singletap', function (ev) {onTap(ev, canvas);}); ++ mc.on('tap press', function (ev) {onTap(ev, canvas);}); + mc.on('panstart panmove', function (ev) {onPan(ev, canvas, displayview);}); +- mc.on('pinchstart pinchmove', function (ev) {onPinch(ev, canvas, displayview);}); +- ++ mc.on('pinchstart pinchmove', function (ev) {onPinch(ev, canvas, displayview);}); + canvas.addEventListener('mousewheel', function (ev) {onZoom(ev, canvas, displayzoom)}, false); + canvas.addEventListener('DOMMouseScroll', function (ev) {onZoom(ev, canvas, displayzoom)}, false); ++ ++ //Add persistent state variables ++ canvas.nodes = {}; ++ canvas.octrees = {}; ++ canvas.unitNode = {}; ++ canvas.unitData = {}; ++ canvas.unitMovieData = {}; ++ canvas.gl = gl; ++ canvas.rootPath = options.getfieldvalue('rootpath', '../../../js/'); ++ canvas.id = options.getfieldvalue('canvasid', '.sim-canvas'); ++ canvas.selector = $('#' + canvas.id); ++ canvas.textcanvas = null; ++ canvas.overlaycanvas = null; ++ ++ typedArraySliceSupport(); + } +- else { +- gl = canvas.gl; +- } + +- // Add context state variables +- canvas.gl = gl; +- canvas.textcanvas = null; +- canvas.overlaycanvas = null; +- canvas.unitNode = {}; +- canvas.unitData = {}; ++ //Add context state variables + canvas.controlSensitivity = options.getfieldvalue('controlsensitivity', 1); +- canvas.id = options.getfieldvalue('canvasid', '.sim-canvas'); +- canvas.rootPath = options.getfieldvalue('rootpath', '../../../js/'); +- canvas.selector = $('#' + canvas.id); + var backgroundcolor = new RGBColor(options.getfieldvalue('backgroundcolor', 'lightcyan')); + if (backgroundcolor.ok) { canvas.backgroundcolor = [backgroundcolor.r/255.0, backgroundcolor.g/255.0, backgroundcolor.b/255.0, 1.0]; } + else { throw Error(sprintf('s%s%s\n','initWebGL error message: cound not find out background color for curent canvas ', canvas)); } +@@ -69,6 +68,7 @@ + play: defaultFor(animation.play, true), + increment: defaultFor(animation.increment, true), + fps: defaultFor(animation.fps, 4), ++ interval: defaultFor(animation.interval, 1000 / animation.fps), + loop: defaultFor(animation.loop, true), + handler: defaultFor(animation.handler, 0) + } +@@ -98,7 +98,8 @@ + canvas.clouds = { + enabled: defaultFor(clouds.enabled, false), + height: defaultFor(clouds.height, 7500), +- quantity: defaultFor(clouds.quantity, 10) ++ quantity: defaultFor(clouds.quantity, 10), ++ hit: defaultFor(clouds.hit, {}) + }; + var dataMarkers = options.getfieldvalue('datamarkers', {}); + canvas.dataMarkers = { +@@ -110,7 +111,8 @@ + animated: defaultFor(dataMarkers.animated, false), + labels: defaultFor(dataMarkers.labels, []), + font: defaultFor(dataMarkers.font, ''), +- marker: defaultFor(dataMarkers.marker, document.getElementById('sim-data-marker-' + canvas.id)) ++ marker: defaultFor(dataMarkers.marker, document.getElementById('sim-data-marker-' + canvas.id)), ++ reposition: defaultFor(dataMarkers.reposition, true) + }; + var draw = options.getfieldvalue('draw', {}); + canvas.draw = { +@@ -133,27 +135,23 @@ + //Override with parameters from URL, if any + //TODO: Make permalinks more robust and less interdependent on UI + if (!canvas.usedparemters) { +- function getJsonFromUrl() { +- var query = location.search.substr(1); +- var result = {}; +- query.split('&').forEach(function(part) { +- var item = part.split('='); +- result[item[0]] = decodeURIComponent(item[1]); +- }); +- return result; +- } +- parameters = getJsonFromUrl(); +- +- if (parameters['view']) { +- canvas.view = JSON.parse(parameters['view']); +- } ++ var parameters = {}; ++ location.search.substr(1).split('&').forEach(function(part) { ++ var item = part.split('='); ++ parameters[item[0]] = decodeURIComponent(item[1]); ++ }); ++ ++ if (parameters['pos']) { canvas.view.position = JSON.parse(parameters['pos']); } ++ if (parameters['rot']) { canvas.view.rotation = JSON.parse(parameters['rot']); } ++ if (parameters['zoom']) { canvas.view.zoom = JSON.parse(parameters['zoom']); } ++ if (parameters['twod']) { canvas.view.twod = JSON.parse(parameters['twod']); } + if (parameters['initial']) { + initial = JSON.parse(parameters['initial']); + if (!initial) { +- if (typeof SolveGlacier == 'function') { ++ if (typeof SolveGlacier === 'function') { + SolveGlacier(); + } +- if (typeof SolveSlr == 'function') { ++ if (typeof SolveSlr === 'function') { + SolveSlr(); + } + } +@@ -162,7 +160,11 @@ + } + } //}}} + function generatePermalink() { //{{{ +- var permalink = window.location.origin + window.location.pathname + '&view=' + JSON.stringify(canvas.view) + '&initial=' + JSON.stringify(initial); ++ var permalink = window.location.origin + window.location.pathname + '?' ++ + '&pos=' + encodeURIComponent(JSON.stringify(canvas.view.position)) ++ + '&rot=' + encodeURIComponent(JSON.stringify(canvas.view.rotation)) ++ + '&zoom=' + encodeURIComponent(JSON.stringify(canvas.view.zoom)) ++ + '&twod=' + encodeURIComponent(JSON.stringify(canvas.view.twod)); + window.prompt('Share this simulation: ', permalink); + } //}}} + function loadShaders(gl, rootPath) { //{{{ +@@ -181,83 +183,6 @@ + } + return gl.textures[imageSource]; + } //}}} +-function Node(gl) { //{{{ +- //Returns a Node object that contains default display states for webgl object. center represents pivot point of rotation. +- return { +- alpha: 1.0, +- buffers: [], +- cullFace: gl.BACK, +- disableDepthTest: false, +- drawMode: gl.TRIANGLES, +- drawOrder: 0, +- enabled: true, +- enableCullFace: true, +- hideOcean: false, +- lineWidth: 1.0, +- maskEnabled: false, +- maskHeight: 150.0, +- maskColor: vec4.fromValues(0.0, 0.0, 1.0, 1.0), +- mesh: null, +- name: 'node', +- shaderName: 'Colored', +- shader: gl.shaders.Colored, +- texture: null, +- useIndexBuffer: true, +- center: vec3.create(), +- scale: vec3.fromValues(1, 1, 1), +- rotation: vec3.create(), +- translation: vec3.create(), +- modelMatrix: mat4.create(), +- rotationMatrix: mat4.create(), +- inverseModelMatrix: mat4.create(), +- inverseRotationMatrix: mat4.create() +- }; +-} //}}} +-function debugNodes(canvasid) { //{{{ +- var canvasid = canvasid || '.sim-canvas'; +- var nodes = document.getElementById(canvasid).nodes; +- console.log(canvasid, 'Nodes:'); +- for (var node in nodes) { +- console.log('name: ', nodes[node].name, ' node: ', nodes[node], ' mesh: ', nodes[node].mesh, ' translation: ', nodes[node].translation, ' center:', nodes[node].center, ' rotation:', nodes[node].rotation); +- } +- return nodes; +-} //}}} +-function updateModelMatrix(node) { //{{{ +- var modelMatrix = mat4.create(); +- +- var translationMatrix = mat4.create(); +- mat4.translate(translationMatrix, translationMatrix, vec3.negate(vec3.create(), node.center)); //scale/rotation centering +- mat4.multiply(modelMatrix, translationMatrix, modelMatrix); +- +- var scaleMatrix = mat4.create(); +- mat4.scale(scaleMatrix, scaleMatrix, node.scale); +- mat4.multiply(modelMatrix, scaleMatrix, modelMatrix); +- +- var rotationMatrix = mat4.create(); +- var zRotationMatrix = mat4.create(); +- mat4.rotate(zRotationMatrix, zRotationMatrix, DEG2RAD * node.rotation[2], [0.0, 0.0, 1.0]); +- mat4.multiply(rotationMatrix, zRotationMatrix, rotationMatrix); +- var yRotationMatrix = mat4.create(); +- mat4.rotate(yRotationMatrix, yRotationMatrix, DEG2RAD * node.rotation[1], [0.0, 1.0, 0.0]); +- mat4.multiply(rotationMatrix, yRotationMatrix, rotationMatrix); +- var xRotationMatrix = mat4.create(); +- mat4.rotate(xRotationMatrix, xRotationMatrix, DEG2RAD * node.rotation[0], [1.0, 0.0, 0.0]); +- mat4.multiply(rotationMatrix, xRotationMatrix, rotationMatrix); +- mat4.multiply(modelMatrix, rotationMatrix, modelMatrix); +- +- mat4.identity(translationMatrix); +- mat4.translate(translationMatrix, translationMatrix, node.center); //relative translation +- mat4.multiply(modelMatrix, translationMatrix, modelMatrix); +- +- mat4.identity(translationMatrix); +- mat4.translate(translationMatrix, translationMatrix, node.translation); //absolute translation +- mat4.multiply(modelMatrix, translationMatrix, modelMatrix); +- +- node.modelMatrix = modelMatrix; +- node.inverseModelMatrix = mat4.invert(mat4.create(), modelMatrix); +- node.rotationMatrix = rotationMatrix; +- node.inverseRotationMatrix = mat4.invert(mat4.create(), rotationMatrix); +-} //}}} + function clamp(value, min, max) { //{{{ + return Math.max(min, Math.min(value, max)); + } //}}} +@@ -265,15 +190,21 @@ + return typeof name !== 'undefined' ? name : value; + } //}}} + function isEmptyOrUndefined(object) { //{{{ +- return object === undefined || Object.getOwnPropertyNames(object).length === 0; ++ return object === undefined || isEmpty(object); + } //}}} ++function isEmpty(object) { //{{{ ++ for (var key in object) { ++ return false; ++ } ++ return true; ++} //}}} + function recover(canvasid, name, value) { //{{{ + //Traverse canvas object tree for property defined by dot delimited string, returning it, or a default value if it is not found. + var object = document.getElementById(canvasid); + var properties = name.split('.'); +- for (var i = 0; i < properties.length; ++i) { ++ for (var i = 0; i < properties.length; i++) { + object = object[properties[i]]; +- if (typeof object === 'undefined') { break; } ++ if (isEmptyOrUndefined(object)) { break; } + } + return defaultFor(object, value); + } //}}} +@@ -325,26 +256,51 @@ + function onTap(ev, canvas) { //{{{ + //Sets up a marker on a canvas that will track a point on the mesh. Can be dismissed by closing the display or clicking the marker. + ev.preventDefault(); +- if (!canvas.dataMarkers.enabled) { return; } +- var hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY); +- canvas.dataMarkers.marker.hit = hit; ++ ++ if (canvas.clouds.enabled) { ++ for (var i = 0; i < canvas.clouds.quantity; i++) { ++ raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.nodes["clouds" + i]); ++ } ++ } ++ var hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.unitNode); ++ if ('cities' in canvas.nodes) { ++ var hitCities = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.nodes.cities); ++ canvas.nodes.cities.hit = hitCities; ++ updateCities(canvas); ++ } ++ + canvas.brush.hit = hit; +- updateMarker(canvas, true); ++ ++ if (canvas.dataMarkers.enabled) { ++ canvas.dataMarkers.marker.selector.closed = false; ++ canvas.dataMarkers.marker.hit = hit; ++ updateMarker(canvas, true); ++ } ++ + brushModify(canvas); + } //}}} + function onPan(ev, canvas, displaylog) { //{{{ + ev.preventDefault(); + +- if (canvas.dataMarkers.enabled == 'on') { +- canvas.brush.hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY); +- brushModify(canvas); ++ if (canvas.dataMarkers.enabled) { ++ if (!isEmptyOrUndefined(canvas.unitNode)) { ++ canvas.brush.hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.unitNode); ++ brushModify(canvas); ++ } + } + +- if (ev.type == 'panstart') { ++ if (canvas.clouds.enabled) { ++ if (!isEmptyOrUndefined(canvas.nodes['overlay'])) { ++ canvas.clouds.hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.nodes['overlay']); ++ updateClouds(canvas); ++ } ++ } ++ ++ if (ev.type === 'panstart') { + canvas.lastDeltaX = 0; + canvas.lastDeltaY = 0; + } +- if (ev.srcEvent.shiftKey || ev.pointers.length == 2) { ++ if (ev.srcEvent.shiftKey || ev.pointers.length === 2) { + if (!canvas.view.panningEnabled) return; + var deltaX = (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth / canvas.view.zoom * 2 * canvas.controlSensitivity * 6.371e6; + var deltaY = (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight / canvas.view.zoom * 2 * canvas.controlSensitivity * 6.371e6; +@@ -360,7 +316,7 @@ + } + + else { +- canvas.view.rotation[0] += (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth * -2 * canvas.controlSensitivity * RAD2DEG; ++ canvas.view.rotation[0] += (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth * 2 * canvas.controlSensitivity * RAD2DEG; + canvas.view.rotation[1] += (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight * -2 * canvas.controlSensitivity * RAD2DEG; + + if (canvas.view.rotation[0] > 360) { canvas.view.rotation[0] -= 360; }; +@@ -374,13 +330,13 @@ + canvas.lastDeltaX = ev.deltaX; + canvas.lastDeltaY = ev.deltaY; + +- repositionMarker(canvas); ++ canvas.dataMarkers.reposition = true; + + if (displaylog) { console.log(canvas.view.rotation); } + } //}}} + function onPinch(ev, canvas, displaylog) { //{{{ + ev.preventDefault(); +- if (ev.type == 'pinchstart') { canvas.view.lastZoom = canvas.view.zoom; } ++ if (ev.type === 'pinchstart') { canvas.view.lastZoom = canvas.view.zoom; } + else { modifyZoom(ev.scale * canvas.view.lastZoom, canvas, displaylog); } + } //}}} + function onZoom(ev, canvas, displaylog) { //{{{ +@@ -390,7 +346,7 @@ + } //}}} + function modifyZoom(value, canvas, displaylog) { //{{{ + canvas.view.zoom = clamp(value, canvas.view.zoomLimits[0], canvas.view.zoomLimits[1]); +- repositionMarker(canvas); ++ canvas.dataMarkers.reposition = true; + if (displaylog) { console.log(canvas.view.zoom); } + } //}}} + function modifyDataMarkersEnabled(value, canvas) { //{{{ +@@ -407,53 +363,45 @@ + canvas.playButton.find('span').addClass('fa-play'); + } + } //}}} +-function onSlideStart(canvas, progressBar) { //{{{ +- if (!isEmptyOrUndefined(canvas.animation)) { +- canvas.animation.increment = false; +- canvas.animation.frame = parseInt($(progressBar).val()); +- //console.log(canvas.animation.frame); +- //updateMarker(canvas, false); +- } +-} //}}} +-function onSlideChange(canvas, progressBar) { //{{{ +- if (!isEmptyOrUndefined(canvas.animation)) { +- canvas.animation.frame = parseInt($(progressBar).val()); +- //console.log("change"); +- updateMarker(canvas, false); +- } +-} //}}} +-function onSlideStop(canvas, progressBar) { //{{{ +- if (!isEmptyOrUndefined(canvas.animation)) { +- canvas.animation.increment = true; +- canvas.animation.frame = parseInt($(progressBar).val()); +- //console.log(canvas.animation.frame); +- //updateMarker(canvas, false); +- } +-} //}}} + //}}} + //{{{ Interaction Functions +-function raycast(canvas, x, y) { //{{{ ++function raycast(canvas, x, y, node) { //{{{ + //Performs raycast on canvas.unitNode.mesh using x/y screen coordinates. Returns hit objects with hit position, coords, and indicies of ray-triangle intersection. + //TODO: Diagnose marker issues with orthographic views and slr-eustatic updates when switching between basins. +- var inverseMVPMatrix = mat4.invert(mat4.create(), mat4.multiply(mat4.create(), canvas.camera.vpMatrix, canvas.unitNode.modelMatrix)); ++ var inverseMVPMatrix = mat4.invert(mat4.create(), mat4.multiply(mat4.create(), canvas.camera.vpMatrix, node.modelMatrix)); + var origin = vec3.transformMat4(vec3.create(), [(x - canvas.width / 2) / (canvas.width / 2), (canvas.height / 2 - y) / (canvas.height / 2), 0], inverseMVPMatrix); + var far = far || vec3.transformMat4(vec3.create(), [(x - canvas.width / 2) / (canvas.width / 2), (canvas.height / 2 - y) / (canvas.height / 2), 1.0], inverseMVPMatrix); + var ray = vec3.subtract(vec3.create(), far, origin); + +- var mesh = canvas.unitNode.mesh; ++ var mesh = node.mesh; ++ + if (!mesh) { return; } +- if (!mesh.octree) { mesh.octree = new GL.Octree(mesh); } ++ if (!node.octree) { node.octree = new GL.Octree(mesh); } + +- var hit = mesh.octree.testRay(origin, ray, 1e3, 1e10); ++ var hit = node.octree.testRay(origin, ray, 1e3, 1e10); + + if(!hit) { return; } +- ++ ++ if (node.name.startsWith("clouds")) { canvas.clouds.selected = node.name; alert("New selected cloud: " + canvas.clouds.selected); } ++ + hit.modelPos = vec3.copy(vec3.create(), hit.pos); +- vec3.transformMat4(hit.pos, hit.pos, canvas.unitNode.modelMatrix); +- vec3.transformMat4(hit.normal, hit.normal, canvas.unitNode.modelMatrix); ++ vec3.transformMat4(hit.pos, hit.pos, node.modelMatrix); ++ vec3.transformMat4(hit.normal, hit.normal, node.modelMatrix); + + return hit; + } //}}} ++function updateCities(canvas) { ++ //Update selected city ++ var hit = canvas.nodes.cities.hit; ++ if (hit) { ++ citiesIndex = Math.floor(hit.indices[0] / ((ArrayMax(canvas.nodes.cities.mesh.getIndexBuffer('triangles').data) + 1) / cities.length)); ++ cityName = cities[citiesIndex]; ++ if (cityName !== $('#gfm-sim-controls-select-city').val()) { ++ $('#gfm-sim-controls-select-city').val(cityName).selectmenu("refresh"); ++ changeCity(canvas); ++ } ++ } ++} + function brushModify(canvas) { //{{{ + //This function takes in the canvas and x/y coordinates, performing a raycast against the mesh, and modifies the mesh using a the canvas.brush.strength and canvas.brush.falloff properties. + //Currently the brush extends to the raycasted element and its immediate neighbors. +@@ -506,27 +454,26 @@ + //Update mesh on GPU + bufferVertices.upload(canvas.gl.DYNAMIC_DRAW); + bufferCoords.upload(canvas.gl.DYNAMIC_DRAW); +- canvas.unitNode.mesh.octree = new GL.Octree(canvas.unitNode.mesh); +- +- //Update clouds if rendered +- //TODO: Steven, once you update the cloud generation in applyoptions.js, modify this code block to move the clouds as well. We'll want to move them individually later, but moving them all is ok for now. +- for (var i = 0; i < canvas.clouds.quantity; i++) { +- if (canvas.nodes['clouds' + i]) { +- var v1 = vec3.fromValues(vertices[hit.indices[0] * 3], vertices[hit.indices[0] * 3 + 1], vertices[hit.indices[0] * 3 + 2]); +- var v2 = vec3.fromValues(vertices[hit.indices[1] * 3], vertices[hit.indices[1] * 3 + 1], vertices[hit.indices[1] * 3 + 2]); +- var v3 = vec3.fromValues(vertices[hit.indices[2] * 3], vertices[hit.indices[2] * 3 + 1], vertices[hit.indices[2] * 3 + 2]); +- vec3.transformMat4(v1, v1, canvas.unitNode.modelMatrix); +- vec3.transformMat4(v2, v2, canvas.unitNode.modelMatrix); +- vec3.transformMat4(v3, v3, canvas.unitNode.modelMatrix); +- var x = (v1[0] + v2[0] + v3[0]) / 3 + Math.floor((Math.random() * (1 + 10000 - (-10000)) + (-10000))); +- var y = (v1[1] + v2[1] + v3[1]) / 3 + Math.floor((Math.random() * (1 + 10000 - (-10000)) + (-10000))); +- var z = (v1[2] + v2[2] + v3[2]) / 3; +- canvas.nodes['clouds' + i].translation = [x, y + canvas.clouds.height, z]; +- updateModelMatrix(canvas.nodes['clouds' + i]); +- } +- } ++ canvas.unitNode.octree = new GL.Octree(canvas.unitNode.mesh); + } + } //}}} ++function updateClouds(canvas) { ++ //Update clouds if rendered ++ //TODO: Steven, the hit now queries the radaroverlay. ++ if (canvas.nodes[canvas.clouds.selected]) { ++ var v1 = vec3.fromValues(vertices[hit.indices[0] * 3], vertices[hit.indices[0] * 3 + 1], vertices[hit.indices[0] * 3 + 2]); ++ var v2 = vec3.fromValues(vertices[hit.indices[1] * 3], vertices[hit.indices[1] * 3 + 1], vertices[hit.indices[1] * 3 + 2]); ++ var v3 = vec3.fromValues(vertices[hit.indices[2] * 3], vertices[hit.indices[2] * 3 + 1], vertices[hit.indices[2] * 3 + 2]); ++ vec3.transformMat4(v1, v1, canvas.unitNode.modelMatrix);//move out of brushModify, perhaps onto onPan ++ vec3.transformMat4(v2, v2, canvas.unitNode.modelMatrix); ++ vec3.transformMat4(v3, v3, canvas.unitNode.modelMatrix); ++ var x = (v1[0] + v2[0] + v3[0]) / 3;// + Math.floor((Math.random() * (1 + 10000 - (-10000)) + (-10000))); ++ var y = (v1[1] + v2[1] + v3[1]) / 3;// + Math.floor((Math.random() * (1 + 10000 - (-10000)) + (-10000))); ++ var z = (v1[2] + v2[2] + v3[2]) / 3; ++ canvas.nodes[canvas.clouds.selected].translation = [x, y + canvas.clouds.height, z]; ++ updateModelMatrix(canvas.nodes[canvas.clouds.selected]); ++ } ++} + function initializeMarker(canvas) { //{{{ + //Initialize data marker and tooltip display once per page load + var marker = $('#' + canvas.dataMarkers.marker.id); +@@ -562,7 +509,9 @@ + marker.on('click touch', function () { + marker.fadeOut(175); + marker.tooltipster('close'); ++ marker.closed = true; + }); ++ marker.closed = false; + canvas.dataMarkers.marker.selector = marker; + } + updateMarker(canvas, true); +@@ -569,10 +518,10 @@ + } //}}} + function repositionMarker(canvas) { //{{{ + //Mover marker to point to mouse position, offset in y by 1 to enable immediate clicking. +- if (isEmptyOrUndefined(canvas.dataMarkers.marker.hit) || !canvas.camera.ready) { return; } ++ //Return if no marker hit exists, the camera is not rendering, or if no reposition has been scheduled. ++ if (isEmptyOrUndefined(canvas.dataMarkers.marker.hit) || !canvas.camera.ready || !canvas.dataMarkers.reposition) { return; } + var size = canvas.dataMarkers.size; + var screenPoint = vec3.transformMat4(vec3.create(), canvas.dataMarkers.marker.hit.pos, canvas.camera.vpMatrix); +- //console.log(canvas, canvas.selector, $(canvas.id) + var x = (screenPoint[0] + 1.0) * (canvas.width / 2) + canvas.selector.offset().left; + var y = (-screenPoint[1] + 1.0) * (canvas.height / 2) + canvas.selector.offset().top; + canvas.dataMarkers.marker.selector.css({ +@@ -579,15 +528,15 @@ + 'left': (Math.round(x) - size[0] / 2) + 'px', + 'top': (Math.round(y) - size[1] + 1) + 'px' + }); +- + if (canvas.dataMarkers.marker.selector.tooltipster('status').state != 'closed') { canvas.dataMarkers.marker.selector.tooltipster('reposition'); } ++ canvas.dataMarkers.reposition = false; + } //}}} + function updateMarker(canvas, reset) { //{{{ + //Retrieve data value fields and plots them on data marker popup if a hit has been registered. + //TODO: Automatically pick up any field of size md.mesh.numberofelements + //If no marker has been placed, no update is needed. If canvas is resimulating and unitNode has not been set yet, wait and try again. +- if (isEmptyOrUndefined(canvas.dataMarkers.marker.hit)) { return; } +- if (isEmptyOrUndefined(canvas.unitNode)) { setTimeout( function(){ updateMarker(canvas, reset); }, 750); return; } ++ if (!canvas.dataMarkers.enabled || isEmptyOrUndefined(canvas.dataMarkers.marker.hit)) { return; } ++ if (isEmptyOrUndefined(canvas.unitNode) || isEmptyOrUndefined(canvas.unitNode.mesh)) { setTimeout( function(){ updateMarker(canvas, reset); }, 750); return; } + + var hit = canvas.dataMarkers.marker.hit; + +@@ -605,41 +554,49 @@ + velocity = md.initialization.vel; + } + +- //Determine data values at hit position. +- var hitCoords = [coords[hit.indices[0]*2], coords[hit.indices[0]*2+1], coords[hit.indices[1]*2], coords[hit.indices[1]*2+1], coords[hit.indices[2]*2], coords[hit.indices[2]*2+1]]; +- var hitLatitude = [latitude[hit.indices[0]], latitude[hit.indices[1]], latitude[hit.indices[2]]]; +- var hitLongitude = [longitude[hit.indices[0]], longitude[hit.indices[1]], longitude[hit.indices[2]]]; +- var hitThickness = [thickness[hit.indices[0]], thickness[hit.indices[1]], thickness[hit.indices[2]]]; +- var hitVelocity = [velocity[hit.indices[0]], velocity[hit.indices[1]], velocity[hit.indices[2]]]; +- var u = hitCoords[0] * hit.uvw[0] + hitCoords[2] * hit.uvw[1] + hitCoords[4] * hit.uvw[2]; +- var v = hitCoords[1] * hit.uvw[0] + hitCoords[3] * hit.uvw[1] + hitCoords[5] * hit.uvw[2]; +- var value = canvas.unitNode.caxis[0] * (1.0 - v) + canvas.unitNode.caxis[1] * v; +- var valueLatitude = Math.abs(hitLatitude[0] * hit.uvw[0] + hitLatitude[1] * hit.uvw[1] + hitLatitude[2] * hit.uvw[2]); +- var valueLongitude = Math.abs(hitLongitude[0] * hit.uvw[0] + hitLongitude[1] * hit.uvw[1] + hitLongitude[2] * hit.uvw[2]); +- var valueThickness = hitThickness[0] * hit.uvw[0] + hitThickness[1] * hit.uvw[1] + hitThickness[2] * hit.uvw[2]; +- var valueVelocity = hitVelocity[0] * hit.uvw[0] + hitVelocity[1] * hit.uvw[1] + hitVelocity[2] * hit.uvw[2]; +- + //Construct new argument array of the data display format for sprintf using first first argument as the formatSpecifier string and the rest as the additional arguments. +- var format = canvas.dataMarkers.format.slice(); +- for (var i = 1; i < format.length; i++) { +- if (format[i].toLowerCase() == 'x') { format[i] = hit.modelPos[0]; } +- else if (format[i].toLowerCase() == 'y') { format[i] = hit.modelPos[1]; } +- else if (format[i].toLowerCase() == 'z') { format[i] = hit.modelPos[2]; } +- else if (format[i].toLowerCase() == 'lat') { format[i] = valueLatitude; } +- else if (format[i].toLowerCase() == 'long') { format[i] = valueLongitude; } +- else if (format[i].toLowerCase() == 'thickness') { format[i] = valueThickness; } +- else if (format[i].toLowerCase() == 'vel') { format[i] = valueVelocity; } +- else if (format[i].toLowerCase() == 'value') { format[i] = value; } ++ var labels = canvas.dataMarkers.labels.slice(); ++ for (var i = 0; i < labels.length; i++) { ++ if (labels[i].toLowerCase() === 'x') { labels[i] = hit.modelPos[0]; } ++ else if (labels[i].toLowerCase() === 'y') { labels[i] = hit.modelPos[1]; } ++ else if (labels[i].toLowerCase() === 'z') { labels[i] = hit.modelPos[2]; } ++ else if (labels[i].toLowerCase() === 'latitude') { ++ var hitLatitude = [latitude[hit.indices[0]], latitude[hit.indices[1]], latitude[hit.indices[2]]]; ++ var valueLatitude = Math.abs(hitLatitude[0] * hit.uvw[0] + hitLatitude[1] * hit.uvw[1] + hitLatitude[2] * hit.uvw[2]); ++ labels[i] = valueLatitude; ++ } ++ else if (labels[i].toLowerCase() === 'longitude') { ++ var hitLongitude = [longitude[hit.indices[0]], longitude[hit.indices[1]], longitude[hit.indices[2]]]; ++ var valueLongitude = Math.abs(hitLongitude[0] * hit.uvw[0] + hitLongitude[1] * hit.uvw[1] + hitLongitude[2] * hit.uvw[2]); ++ labels[i] = valueLongitude; ++ } ++ else if (labels[i].toLowerCase() === 'thickness') { ++ var hitThickness = [thickness[hit.indices[0]], thickness[hit.indices[1]], thickness[hit.indices[2]]]; ++ var valueThickness = hitThickness[0] * hit.uvw[0] + hitThickness[1] * hit.uvw[1] + hitThickness[2] * hit.uvw[2]; ++ labels[i] = valueThickness; ++ } ++ else if (labels[i].toLowerCase() === 'velocity') { ++ var hitVelocity = [velocity[hit.indices[0]], velocity[hit.indices[1]], velocity[hit.indices[2]]]; ++ var valueVelocity = hitVelocity[0] * hit.uvw[0] + hitVelocity[1] * hit.uvw[1] + hitVelocity[2] * hit.uvw[2]; ++ labels[i] = valueVelocity; ++ } ++ else if (labels[i].toLowerCase() === 'value') { ++ var hitCoords = [coords[hit.indices[0]*2], coords[hit.indices[0]*2+1], coords[hit.indices[1]*2], coords[hit.indices[1]*2+1], coords[hit.indices[2]*2], coords[hit.indices[2]*2+1]]; ++ var u = hitCoords[0] * hit.uvw[0] + hitCoords[2] * hit.uvw[1] + hitCoords[4] * hit.uvw[2]; ++ var v = hitCoords[1] * hit.uvw[0] + hitCoords[3] * hit.uvw[1] + hitCoords[5] * hit.uvw[2]; ++ var value = canvas.unitNode.caxis[0] * (1.0 - v) + canvas.unitNode.caxis[1] * v; ++ labels[i] = value; ++ } + } + + //Apply changes to tooltip +- $('#tooltip-content-data-marker-' + canvas.id).html(sprintf.apply(null, format)); ++ $('#tooltip-content-data-marker-' + canvas.id).html(sprintf.apply(null, canvas.dataMarkers.format.concat(labels))); + $('#tooltip-content-data-marker-' + canvas.id).css({'font': canvas.dataMarkers.font}); + + //If animated, setup animation loop to update plot as movie plays. + if (canvas.dataMarkers.animated) { +- var isEmpty = (canvas.dataMarkers.values.length == 0); +- var lastUpdatedIndex = (canvas.dataMarkers.values.length-1); ++ var isEmpty = (canvas.dataMarkers.values.length === 0); ++ var lastUpdatedIndex = (canvas.dataMarkers.values.length - 1); + var newMovieFrame = (!isEmpty && canvas.dataMarkers.values[lastUpdatedIndex][0] != canvas.animation.frame); + //If new data marker has been placed, reinitialize plot. If not, push new value into plot value array. + if (reset) { +@@ -646,7 +603,7 @@ + canvas.dataMarkers.values = []; + newMovieFrame = true; + for (var currentFrame = 0; currentFrame < (canvas.unitNode.movieLength); currentFrame++) { +- coords = canvas.unitNode.texcoords[currentFrame]; ++ coords = canvas.unitMovieData[currentFrame]; + var hitCoords = [coords[hit.indices[0]*2], coords[hit.indices[0]*2+1], coords[hit.indices[1]*2], coords[hit.indices[1]*2+1], coords[hit.indices[2]*2], coords[hit.indices[2]*2+1]]; + var u = hitCoords[0] * hit.uvw[0] + hitCoords[2] * hit.uvw[1] + hitCoords[4] * hit.uvw[2]; + var v = hitCoords[1] * hit.uvw[0] + hitCoords[3] * hit.uvw[1] + hitCoords[5] * hit.uvw[2]; +@@ -655,7 +612,13 @@ + } + } + else { ++ if (canvas.animation.lastFrame > canvas.animation.frame) { ++ canvas.dataMarkers.values = []; ++ } + if (isEmpty || newMovieFrame) { ++ coords = canvas.unitMovieData[canvas.animation.frame]; ++ var hitValues = [coords[hit.indices[0]], coords[hit.indices[1]], coords[hit.indices[2]]]; ++ var value = hitValues[0] * hit.uvw[0] + hitValues[1] * hit.uvw[1] + hitValues[2] * hit.uvw[2]; + canvas.dataMarkers.values.push([canvas.animation.frame, value]); + } + } +@@ -663,7 +626,7 @@ + //Replot data marker popup using update data value array. + if (isEmpty || newMovieFrame) { + var dataLabels = {'latitude': valueLatitude, 'longitude': valueLongitude, 'thickness': valueThickness, 'velocity': valueVelocity, 'value': value}; +- var dataDisplay = canvas.dataMarkers.values.slice(0, canvas.animation.frame+1); ++ var dataDisplay = canvas.dataMarkers.values.slice(0, canvas.animation.frame + 1); + plot( + 'id', '#sim-plot', + 'type', 'bar', +@@ -679,12 +642,21 @@ + ); + } + } +- repositionMarker(canvas); +- if (reset) { ++ canvas.dataMarkers.reposition = true; ++ if (reset && !canvas.dataMarkers.marker.selector.closed) { + canvas.dataMarkers.marker.selector.fadeIn(175); + canvas.dataMarkers.marker.selector.tooltipster('open'); + } + } //}}} ++function animateValue(current, target, duration, stepCallback, doneCallback) { //{{{ ++ //Animates scalar value for length duration, calling callback each step. ++ //TODO: Specify lerp easing as option (cubic, linear, cosine). ++ $({'value':current}).animate({'value':target}, { ++ duration: duration, ++ step: stepCallback, ++ done: doneCallback ++ }); ++} //}}} + //}}} + //{{{ Drawing Functions + function updateCameraMatrix(canvas) { //{{{ +@@ -706,12 +678,12 @@ + + //Calculate rotation around camera focal point about worldspace origin + if (canvas.view.twod) { +- mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, DEG2RAD * 0, [0, 1, 0]); ++ mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, -DEG2RAD * 0, [0, 1, 0]); + mat4.rotate(elevationRotationMatrix, elevationRotationMatrix, DEG2RAD * 90, [1, 0, 0]); + mat4.multiply(rotationMatrix, elevationRotationMatrix, azimuthRotationMatrix); + } + else { +- mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, DEG2RAD * canvas.view.rotation[0], [0, 1, 0]); ++ mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, -DEG2RAD * (canvas.view.rotation[0] + 90), [0, 1, 0]); + mat4.rotate(elevationRotationMatrix, elevationRotationMatrix, DEG2RAD * canvas.view.rotation[1], [1, 0, 0]); + mat4.multiply(rotationMatrix, elevationRotationMatrix, azimuthRotationMatrix); + } +@@ -734,6 +706,7 @@ + + vec3.transformMat4(canvas.camera.position, cameraPosition, canvas.camera.vpInverseMatrix); + canvas.camera.ready = true; ++ repositionMarker(canvas); + }//}}} + function drawSceneGraphNode(canvas, node) { //{{{ + if (!node.enabled) { return; } +@@ -748,7 +721,7 @@ + mat4.multiply(mvMatrix, canvas.camera.vMatrix, node.modelMatrix); + + var normalMatrix = mat4.create(); +- mat4.invert(normalMatrix, mvMatrix); ++ mat4.invert(normalMatrix, node.modelMatrix); + mat4.transpose(normalMatrix, normalMatrix); + + if (node.texture) { node.texture.bind(0); } +@@ -768,23 +741,23 @@ + vec3.sub(cameraPositionRelative, origin, node.translation); + cameraHeight = vec3.length(cameraPositionRelative); + +- var atm = { //Default Values +- wavelength_r: 0.65, //0.65 Red wavelength (micrometers) +- wavelength_g: 0.57, //0.57 Green wavelength (micrometers) +- wavelength_b: 0.475, //0.475 Green wavelength (micrometers) +- eSun: 100.0, //20.0 Sun intensity +- kRayleigh: 0.0025, //0.0025 Rayleigh scattering amount +- kMie: 0.000, //0.01 Mie scattering amount +- g: -0.99, //-0.99 Mie phase asymmetry/direction factor +- hdr_exposure: 0.8, //0.8 High Dynamic Range Exposure +- scale: 1.25, //1.025 Scale of atmosphere. WARNING: Change atmosphereScale in applyoptions.js, and scaling constants. +- scaleDepth: 0.25, //0.25 Percentage altitude at which the atmosphere's average density is found +- a: -0.00287, //-0.00287 Scaling constant a +- b: 0.459, //0.459 Scaling constant b +- c: 3.83, //3.83 Scaling constant c +- d: -6.80, //-6.80 Scaling constant d +- e: 3.6, //5.25 Scaling constant e. Lower when increasing atmosphere scale. +- attenuation: 0.5 //0.5 Strength of atmospheric scattering on ground shading. ++ var atm = { //Default Values ++ wavelength_r: 0.65, //0.65 Red wavelength (micrometers) ++ wavelength_g: 0.57, //0.57 Green wavelength (micrometers) ++ wavelength_b: 0.475, //0.475 Green wavelength (micrometers) ++ eSun: 100.0, //20.0 Sun intensity ++ kRayleigh: 0.0025, //0.0025 Rayleigh scattering amount ++ kMie: 0.000, //0.01 Mie scattering amount ++ g: -0.99, //-0.99 Mie phase asymmetry/direction factor ++ hdr_exposure: 0.8, //0.8 High Dynamic Range Exposure ++ scale: 1.25, //1.025 Scale of atmosphere. WARNING: Change atmosphereScale in applyoptions.js, and scaling constants. ++ scaleDepth: 0.25, //0.25 Percentage altitude at which the atmosphere's average density is found ++ a: -0.00287, //-0.00287 Scaling constant a ++ b: 0.459, //0.459 Scaling constant b ++ c: 3.83, //3.83 Scaling constant c ++ d: -6.80, //-6.80 Scaling constant d ++ e: 3.6, //5.25 Scaling constant e. Lower when increasing atmosphere scale. ++ attenuation: 0.5 //0.5 Strength of atmospheric scattering on ground shading. + }; + + var inv_wavelength4 = [1.0 / Math.pow(atm.wavelength_r, 4), 1.0 / Math.pow(atm.wavelength_g, 4), 1.0 / Math.pow(atm.wavelength_b, 4)]; +@@ -797,14 +770,19 @@ + m4MVP: mvpMatrix, + m4Normal: normalMatrix, + m4Model: node.modelMatrix, +- //u_lightPosition: [-lightOrigin[0], -lightOrigin[1], -lightOrigin[2]], +- u_lightPosition: [1.0, 1.0, 1.0], +- u_diffuseColor: [1.0, 0.9, 0.9], ++ u_lightPosition: lightOrigin, ++ //u_lightPosition: [1.0, 1.0, 1.0], ++ u_diffuseColor: node.diffuseColor, + u_texture: 0, + u_alpha: node.alpha, ++ u_maskZerosColor: node.maskZerosColor, ++ u_maskZerosEnabled: node.maskZerosEnabled, ++ u_maskZerosTolerance: node.maskZerosTolerance, ++ u_maskZerosZeroValue: node.maskZerosZeroValue, + u_maskEnabled: node.maskEnabled, + u_maskHeight: node.maskHeight, + u_maskColor: node.maskColor, ++ u_pointSize: node.pointSize, + v3CameraPosition: origin, + v3Translate: node.translation, + v3LightPos: lightOrigin, +@@ -840,10 +818,10 @@ + //TODO: Come up with better way to check if shaders are ready, or move outside of main draw function + var nodes = canvas.nodes; + if (!canvas.draw.ready) { +- if (nodes.length !== 0) { ++ if (Object.keys(nodes).length !== 0) { + canvas.draw.ready = true; + for (var node in nodes) { +- if (nodes[node].shader.ready == false) { ++ if (nodes[node].shader.ready === false) { + canvas.draw.ready = false; + break; + } +@@ -854,9 +832,6 @@ + + //Begin rendering nodes + if (canvas.draw.ready) { +- if (canvas.textcanvas) { canvas.textcanvas.draw(canvas); } +- if (canvas.overlaycanvas) { canvas.overlaycanvas.draw(canvas); } +- + var rect = canvas.getBoundingClientRect(); + canvas.width = rect.width; + canvas.height = rect.height; +@@ -869,10 +844,13 @@ + + updateCameraMatrix(canvas); + ++ if (canvas.textcanvas) { canvas.textcanvas.draw(canvas); } ++ if (canvas.overlaycanvas) { canvas.overlaycanvas.draw(canvas); } ++ + var drawPassNumber = 3; +- for (var i = drawPassNumber - 1; i >= 0; i--) { ++ for (var i = drawPassNumber - 1; i >= 0; --i) { + for (var node in nodes) { +- if (nodes[node].drawOrder == i) { drawSceneGraphNode(canvas, nodes[node]); } ++ if (nodes[node].drawOrder === i) { drawSceneGraphNode(canvas, nodes[node]); } + } + } + } +Index: ../trunk-jpl/src/m/plot/applyoptions.js +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/applyoptions.js (revision 21768) +@@ -1,4 +1,4 @@ +-function applyoptions(md, data, datatype, options, canvas, gl, node){ //{{{ ++function applyoptions(md, data, options, canvas){ //{{{ + //APPLYOPTIONS - apply colobar, text, cloud, and expdisp options to current plot + // + // Usage: +@@ -7,14 +7,11 @@ + // See also: PLOTMODEL, PARSE_OPTIONS + + //{{{ colorbar ++ var gl = canvas.gl; + if (options.exist('colorbar')) { + if (options.getfieldvalue('colorbar')==1) { +- //{{{ Handle movie data +- if (datatype == 5) { +- data = data[0]; +- } //}}} + //{{{ Variable options initialization +- var caxis = options.getfieldvalue('caxis',[ArrayMin(data), ArrayMax(data)]); ++ var caxis = options.getfieldvalue('caxis'); + var colorbarinnerlabels = options.getfieldvalue('colorbarinnerlabels','off'); + var ccanvasid, ctitleid, clabelsid, ccanvas, ctitle, clabels, ccontext, cmap, colorbar, cwidth, cheight, cgradient, color, y, x; + //}}} +@@ -23,14 +20,31 @@ + var cdivisions = options.getfieldvalue('colorbarnticks', 6); + var caxisdelta = caxis[1] - caxis[0]; + var precision = options.getfieldvalue('colorbarprecision', 3); ++ var format = options.getfieldvalue('colorbarformat', 'f').toLowerCase(); + if (options.getfieldvalue('log','off')!='off') { + for (var i=cdivisions; i >= 0; i--) { + var scale = (Math.log10(caxis[1])-Math.log10(caxis[0]))/Math.log10(options.getfieldvalue('log', 10)); +- labels[i] = (Math.pow(options.getfieldvalue('log', 10), Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10))+scale*(cdivisions-i)/cdivisions)).toFixed(precision); ++ if (format === 'f') { ++ labels[i] = (Math.pow(options.getfieldvalue('log', 10), Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10))+scale*(cdivisions-i)/cdivisions)).toFixed(precision); ++ } ++ else if (format === 'e') { ++ labels[i] = (Math.pow(options.getfieldvalue('log', 10), Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10))+scale*(cdivisions-i)/cdivisions)).toPrecision(precision); ++ } ++ else { ++ labels[i] = (Math.pow(options.getfieldvalue('log', 10), Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10))+scale*(cdivisions-i)/cdivisions)).toFixed(precision); ++ } + } + } else { + for (var i=cdivisions; i >= 0; i--) { +- labels[i] = (caxisdelta*(cdivisions-i)/cdivisions+caxis[0]).toFixed(precision); ++ if (format === 'f') { ++ labels[i] = (caxisdelta*(cdivisions-i)/cdivisions+caxis[0]).toFixed(precision); ++ } ++ else if (format === 'e') { ++ labels[i] = (caxisdelta*(cdivisions-i)/cdivisions+caxis[0]).toPrecision(precision); ++ } ++ else { ++ labels[i] = (caxisdelta*(cdivisions-i)/cdivisions+caxis[0]).toFixed(precision); ++ } + } + } //}}} + //{{{ Initialize colorbar canvas +@@ -116,166 +130,8 @@ + tcontext.fillStyle = tgradient; + tcontext.fillRect(0, 0, 256, 256); + tURL = tcanvas.toDataURL(); +- node.texture = initTexture(gl, tURL); +- node.textureCanvas = tcanvas; +- node.caxis = options.getfieldvalue('caxis',[ArrayMin(data), ArrayMax(data)]); ++ canvas.unitNode.texture = initTexture(canvas.gl, tURL); + //}}} +- //{{{ expdisp contours +- if (options.exist('expdisp')) { +- canvas.nodes.expdisp = Node(gl, options); +- var node = canvas.nodes.expdisp; +- +- //declare variables: {{{ +- var vertices = []; +- var indices = []; +- var colors = []; +- var rgbcolor = []; +- var xmin, xmax; +- var ymin, ymax; +- var zmin, zmax; +- var scale; +- +- //Process data and model +- var x = options.getfieldvalue('expdisp').x; +- var y = options.getfieldvalue('expdisp').y; +- var z = Array.apply(null, Array(x.length)).map(Number.prototype.valueOf, 0); +- +- if (options.getfieldvalue('expdisp').z) { +- z = options.getfieldvalue('expdisp').z; +- } +- //}}} +- +- //Compute coordinates and data range: //{{{ +- var modelxlim = [ArrayMin(x), ArrayMax(x)]; +- var modelylim = [ArrayMin(y), ArrayMax(y)]; +- var modelzlim = [ArrayMin(z), ArrayMax(z)]; +- var xlim = options.getfieldvalue('xlim', modelxlim); +- var ylim = options.getfieldvalue('ylim', modelylim); +- var zlim = options.getfieldvalue('zlim', modelzlim); +- xmin = xlim[0]; +- xmax = xlim[1]; +- ymin = ylim[0]; +- ymax = ylim[1]; +- zmin = zlim[0]; +- zmax = zlim[1]; +- //}}} +- +- //Compute scaling: //{{{ +- var scale = 1 / (xmax - xmin); +- node.shaderName = 'colored'; +- node.shader = gl.shaders[node.shaderName].program; +- node.scale = [scale, scale, scale*options.getfieldvalue('heightscale', 1)]; +- node.translation = [(xmin + xmax) / (-2 / scale), (ymin + ymax) / (-2 / scale), (zmin + zmax) / (-2 / scale)]; +- node.modelMatrix = updateModelMatrix(node); +- node.drawMode = gl.LINE_LOOP; +- node.drawOrder = 0; +- node.useIndexBuffer = false; +- node.disableDepthTest = true; +- //}}} +- +- //some defaults: +- colors.itemSize = 4; +- +- //retrieve some options +- var linewidth=options.getfieldvalue('linewidth', 1); +- var edgecolor=options.getfieldvalue('edgecolor','black'); //RGBCOLOR? +- +- vertices.itemSize = 3; +- for(var i=0; i < x.length; i++){ +- vertices[vertices.length] = x[i]; +- vertices[vertices.length] = y[i]; +- vertices[vertices.length] = z[i]; +- +- //edgecolor +- rgbcolor = [0.0, 0.0, 0.0]; +- colors[colors.length] = rgbcolor[0]; +- colors[colors.length] = rgbcolor[1]; +- colors[colors.length] = rgbcolor[2]; +- colors[colors.length] = 1.0; +- } +- +- //Initalize buffers: +- node.arrays = [vertices, colors]; +- node.buffers = initBuffers(gl, node.arrays); +- } //}}} +- //{{{ cloud of points +- if (options.exist('cloud')) { +- canvas.nodes.cloud = Node(gl, options); +- var node = canvas.nodes.cloud; +- +- //declare variables: {{{ +- var vertices = []; +- var indices = []; +- var colors = []; +- var rgbcolor = []; +- var xmin, xmax; +- var ymin, ymax; +- var zmin, zmax; +- var scale; +- +- //Process data and model +- var x = options.getfieldvalue('cloud').x; +- var y = options.getfieldvalue('cloud').y; +- var z = Array.apply(null, Array(x.length)).map(Number.prototype.valueOf, 0); +- +- if (options.getfieldvalue('cloud').z) { +- z = options.getfieldvalue('cloud').z; +- } +- //}}} +- +- //Compute coordinates and data range: //{{{ +- var modelxlim = [ArrayMin(x), ArrayMax(x)]; +- var modelylim = [ArrayMin(y), ArrayMax(y)]; +- var modelzlim = [ArrayMin(z), ArrayMax(z)]; +- var xlim = options.getfieldvalue('xlim', modelxlim); +- var ylim = options.getfieldvalue('ylim', modelylim); +- var zlim = options.getfieldvalue('zlim', modelzlim); +- xmin = xlim[0]; +- xmax = xlim[1]; +- ymin = ylim[0]; +- ymax = ylim[1]; +- zmin = zlim[0]; +- zmax = zlim[1]; +- //}}} +- +- //Compute scaling: //{{{ +- var scale = 1 / (xmax - xmin); +- node.shaderName = 'colored'; +- node.shader = gl.shaders[node.shaderName].program; +- node.scale = [scale, scale, scale*options.getfieldvalue('heightscale', 1)]; +- node.translation = [(xmin + xmax) / (-2 / scale), (ymin + ymax) / (-2 / scale), (zmin + zmax) / (-2 / scale)]; +- node.modelMatrix = updateModelMatrix(node); +- node.drawMode = gl.POINTS; +- node.drawOrder = 0; +- node.useIndexBuffer = false; +- node.disableDepthTest = true; +- //}}} +- +- //some defaults: +- colors.itemSize = 4; +- +- //retrieve some options +- var linewidth=options.getfieldvalue('linewidth', 1); +- var edgecolor=options.getfieldvalue('edgecolor','black'); //RGBCOLOR? +- +- vertices.itemSize = 3; +- for(var i=0; i < x.length; i++){ +- vertices[vertices.length] = x[i]; +- vertices[vertices.length] = y[i]; +- vertices[vertices.length] = z[i]; +- +- //edgecolor +- rgbcolor = [0.0, 0.0, 0.0]; +- colors[colors.length] = rgbcolor[0]; +- colors[colors.length] = rgbcolor[1]; +- colors[colors.length] = rgbcolor[2]; +- colors[colors.length] = 1.0; +- } +- +- //Initalize buffers: +- node.arrays = [vertices, colors]; +- node.buffers = initBuffers(gl, node.arrays); +- } //}}} + //{{{ text display + if (options.exist('textlabels')) { + var textcanvas, textcanvasid; +@@ -324,39 +180,39 @@ + var overlaycanvasid = options.getfieldvalue('latlongoverlayid', options.getfieldvalue('canvasid')+'-overlay'); + var overlaycanvas = $('#'+overlaycanvasid)[0]; + var latitudes = { +- //"-90": 1, +- //"-65": .999, +- "-60": 0.994046875, +- //"-55": 0.983187500000002, +- //"-50": 0.97173550854167, +- "-45": 0.955729166666666, +- //"-40": 0.94218750000000218, +- //"-35": 0.94218750000000218, +- "-30": 0.9226562500000024, +- //"-25": 0.87934895833333526, +- //"-20": 0.856572916666669, +- //"-15": 0.830729166666665, +- //"-10": 0.803552708333336, +- //"-5": 0.77395833333333541, +- "0": 0.74218749999999811, +- //"5": 0.70950364583333347, +- //"10": 0.67479166666666823, +- //"15": 0.63932291666666663, +- //"20": 0.60171875, +- //"25": 0.563453125, +- "30": 0.523390625000001, +- //"35": 0.48401875, +- //"40": 0.44296875, +- "45": 0.4020001, +- //"50": 0.3578125, +- //"55": 0.311875, +- "60": 0.26953124999999978, +- //"65": 0.225390625, +- //"70": 0.18125, +- //"75": 0.13541666666666671, +- //"80": 0.08953125, +- //"85": 0.046250000000000013, +- //"90": 0.0, ++ //'-90': 1, ++ //'-65': .999, ++ '-60': 0.994046875, ++ //'-55': 0.983187500000002, ++ //'-50': 0.97173550854167, ++ '-45': 0.955729166666666, ++ //'-40': 0.94218750000000218, ++ //'-35': 0.94218750000000218, ++ '-30': 0.9226562500000024, ++ //'-25': 0.87934895833333526, ++ //'-20': 0.856572916666669, ++ //'-15': 0.830729166666665, ++ //'-10': 0.803552708333336, ++ //'-5': 0.77395833333333541, ++ '0': 0.74218749999999811, ++ //'5': 0.70950364583333347, ++ //'10': 0.67479166666666823, ++ //'15': 0.63932291666666663, ++ //'20': 0.60171875, ++ //'25': 0.563453125, ++ '30': 0.523390625000001, ++ //'35': 0.48401875, ++ //'40': 0.44296875, ++ '45': 0.4020001, ++ //'50': 0.3578125, ++ //'55': 0.311875, ++ '60': 0.26953124999999978, ++ //'65': 0.225390625, ++ //'70': 0.18125, ++ //'75': 0.13541666666666671, ++ //'80': 0.08953125, ++ //'85': 0.046250000000000013, ++ //'90': 0.0, + } + var longitudes = [-150, -120, -90, -60, -30, 0, 30, 60, 90, 120, 150, 180]; + overlaycanvas.draw = function(canvas) { +@@ -400,96 +256,197 @@ + var is2d = meshresults[4]; + var isplanet = meshresults[5]; + +- var modelxlim = [ArrayMin(x), ArrayMax(x)]; +- var modelylim = [ArrayMin(y), ArrayMax(y)]; +- var modelzlim = [ArrayMin(z), ArrayMax(z)]; +- var xlim = options.getfieldvalue('xlim', modelxlim); +- var ylim = options.getfieldvalue('ylim', modelylim); +- var zlim = options.getfieldvalue('zlim', modelzlim); +- xmin = xlim[0]; +- xmax = xlim[1]; +- ymin = ylim[0]; +- ymax = ylim[1]; +- zmin = zlim[0]; +- zmax = zlim[1]; ++ var xlim = options.getfieldvalue('xlim', [ArrayMin(x), ArrayMax(x)]); ++ var ylim = options.getfieldvalue('ylim', [ArrayMin(y), ArrayMax(y)]); ++ var zlim = options.getfieldvalue('zlim', [ArrayMin(z), ArrayMax(z)]); ++ ++ var global = vec3.length([(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2]) < 6371000/10; //tolerance for global models = center is 637100 meters away from center of earth ++ var translation = global ? [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2] : [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) - 6371000, (zlim[0] + zlim[1]) / 2]; + +- var global = vec3.length([(xmin + xmax) / 2, (ymin + ymax) / 2, (zmin + zmax) / 2]) < 6371000/10; //tolerance for global models = center is 637100 meters away from center of earth +- var atmosphereScale = 1.25; +- var translation = global ? [(xmin + xmax) / 2, (ymin + ymax) / 2, (zmin + zmax) / 2] : [(xmin + xmax) / 2, (ymin + ymax) - 6371000, (zmin + zmax) / 2]; +- +- if (options.getfieldvalue('render',[]).indexOf('sky')!=-1) { +- //atmosphere +- var node = Node(gl); +- node.name = "atmosphere"; +- node.shaderName = "SkyFromSpace"; +- node.shader = gl.shaders[node.shaderName]; +- node.drawOrder = 1; +- node.cullFace = gl.FRONT; +- node.enableCullFace = true; +- node.mesh = GL.Mesh.icosahedron({size: 6371000*atmosphereScale, subdivisions: 6}); +- node.rotation = [0, 0, 0]; +- node.translation = translation; +- node.center = [0, 0, 0]; +- updateModelMatrix(node); +- canvas.nodes[node.name] = node; ++ var renderObjects = options.getfieldvalue('render',{}); ++ if ('sky' in renderObjects && !('sky' in canvas.nodes)) { ++ var object = renderObjects.sky; ++ object = { ++ enabled: defaultFor(object.enabled, true), ++ scale: defaultFor(object.scale, 1), ++ }; ++ if (object.enabled) { ++ var atmosphereScale = 1.25; ++ var mesh = GL.Mesh.icosahedron({size: 6371000 * atmosphereScale, subdivisions: 5}); ++ var texture = initTexture(gl, canvas.rootPath + 'textures/TychoSkymapII_t4_2k.jpg'); ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'sky', ++ 'shaderName', 'SkyFromSpace', ++ 'cullFace', gl.FRONT, ++ 'mesh', mesh, ++ 'texture',texture, ++ 'translation',translation ++ ); ++ } + } +- if (options.getfieldvalue('render',[]).indexOf('space')!=-1) { +- //skysphere +- node = Node(gl); +- node.name = "skysphere"; +- node.shaderName = "Textured"; +- node.shader = gl.shaders[node.shaderName]; +- node.drawOrder = 2; +- node.cullFace = gl.FRONT; +- node.enableCullFace = true; +- node.mesh = GL.Mesh.sphere({size: 6371000*20}); +- node.texture = initTexture(gl, canvas.rootPath+'textures/TychoSkymapII_t4_2k.jpg'); +- node.rotation = [0, 0, 0]; +- node.translation = translation; +- node.center = [0, 0, 0]; +- updateModelMatrix(node); +- canvas.nodes[node.name] = node; ++ if ('space' in renderObjects && !('space' in canvas.nodes)) { ++ var object = renderObjects.space; ++ object = { ++ enabled: defaultFor(object.enabled, true), ++ scale: defaultFor(object.scale, 1), ++ }; ++ if (object.enabled) { ++ var mesh = GL.Mesh.sphere({size: 6371000 * 20}); ++ var texture = initTexture(gl, canvas.rootPath + 'textures/TychoSkymapII_t4_2k.jpg'); ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'space', ++ 'shaderName', 'Textured', ++ 'cullFace', gl.FRONT, ++ 'drawOrder', 2, ++ 'mesh', mesh, ++ 'texture',texture, ++ 'translation',translation ++ ); ++ } + } ++ if ('coastlines' in renderObjects && !('coastlines' in canvas.nodes)) { ++ var object = renderObjects.coastlines; ++ object = { ++ enabled: defaultFor(object.enabled, false), ++ scale: defaultFor(object.scale, 1), ++ x: defaultFor(object.x, {}), ++ y: defaultFor(object.y, {}), ++ z: defaultFor(object.z, {}) ++ }; ++ if (object.enabled) { ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'coastlines', ++ 'shaderName', 'Colored', ++ 'drawMode', gl.LINE_STRIP, ++ 'lineWidth', options.getfieldvalue('linewidth', 1), ++ 'scale', [object.scale, object.scale, object.scale], ++ 'rotation', [-90, 0, 0] ++ ); ++ node.patch('Vertices', [object.x, object.y, object.z], 'FaceColor', 'none'); ++ } ++ } ++ if ('graticule' in renderObjects && !('graticule' in canvas.nodes)) { ++ var object = renderObjects.graticule; ++ object = { ++ enabled: defaultFor(object.enabled, false), ++ scale: defaultFor(object.scale, 1), ++ x: defaultFor(object.x, {}), ++ y: defaultFor(object.y, {}), ++ z: defaultFor(object.z, {}) ++ }; ++ if (object.enabled) { ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'graticule', ++ 'shaderName', 'Colored', ++ 'drawMode', gl.LINE_STRIP, ++ 'lineWidth', options.getfieldvalue('linewidth', 1), ++ 'scale', [object.scale, object.scale, object.scale], ++ 'rotation', [-90, 0, 0] ++ ); ++ node.patch('Vertices', [object.x, object.y, object.z], 'FaceColor', 'none'); ++ } ++ } ++ if ('cities' in renderObjects && !('cities' in canvas.nodes)) { ++ var object = renderObjects.cities; ++ object = { ++ enabled: defaultFor(object.enabled, false), ++ scale: defaultFor(object.scale, 1), ++ size: defaultFor(object.size, 1.5), ++ color: defaultFor(object.color, 'black'), ++ x: defaultFor(object.x, {}), ++ y: defaultFor(object.y, {}), ++ z: defaultFor(object.z, {}), ++ indices: defaultFor(object.indices, {}) ++ }; ++ if (object.enabled) { ++ var mesh = GL.Mesh.icosahedron({size: object.size, subdivisions: 1}); ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'cities', ++ 'shaderName', 'Colored', ++ 'diffuseColor', object.color, ++ 'lineWidth', options.getfieldvalue('linewidth', 1), ++ 'scale', [object.scale, object.scale, object.scale], ++ 'rotation', [-90, 0, 0] ++ ); ++ node.geometryShader('Mesh', mesh, 'Vertices', [object.x, object.y, object.z], 'Indices', object.indices); ++ } ++ } ++ if ('city' in renderObjects) { ++ var object = renderObjects.city; ++ object = { ++ enabled: defaultFor(object.enabled, false), ++ name: defaultFor(object.name, 'NY'), ++ size: defaultFor(object.size, 15000), ++ color: defaultFor(object.color, 'magenta'), ++ x: defaultFor(object.x, {}), ++ y: defaultFor(object.y, {}), ++ z: defaultFor(object.z, {}) ++ }; ++ if (object.enabled) { ++ //city ++ var mesh = GL.Mesh.sphere({size: object.size}); ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'city', ++ 'shaderName', 'Colored', ++ 'diffuseColor', object.color, ++ 'mesh', mesh, ++ 'translation', [object.x, object.z, -object.y] ++ ); ++ ++ var overlaycanvasid = options.getfieldvalue('overlayid', options.getfieldvalue('canvasid')+'-overlay'); ++ var overlaycanvas = $('#'+overlaycanvasid)[0]; ++ overlaycanvas.draw = function(canvas) { ++ var rect = overlaycanvas.getBoundingClientRect(); ++ overlaycanvas.width = rect.width; ++ overlaycanvas.height = rect.height; ++ var ctx = overlaycanvas.getContext('2d'); ++ var node = canvas.nodes['city']; ++ node.translation = [object.x, object.z, -object.y]; ++ node.updateModelMatrix(); ++ var screenPoint = vec3.transformMat4(vec3.create(), node.translation, canvas.camera.vpMatrix); ++ var x = (screenPoint[0] + 1.0) * (canvas.width / 2) + canvas.selector.offset().left; ++ var y = (-screenPoint[1] + 1.0) * (canvas.height / 2) + canvas.selector.offset().top; ++ ++ ctx.font = String(options.getfieldvalue('colorbarfontsize', 22))+'px Arial Black, sans-serif'; ++ ctx.fillStyle = options.getfieldvalue('colorbarfontcolor','black'); ++ ctx.strokeStyle = 'white'; ++ ctx.textAlign = 'center'; ++ ctx.textBaseline = 'middle'; ++ ctx.fillText(object.name, x, y); ++ ctx.strokeText(object.name, x, y); ++ } ++ canvas.overlaycanvas = overlaycanvas; ++ } ++ } + if (canvas.clouds.enabled) { + //clouds + for (var i = 0; i < canvas.clouds.quantity; i++) { +- node = Node(gl); +- node.name = "clouds" + i; +- node.shaderName = "Clouds"; +- node.shader = gl.shaders[node.shaderName]; +- node.drawOrder = 2; +- node.cullFace = gl.BACK; +- node.enableCullFace = true; +- node.mesh = GL.Mesh.fromURL(canvas.rootPath+'obj/cloud.obj'); +- node.rotation = [0, 0, 0]; +- node.scale = [2500, 2500, 2500]; +- node.translation = [translation[0], translation[1] - 405000, translation[2]]; +- node.center = [0, 0, 0]; +- node.animation = {"time": Date.now(),"target": node.translation,"current": node.translation}; +- updateModelMatrix(node); +- canvas.nodes[node.name] = node; +- //canvas.clouds.list ++ var mesh = GL.Mesh.fromURL(canvas.rootPath+'obj/cloud.obj'); ++ translation = [translation[0] + Math.floor((Math.random() * (1 + 12000 - (-12000)) + (-12000))), translation[1] - 405000, translation[2] + Math.floor((Math.random() * (1 + 12000 - (-12000)) + (-12000)))]; ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'clouds' + i, ++ 'shaderName', 'Textured', ++ 'animation', {'time': Date.now(),'target': translation,'current': translation}, ++ 'diffuseColor', [0.7,0.7,0.7,1.0], ++ 'mesh', mesh, ++ 'scale', [2500, 2500, 2500], ++ 'translation', translation ++ ); + } +- //TODO: Steven, please add total cloud nodes, randomly spread over the mesh, giving each one a new name and adding them to the canvas.clouds.list so that we can track them later. +- + } +- if (options.getfieldvalue('render',[]).indexOf('latlong')!=-1) { +- //latlong +- node = Node(gl); +- node.name = "clouds"; +- node.shaderName = "Clouds"; +- node.shader = gl.shaders[node.shaderName]; +- node.drawOrder = 2; +- node.cullFace = gl.BACK; +- node.enableCullFace = true; +- node.mesh = GL.Mesh.fromURL(canvas.rootPath+'obj/cloud.obj'); +- node.rotation = [0, 0, 0]; +- node.scale = [2500, 2500, 2500]; +- node.translation = [translation[0], translation[1] - 405000, translation[2]]; +- node.center = [0, 0, 0]; +- node.animation = {"time": Date.now(),"target": node.translation,"current": node.translation}; +- updateModelMatrix(node); +- canvas.nodes[node.name] = node; +- } + } //}}} + } //}}} +Index: ../trunk-jpl/src/m/plot/plot_transient_movie.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_transient_movie.m (revision 21767) ++++ ../trunk-jpl/src/m/plot/plot_transient_movie.m (revision 21768) +@@ -6,7 +6,7 @@ + % See also: PLOTMODEL, PLOT_UNIT, PLOT_MANAGER + + %prepare subplot +- subplot(width,width,i); ++ subplot(width,width,i); + + %xlim + if exist(options,'transient_movie_field'), +Index: ../trunk-jpl/src/m/plot/webgl_node.js +=================================================================== +--- ../trunk-jpl/src/m/plot/webgl_node.js (nonexistent) ++++ ../trunk-jpl/src/m/plot/webgl_node.js (revision 21768) +@@ -0,0 +1,464 @@ ++//NODE class definition //{{{ ++// Description: ++// Contains all information for rendering an object in WebGL, including mesh, materials, shaders, and other attributes. ++// Usage: ++// node=new Node('canvas', canvas); ++ ++function Node() { //{{{ ++ //properties ++ // {{{ ++ var args = Array.prototype.slice.call(arguments); ++ var options = new pairoptions(args.slice(0,args.length)); ++ ++ this.canvas = options.getfieldvalue('canvas', null), ++ this.options = options.getfieldvalue('options', null), ++ this.gl = canvas.gl; ++ ++ this.alpha = options.getfieldvalue('alpha', 1.0), ++ this.animation = options.getfieldvalue('animation', {}), ++ this.arrays = options.getfieldvalue('arrays', {}), ++ this.caxis = options.getfieldvalue('caxis', [0.0, 1.0]), ++ this.center = options.getfieldvalue('center', vec3.create()), ++ this.cullFace = options.getfieldvalue('cullFace', this.gl.BACK), ++ this.computeIndices = options.getfieldvalue('computeIndices', true), ++ this.disableDepthTest = options.getfieldvalue('disableDepthTest', false), ++ this.diffuseColor = options.getfieldvalue('diffuseColor', [0.0, 0.0, 0.0, 1.0]), ++ this.drawMode = options.getfieldvalue('drawMode', this.gl.TRIANGLES), ++ this.drawOrder = options.getfieldvalue('drawOrder', 1), ++ this.enabled = options.getfieldvalue('enabled', true), ++ this.enableCullFace = options.getfieldvalue('enableCullFace', true), ++ this.hideOcean = options.getfieldvalue('hideOcean', false), ++ this.lineWidth = options.getfieldvalue('lineWidth', 1.0), ++ this.log = options.getfieldvalue('log', false), ++ this.maskColor = options.getfieldvalue('maskColor', vec4.fromValues(0.0, 0.0, 1.0, 1.0)), ++ this.maskEnabled = options.getfieldvalue('maskEnabled', false), ++ this.maskHeight = options.getfieldvalue('maskHeight', 150.0), ++ this.maskZerosColor = options.getfieldvalue('maskZerosColor', [1.0, 1.0, 1.0, 1.0]), ++ this.maskZerosEnabled = options.getfieldvalue('maskZerosEnabled', false), ++ this.maskZerosTolerance = options.getfieldvalue('maskZerosTolerance', 1e-6), ++ this.maskZerosZeroValue = options.getfieldvalue('maskZerosZeroValue', 0.5), ++ this.mesh = options.getfieldvalue('mesh', undefined), ++ this.name = options.getfieldvalue('name', 'node'), ++ this.nanIndices = options.getfieldvalue('nanIndices', new Set()), ++ this.octree = options.getfieldvalue('octree', undefined), ++ this.pointSize = options.getfieldvalue('pointSize', 15.0), ++ this.shaderName = options.getfieldvalue('shaderName', 'Colored'), ++ this.shader = options.getfieldvalue('shader', this.gl.shaders[this.shaderName]), ++ this.texture = options.getfieldvalue('texture', undefined), ++ this.scale = options.getfieldvalue('scale', vec3.fromValues(1, 1, 1)), ++ this.rotation = options.getfieldvalue('rotation', vec3.create()), ++ this.translation = options.getfieldvalue('translation', vec3.create()), ++ this.modelMatrix = options.getfieldvalue('modelMatrix', mat4.create()), ++ this.rotationMatrix = options.getfieldvalue('rotationMatrix', mat4.create()), ++ this.inverseModelMatrix = options.getfieldvalue('inverseModelMatrix', mat4.create()), ++ this.inverseRotationMatrix = options.getfieldvalue('inverseRotationMatrix', mat4.create()) ++ //}}} ++ //initialize {{{ ++ //if (this.name in canvas.nodes) abort? ++ this.updateModelMatrix(); ++ this.updateDiffuseColor(); ++ canvas.nodes[this.name] = this; ++ //}}} ++} //}}} ++Node.prototype.updateModelMatrix = function() { //{{{ ++ //Update the model matrix if rotation, scale, or translation have been manually modified. ++ var modelMatrix = mat4.create(); ++ ++ var translationMatrix = mat4.create(); ++ mat4.translate(translationMatrix, translationMatrix, vec3.negate(vec3.create(), this.center)); //scale/rotation centering ++ mat4.multiply(modelMatrix, translationMatrix, modelMatrix); ++ ++ var scaleMatrix = mat4.create(); ++ mat4.scale(scaleMatrix, scaleMatrix, this.scale); ++ mat4.multiply(modelMatrix, scaleMatrix, modelMatrix); ++ ++ var rotationMatrix = mat4.create(); ++ var zRotationMatrix = mat4.create(); ++ mat4.rotate(zRotationMatrix, zRotationMatrix, DEG2RAD * this.rotation[2], [0.0, 0.0, 1.0]); ++ mat4.multiply(rotationMatrix, zRotationMatrix, rotationMatrix); ++ var yRotationMatrix = mat4.create(); ++ mat4.rotate(yRotationMatrix, yRotationMatrix, DEG2RAD * this.rotation[1], [0.0, 1.0, 0.0]); ++ mat4.multiply(rotationMatrix, yRotationMatrix, rotationMatrix); ++ var xRotationMatrix = mat4.create(); ++ mat4.rotate(xRotationMatrix, xRotationMatrix, DEG2RAD * this.rotation[0], [1.0, 0.0, 0.0]); ++ mat4.multiply(rotationMatrix, xRotationMatrix, rotationMatrix); ++ mat4.multiply(modelMatrix, rotationMatrix, modelMatrix); ++ ++ mat4.identity(translationMatrix); ++ mat4.translate(translationMatrix, translationMatrix, this.center); //relative translation ++ mat4.multiply(modelMatrix, translationMatrix, modelMatrix); ++ ++ mat4.identity(translationMatrix); ++ mat4.translate(translationMatrix, translationMatrix, this.translation); //absolute translation ++ mat4.multiply(modelMatrix, translationMatrix, modelMatrix); ++ ++ this.modelMatrix = modelMatrix; ++ this.inverseModelMatrix = mat4.invert(mat4.create(), modelMatrix); ++ this.rotationMatrix = rotationMatrix; ++ this.inverseRotationMatrix = mat4.invert(mat4.create(), rotationMatrix); ++} //}}} ++Node.prototype.updateDiffuseColor = function() { //{{{ ++ //Update the diffuse color with an RGB color name or vec4 containing r, g, b, and alpha values from 0.0 to 1.0 ++ var color = this.diffuseColor; ++ if (typeof color === 'string') { ++ color = new RGBColor(color); ++ if (color.ok) color = [color.r/255.0, color.g/255.0, color.b/255.0, 1.0]; ++ else throw Error(sprintf("s%s%s\n","initWebGL error message: cound not find out edgecolor color for curent canvas ", canvas)); ++ } ++ this.diffuseColor = color; ++} //}}} ++Node.prototype.transform = function() { //{{{ ++ //Transforms the translation, rotation, or scle fo the node and updates the model matrix. ++ var args = Array.prototype.slice.call(arguments); ++ var options = new pairoptions(args.slice(0,args.length)); ++ ++ var translation = options.getfieldvalue('translation', undefined); ++ var rotation = options.getfieldvalue('rotation', undefined); ++ var scale = options.getfieldvalue('scale', undefined); ++ ++ if (!isEmptyOrUndefined(translation)) this.translation = translation; ++ if (!isEmptyOrUndefined(rotation)) this.rotation = rotation; ++ if (!isEmptyOrUndefined(scale)) this.scale = scale; ++ this.updateModelMatrix(); ++} //}}} ++Node.prototype.patch = function() { //{{{ ++ //Emulates the behavior of MATLAB patch function by constructing a mesh from arguments. ++ //Limitations: ++ // -Expects pair labeled arguments ('FaceColor','none',...). ++ // -Only handles Face/Vertices/FaceVertexCData element/node plots. ++ // -Only supports FaceColor 'interp' and 'none'. ++ ++ var args = Array.prototype.slice.call(arguments); ++ var options = new pairoptions(args.slice(0,args.length)); ++ ++ var faces = options.getfieldvalue('Faces', undefined); ++ var vertices = options.getfieldvalue('Vertices', undefined); ++ var faceVertexCData = options.getfieldvalue('FaceVertexCData', undefined); ++ var faceColor = options.getfieldvalue('FaceColor', 'interp'); ++ var edgeColor = options.getfieldvalue('EdgeColor', this.diffuseColor); ++ var lineWidth = options.getfieldvalue('linewidth', 1); ++ ++ this.faces = faces; ++ this.vertices = vertices; ++ this.diffuseColor = edgeColor; ++ this.updateDiffuseColor(); ++ ++ this.patchVertices(faceVertexCData, faces, vertices); ++ this.patchCoords(faceVertexCData, faces, vertices); ++ this.patchIndices(faces, faceColor); ++ ++ this.mesh = GL.Mesh.load(this.arrays, null, null, this.gl); ++ //this.mesh.computeNormals(); ++ this.computeOctree(); ++} //}}} ++Node.prototype.patchVertices = function(faceVertexCData, faces, vertices) { //{{{ ++ //Patch subfunction for processing xyz vertices. ++ var vertexArray; ++ var face; ++ ++ if (isEmptyOrUndefined(faceVertexCData)) { ++ vertexArray = new Float32Array(vertices[0].length * 3); ++ for(var i = 0, v = 0; i < vertices[0].length; i++) { ++ vertexArray[v++] = vertices[0][i]; ++ vertexArray[v++] = vertices[1][i]; ++ vertexArray[v++] = vertices[2][i]; ++ } ++ } ++ else if (!Array.isArray(faceVertexCData[0])) { //indexed plot - faceVertexCData = [0, 2.32, 231.1, ...] ++ if (faceVertexCData.length === faces.length) { //element plot ++ vertexArray = new Float32Array(faces.length * 3 * 3); ++ for(var i = 0, v = 0, t = 0; i < faces.length; i++) { ++ face = [faces[i][0] - 1, faces[i][1] - 1, faces[i][2] - 1]; ++ for(var j = 0; j < face.length; j++) { ++ if (isNaN(faceVertexCData[i])) { ++ this.nanIndices.add(i); ++ vertexArray[v++] = 0.0; ++ vertexArray[v++] = 0.0; ++ vertexArray[v++] = 0.0; ++ } ++ else { ++ vertexArray[v++] = vertices[0][face[j]]; ++ vertexArray[v++] = vertices[1][face[j]]; ++ vertexArray[v++] = vertices[2][face[j]]; ++ } ++ } ++ } ++ this.computeIndices = false; ++ } ++ else if (faceVertexCData.length === vertices[0].length) { //node plot ++ vertexArray = new Float32Array(vertices[0].length * 3); ++ for(var i = 0, v = 0, t = 0; i < vertices[0].length; i++) { ++ if (isNaN(faceVertexCData[i])) { ++ this.nanIndices.add(i); ++ vertexArray[v++] = 0.0; ++ vertexArray[v++] = 0.0; ++ vertexArray[v++] = 0.0; ++ } ++ else { ++ vertexArray[v++] = vertices[0][i]; ++ vertexArray[v++] = vertices[1][i]; ++ vertexArray[v++] = vertices[2][i]; ++ } ++ } ++ } ++ } ++ else if (Array.isArray(faceVertexCData[0])) { //JS specific: precomputed UV coord plot - faceVertexCData = [[0, 0.99, 0.4, ...],[0, 0.99, 0.4, ...]] ++ if (faceVertexCData[0].length === faces.length) { //element plot ++ vertexArray = new Float32Array(faces.length * 3 * 3); ++ for(var i = 0, v = 0, t = 0; i < faces.length; i++) { ++ face = [faces[i][0] - 1, faces[i][1] - 1, faces[i][2] - 1]; ++ for(var j = 0; j < face.length; j++) { ++ vertexArray[v++] = vertices[0][face[j]]; ++ vertexArray[v++] = vertices[1][face[j]]; ++ vertexArray[v++] = vertices[2][face[j]]; ++ } ++ } ++ this.computeIndices = false; ++ } ++ else if (faceVertexCData[0].length === vertices[0].length) { //node plot ++ vertexArray = new Float32Array(vertices[0].length * 3); ++ for(var i = 0, v = 0, t = 0; i < vertices[0].length; i++) { ++ vertexArray[v++] = vertices[0][i]; ++ vertexArray[v++] = vertices[1][i]; ++ vertexArray[v++] = vertices[2][i]; ++ } ++ } ++ } ++ this.arrays.vertices = vertexArray; ++} //}}} ++Node.prototype.patchCoords = function(faceVertexCData, faces, vertices) { //{{{ ++ //Patch subfunction for processing texture coords/UVs. ++ var coordArray; ++ var cramge; ++ var caxis = this.caxis; ++ var face; ++ ++ if (isEmptyOrUndefined(faceVertexCData)) { return; } ++ ++ //Use logarithmic scaling if it is valid ++ if (this.log !== false && this.log !== 'off') { ++ caxis = [ ++ Math.log10(caxis[0]) / Math.log10(this.log), ++ Math.log10(caxis[1]) / Math.log10(this.log) ++ ]; ++ } ++ ++ if (!Array.isArray(faceVertexCData[0])) { //indexed plot - faceVertexCData = [0, 2.32, 231.1, ...] ++ if (faceVertexCData.length === faces.length) { //element plot ++ coordArray = new Float32Array(faces.length * 3 * 2); ++ crange = caxis[1] - caxis[0]; ++ for(var i = 0, v = 0, t = 0; i < faces.length; i++) { ++ face = [faces[i][0] - 1, faces[i][1] - 1, faces[i][2] - 1]; ++ for(var j = 0; j < face.length; j++) { ++ if (isNaN(faceVertexCData[i])) { ++ this.nanIndices.add(i); ++ coordArray[t++] = 0.0; ++ coordArray[t++] = 0.0; ++ } ++ else { ++ coordArray[t++] = 0.5; ++ coordArray[t++] = clamp((faceVertexCData[i] - caxis[0]) / crange, 0.0, 1.0); ++ } ++ } ++ } ++ this.computeIndices = false; ++ } ++ else if (faceVertexCData.length === vertices[0].length) { //node plot ++ coordArray = new Float32Array(vertices[0].length * 2); ++ crange = caxis[1] - caxis[0]; ++ for(var i = 0, v = 0, t = 0; i < vertices[0].length; i++) { ++ if (isNaN(faceVertexCData[i])) { ++ this.nanIndices.add(i); ++ coordArray[t++] = 0.0; ++ coordArray[t++] = 0.0; ++ } ++ else { ++ coordArray[t++] = 0.5; ++ coordArray[t++] = clamp((faceVertexCData[i] - caxis[0]) / crange, 0.0, 1.0); ++ } ++ } ++ } ++ } ++ else if (Array.isArray(faceVertexCData[0])) { //JS specific: precomputed UV coord plot - faceVertexCData = [[0, 0.99, 0.4, ...],[0, 0.99, 0.4, ...]] ++ if (faceVertexCData[0].length === faces.length) { //element plot ++ coordArray = new Float32Array(faces.length * 3 * 2); ++ for(var i = 0, v = 0, t = 0; i < faces.length; i++) { ++ face = [faces[i][0] - 1, faces[i][1] - 1, faces[i][2] - 1]; ++ for(var j = 0; j < face.length; j++) { ++ coordArray[t++] = faceVertexCData[0][i]; ++ coordArray[t++] = faceVertexCData[1][i]; ++ } ++ } ++ this.computeIndices = false; ++ } ++ else if (faceVertexCData[0].length === vertices[0].length) { //node plot ++ coordArray = new Float32Array(vertices[0].length * 2); ++ for(var i = 0, v = 0, t = 0; i < vertices[0].length; i++) { ++ coordArray[t++] = faceVertexCData[0][i]; ++ coordArray[t++] = faceVertexCData[1][i]; ++ } ++ } ++ } ++ this.arrays.coords = coordArray; ++} //}}} ++Node.prototype.patchIndices = function(faces, faceColor) { //{{{ ++ //Patch subfunction for processing faces/elements/triangles/indices. ++ var indexArray; ++ var face; ++ ++ if (faceColor === 'none') { //Check for wireframe mesh rendering ++ if (this.drawMode === this.gl.TRIANGLES) { //NOTE: Stopgap to allow gl.LINE_STRIP nodes render normally. Only use case for faceColor === 'none' is for plot_mesh ++ this.drawMode = this.gl.LINES; ++ } ++ } ++ ++ if (this.computeIndices === true && !isEmptyOrUndefined(faces)) { ++ if (!isEmptyOrUndefined(faces[0])) { //Check for 2D format and process if needed ++ if (faceColor !== 'none') { //Check for triangle rendering ++ indexArray = new Uint16Array(faces.length * 3); ++ for(var i = 0, f = 0; i < faces.length; i++) { ++ face = [faces[i][0] - 1, faces[i][1] - 1, faces[i][2] - 1]; ++ if (this.nanIndices.has(face[0]) || this.nanIndices.has(face[1]) || this.nanIndices.has(face[2])) continue; //Skip triangle if contains NaN value. ++ indexArray[f++] = faces[i][0] - 1; ++ indexArray[f++] = faces[i][1] - 1; ++ indexArray[f++] = faces[i][2] - 1; ++ } ++ } ++ else { //Check for wireframe mesh rendering ++ indexArray = new Uint16Array(faces.length * 6); ++ for(var i = 0, f = 0; i < faces.length; i++) { ++ indexArray[f++] = faces[i][0] - 1; ++ indexArray[f++] = faces[i][1] - 1; ++ indexArray[f++] = faces[i][1] - 1; ++ indexArray[f++] = faces[i][2] - 1; ++ indexArray[f++] = faces[i][2] - 1; ++ indexArray[f++] = faces[i][0] - 1; ++ } ++ } ++ } ++ else { //Else, assume face indices have already been processed ++ indexArray = faces; ++ } ++ this.arrays.triangles = indexArray; ++ } ++} //}}} ++Node.prototype.updateBuffer = function() { //{{{ ++ //Updates the mesh buffers provided in place. ++ //NOTE: Only support coord buffers currently. ++ var args = Array.prototype.slice.call(arguments); ++ var options = new pairoptions(args.slice(0,args.length)); ++ ++ var coords = options.getfieldvalue('Coords', undefined); ++ var cacheIndex = options.getfieldvalue('CacheIndex', false); ++ ++ if (!isEmptyOrUndefined(coords)) { ++ this.patchCoords(coords, this.faces, this.vertices); ++ var buffer = this.mesh.getBuffer("coords"); ++ buffer.data = this.arrays.coords; ++ buffer.upload(this.gl.DYNAMIC_DRAW); ++ } ++} //}}} ++Node.prototype.computeOctree = function() { //{{{ ++ //Computes and caches octrees for a node. ++ var octree = this.canvas.octrees[this.name]; ++ if (isEmptyOrUndefined(octree)) { ++ octree = new GL.Octree(this.mesh); ++ } ++ this.canvas.octrees[this.name] = octree; ++ this.octree = octree; ++} //}}} ++Node.prototype.geometryShader = function() { //{{{ ++ //Emulates OpenGL geometry shaders by rendering each point as a mesh. ++ //Parameters: ++ // Mesh - the geometry to duplicate for each point. ++ // Vertices - the list of points to shade. ++ // Indices - (optional) ordered list for non-ordered Vertices objects. ++ ++ var args = Array.prototype.slice.call(arguments); ++ var options = new pairoptions(args.slice(0,args.length)); ++ ++ var mesh = options.getfieldvalue('Mesh', undefined); ++ var vertices = options.getfieldvalue('Vertices', undefined); ++ var indices = options.getfieldvalue('Indices', undefined); ++ ++ //For handling key-value object arrays, like xcity ++ for (var i = 0; i < vertices.length; i++) { ++ if (!Array.isArray(vertices[i])) { ++ var array = []; ++ var coordinateObject = vertices[i]; ++ var j = 0; ++ if (isEmptyOrUndefined(indices)) { ++ for (var key in object) { ++ array[j++] = coordinateObject[key]; ++ } ++ } ++ else { ++ for (var k = 0; k < indices.length; k++) { ++ array[j++] = coordinateObject[indices[k]]; ++ } ++ } ++ vertices[i] = array; ++ } ++ } ++ ++ var x = vertices[0]; ++ var y = vertices[1]; ++ var z = vertices[2]; ++ var meshVertices = mesh.getBuffer('vertices').data; ++ var meshIndicies = mesh.getIndexBuffer('triangles').data; ++ var indicies = new Uint16Array(meshIndicies.length * x.length); ++ var size = meshVertices.length * x.length / 3; ++ newX = new Float32Array(size); ++ newY = new Float32Array(size); ++ newZ = new Float32Array(size); ++ ++ //For each vertex in vertices, instantiate mesh geomtry centered around that point. ++ for(var i = 0, v = 0, e = 0; i < x.length; i++){ ++ var vector = [x[i], y[i], z[i]]; ++ for (var j = 0; j < meshVertices.length;) { ++ newX[v] = meshVertices[j++] + x[i]; ++ newY[v] = meshVertices[j++] + y[i]; ++ newZ[v++] = meshVertices[j++] + z[i]; ++ } ++ var offset = i * meshVertices.length / 3; ++ for (var j = 0; j < meshIndicies.length;) { ++ indicies[e++] = meshIndicies[j++] + offset; ++ } ++ } ++ ++ this.patch('Faces', indicies, 'Vertices', [newX, newY, newZ], 'FaceColor', 'interp'); ++} //}}} ++Node.prototype.scaleVertices = function(md, x, y, z, scale) { //{{{ ++ //Scales and returns vertices x, y, and z by factor scale. Uses md.geometry.scale for heightscaling in 3d meshes. ++ if (md.mesh.classname() === 'mesh3dsurface') { ++ var xyz, magnitude; ++ x = x.slice(); ++ y = y.slice(); ++ z = z.slice(); ++ for(var i = 0; i < x.length; i++) { ++ xyz = vec3.fromValues(x[i], y[i], z[i]); ++ magnitude = 1 + md.geometry.surface[i] * scale / vec3.length(xyz); ++ vec3.scale(xyz, xyz, magnitude); ++ x[i] = xyz[0]; ++ y[i] = xyz[1]; ++ z[i] = xyz[2]; ++ } ++ } ++ else { ++ z = z.slice(); ++ var zMin = ArrayMin(md.geometry.surface); ++ for(var i = 0; i < z.length; i++) { ++ z[i] = (z[i] - zMin) * scale + zMin; ++ } ++ } ++ return [x, y, z]; ++} //}}} ++Node.prototype.mergeVertices = function(x1, y1, z1, elements1, x2, y2, z2, elements2) { //{{{ ++ //Merges and returns two sets of indexed xyz vertices. ++ elements2 = elements2.slice(); ++ for (var i = 0, offset = x1.length; i < elements2.length; i++) { ++ elements2[i] = [elements2[i][0] + offset, elements2[i][1] + offset, elements2[i][2] + offset]; ++ } ++ return {x:x1.concat(x2), y:y1.concat(y2), z:z1.concat(z2), elements:elements1.concat(elements2)}; ++} //}}} ++//}}} +Index: ../trunk-jpl/src/m/plot/plot_manager.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_manager.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/plot_manager.js (revision 21768) +@@ -13,7 +13,7 @@ + var data = options.getfieldvalue('data'); + var canvas = initCanvas(options); + var gl = canvas.gl; +- //TODO: each plot_ should add their node to the canvas.node array ++ + //figure out if this is a special plot + if (typeof data === 'string'){ + +@@ -80,9 +80,9 @@ + plot_mesh(md,options,canvas); + return; + case 'none': +- if (!(options.exist('overlay'))){ +- plot_none(md,options,nlines,ncols,i); +- } ++ //if (!(options.exist('overlay'))){ ++ // plot_none(md,options,nlines,ncols,i); ++ //} + return; + case 'penalties': + plot_penalties(md,options,subplotwidth,i); +@@ -150,7 +150,7 @@ + plot_thermaltransient_results(md,options,subplotwidth,i); + return; + case 'transient_movie': +- plot_transient_movie(md,options,subplotwidth,i); ++ plot_transient_movie(md,options,canvas); + return; + case 'transient_results': + plot_transient_results(md,options,subplotwidth,i); +@@ -204,5 +204,5 @@ + //plot unit + plot_unit(md,data2,datatype,options,canvas); + +- applyoptions(md,data2,datatype,options,canvas,gl,canvas.nodes[canvas.nodes.length-1]); ++ applyoptions(md,data2,options,canvas); + } //}}} +Index: ../trunk-jpl/src/m/plot/plot_unit.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_unit.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/plot_unit.js (revision 21768) +@@ -6,7 +6,14 @@ + // + // See also: PLOTMODEL, PLOT_MANAGER + +- //{{{ declare variables: ++ //if ('unit' in canvas.nodes) { ++ // if ( ++ // canvas.nodes.unit.updateBuffer('Coords', data); ++ // return; ++ //} ++ //else { ++ ++ //{{{ declare variables: + //Process data and model + var meshresults = processmesh(md, data, options); + var x = meshresults[0]; +@@ -15,78 +22,64 @@ + var elements = meshresults[3]; + var is2d = meshresults[4]; + var isplanet = meshresults[5]; ++ if (md.mesh.classname() !== 'mesh3dsurface') z = md.geometry.surface; + +- var vertices = new Float32Array(x.length * 3); +- var texcoords = new Float32Array(x.length * 2); +- var indices = new Uint16Array(elements.length * 3); +- var nanindices = {}; +- var xmin, xmax; +- var ymin, ymax; +- var zmin, zmax; +- var datamin, datamax, datadelta; +- var matrixscale, vertexscale; +- //Compue scaling through matrices for 2d meshes and vertices for 3d meshes +- if (!md.geometry.surface) { +- md.geometry.surface=NewArrayFill(md.mesh.x.length, 0); ++ //Compute coordinates and data range: ++ var xlim = options.getfieldvalue('xlim', [ArrayMin(x), ArrayMax(x)]); ++ var ylim = options.getfieldvalue('ylim', [ArrayMin(y), ArrayMax(y)]); ++ var zlim = options.getfieldvalue('zlim', [ArrayMin(z), ArrayMax(z)]); ++ ++ //Handle heightscale ++ var vertices, scale; ++ if (md.mesh.classname() !== 'mesh3dsurface') { ++ vertices = [x, y, z]; ++ scale = [1, 1, options.getfieldvalue('heightscale', 1)]; + } +- if (md.mesh.classname() == 'mesh3dsurface') { +- matrixscale = 1; +- vertexscale = options.getfieldvalue('heightscale', 1); +- } + else { +- if (md.geometry.surface) { +- z=md.geometry.surface; +- } +- matrixscale = options.getfieldvalue('heightscale', 1); +- vertexscale = 0; ++ vertices = Node.prototype.scaleVertices(md, x, y, z, options.getfieldvalue('heightscale', 1)); ++ scale = [1, 1, 1]; + } +- //}}} +- +- //Compute coordinates and data range: +- var modelxlim = [ArrayMin(x), ArrayMax(x)]; +- var modelylim = [ArrayMin(y), ArrayMax(y)]; +- var modelzlim = [ArrayMin(z), ArrayMax(z)]; +- var xlim = options.getfieldvalue('xlim', modelxlim); +- var ylim = options.getfieldvalue('ylim', modelylim); +- var zlim = options.getfieldvalue('zlim', modelzlim); +- xmin = xlim[0]; +- xmax = xlim[1]; +- ymin = ylim[0]; +- ymax = ylim[1]; +- zmin = zlim[0]; +- zmax = zlim[1]; +- var caxis; +- ++ + //Compute gl variables: +- var gl = canvas.gl; +- var node = Node(gl); +- canvas.nodes[canvas.nodes.length] = node; ++ var edgecolor = options.getfieldvalue('edgecolor', 'black'); ++ var maskzeros = options.getfieldvalue('maskzeros', {}); ++ var node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'unit', ++ 'shaderName', 'Textured', ++ 'alpha', options.getfieldvalue('alpha', 1.0), ++ 'caxis', options.getfieldvalue('caxis',[ArrayMin(data), ArrayMax(data)]), ++ //'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, md.mesh.classname() === 'mesh3dsurface' ? (zlim[0] + zlim[1]) / 2 : zlim[0]], ++ 'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2], ++ 'diffuseColor', edgecolor, ++ 'enabled', options.getfieldvalue('nodata','off') == 'off', ++ 'log', options.getfieldvalue('log',false), ++ 'maskEnabled', options.getfieldvalue('innermask','off') == 'on', ++ 'maskHeight', options.getfieldvalue('innermaskheight', 150.0) / options.getfieldvalue('heightscale', 1), ++ 'maskColor', options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]), ++ 'maskZerosColor', defaultFor(maskzeros.color,[1.0, 1.0, 1.0, 1.0]), ++ 'maskZerosEnabled', defaultFor(maskzeros.enabled,false), ++ 'maskZerosTolerance', defaultFor(maskzeros.tolerance,1e-3), ++ 'maskZerosZeroValue', defaultFor(maskzeros.zeroValue,0.5), ++ 'rotation', [-90, 0, 0], ++ 'scale', scale ++ ); ++ //} + canvas.unitNode = node; + canvas.unitData = data; +- node.name = "unit"; +- node.shaderName = "Textured"; +- node.shader = gl.shaders[node.shaderName]; +- node.scale = [1, 1, matrixscale]; +- node.rotation = [-90, 0, 0]; +- node.translation = [0, 0, 0]; +- node.center = [(xmin + xmax) / 2, (ymin + ymax) / 2, (zmin + zmax) / 2]; +- node.alpha = options.getfieldvalue('alpha', 1.0); +- node.drawOrder = 1; +- node.maskEnabled = options.getfieldvalue('innermask','off') == 'on'; +- node.maskHeight = options.getfieldvalue('innermaskheight', 150.0); +- node.maskColor = options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]); +- node.enabled = options.getfieldvalue('nodata','off') == 'off'; +- updateModelMatrix(node); +- ++ //}}} + switch(datatype){ + //{{{ element plot + case 1: ++ //WARNING: NaN are not properly found (NaN != NaN = true) + pos=ArrayFindNot(data, NaN); //needed for element on water + if (elements[0].length==6){ //prisms + } + else if (elements[0].length==4){ //tetras + } +- else{ //2D triangular elements ++ else{ //triangular elements ++ node.patch('Faces', elements, 'Vertices', vertices, 'FaceVertexCData', data, 'FaceColor', 'flat', 'EdgeColor', edgecolor); + } + break; + //}}} +@@ -97,55 +90,8 @@ + else if (elements[0].length==4){ //tetras + } + else{ //triangular elements +- caxis = options.getfieldvalue('caxis',[ArrayMin(data), ArrayMax(data)]); +- if (options.getfieldvalue('log','off')!='off') caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10)), Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log', 10))]; +- datamin = caxis[0]; +- datamax = caxis[1]; +- datadelta = datamax - datamin; +- +- var xyz = vec3.create(); +- var direction = vec3.create(); +- var vertex = vec3.create(); +- var magnitude; +- +- for(var i = 0, vindex = 0, tindex = 0; i < x.length; i++){ +- //Check for NaN values and remove from indices array as necessary, but preserve vertex array spacing +- if (isNaN(x[i]) || isNaN(y[i]) || isNaN(z[i]) || isNaN(data[i])) { +- nanindices[i] = i; +- vertices[vindex++] = vertex[0]; +- vertices[vindex++] = vertex[1]; +- vertices[vindex++] = vertex[2]; +- +- texcoords[tindex++] = 0.5; +- texcoords[tindex++] = 0.0; +- continue; +- } +- +- //Scale vertices +- xyz = vec3.fromValues(x[i], y[i], z[i]); +- magnitude = vec3.length(xyz) + md.geometry.surface[i] * vertexscale; +- vec3.normalize(direction, xyz); +- vec3.scale(vertex, direction, magnitude); +- vertices[vindex++] = vertex[0]; +- vertices[vindex++] = vertex[1]; +- vertices[vindex++] = vertex[2]; +- +- texcoords[tindex++] = 0.5; +- texcoords[tindex++] = clamp((data[i] - datamin) / datadelta, 0.0, 1.0); +- } +- +- //linearize the elements array: +- var element; +- for(var i = 0, iindex = 0; i < elements.length; i++){ +- element = [elements[i][0] - 1, elements[i][1] - 1, elements[i][2] - 1]; +- if (element[0] in nanindices || element[1] in nanindices || element[2] in nanindices) continue; +- indices[iindex++] = element[0]; +- indices[iindex++] = element[1]; +- indices[iindex++] = element[2]; +- } ++ node.patch('Faces', elements, 'Vertices', vertices, 'FaceVertexCData', data, 'FaceColor', 'interp', 'EdgeColor', edgecolor); + } +- node.mesh = GL.Mesh.load({vertices: vertices, coords: texcoords, triangles: indices}, null, null, gl); +- node.mesh.octree = new GL.Octree(node.mesh); + break; + //}}} + //{{{ quiver plot +@@ -158,135 +104,7 @@ + } + break; + //}}} +- //{{{ node transient plot +- case 5: +- if (elements[0].length==6){ //prisms +- } +- else if (elements[0].length==4){//tetras +- } +- else{ //triangular elements +- var xyz = vec3.create(); +- var direction = vec3.create(); +- var vertex = vec3.create(); +- var magnitude; +- var timestamps = data[data.length-1]; +- for(var i = 0, vindex = 0, tindex = 0; i < x.length; i++){ +- //Check for NaN values and remove from indices array as necessary, but preserve vertex array spacing +- if (isNaN(x[i]) || isNaN(y[i]) || isNaN(z[i]) || isNaN(data[i][0])) { +- nanindices[i] = i; +- } +- else { +- //Scale vertices +- xyz = vec3.fromValues(x[i], y[i], z[i]); +- magnitude = vec3.length(xyz) + md.geometry.surface[i] * vertexscale; +- vec3.normalize(direction, xyz); +- vec3.scale(vertex, direction, magnitude); +- } +- vertices[vindex++] = vertex[0]; +- vertices[vindex++] = vertex[1]; +- vertices[vindex++] = vertex[2]; +- } +- //Transpose data to obtain column addressable data matrix +- data = data[0].map(function(col, i) { +- return data.map(function(row) { +- return row[i] +- }) +- }); +- //Prevent evaluation of datasubarray min/max if caxis exists +- if (options.exist('caxis')) caxis = options.getfieldvalue('caxis'); +- else caxis = [ArrayMin(data[0]), ArrayMax(data[0].slice(0,-1))]; +- if (options.getfieldvalue('log','off')!='off') caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10)), Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log', 10))]; +- //Prepare texcoords to hold array of data values +- texcoords = []; +- for(var i = 0; i < data.length; i++){ +- datamin = caxis[0]; +- datamax = caxis[1]; +- datadelta = datamax - datamin; +- //Precalculate arrays for each datasubarray, trimming off timestamp value by using x.length instead of data[i].length +- texcoords[i] = new Float32Array(x.length * 2); +- for(var j = 0, index = 0; j < x.length; j++){ +- texcoords[i][index++] = 0.5; +- texcoords[i][index++] = clamp((data[i][j] - datamin) / datadelta, 0.0, 1.0); +- } +- } +- +- //linearize the elements array: +- var element; +- for(var i = 0, iindex = 0; i < elements.length; i++){ +- element = [elements[i][0] - 1, elements[i][1] - 1, elements[i][2] - 1]; +- if (element[0] in nanindices || element[1] in nanindices || element[2] in nanindices) continue; +- indices[iindex++] = element[0]; +- indices[iindex++] = element[1]; +- indices[iindex++] = element[2]; +- } +- +- //Initialize movie loop +- node.movieLoop = canvas.animation.loop; +- node.movieInterval = 1000 / canvas.animation.fps; +- node.movieTimestamps = timestamps; +- node.movieLength = timestamps.length; +- node.movieFrame = 0; +- canvas.dataMarkers.values = []; +- var quiverVelFrames = {}; +- for(var i=0; i < md.results.length; i++){ +- quiverVelFrames[Math.floor(md.results[i].time)] = md.results[i]; +- } +- +- if (canvas.animation.handler !== 0) { +- console.log("clearing..."); +- clearInterval(canvas.animation.handler) +- } +- //TODO: Move this into webgl.js +- canvas.animation.handler = setInterval(function () { +- node.movieFrame = canvas.animation.frame; +- if (canvas.animation.play && canvas.animation.increment) { +- if (node.movieFrame == node.movieLength - 1) { +- if (node.movieLoop) { +- node.movieFrame = 0; +- } +- else { +- toggleMoviePlay(canvas); +- } +- } +- else { +- node.movieFrame = node.movieFrame + 1; +- } +- if (canvas.animation.lastFrame != canvas.animation.frame) { +- updateMarker(canvas, false); +- } +- } +- +- if (canvas.progressBar) { +- canvas.progressBar.val(node.movieFrame); +- canvas.progressBar.slider('refresh'); +- } +- if (canvas.timeLabel) { canvas.timeLabel.html(node.movieTimestamps[node.movieFrame].toFixed(0) + " " + options.getfieldvalue("movietimeunit","yr")); } +- +- var buffer = node.mesh.getBuffer("coords"); +- buffer.data = texcoords[node.movieFrame]; +- buffer.upload(canvas.gl.DYNAMIC_DRAW); +- node.mesh.octree = new GL.Octree(node.mesh); +- node.texcoords = texcoords; +- if(options.getfieldvalue('quiver') == 'on'){ +- plot_quiver(md, options, canvas, {vel: quiverVelFrames[node.movieFrame].Vel, vx: quiverVelFrames[node.movieFrame].Vx, vy: quiverVelFrames[node.movieFrame].Vy}); +- } +- canvas.animation.lastFrame = canvas.animation.frame; +- canvas.animation.frame = node.movieFrame; +- }, node.movieInterval); +- +- if (canvas.progressBar) { +- canvas.animation.frame = 0; +- canvas.progressBar.val(0); +- canvas.progressBar.attr('max', node.movieLength-1); +- canvas.progressBar.slider('refresh'); +- } +- +- } +- node.mesh = GL.Mesh.load({vertices: vertices, coords: texcoords[0], triangles: indices}, null, null, gl); +- node.mesh.octree = new GL.Octree(node.mesh); +- break; +- //}}} + default: +- throw Error(sprintf("%s%i%s\n",'case ', datatype,' not supported')); ++ throw Error(sprintf('%s%i%s\n','case ', datatype,' not supported')); + } + } //}}} +Index: ../trunk-jpl/src/m/plot/plot_overlay.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_overlay.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/plot_overlay.js (revision 21768) +@@ -6,18 +6,11 @@ + // + // See also: PLOTMODEL, PLOT_MANAGER + ++ if ('overlay' in canvas.nodes && options.getfieldvalue('cachenodes','on') === 'on') return; ++ + //{{{ declare variables: +- var vertices = []; +- var indices = []; +- var texcoords = []; +- var nanindices = {}; +- var xmin, xmax; +- var ymin, ymax; +- var zmin, zmax; +- var matrixscale, vertexscale; +- + //Process data and model +- var meshresults = processmesh(md, data, options); ++ var meshresults = processmesh(md, [], options); + var x = meshresults[0]; + var y = meshresults[1]; + var z = meshresults[2]; +@@ -24,139 +17,74 @@ + var elements = meshresults[3]; + var is2d = meshresults[4]; + var isplanet = meshresults[5]; +- +- //Compue scaling through matrices for 2d meshes and vertices for 3d meshes +- if (!md.geometry.surface) { +- md.geometry.surface=NewArrayFill(md.mesh.x.length, 0); ++ if (md.mesh.classname() !== 'mesh3dsurface') z = md.geometry.surface; ++ ++ //Compute coordinates and data range: ++ var xlim = options.getfieldvalue('xlim', [ArrayMin(x), ArrayMax(x)]); ++ var ylim = options.getfieldvalue('ylim', [ArrayMin(y), ArrayMax(y)]); ++ var zlim = options.getfieldvalue('zlim', [ArrayMin(md.geometry.surface), ArrayMax(md.geometry.surface)]); ++ ++ //Handle radaroverlay ++ if (md.radaroverlay.outerx) { ++ var result = Node.prototype.mergeVertices(x, y, z, elements, md.radaroverlay.outerx, md.radaroverlay.outery, md.radaroverlay.outerheight, md.radaroverlay.outerindex); ++ x = result.x; ++ y = result.y; ++ z = result.z; ++ elements = result.elements; + } +- if (md.mesh.classname() == 'mesh3dsurface') { +- matrixscale = 1; +- vertexscale = options.getfieldvalue('heightscale', 1); ++ ++ //Handle heightscale ++ var vertices, scale; ++ if (md.mesh.classname() !== 'mesh3dsurface') { ++ vertices = [x, y, z]; ++ scale = [1, 1, options.getfieldvalue('heightscale', 1)]; + } + else { +- if (md.geometry.surface) { +- z=md.geometry.surface; +- } +- matrixscale = options.getfieldvalue('heightscale', 1); +- vertexscale = 0; ++ vertices = Node.prototype.scaleVertices(md, x, y, z, options.getfieldvalue('heightscale', 1)); ++ scale = [1, 1, 1]; + } +- //}}} + +- //Compute coordinates and data range: +- var modelxlim = [ArrayMin(x), ArrayMax(x)]; +- var modelylim = [ArrayMin(y), ArrayMax(y)]; +- var modelzlim = [ArrayMin(z), ArrayMax(z)]; +- var xlim = options.getfieldvalue('xlim', modelxlim); +- var ylim = options.getfieldvalue('ylim', modelylim); +- var zlim = options.getfieldvalue('zlim', modelzlim); +- xmin = xlim[0]; +- xmax = xlim[1]; +- ymin = ylim[0]; +- ymax = ylim[1]; +- zmin = zlim[0]; +- zmax = zlim[1]; +- + //Compute gl variables: +- var gl = canvas.gl; +- var node = Node(gl); +- canvas.nodes[canvas.nodes.length] = node; +- node.name = "overlay"; +- node.shaderName = (options.getfieldvalue('render',[]).indexOf('ground')!=-1) ? "GroundFromSpace" : "Textured"; +- node.shader = gl.shaders[node.shaderName]; +- node.scale = [1, 1, matrixscale]; +- node.rotation = [-90, 0, 0]; +- node.translation = [0, 0, 0]; +- node.center = [(xmin + xmax) / 2, (ymin + ymax) / 2, (zmin + zmax) / 2]; +- node.texture = initTexture(gl, options.getfieldvalue('overlay_image')); +- node.alpha = options.getfieldvalue('outeralpha', 1.0); +- node.drawOrder = 1; +- node.maskEnabled = options.getfieldvalue('outermask','off') == 'on'; +- node.maskHeight = options.getfieldvalue('outermaskheight', 150.0); +- node.maskColor = options.getfieldvalue('outermaskcolor',[0.0, 0.0, 1.0, 1.0]); +- updateModelMatrix(node); ++ var edgecolor = options.getfieldvalue('edgecolor', 'black'); ++ var texture = initTexture(gl, options.getfieldvalue('overlay_image')); ++ var node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'overlay', ++ 'shaderName', 'ground' in options.getfieldvalue('render', {}) ? 'GroundFromSpace' : 'Textured', ++ 'alpha', options.getfieldvalue('outeralpha', 1.0), ++ //'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, md.mesh.classname() === 'mesh3dsurface' ? (zlim[0] + zlim[1]) / 2 : zlim[0]], ++ 'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2], ++ 'diffuseColor', 'white', ++ 'maskEnabled', options.getfieldvalue('outermask','off') == 'on', ++ 'maskHeight', options.getfieldvalue('outermaskheight', 150.0), ++ 'maskColor', options.getfieldvalue('outermaskcolor',[0.0, 0.0, 1.0, 1.0]), ++ 'texture', texture, ++ 'rotation', [-90, 0, 0], ++ 'scale', scale ++ ); ++ //}}} + +- //Handle outer radaroverlay +- if (md.radaroverlay.outerx) { +- var newelements = []; +- for (var i = 0; i < md.radaroverlay.outerindex.length; i++) { +- newelements[newelements.length] = [md.radaroverlay.outerindex[i][0] + x.length, md.radaroverlay.outerindex[i][1] + y.length, md.radaroverlay.outerindex[i][2] + z.length]; +- } +- x = [].concat(x, md.radaroverlay.outerx); +- y = [].concat(y, md.radaroverlay.outery); +- z = [].concat(z, md.radaroverlay.outerheight); +- elements = [].concat(elements, newelements); +- +- //Reclaculate bounds based on otuer radaroverlay +- modelxlim = [ArrayMin(x), ArrayMax(x)]; +- modelylim = [ArrayMin(y), ArrayMax(y)]; +- modelzlim = [ArrayMin(z), ArrayMax(z)]; +- xmin = xlim[0]; +- xmax = xlim[1]; +- ymin = ylim[0]; +- ymax = ylim[1]; +- zmin = zlim[0]; +- zmax = zlim[1]; +- +- node.center = [node.center[0], node.center[1], -zmax]; +- } ++ var xRange = xlim[1] - xlim[0]; ++ var yRange = ylim[1] - ylim[0]; ++ var coordArray = [new Array(x.length), new Array(x.length)]; ++ //generate mesh: + +- var xrange = modelxlim[1] - modelxlim[0]; +- var yrange = modelylim[1] - modelylim[0]; +- +- var xyz = vec3.create(); +- var direction = vec3.create(); +- var vertex = vec3.create(); +- var magnitude; +- +- //generate mesh: +- for(var i = 0; i < x.length; i++){ +- //Check for NaN values and remove from indices array as necessary, but preserve vertex array spacing +- if (isNaN(x[i]) || isNaN(y[i]) || isNaN(z[i])) { +- nanindices[i] = i; +- vertices[vertices.length] = vertex[0]; +- vertices[vertices.length] = vertex[1]; +- vertices[vertices.length] = vertex[2]; +- +- texcoords[texcoords.length] = 0.0; +- texcoords[texcoords.length] = 0.0; +- continue; +- } +- +- if (md.mesh.classname() == 'mesh3dsurface') { +- //Scale vertices +- xyz = vec3.fromValues(x[i], y[i], z[i]); +- magnitude = vec3.length(xyz) + md.geometry.surface[i] * vertexscale; +- vec3.normalize(direction, xyz); +- vec3.scale(vertex, direction, magnitude); +- vertices[vertices.length] = vertex[0]; +- vertices[vertices.length] = vertex[1]; +- vertices[vertices.length] = vertex[2]; +- +- texcoords[texcoords.length] = Math.atan2(vertex[1], vertex[0]) / (2 * Math.PI) + 0.5; +- texcoords[texcoords.length] = Math.asin(vertex[2] / magnitude) / Math.PI + 0.5; +- } +- else { +- //Scale vertices +- xyz = vec3.fromValues(x[i], y[i], z[i]); ++ if (md.mesh.classname() == 'mesh3dsurface') { ++ var xyz, magnitude; ++ for(var i = 0; i < x.length; i++){ ++ xyz = vec3.fromValues(vertices[0][i], vertices[1][i], vertices[2][i]); + magnitude = vec3.length(xyz); +- vec3.normalize(direction, xyz); +- vec3.scale(vertex, direction, magnitude); +- vertices[vertices.length] = vertex[0]; +- 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; ++ ++ coordArray[0][i] = Math.atan2(xyz[1], xyz[0]) / (2 * Math.PI) + 0.5; ++ coordArray[1][i] = Math.asin(xyz[2] / magnitude) / Math.PI + 0.5; + } + } +- //linearize the elements array: +- var element; +- for(var i = 0; i < elements.length; i++){ +- element = [elements[i][0] - 1, elements[i][1] - 1, elements[i][2] - 1]; +- if (element[0] in nanindices || element[1] in nanindices || element[2] in nanindices) continue; +- indices[indices.length] = element[0]; +- indices[indices.length] = element[1]; +- indices[indices.length] = element[2]; ++ else { ++ for(var i = 0; i < x.length; i++){ ++ coordArray[0][i] = (vertices[0][i] - xlim[0]) / xRange; ++ coordArray[1][i] = (vertices[1][i] - ylim[0]) / yRange; ++ } + } +- node.mesh = GL.Mesh.load({vertices: vertices, coords: texcoords, triangles: indices}, null, null, gl); ++ node.patch('Faces', elements, 'Vertices', vertices, 'FaceVertexCData', coordArray, 'FaceColor', 'interp', 'EdgeColor', edgecolor); + } //}}} +Index: ../trunk-jpl/src/m/plot/plot_transient_movie.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_transient_movie.js (nonexistent) ++++ ../trunk-jpl/src/m/plot/plot_transient_movie.js (revision 21768) +@@ -0,0 +1,100 @@ ++function plot_transient_movie(md, options, canvas) { //{{{ ++ //PLOT_TRANSIENT_MOVIE - plot a transient result as a movie ++ // ++ // Usage: ++ // plot_transient_movie(md, options, canvas); ++ // ++ // See also: PLOTMODEL, PLOT_MANAGER ++ ++ //loop over the time steps ++ var data = options.getfieldvalue('transient_field_data'); ++ var datatype; ++ var steps = new Array(data.length); ++ for (i = 0; i < steps.length; i++) { ++ steps[i] = i; ++ } ++ ++ //calculate caxis ++ if (!options.exist('caxis')) { ++ var range = [Infinity, -Infinity]; ++ var dataresults; ++ for (var i in steps) { ++ dataresults = processdata(md, data[i], options); ++ range[1] = Math.min(range[0], ArrayMin(dataresults[0])); ++ range[2] = Math.max(range[1], ArrayMax(dataresults[0])); ++ } ++ datatype = dataresults[1]; ++ options.addfielddefault('caxis', range); ++ ++ } ++ ++ //Create unit node if it does not already exist ++ if (!('unit' in canvas.nodes)) { ++ var dataresults = processdata(md, data[i],options); ++ var data2 = dataresults[0]; ++ var datatype = dataresults[1]; ++ ++ //plot unit ++ plot_unit(md,data2,datatype,options,canvas); ++ } ++ ++ //display movie ++ var node = canvas.nodes.unit; ++ node.options = options; ++ node.alpha = options.getfieldvalue('alpha', 1.0); ++ node.caxis = options.getfieldvalue('caxis'); ++ node.enabled = options.getfieldvalue('nodata', 'off') == 'off'; ++ node.log = options.getfieldvalue('log', false); ++ canvas.unitMovieData = data; ++ canvas.animation.frame = 0; ++ canvas.animation.handler = setInterval(function () { ++ //Update current animation frame ++ var frame = canvas.animation.frame; ++ if (canvas.animation.play) { ++ if (canvas.animation.increment) { ++ if (frame > steps.length - 1) { ++ if (node.movieLoop) { ++ frame = 0; ++ } ++ else { ++ toggleMoviePlay(canvas); ++ } ++ } ++ else { ++ frame = (frame + 1) % steps.length; ++ } ++ } ++ } ++ ++ //If frame has changed, update unit node and data marker display. ++ if (frame !== canvas.animation.lastFrame) { ++ node.updateBuffer('Coords', data[frame]); ++ canvas.unitData = data[frame]; ++ if (canvas.dataMarkers.enabled) { ++ updateMarker(canvas, false); ++ } ++ if (canvas.progressBar) { ++ canvas.progressBar.val(frame).slider('refresh'); ++ } ++ if (canvas.timeLabel) { ++ canvas.timeLabel.html(steps[frame].toFixed(0) + " " + options.getfieldvalue("movietimeunit","yr")); ++ } ++ if (!isEmptyOrUndefined(canvas.nodes.quiver)) { ++ plot_quiver(md,options,canvas,false); ++ } ++ } ++ ++ //Save new frame info. ++ canvas.animation.lastFrame = canvas.animation.frame; ++ canvas.animation.frame = frame; ++ }, canvas.animation.interval); ++ ++ //Update progress bar with new frame info. ++ if (canvas.progressBar) { ++ canvas.progressBar.val(canvas.animation.frame); ++ canvas.progressBar.attr('max', steps.length - 1); ++ canvas.progressBar.slider('refresh'); ++ } ++ ++ applyoptions(md, [], options, canvas); ++} //}}} +Index: ../trunk-jpl/src/m/plot/plotdoc.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plotdoc.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/plotdoc.js (revision 21768) +@@ -4,20 +4,25 @@ + // Usage: + // plotdoc() + +- //TODO: Standardize image to overlay_image, heightscale to scaling, colorbarfontsize/color, clarify innermask/outermask, edgecolor implementation, check colormap, ++ //TODO: rename innermask/outermask/maskzero and combine + +- console.log(' WARNING: starred methods (*) are experimental and not guarenteed to be stable'); + console.log(' Plot usage: plotmodel(model,varargin)'); + console.log(' Options: '); + console.log(' "canvasid": canvas id'); + console.log(' "data" : what we want to plot'); +- console.log(' Available values for "data" are: '); +- console.log(' - any field of the model structure. ex: plot(md,"data","vel"), or plot(md,"data",md.initialization.vel)'); +- console.log(' - "mesh": draw mesh using trisurf'); +- console.log(' - "quiver": quiver plot'); +- console.log(' "2d": renders orthographic camera with view set to [0, 90] (default "off", ex: "on", "off")'); ++ console.log(' Available values for "data" are: '); ++ console.log(' - any field of the model structure. ex: plot(md,"data","vel"), or plot(md,"data",md.initialization.vel)'); ++ console.log(' - "mesh": draw mesh using trisurf'); ++ console.log(' - "quiver": quiver plot'); + console.log(' "backgroundcolor": plot background color. (default "lightcyan", ex: "green","blue")'); + console.log(' "brush": specify brush options (default {"strength":0.075,"falloff":0.5})'); ++ console.log(' "enabled": toggle brush (default false, ex: true)'); ++ console.log(' "strength": value that brush will change data points by (ex: 0.075)'); ++ console.log(' "falloff": multiplier that brush will decrease strength by for each successive point away from brush center (ex: 0.5)'); ++ console.log(' "clouds": specify brush options (default {"strength":0.075,"falloff":0.5})'); ++ console.log(' "enabled": toggle clouds (default false, ex: true)'); ++ console.log(' "height": height to spawn clouds at (ex: 7500)'); ++ console.log(' "quantity": quantity of clouds to spawn (ex: 10)'); + console.log(' "caxis": modify colorbar range. (array of type [a, b] where b>=a)'); + console.log(' "colorbar": add colorbar (default "off", ex: "on", "off")'); + console.log(' "colorbarid": colorbar canvas id (string)'); +@@ -31,18 +36,26 @@ + console.log(' "colorbarheight": multiplier (default 1) to the default height colorbar'); + console.log(' "colormap": same as standard matlab option (default "jet", ex: "hsv","cool","spring","gray","Ala","Rignot",...)'); + console.log(' "controlsensitivity": sensitivty of view/zoom changes as a percentage of default (default 1, ex: 0.5, 2.75)'); +- console.log(' "datamarkers": toggle data marker displays (default "on", ex: "on", "off")'); +- console.log(' "datamarkers_image": toggle data marker displays (default "on", ex: "on", "off")'); +- console.log(' "datamarkerssize": specifiy the width and height of the data markers (default [32,32], ex: [24,32], [105,10])'); +- console.log(' "datamarkersoptions": specifiy options for data markers (default {"enabled":"on","image":canvas.rootPath+"textures/data_marker.svg","size":[32,32],"format":["X: %.2e
Y: %.2e
Z: %.2e]
Value: %0.1f","x","y","z","value"]}'); ++ console.log(' "datamarkers": object cotaining data marker parameters. See webgl.js for defaults. (ex: {"enabled":true,"format":["
"],"labels":["thickness","velocity","value"],"animated":true})'); ++ console.log(' "enabled": toggle data marker displays (default true, ex: false)'); ++ console.log(' "image": image used for marking the clicked point (ex: "/textures/data_marker.svg")'); ++ console.log(' "labels": when displaying a sim-plot graph, display these model fields. (ex: ["thickness","velocity","value"])'); ++ console.log(' "font": font to be used for display (ex: "24px "Comic Sans MS", cursive")'); ++ console.log(' "format": an array compatible with sprintf that will be displayed as html (ex: ["X: %.2e
Y: %.2e
Z: %.2e]
Value: %0.1f","x","y","z","value"])'); ++ console.log(' "size": specifiy the width and height of the data markers (default [32,32], ex: [24,32], [105,10])'); + console.log(' "displayview": print view value to console (default "off", ex: "on", "off")'); + console.log(' "displayzoom": print zoom value to console (default "off", ex: "on", "off")'); + console.log(' "edgecolor": same as standard matlab option EdgeColor (default "black", ex: color name: "blue" or RGB array: [0.5, 0.2, 0.8])'); + console.log(' "heightscale": scaling factor to accentuate height. (default 1, ex: 0.5, 100)'); +- console.log(' "linewidth*": line width for mesh, quiver, and contour plots, currently limited by WebGL to 1. (default 1, ex: 2, 5)'); ++ console.log(' "linewidth": line width for mesh, quiver, and contour plots, currently limited by WebGL to 1. (default 1, ex: 2, 5)'); + console.log(' "log": value of log (default 10, ex: 2, Math.E)'); + console.log(' "mask": list of flags of size numberofnodes or numberofelements. Only "true" values are plotted '); +- console.log(' "movieoptions": specify movie options (default {"fps":4,"loop":true})'); ++ console.log(' "movies": object cotaining transient plot animation options (ex: {"fps":4,"loop":true})'); ++ console.log(' "maskzeros": object cotaining transient plot animation options (ex: "enabled":true,"color":[1.0, 1.0, 1.0, 1.0],"tolerance":1e-3,"zeroValue":0.5})'); ++ console.log(' "enabled": toggle maskzeros (default false, ex: true)'); ++ console.log(' "color": RGBA color value array with ranges 0.0 to 1.0 (ex: [1.0, 1.0, 1.0, 1.0])'); ++ console.log(' "tolerance": values within this tolerance of the zeroValue will be masked. (default: 1e-3, ex: 2.5e-2)'); ++ console.log(' "zeroValue": the percentage value with range 0.0, to 1.0 of the caxis value around which the data will be masked with the color. (default: 0.5, ex: 0, 1.0, 0.75)'); + console.log(' "innermask*": Special mask that colors all parts of a data mesh below a height a certain color. provide innermaskheight and innermaskcolor options also (default "off", ex: "on", "off")'); + console.log(' "outermask*": Special mask that colors all parts of a overlay mesh below a height a certain color. provide outermaskheight and outermaskcolor options also (default "off", ex: "on", "off")'); + console.log(' "overlay": overlay a radar amplitude image behind (default "off", ex: "on", "off")'); +@@ -50,20 +63,51 @@ + console.log(' "quiver": add quiver plot overlay for velocities. (default "off", ex: "on", "off")'); + console.log(' "scaling": scaling factor used by quiver plots. Default is 0.4'); + console.log(' "alpha": transparency coefficient 0.0 to 1.0, the lower, the more transparent. (default 1.0, ex: 0.5, 0.25)'); +- console.log(' "azlim": azimuth view limits (ex: [0, 180])'); +- console.log(' "ellim": elevation view limits (ex: [-90, 90])'); +- console.log(' "origin": initial camera offset from model center (default [0,0,0.0], ex: [-2, 1.5, 0.01])'); +- console.log(' "render": toggle sky, ground, and space rendering. (default [], ex: ["sky", "space"], ["ground"])'); +- console.log(' "viewPanning": enable view origin panning with two-finger touch or shift+mouse drag. (default "off", ex: "on", "off")'); +- console.log(' "view": initial azimuth and elevation angles for camera (default [0,90], ex: [90, 180]'); ++ console.log(' "render": a object containing a list of default object to render. (default {}, ex: {"sky", "space"})'); ++ console.log(' "sky": render the atmosphere. (ex: {"enabled":true})'); ++ console.log(' "enabled": toggle sky (default false, ex: true)'); ++ console.log(' "space": render space. (ex: {"enabled":true})'); ++ console.log(' "enabled": toggle space (default false, ex: true)'); ++ console.log(' "coastlines": render coastlines. (ex: {"enabled":true})'); ++ console.log(' "enabled": toggle coastlines (default false, ex: true)'); ++ console.log(' "scale": scale coastlines factor (default 1.0, ex: 1.004)'); ++ console.log(' "x": x coordinate array. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "y": y coordinate array. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "z": z coordinate array. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "city": render city. (ex: {"enabled":true})'); ++ console.log(' "enabled": toggle city (default false, ex: true)'); ++ console.log(' "size": radius of city sphere, in meters (default 1.0, ex: 150000)'); ++ console.log(' "color": color of city sphere (ex: "magenta")'); ++ console.log(' "x": x coordinate of city. (ex: 0.0)'); ++ console.log(' "y": y coordinate of city. (ex: 0.0)'); ++ console.log(' "z": z coordinate of city. (ex: 6356700.0)'); ++ console.log(' "cities": render cities. (ex: {"enabled":true})'); ++ console.log(' "enabled": toggle cities (default false, ex: true)'); ++ console.log(' "size": radius of cities spheres, in meters (default 1.0, ex: 80000)'); ++ console.log(' "color": color of cities spheres (ex: "darkviolet")'); ++ console.log(' "x": x coordinate array of cities. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "y": y coordinate array of cities. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "z": z coordinate array of cities. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "graticule": render graticule. (ex: {"enabled":true})'); ++ console.log(' "enabled": toggle graticule (default false, ex: true)'); ++ console.log(' "scale": scale graticule factor (default 1.0, ex: 1.004)'); ++ console.log(' "x": x coordinate array. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "y": y coordinate array. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "z": z coordinate array. (ex: [0.0, 10.0, -25.0,...])'); ++ console.log(' "view": object cotaining view parameters. See webgl.js for defaults. (ex: {"position":[0.0,0.0,0.0],"rotation":[0.0,0.0,0.0],"zoom":1.0,"zoomLimits":[0.01,100.0],"azimuthLimits":[-180,180.0],"elevationLimits":[-90,90.0],"panningEnabled":false,"twod":false})'); ++ console.log(' "position": camera position (ex: [0.0,0.0,0.0])'); ++ console.log(' "rotation": camera rotation (ex: [0.0,0.0,0.0])'); ++ console.log(' "zoom": initial camera zoom as a percentage of default (default 1, ex: 1.5, 0.01)'); ++ console.log(' "zoomLimits": zoom view limits (ex: [0.05, 10])'); ++ console.log(' "azimuthLimits": zoom view limits (ex: [0.05, 10])'); ++ console.log(' "elevationLimits": zoom view limits (ex: [0.05, 10])'); ++ console.log(' "panningEnabled": controls panning with shift + drag mouse or pan gestures (default: false, ex: true)'); ++ console.log(' "twod": controls twod orthographic view (default: false, ex: true)'); + console.log(' "xlim": x coordinates to fit inside camera (ex: [0, 500])'); + console.log(' "ylim": y coordinates to fit inside camera (ex: [0, 500])'); + console.log(' "zlim": z coordinates to fit inside camera (ex: [0, 500])'); +- console.log(' "zoomlim": zoom view limits (ex: [0.05, 10])'); +- console.log(' "zoom": initial camera zoom as a percentage of default (default 1, ex: 1.5, 0.01)'); +- console.log(' "cloud*": plot a cloud of points, given a flat array of 3d coordinates (ex: [0.0, 0.0, 0.0, 1.0, 1.0, 1.0])'); +- console.log(' "expdisp*": plot exp file on top of a data plot. provide exp file as an argument (use a cell of strings if more than one)'); +- console.log(' "textlabels*": plot text labels rendered in 3d space, using an array of text/coordinate pairs (ex: [{"pos":[0.0,0.0,0.0],"text":"origin"}])'); ++ console.log(' "transient_field_data": array of data objects (ex: [[0.0,1.0, 2.5, 12.0...],[0.0,1.0, 2.5, 12.0...],...])'); ++ console.log(' "textlabels": plot text labels rendered in 3d space, using an array of text/coordinate pairs (ex: [{"pos":[0.0,0.0,0.0],"text":"origin"}])'); + + console.log(' '); + console.log(' Examples:'); +Index: ../trunk-jpl/src/m/plot/processdata.js +=================================================================== +--- ../trunk-jpl/src/m/plot/processdata.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/processdata.js (revision 21768) +@@ -14,9 +14,6 @@ + // + // See also: PLOTMODEL, PROCESSMESH + +- //variables: +- var datatype; +- + //check format + if ( data.length ==0 | data === [] | typeof data === 'number' | ArrayAnyNaN(data) ){ + throw Error('plotmodel error message: data provided is empty'); +@@ -34,6 +31,7 @@ + } + + //needed later on ++ var numberofvertices2d, numberofelements2d; + if ('numberofvertices2d' in md.mesh){ + numberofvertices2d=md.mesh.numberofvertices2d; + numberofelements2d=md.mesh.numberofelements2d; +@@ -44,10 +42,10 @@ + } + + //initialize datatype +- datatype=0; ++ var datatype=0; + + //get datasize +- datasize=data.length; ++ var datasize=data.length; + + //transpose data if necessary + if (data[0].length > data.length){ +@@ -63,7 +61,7 @@ + + + //quiver? +- if (data[0].length>1){ ++ if (Array.isArray(data[0])){ + datatype=3; + + //check number of columns, add zeros if necessary, +@@ -114,7 +112,7 @@ + } + + //element data +- if (datasize==md.mesh.numberofelements & data[0].length==1){ ++ if (datasize==md.mesh.numberofelements & !Array.isArray(data[0])){ + + //Initialize datatype if non patch + if(datatype!=4 & datatype!=5){ +@@ -157,7 +155,7 @@ + } + + //node data +- if (datasize==md.mesh.numberofvertices){ ++ if (datasize==md.mesh.numberofvertices & !Array.isArray(data[0])){ + datatype=2; + + //Mask? +Index: ../trunk-jpl/src/m/plot/plot_quiver.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_quiver.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/plot_quiver.js (revision 21768) +@@ -1,4 +1,4 @@ +-function plot_quiver(md, options, canvas, updateVel) { //{{{ ++function plot_quiver(md, options, canvas, noCacheNodesOverride) { //{{{ + //PLOT_QUIVER - quiver plot with colors + // + // Usage: +@@ -6,18 +6,11 @@ + // + // See also: PLOTMODEL, PLOT_MANAGER + ++ if ('quiver' in canvas.nodes && noCacheNodesOverride && options.getfieldvalue('cachenodes','on') === 'on') return; ++ + //{{{ declare variables: +- var vertices = []; +- var indices = []; +- var colors = []; +- var xmin, xmax; +- var ymin, ymax; +- var zmin, zmax; +- var scale, matrixscale, vertexscale; +- + //Process data and model +- var meshresults = processmesh(md,[], options); +- ++ var meshresults = processmesh(md, [], options); + var x = meshresults[0]; + var y = meshresults[1]; + var z = meshresults[2]; +@@ -24,66 +17,50 @@ + var elements = meshresults[3]; + var is2d = meshresults[4]; + var isplanet = meshresults[5]; +- var v = updateVel != undefined ? updateVel.vel : md.initialization.vel; +- var vx = updateVel != undefined ? updateVel.vx : md.initialization.vx; +- var vy = updateVel != undefined ? updateVel.vy : md.initialization.vy; ++ if (md.mesh.classname() !== 'mesh3dsurface') z = md.geometry.surface; + +- //Compue scaling through matrices for 2d meshes and vertices for 3d meshes +- if (!md.geometry.surface) { +- md.geometry.surface=NewArrayFill(md.mesh.x.length, 0); ++ //Compute coordinates and data range: ++ var xlim = options.getfieldvalue('xlim', [ArrayMin(x), ArrayMax(x)]); ++ var ylim = options.getfieldvalue('ylim', [ArrayMin(y), ArrayMax(y)]); ++ var zlim = options.getfieldvalue('zlim', [ArrayMin(z), ArrayMax(z)]); ++ ++ //Only displaying velocity fields for now ++ var v = isEmptyOrUndefined(md.results) ? md.initialization.vel : md.results[canvas.animation.frame].Vel; ++ var vx = isEmptyOrUndefined(md.results) ? md.initialization.vx : md.results[canvas.animation.frame].Vx; ++ var vy = isEmptyOrUndefined(md.results) ? md.initialization.vy : md.results[canvas.animation.frame].Vy; ++ ++ //Handle heightscale ++ var vertices, scale; ++ if (md.mesh.classname() !== 'mesh3dsurface') { ++ vertices = [x, y, z]; ++ scale = [1, 1, options.getfieldvalue('heightscale', 1)]; + } +- if (md.mesh.classname() == 'mesh3dsurface') { +- matrixscale = 1; +- vertexscale = options.getfieldvalue('heightscale', 1); +- } + else { +- if (md.geometry.surface) { +- z=md.geometry.surface; +- } +- matrixscale = options.getfieldvalue('heightscale', 1); +- vertexscale = 0; ++ vertices = Node.prototype.scaleVertices(md, x, y, z, options.getfieldvalue('heightscale', 1)); ++ scale = [1, 1, 1]; + } +- //}}} +- +- //Compute coordinates and data range: +- var modelxlim = [ArrayMin(x), ArrayMax(x)]; +- var modelylim = [ArrayMin(y), ArrayMax(y)]; +- var modelzlim = [ArrayMin(z), ArrayMax(z)]; +- var xlim = options.getfieldvalue('xlim', modelxlim); +- var ylim = options.getfieldvalue('ylim', modelylim); +- var zlim = options.getfieldvalue('zlim', modelzlim); +- xmin = xlim[0]; +- xmax = xlim[1]; +- ymin = ylim[0]; +- ymax = ylim[1]; +- zmin = zlim[0]; +- zmax = zlim[1]; +- ++ + //Compute gl variables: +- var gl = canvas.gl; +- var node = Node(gl); +- canvas.nodes["velocity"] = node; +- node.name = "quiver"; +- node.shaderName = "Colored"; +- node.shader = gl.shaders[node.shaderName]; +- node.lineWidth = options.getfieldvalue('linewidth', 1); +- node.scale = [1, 1, matrixscale]; +- node.rotation = [-90, 0, 0]; +- node.translation = [0, 0, 0]; +- node.center = [(xmin + xmax) / 2, (ymin + ymax) / 2, (zmin + zmax) / 2]; +- node.drawMode = gl.LINES; +- node.useIndexBuffer = false; +- node.drawOrder = 0; +- node.maskEnabled = options.getfieldvalue('innermask','off') == 'on'; +- node.maskHeight = options.getfieldvalue('innermaskheight', 150.0)*options.getfieldvalue('heightscale', 1); +- node.maskColor = options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]); +- updateModelMatrix(node); +- +- //retrieve some options +- var edgecolor=new RGBColor(options.getfieldvalue('edgecolor','black')); +- if (edgecolor.ok) edgecolor = [edgecolor.r/255.0, edgecolor.g/255.0, edgecolor.b/255.0, 1.0]; +- else throw Error(sprintf("s%s%s\n","initWebGL error message: cound not find out edgecolor color for curent canvas ", canvas)); +- ++ var edgecolor = options.getfieldvalue('edgecolor', 'black'); ++ var node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'quiver', ++ 'shaderName', 'Colored', ++ 'alpha', options.getfieldvalue('alpha', 1.0), ++ //'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, md.mesh.classname() === 'mesh3dsurface' ? (zlim[0] + zlim[1]) / 2 : zlim[0]], ++ 'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2], ++ 'drawMode', canvas.gl.LINES, ++ 'diffuseColor', edgecolor, ++ 'lineWidth', options.getfieldvalue('linewidth', 1), ++ 'maskEnabled', options.getfieldvalue('innermask','off') == 'on', ++ 'maskHeight', options.getfieldvalue('innermaskheight', 150.0) / options.getfieldvalue('heightscale', 1), ++ 'maskColor', options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]), ++ 'rotation', [-90, 0, 0], ++ 'scale', scale ++ ); ++ ++ + //{{{ node plot + if (elements[0].length==6){ //prisms + } +@@ -90,49 +67,37 @@ + else if (elements[0].length==4){ //tetras + } + else{ //2D triangular elements ++ //Create arow vertices, and use vx/vy to determine rotation before adding to quiver mesh. ++ var verticesArrow = [vec3.fromValues(0.0, 0.0, 0.0), vec3.fromValues(1.0, 0.0, 0.0), vec3.fromValues(0.667, -0.167, 0.0), vec3.fromValues(1.0, 0.0, 0.0), vec3.fromValues(0.667, 0.166, 0.0), vec3.fromValues(1.0, 0.0, 0.0)]; ++ ++ var newX = []; ++ var newY = []; ++ var newZ = []; + var xyz = vec3.create(); +- var xyz = vec3.create(); +- var direction = vec3.create(); + var vertex = vec3.create(); +- var vertexBase = vec3.create(); +- var verticesArrow = [vec3.fromValues(0.0, 0.0, 0.0), vec3.fromValues(1.0, 0.0, 0.0), vec3.fromValues(0.667, -0.167, 0.0), vec3.fromValues(1.0, 0.0, 0.0), vec3.fromValues(0.667, 0.166, 0.0), vec3.fromValues(1.0, 0.0, 0.0)]; +- var magnitude; +- var color = edgecolor; + var scaling = options.getfieldvalue('scaling', 1); +- var scale; +- for(var i = 0; i < x.length; i++){ +- //Check for NaN values and remove from indices array as necessary, but preserve vertex array spacing +- if (isNaN(x[i]) || isNaN(y[i]) || isNaN(z[i])) continue; +- //Scale vertices ++ var heightScale = options.getfieldvalue('heightscale', 1); ++ var arrowScale; ++ var modelMatrix = mat4.create(); ++ var scaleMatrix = mat4.create(); ++ var rotationMatrix = mat4.create(); ++ ++ for(var i = 0, iX = 0, iY = 0, iZ = 0; i < x.length; i++){ + xyz = vec3.fromValues(x[i], y[i], z[i]); +- magnitude = vec3.length(xyz) + md.geometry.surface[i] * vertexscale; +- vec3.normalize(direction, xyz); +- vec3.scale(vertex, direction, magnitude); +- vec3.copy(vertexBase, vertex); +- +- scale = scaling*v[i]; +- var modelMatrix = mat4.create(); +- var scaleMatrix = mat4.create(); +- var rotationMatrix = mat4.create(); +- mat4.scale(scaleMatrix, scaleMatrix, vec3.fromValues(scale, scale, scale)); +- mat4.rotate(rotationMatrix, rotationMatrix, Math.atan2(vy[i], vx[i]), [0.0, 0.0, 1.0]); ++ arrowScale = v[i] * scaling; ++ scaleMatrix = mat4.create(); ++ mat4.scale(scaleMatrix, mat4.create(), vec3.fromValues(arrowScale, arrowScale, arrowScale)); ++ mat4.rotate(rotationMatrix, mat4.create(), Math.atan2(vy[i], vx[i]), [0.0, 0.0, 1.0]); + mat4.multiply(modelMatrix, rotationMatrix, scaleMatrix); +- +- var temp = vec3.fromValues(0.0, 0.0, 0.0); + for (var j = 0; j < 6; j++){ + vec3.transformMat4(vertex, verticesArrow[j], modelMatrix); +- vec3.add(vertex, vertex, vertexBase); +- vertices[vertices.length] = vertex[0]; +- vertices[vertices.length] = vertex[1]; +- vertices[vertices.length] = vertex[2]; +- +- colors[colors.length] = color[0]; +- colors[colors.length] = color[1]; +- colors[colors.length] = color[2]; +- colors[colors.length] = color[3]; ++ vec3.add(vertex, vertex, xyz); ++ newX[iX++] = vertex[0]; ++ newY[iY++] = vertex[1]; ++ newZ[iZ++] = vertex[2]; + } + } ++ node.patch('Vertices', [newX, newY, newZ], 'FaceColor', 'none'); + } + //}}} +- node.mesh = GL.Mesh.load({vertices: vertices, colors: colors}, null, null, gl); + } //}}} +Index: ../trunk-jpl/src/m/plot/plot_mesh.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_mesh.js (revision 21767) ++++ ../trunk-jpl/src/m/plot/plot_mesh.js (revision 21768) +@@ -6,18 +6,11 @@ + // + // See also: PLOTMODEL, PLOT_MANAGER + ++ if ('mesh' in canvas.nodes && options.getfieldvalue('cachenodes','on') === 'on') return; ++ + //{{{ declare variables: +- var vertices = []; +- var indices = []; +- var colors = []; +- var nanindices = {}; +- var xmin, xmax; +- var ymin, ymax; +- var zmin, zmax; +- var scale, matrixscale, vertexscale; +- + //Process data and model +- var meshresults = processmesh(md,[], options); ++ var meshresults = processmesh(md, [], options); + var x = meshresults[0]; + var y = meshresults[1]; + var z = meshresults[2]; +@@ -25,62 +18,42 @@ + var is2d = meshresults[4]; + var isplanet = meshresults[5]; + +- //Compue scaling through matrices for 2d meshes and vertices for 3d meshes +- if (!md.geometry.surface) { +- md.geometry.surface=NewArrayFill(md.mesh.x.length, 0); ++ //Compute coordinates and data range: ++ var xlim = options.getfieldvalue('xlim', [ArrayMin(x), ArrayMax(x)]); ++ var ylim = options.getfieldvalue('ylim', [ArrayMin(y), ArrayMax(y)]); ++ var zlim = options.getfieldvalue('zlim', [ArrayMin(z), ArrayMax(z)]); ++ ++ //Handle heightscale ++ var vertices, scale; ++ if (md.mesh.classname() !== 'mesh3dsurface') { ++ vertices = [x, y, z]; ++ scale = [1, 1, options.getfieldvalue('heightscale', 1)]; + } +- if (md.mesh.classname() == 'mesh3dsurface') { +- matrixscale = 1; +- vertexscale = options.getfieldvalue('heightscale', 1); +- } + else { +- if (md.geometry.surface) { +- z=md.geometry.surface; +- } +- matrixscale = options.getfieldvalue('heightscale', 1); +- vertexscale = 0; ++ vertices = Node.prototype.scaleVertices(md, x, y, z, options.getfieldvalue('heightscale', 1)); ++ scale = [1, 1, 1]; + } ++ ++ //Compute gl variables: ++ var edgecolor = options.getfieldvalue('edgecolor', 'black'); ++ var node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'name', 'mesh', ++ 'shaderName', 'Colored', ++ 'alpha', options.getfieldvalue('alpha', 1.0), ++ //'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, md.mesh.classname() === 'mesh3dsurface' ? (zlim[0] + zlim[1]) / 2 : zlim[0]], ++ 'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2], ++ 'drawMode', canvas.gl.LINES, ++ 'diffuseColor', edgecolor, ++ 'lineWidth', options.getfieldvalue('linewidth', 1), ++ 'maskEnabled', options.getfieldvalue('innermask','off') == 'on', ++ 'maskHeight', options.getfieldvalue('innermaskheight', 150.0) / options.getfieldvalue('heightscale', 1), ++ 'maskColor', options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]), ++ 'rotation', [-90, 0, 0], ++ 'scale', scale ++ ); + //}}} +- +- //Compute coordinates and data range: +- var modelxlim = [ArrayMin(x), ArrayMax(x)]; +- var modelylim = [ArrayMin(y), ArrayMax(y)]; +- var modelzlim = [ArrayMin(z), ArrayMax(z)]; +- var xlim = options.getfieldvalue('xlim', modelxlim); +- var ylim = options.getfieldvalue('ylim', modelylim); +- var zlim = options.getfieldvalue('zlim', modelzlim); +- xmin = xlim[0]; +- xmax = xlim[1]; +- ymin = ylim[0]; +- ymax = ylim[1]; +- zmin = zlim[0]; +- zmax = zlim[1]; +- +- //Compute gl variables: +- var gl = canvas.gl; +- gl.makeCurrent(); +- var node = Node(gl); +- canvas.nodes[canvas.nodes.length] = node; +- node.name = "mesh"; +- node.shaderName = "Colored"; +- node.shader = gl.shaders[node.shaderName]; +- node.lineWidth = options.getfieldvalue('linewidth', 1); +- node.scale = [1, 1, matrixscale]; +- node.rotation = [-90, 0, 0]; +- node.translation = [0, 0, 0]; +- node.center = [(xmin + xmax) / 2, (ymin + ymax) / 2, (zmin + zmax) / 2]; +- node.drawMode = gl.LINES; +- node.drawOrder = 0; +- node.maskEnabled = options.getfieldvalue('innermask','off') == 'on'; +- node.maskHeight = options.getfieldvalue('innermaskheight', 150.0)*options.getfieldvalue('heightscale', 1); +- node.maskColor = options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]); +- updateModelMatrix(node); +- +- //retrieve some options +- var edgecolor = new RGBColor(options.getfieldvalue('edgecolor','black')); +- if (edgecolor.ok) edgecolor = [edgecolor.r/255.0, edgecolor.g/255.0, edgecolor.b/255.0, 1.0]; +- else throw Error(sprintf("s%s%s\n","initWebGL error message: cound not find out edgecolor color for curent canvas ", canvas)); +- + //{{{ node plot + if (elements[0].length==6){ //prisms + } +@@ -87,53 +60,10 @@ + else if (elements[0].length==4){ //tetras + } + else{ //2D triangular elements +- var xyz = vec3.create(); +- var direction = vec3.create(); +- var vertex = vec3.create(); +- var magnitude; +- var color = edgecolor; +- for(var i = 0; i < x.length; i++){ +- //Check for NaN values and remove from indices array as necessary, but preserve vertex array spacing +- if (isNaN(x[i]) || isNaN(y[i]) || isNaN(z[i])) { +- nanindices[i] = i; +- vertices[vertices.length] = vertex[0]; +- vertices[vertices.length] = vertex[1]; +- vertices[vertices.length] = vertex[2]; +- +- colors[colors.length] = color[0]; +- colors[colors.length] = color[1]; +- colors[colors.length] = color[2]; +- colors[colors.length] = color[3]; +- continue; +- } +- //Scale vertices +- xyz = vec3.fromValues(x[i], y[i], z[i]); +- magnitude = vec3.length(xyz) + md.geometry.surface[i] * vertexscale; +- vec3.normalize(direction, xyz); +- vec3.scale(vertex, direction, magnitude); +- vertices[vertices.length] = vertex[0]; +- vertices[vertices.length] = vertex[1]; +- vertices[vertices.length] = vertex[2]; +- +- colors[colors.length] = color[0]; +- colors[colors.length] = color[1]; +- colors[colors.length] = color[2]; +- colors[colors.length] = color[3]; +- } +- +- //linearize the elements array: +- var element; +- for(var i = 0; i < elements.length; i++){ +- element = [elements[i][0] - 1, elements[i][1] - 1, elements[i][2] - 1]; +- if (element[0] in nanindices || element[1] in nanindices || element[2] in nanindices) continue; +- indices[indices.length] = element[0]; +- indices[indices.length] = element[1]; +- indices[indices.length] = element[1]; +- indices[indices.length] = element[2]; +- indices[indices.length] = element[2]; +- indices[indices.length] = element[0]; +- } ++ node.patch('Faces', elements, 'Vertices', vertices, 'FaceColor', 'none', 'EdgeColor', edgecolor); + } + //}}} +- node.mesh = GL.Mesh.load({vertices: vertices, colors: colors, triangles: indices}, null, null, gl); ++ //options=options.addfielddefault('title','Mesh'); ++ //options=addfielddefault('colorbar','off'); ++ //applyoptions(md,[],options,canvas); + } //}}} +Index: ../trunk-jpl/src/m/classes/clusters/generic.js +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/generic.js (revision 21767) ++++ ../trunk-jpl/src/m/classes/clusters/generic.js (revision 21768) +@@ -171,4 +171,4 @@ + } + return buf; + } //}}} +-} ++} Index: /issm/oecreview/Archive/21724-22754/ISSM-21768-21769.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21768-21769.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21768-21769.diff (revision 22755) @@ -0,0 +1,29 @@ +Index: ../trunk-jpl/src/m/miscellaneous/transientrestart.m +=================================================================== +--- ../trunk-jpl/src/m/miscellaneous/transientrestart.m (revision 21768) ++++ ../trunk-jpl/src/m/miscellaneous/transientrestart.m (revision 21769) +@@ -1,11 +1,22 @@ +-function md = transientrestart(md) ++function md = transientrestart(md,step) + %TRANSIENTRESTART - reinitialize model from last transient step + % + % Usage: + % md = transientrestart(md) ++% md = transientrestart(md,step) ++% ++% By default, transientrestart will use the last step provided in md.results.TransientSolution + + %Get result and save it again +-results = md.results.TransientSolution(end); ++if nargin==1, ++ step = numel(md.results.TransientSolution(end)); ++end ++if step<1, ++ error('step needs to be >0'); ++elseif step>numel(md.results.TransientSolution) ++ error(['md.results.TransientSolution has only ' num2str(numel(md.results.TransientSolution)) ' steps']); ++end ++results = md.results.TransientSolution(step); + + newname = ['TransientSolution' num2str(numel(fields(md.results))+1)]; + if isfield(md.results,newname) Index: /issm/oecreview/Archive/21724-22754/ISSM-21769-21770.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21769-21770.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21769-21770.diff (revision 22755) @@ -0,0 +1,35 @@ +Index: ../trunk-jpl/src/m/classes/clusters/pfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 21769) ++++ ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 21770) +@@ -10,7 +10,7 @@ + % {{{ + name = 'pfe' + login = ''; +- modules = {'comp-intel/2016.2.181' 'mpi-sgi/mpt'}; ++ modules = {'comp-intel/2015.0.090' 'mpi-sgi/mpt.2.12r26' 'math/intel_mkl_64_10.0.011'}; + numnodes = 20; + cpuspernode = 8; + port = 1025; +@@ -162,8 +162,8 @@ + fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); +- fprintf(fid,'module load comp-intel/2016.2.181\n'); +- fprintf(fid,'module load mpi-sgi/mpt\n'); ++ fprintf(fid,'module load comp-intel/2015.0.090\n'); ++ fprintf(fid,'module load mpi-sgi/mpt.2.12r16\n'); + fprintf(fid,'export PATH="$PATH:."\n\n'); + fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME +@@ -225,8 +225,8 @@ + fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); +- fprintf(fid,'module load comp-intel/2016.2.181\n'); +- fprintf(fid,'module load mpi-sgi/mpt\n'); ++ fprintf(fid,'module load comp-intel/2015.0.090\n'); ++ fprintf(fid,'module load mpi-sgi/mpt.2.12r16\n'); + fprintf(fid,'export PATH="$PATH:."\n\n'); + fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME Index: /issm/oecreview/Archive/21724-22754/ISSM-21770-21771.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21770-21771.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21770-21771.diff (revision 22755) @@ -0,0 +1,46 @@ +Index: ../trunk-jpl/src/m/classes/clusters/pfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 21770) ++++ ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 21771) +@@ -10,7 +10,7 @@ + % {{{ + name = 'pfe' + login = ''; +- modules = {'comp-intel/2015.0.090' 'mpi-sgi/mpt.2.12r26' 'math/intel_mkl_64_10.0.011'}; ++ modules = {'comp-intel/2016.2.181' 'mpi-sgi/mpt'}; + numnodes = 20; + cpuspernode = 8; + port = 1025; +@@ -162,8 +162,8 @@ + fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); +- fprintf(fid,'module load comp-intel/2015.0.090\n'); +- fprintf(fid,'module load mpi-sgi/mpt.2.12r16\n'); ++ fprintf(fid,'module load comp-intel/2016.2.181\n'); ++ fprintf(fid,'module load mpi-sgi/mpt\n'); + fprintf(fid,'export PATH="$PATH:."\n\n'); + fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME +@@ -225,8 +225,8 @@ + fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); +- fprintf(fid,'module load comp-intel/2015.0.090\n'); +- fprintf(fid,'module load mpi-sgi/mpt.2.12r16\n'); ++ fprintf(fid,'module load comp-intel/2016.2.181\n'); ++ fprintf(fid,'module load mpi-sgi/mpt\n'); + fprintf(fid,'export PATH="$PATH:."\n\n'); + fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME +@@ -352,8 +352,8 @@ + fprintf(fid,'#PBS -o %s.outlog \n',modelname); + fprintf(fid,'#PBS -e %s.errlog \n\n',modelname); + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); +- fprintf(fid,'module load comp-intel/2015.0.090\n'); +- fprintf(fid,'module load test/mpt.2.11r8\n'); ++ fprintf(fid,'module load comp-intel/2016.2.181\n'); ++ fprintf(fid,'module load mpi-sgi/mpt\n'); + fprintf(fid,'module load netcdf/4.0\n'); + fprintf(fid,'module load mpi-mvapich2/1.4.1/gcc\n'); + fprintf(fid,'module load gcc/4.4.4\n'); Index: /issm/oecreview/Archive/21724-22754/ISSM-21771-21772.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21771-21772.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21771-21772.diff (revision 22755) @@ -0,0 +1,131 @@ +Index: ../trunk-jpl/src/m/classes/timestepping.py +=================================================================== +--- ../trunk-jpl/src/m/classes/timestepping.py (revision 21771) ++++ ../trunk-jpl/src/m/classes/timestepping.py (revision 21772) +@@ -65,6 +65,7 @@ + def marshall(self,prefix,md,fid): # {{{ + + yts=md.constants.yts ++ WriteData(fid,prefix,'name','md.timestepping.type','data',1,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','start_time','format','Double','scale',yts) + WriteData(fid,prefix,'object',self,'fieldname','final_time','format','Double','scale',yts) + WriteData(fid,prefix,'object',self,'fieldname','time_step','format','Double','scale',yts) +Index: ../trunk-jpl/src/m/classes/timeadaptation.m +=================================================================== +--- ../trunk-jpl/src/m/classes/timeadaptation.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/timeadaptation.m (revision 21772) +@@ -0,0 +1,90 @@ ++%TIMESTEPPING Class definition ++% ++% Usage: ++% timeadaptation=timeadaptation(); ++ ++classdef timeadaptation ++ properties (SetAccess=public) ++ start_time = 0.; ++ final_time = 0.; ++ time_step_min = 0.; ++ time_step_max = 0.; ++ cfl_coefficient = 0.; ++ interp_forcings = 1; ++ end ++ methods ++ function self = timeadaptation(varargin) % {{{ ++ switch nargin ++ case 0 ++ self=setdefaultparameters(self); ++ case 1 ++ self=structtoobj(timeadaptation(),varargin{1}); ++ otherwise ++ error('constructor not supported'); ++ end ++ end % }}} ++ function self = setdefaultparameters(self) % {{{ ++ ++ %time between 2 time steps ++ self.time_step_min = 0.01; ++ self.time_step_max = 1.; ++ ++ %final time ++ self.final_time=10.*self.time_step_max; ++ ++ %default CFL coefficient ++ self.cfl_coefficient=0.5; ++ ++ %should we interpolate forcings between timesteps? ++ self.interp_forcings=1; ++ end % }}} ++ function md = checkconsistency(self,md,solution,analyses) % {{{ ++ ++ md = checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','timestepping.time_step_min','numel',[1],'>=',0,'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','timestepping.time_step_max','numel',[1],'>=',0,'NaN',1,'Inf',1); ++ if (self.time_step_min>self.time_step_max) ++ md = checkmessage(md,['base not equal to bed on grounded ice!']); ++ end ++ md = checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1); ++ md = checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0 1]); ++ if self.final_time-self.start_time<0, ++ md = checkmessage(md,'timestepping.final_time should be larger than timestepping.start_time'); ++ end ++ end % }}} ++ function disp(self) % {{{ ++ disp(sprintf(' timeadaptation parameters:')); ++ ++ unit = 'yr'; ++ fielddisplay(self,'start_time',['simulation starting time [' unit ']']); ++ fielddisplay(self,'final_time',['final time to stop the simulation [' unit ']']); ++ fielddisplay(self,'time_step_min',['minimum length of time step [' unit ']']); ++ fielddisplay(self,'time_step_max',['maximum length of time step [' unit ']']); ++ fielddisplay(self,'cfl_coefficient','coefficient applied to cfl condition'); ++ fielddisplay(self,'interp_forcings','interpolate in time between requested forcing values ? (0 or 1)'); ++ ++ end % }}} ++ function marshall(self,prefix,md,fid) % {{{ ++ ++ scale = md.constants.yts; ++ WriteData(fid,prefix,'name','md.timestepping.type','data',2,'format','Integer'); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','start_time','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','final_time','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','time_step_min','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','time_step_max','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','cfl_coefficient','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','interp_forcings','format','Boolean'); ++ end % }}} ++ function savemodeljs(self,fid,modelname) % {{{ ++ ++ writejsdouble(fid,[modelname '.timeadaptation.start_time'],self.start_time); ++ writejsdouble(fid,[modelname '.timeadaptation.final_time'],self.final_time); ++ writejsdouble(fid,[modelname '.timeadaptation.time_step_min'],self.time_step_min); ++ writejsdouble(fid,[modelname '.timeadaptation.time_step_max'],self.time_step_max); ++ writejsdouble(fid,[modelname '.timeadaptation.cfl_coefficient'],self.cfl_coefficient); ++ writejsdouble(fid,[modelname '.timeadaptation.interp_forcings'],self.interp_forcings); ++ ++ end % }}} ++ end ++end +Index: ../trunk-jpl/src/m/classes/timestepping.js +=================================================================== +--- ../trunk-jpl/src/m/classes/timestepping.js (revision 21771) ++++ ../trunk-jpl/src/m/classes/timestepping.js (revision 21772) +@@ -53,6 +53,7 @@ + var scale; + scale = md.constants.yts; + ++ WriteData(fid,prefix,'name','md.timestepping.type','data',1,'format','Integer'); + WriteData(fid,prefix,'object',this,'fieldname','start_time','format','Double','scale',scale); + WriteData(fid,prefix,'object',this,'fieldname','final_time','format','Double','scale',scale); + WriteData(fid,prefix,'object',this,'fieldname','time_step','format','Double','scale',scale); +Index: ../trunk-jpl/src/m/classes/timestepping.m +=================================================================== +--- ../trunk-jpl/src/m/classes/timestepping.m (revision 21771) ++++ ../trunk-jpl/src/m/classes/timestepping.m (revision 21772) +@@ -63,6 +63,7 @@ + function marshall(self,prefix,md,fid) % {{{ + + scale = md.constants.yts; ++ WriteData(fid,prefix,'name','md.timestepping.type','data',1,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','start_time','format','Double','scale',scale); + WriteData(fid,prefix,'object',self,'fieldname','final_time','format','Double','scale',scale); + WriteData(fid,prefix,'object',self,'fieldname','time_step','format','Double','scale',scale); Index: /issm/oecreview/Archive/21724-22754/ISSM-21772-21773.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21772-21773.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21772-21773.diff (revision 22755) @@ -0,0 +1,373 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21772) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21773) +@@ -18,7 +18,7 @@ + void CreateParameters(Parameters* parameters,IoModel* iomodel,char* rootpath,FILE* toolkitsoptionsfid,const int solution_type){ + + int i,j,m,k; +- int numoutputs,materialtype,smb_model,basalforcing_model; ++ int numoutputs,materialtype,smb_model,basalforcing_model,timestepping_type; + char** requestedoutputs = NULL; + IssmDouble time; + +@@ -45,12 +45,6 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.settings.output_frequency",SettingsOutputFrequencyEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.settings.recording_frequency",SettingsRecordingFrequencyEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.constants.yts",ConstantsYtsEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.start_time",TimesteppingStartTimeEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.final_time",TimesteppingFinalTimeEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_adapt",TimesteppingTimeAdaptEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_step",TimesteppingTimeStepEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.cfl_coefficient",TimesteppingCflCoefficientEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.interp_forcings",TimesteppingInterpForcingsEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.settings.lowmem",SettingsLowmemEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.debug.profiling",DebugProfilingEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.mesh.average_vertex_connectivity",MeshAverageVertexConnectivityEnum)); +@@ -141,6 +135,30 @@ + /*some parameters that did not come with the iomodel: */ + parameters->AddObject(new IntParam(SolutionTypeEnum,solution_type)); + ++ /*Time stepping*/ ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.type",TimesteppingTypeEnum)); ++ iomodel->FindConstant(×tepping_type,"md.timestepping.type"); ++ switch(timestepping_type){ ++ case FixedTimesteppingEnum: ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.start_time",TimesteppingStartTimeEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.final_time",TimesteppingFinalTimeEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_adapt",TimesteppingTimeAdaptEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_step",TimesteppingTimeStepEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.cfl_coefficient",TimesteppingCflCoefficientEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.interp_forcings",TimesteppingInterpForcingsEnum)); ++ break; ++ case TimeAdaptationEnum: ++ parameters->AddObject(new BoolParam(TimesteppingTimeAdaptEnum,true)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.start_time",TimesteppingStartTimeEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.final_time",TimesteppingFinalTimeEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_step_min",TimesteppingTimeStepMinEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_step_max",TimesteppingTimeStepMaxEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.cfl_coefficient",TimesteppingCflCoefficientEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.interp_forcings",TimesteppingInterpForcingsEnum)); ++ break; ++ default: ++ _error_(EnumToStringx(timestepping_type) <<" not supported yet"); ++ } + iomodel->FindConstant(&time,"md.timestepping.start_time"); + parameters->AddObject(new DoubleParam(TimeEnum,time)); + parameters->AddObject(new IntParam(StepEnum,0)); +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21772) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21773) +@@ -43,7 +43,6 @@ + femmodel->parameters->FindParam(&step,StepEnum); + femmodel->parameters->FindParam(&time,TimeEnum); + femmodel->parameters->FindParam(&finaltime,TimesteppingFinalTimeEnum); +- femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + femmodel->parameters->FindParam(&yts,ConstantsYtsEnum); + femmodel->parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); + femmodel->parameters->FindParam(&output_frequency,SettingsOutputFrequencyEnum); +@@ -77,6 +76,9 @@ + if(time+dt>finaltime) dt=finaltime-time; + femmodel->parameters->SetParam(dt,TimesteppingTimeStepEnum); + } ++ else{ ++ femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); ++ } + step+=1; + time+=dt; + femmodel->parameters->SetParam(time,TimeEnum); +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 21772) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 21773) +@@ -602,6 +602,7 @@ + if(strcmp(record_name,"md.calving.law")==0) integer = IoCodeToEnumCalving(integer); + if(strcmp(record_name,"md.hydrology.model")==0) integer = IoCodeToEnumHydrology(integer); + if(strcmp(record_name,"md.materials.type")==0) integer = IoCodeToEnumMaterials(integer); ++ if(strcmp(record_name,"md.timestepping.type")==0) integer = IoCodeToEnumTimestepping(integer); + + /*Broadcast to other cpus*/ + ISSM_MPI_Bcast(&integer,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21772) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21773) +@@ -2070,12 +2070,11 @@ + IssmDouble dt; + + /*intermediary: */ +- Element *element = NULL; + IssmDouble min_dt = 0; + IssmDouble node_min_dt = 0; + + /*Go through elements, and figure out the minimum of the time steps for each element (using CFL criterion): */ +- element=(Element*)elements->GetObjectByOffset(0); min_dt=element->TimeAdapt(); ++ Element* element=(Element*)elements->GetObjectByOffset(0); min_dt=element->TimeAdapt(); + + for (i=1;iSize();i++){ + element=xDynamicCast(elements->GetObjectByOffset(i)); +@@ -2088,6 +2087,17 @@ + ISSM_MPI_Bcast(&node_min_dt,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + min_dt=node_min_dt; + ++ /*Constrain dt if necessary*/ ++ int timestepping_type; ++ IssmDouble dt_low,dt_high; ++ parameters->FindParam(×tepping_type,TimesteppingTypeEnum); ++ if(timestepping_type==TimeAdaptationEnum){ ++ parameters->FindParam(&dt_low,TimesteppingTimeStepMinEnum); ++ parameters->FindParam(&dt_high,TimesteppingTimeStepMaxEnum); ++ if(min_dtdt_high) min_dt = dt_high; ++ } ++ + /*Assign output pointers:*/ + *pdt=min_dt; + } +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21772) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21773) +@@ -29,6 +29,11 @@ + InputToSmoothEnum, + SmoothThicknessMultiplierEnum, + LevelsetStabilizationEnum, ++ TimesteppingTypeEnum, ++ FixedTimesteppingEnum, ++ TimeAdaptationEnum, ++ TimesteppingTimeStepMinEnum, ++ TimesteppingTimeStepMaxEnum, + /*}}}*/ + /*Model fields {{{*/ + AutodiffIsautodiffEnum, +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21772) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21773) +@@ -37,6 +37,11 @@ + case InputToSmoothEnum : return "InputToSmooth"; + case SmoothThicknessMultiplierEnum : return "SmoothThicknessMultiplier"; + case LevelsetStabilizationEnum : return "LevelsetStabilization"; ++ case TimesteppingTypeEnum : return "TimesteppingType"; ++ case FixedTimesteppingEnum : return "FixedTimestepping"; ++ case TimeAdaptationEnum : return "TimeAdaptation"; ++ case TimesteppingTimeStepMinEnum : return "TimesteppingTimeStepMin"; ++ case TimesteppingTimeStepMaxEnum : return "TimesteppingTimeStepMax"; + case AutodiffIsautodiffEnum : return "AutodiffIsautodiff"; + case AutodiffNumDependentsEnum : return "AutodiffNumDependents"; + case AutodiffDependentObjectsEnum : return "AutodiffDependentObjects"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21772) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21773) +@@ -37,6 +37,11 @@ + else if (strcmp(name,"InputToSmooth")==0) return InputToSmoothEnum; + else if (strcmp(name,"SmoothThicknessMultiplier")==0) return SmoothThicknessMultiplierEnum; + else if (strcmp(name,"LevelsetStabilization")==0) return LevelsetStabilizationEnum; ++ else if (strcmp(name,"TimesteppingType")==0) return TimesteppingTypeEnum; ++ else if (strcmp(name,"FixedTimestepping")==0) return FixedTimesteppingEnum; ++ else if (strcmp(name,"TimeAdaptation")==0) return TimeAdaptationEnum; ++ else if (strcmp(name,"TimesteppingTimeStepMin")==0) return TimesteppingTimeStepMinEnum; ++ else if (strcmp(name,"TimesteppingTimeStepMax")==0) return TimesteppingTimeStepMaxEnum; + else if (strcmp(name,"AutodiffIsautodiff")==0) return AutodiffIsautodiffEnum; + else if (strcmp(name,"AutodiffNumDependents")==0) return AutodiffNumDependentsEnum; + else if (strcmp(name,"AutodiffDependentObjects")==0) return AutodiffDependentObjectsEnum; +@@ -131,15 +136,15 @@ + else if (strcmp(name,"HydrologyshreveStabilization")==0) return HydrologyshreveStabilizationEnum; + else if (strcmp(name,"Hydrologydc")==0) return HydrologydcEnum; + else if (strcmp(name,"SedimentHead")==0) return SedimentHeadEnum; +- else if (strcmp(name,"SedimentHeadOld")==0) return SedimentHeadOldEnum; ++ else stage=2; ++ } ++ if(stage==2){ ++ if (strcmp(name,"SedimentHeadOld")==0) return SedimentHeadOldEnum; + else if (strcmp(name,"SedimentHeadResidual")==0) return SedimentHeadResidualEnum; + else if (strcmp(name,"EffectivePressure")==0) return EffectivePressureEnum; + else if (strcmp(name,"EplHead")==0) return EplHeadEnum; + else if (strcmp(name,"EplHeadOld")==0) return EplHeadOldEnum; +- else stage=2; +- } +- if(stage==2){ +- if (strcmp(name,"EplHeadSlopeX")==0) return EplHeadSlopeXEnum; ++ else if (strcmp(name,"EplHeadSlopeX")==0) return EplHeadSlopeXEnum; + else if (strcmp(name,"EplHeadSlopeY")==0) return EplHeadSlopeYEnum; + else if (strcmp(name,"EplZigZagCounter")==0) return EplZigZagCounterEnum; + else if (strcmp(name,"HydrologydcMaxIter")==0) return HydrologydcMaxIterEnum; +@@ -254,15 +259,15 @@ + else if (strcmp(name,"NewDamage")==0) return NewDamageEnum; + else if (strcmp(name,"StressIntensityFactor")==0) return StressIntensityFactorEnum; + else if (strcmp(name,"CalvingLaw")==0) return CalvingLawEnum; +- else if (strcmp(name,"CalvingCalvingrate")==0) return CalvingCalvingrateEnum; ++ else stage=3; ++ } ++ if(stage==3){ ++ if (strcmp(name,"CalvingCalvingrate")==0) return CalvingCalvingrateEnum; + else if (strcmp(name,"CalvingMeltingrate")==0) return CalvingMeltingrateEnum; + else if (strcmp(name,"CalvingLevermann")==0) return CalvingLevermannEnum; + else if (strcmp(name,"CalvingDev")==0) return CalvingDevEnum; + else if (strcmp(name,"CalvingMinthickness")==0) return CalvingMinthicknessEnum; +- else stage=3; +- } +- if(stage==3){ +- if (strcmp(name,"DefaultCalving")==0) return DefaultCalvingEnum; ++ else if (strcmp(name,"DefaultCalving")==0) return DefaultCalvingEnum; + else if (strcmp(name,"CalvinglevermannCoeff")==0) return CalvinglevermannCoeffEnum; + else if (strcmp(name,"CalvinglevermannMeltingrate")==0) return CalvinglevermannMeltingrateEnum; + else if (strcmp(name,"CalvingdevCoeff")==0) return CalvingdevCoeffEnum; +@@ -377,15 +382,15 @@ + else if (strcmp(name,"BalancethicknessOmega")==0) return BalancethicknessOmegaEnum; + else if (strcmp(name,"BalancethicknessD0")==0) return BalancethicknessD0Enum; + else if (strcmp(name,"Smb")==0) return SmbEnum; +- else if (strcmp(name,"SmbAnalysis")==0) return SmbAnalysisEnum; ++ else stage=4; ++ } ++ if(stage==4){ ++ if (strcmp(name,"SmbAnalysis")==0) return SmbAnalysisEnum; + else if (strcmp(name,"SmbSolution")==0) return SmbSolutionEnum; + else if (strcmp(name,"SmbNumRequestedOutputs")==0) return SmbNumRequestedOutputsEnum; + else if (strcmp(name,"SmbRequestedOutputs")==0) return SmbRequestedOutputsEnum; + else if (strcmp(name,"SmbIsInitialized")==0) return SmbIsInitializedEnum; +- else stage=4; +- } +- if(stage==4){ +- if (strcmp(name,"SmbDzini")==0) return SmbDziniEnum; ++ else if (strcmp(name,"SmbDzini")==0) return SmbDziniEnum; + else if (strcmp(name,"SmbDini")==0) return SmbDiniEnum; + else if (strcmp(name,"SmbReini")==0) return SmbReiniEnum; + else if (strcmp(name,"SmbGdnini")==0) return SmbGdniniEnum; +@@ -500,15 +505,15 @@ + else if (strcmp(name,"MassFlux")==0) return MassFluxEnum; + else if (strcmp(name,"MeltingOffset")==0) return MeltingOffsetEnum; + else if (strcmp(name,"Misfit")==0) return MisfitEnum; +- else if (strcmp(name,"Pressure")==0) return PressureEnum; ++ else stage=5; ++ } ++ if(stage==5){ ++ if (strcmp(name,"Pressure")==0) return PressureEnum; + else if (strcmp(name,"PressurePicard")==0) return PressurePicardEnum; + else if (strcmp(name,"AndroidFrictionCoefficient")==0) return AndroidFrictionCoefficientEnum; + else if (strcmp(name,"ResetPenalties")==0) return ResetPenaltiesEnum; + else if (strcmp(name,"SurfaceAbsVelMisfit")==0) return SurfaceAbsVelMisfitEnum; +- else stage=5; +- } +- if(stage==5){ +- if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum; ++ else if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum; + else if (strcmp(name,"SurfaceAverageVelMisfit")==0) return SurfaceAverageVelMisfitEnum; + else if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; + else if (strcmp(name,"SurfaceLogVxVyMisfit")==0) return SurfaceLogVxVyMisfitEnum; +@@ -623,15 +628,15 @@ + else if (strcmp(name,"Outputdefinition21")==0) return Outputdefinition21Enum; + else if (strcmp(name,"Outputdefinition22")==0) return Outputdefinition22Enum; + else if (strcmp(name,"Outputdefinition23")==0) return Outputdefinition23Enum; +- else if (strcmp(name,"Outputdefinition24")==0) return Outputdefinition24Enum; ++ else stage=6; ++ } ++ if(stage==6){ ++ if (strcmp(name,"Outputdefinition24")==0) return Outputdefinition24Enum; + else if (strcmp(name,"Outputdefinition25")==0) return Outputdefinition25Enum; + else if (strcmp(name,"Outputdefinition26")==0) return Outputdefinition26Enum; + else if (strcmp(name,"Outputdefinition27")==0) return Outputdefinition27Enum; + else if (strcmp(name,"Outputdefinition28")==0) return Outputdefinition28Enum; +- else stage=6; +- } +- if(stage==6){ +- if (strcmp(name,"Outputdefinition29")==0) return Outputdefinition29Enum; ++ else if (strcmp(name,"Outputdefinition29")==0) return Outputdefinition29Enum; + else if (strcmp(name,"Outputdefinition30")==0) return Outputdefinition30Enum; + else if (strcmp(name,"Outputdefinition31")==0) return Outputdefinition31Enum; + else if (strcmp(name,"Outputdefinition32")==0) return Outputdefinition32Enum; +@@ -746,15 +751,15 @@ + else if (strcmp(name,"OutputFileName")==0) return OutputFileNameEnum; + else if (strcmp(name,"InputFileName")==0) return InputFileNameEnum; + else if (strcmp(name,"LockFileName")==0) return LockFileNameEnum; +- else if (strcmp(name,"RestartFileName")==0) return RestartFileNameEnum; ++ else stage=7; ++ } ++ if(stage==7){ ++ if (strcmp(name,"RestartFileName")==0) return RestartFileNameEnum; + else if (strcmp(name,"ToolkitsOptionsAnalyses")==0) return ToolkitsOptionsAnalysesEnum; + else if (strcmp(name,"ToolkitsOptionsStrings")==0) return ToolkitsOptionsStringsEnum; + else if (strcmp(name,"QmuErrName")==0) return QmuErrNameEnum; + else if (strcmp(name,"QmuInName")==0) return QmuInNameEnum; +- else stage=7; +- } +- if(stage==7){ +- if (strcmp(name,"QmuOutName")==0) return QmuOutNameEnum; ++ else if (strcmp(name,"QmuOutName")==0) return QmuOutNameEnum; + else if (strcmp(name,"Regular")==0) return RegularEnum; + else if (strcmp(name,"Scaled")==0) return ScaledEnum; + else if (strcmp(name,"Separate")==0) return SeparateEnum; +@@ -869,15 +874,15 @@ + else if (strcmp(name,"NodeSId")==0) return NodeSIdEnum; + else if (strcmp(name,"ElementSId")==0) return ElementSIdEnum; + else if (strcmp(name,"VectorParam")==0) return VectorParamEnum; +- else if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; ++ else stage=8; ++ } ++ if(stage==8){ ++ if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; + else if (strcmp(name,"Segment")==0) return SegmentEnum; + else if (strcmp(name,"SegmentRiftfront")==0) return SegmentRiftfrontEnum; + else if (strcmp(name,"SpcDynamic")==0) return SpcDynamicEnum; + else if (strcmp(name,"SpcStatic")==0) return SpcStaticEnum; +- else stage=8; +- } +- if(stage==8){ +- if (strcmp(name,"SpcTransient")==0) return SpcTransientEnum; ++ else if (strcmp(name,"SpcTransient")==0) return SpcTransientEnum; + else if (strcmp(name,"StringArrayParam")==0) return StringArrayParamEnum; + else if (strcmp(name,"StringParam")==0) return StringParamEnum; + else if (strcmp(name,"Seg")==0) return SegEnum; +@@ -992,15 +997,15 @@ + else if (strcmp(name,"P1bubblecondensed")==0) return P1bubblecondensedEnum; + else if (strcmp(name,"P2")==0) return P2Enum; + else if (strcmp(name,"P2bubble")==0) return P2bubbleEnum; +- else if (strcmp(name,"P2bubblecondensed")==0) return P2bubblecondensedEnum; ++ else stage=9; ++ } ++ if(stage==9){ ++ if (strcmp(name,"P2bubblecondensed")==0) return P2bubblecondensedEnum; + else if (strcmp(name,"P2xP1")==0) return P2xP1Enum; + else if (strcmp(name,"P1xP2")==0) return P1xP2Enum; + else if (strcmp(name,"P1xP3")==0) return P1xP3Enum; + else if (strcmp(name,"P2xP4")==0) return P2xP4Enum; +- else stage=9; +- } +- if(stage==9){ +- if (strcmp(name,"P1P1")==0) return P1P1Enum; ++ else if (strcmp(name,"P1P1")==0) return P1P1Enum; + else if (strcmp(name,"P1P1GLS")==0) return P1P1GLSEnum; + else if (strcmp(name,"MINI")==0) return MINIEnum; + else if (strcmp(name,"MINIcondensed")==0) return MINIcondensedEnum; +Index: ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 21772) ++++ ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 21773) +@@ -120,6 +120,13 @@ + default: _error_("Marshalled materials code \""<(alpha2)); ++ _assert_(!xIsInf(alpha2)); ++ + /*Assign output pointers:*/ + *palpha2=alpha2; + }/*}}}*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21774-21775.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21774-21775.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21774-21775.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 21774) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 21775) +@@ -21,6 +21,7 @@ + #include + #include + #include ++#include + + #include "./classes.h" + #include "../shared/io/io.h" Index: /issm/oecreview/Archive/21724-22754/ISSM-21775-21776.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21775-21776.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21775-21776.diff (revision 22755) @@ -0,0 +1,24 @@ +Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21775) ++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21776) +@@ -247,9 +247,16 @@ + /*Deal with friction parameters*/ + int frictionlaw; + iomodel->FindConstant(&frictionlaw,"md.friction.law"); +- if(frictionlaw==4 || frictionlaw==6) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); +- if(frictionlaw==3 || frictionlaw==1) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); +- if(frictionlaw==9) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); ++ if(frictionlaw==4 || frictionlaw==6){ ++ parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); ++ parameters->AddObject(new BoolParam(FrictionCouplingEnum,false)); ++ } ++ if(frictionlaw==3 || frictionlaw==1){ ++ parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); ++ } ++ if(frictionlaw==9){ ++ parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); ++ } + }/*}}}*/ + + /*Finite Element Analysis*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21776-21777.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21776-21777.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21776-21777.diff (revision 22755) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21776) ++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21777) +@@ -249,7 +249,6 @@ + iomodel->FindConstant(&frictionlaw,"md.friction.law"); + if(frictionlaw==4 || frictionlaw==6){ + parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); +- parameters->AddObject(new BoolParam(FrictionCouplingEnum,false)); + } + if(frictionlaw==3 || frictionlaw==1){ + parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); +@@ -256,6 +255,7 @@ + } + if(frictionlaw==9){ + parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); ++ parameters->AddObject(new BoolParam(FrictionCouplingEnum,false)); + } + }/*}}}*/ + Index: /issm/oecreview/Archive/21724-22754/ISSM-21777-21778.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21777-21778.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21777-21778.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21777) ++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21778) +@@ -255,7 +255,7 @@ + } + if(frictionlaw==9){ + parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); +- parameters->AddObject(new BoolParam(FrictionCouplingEnum,false)); ++ parameters->AddObject(new IntParam(FrictionCouplingEnum,0)); + } + }/*}}}*/ + Index: /issm/oecreview/Archive/21724-22754/ISSM-21778-21779.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21778-21779.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21778-21779.diff (revision 22755) @@ -0,0 +1,56 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21778) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21779) +@@ -3178,8 +3178,6 @@ + + /*Intermediaries*/ + IssmDouble phi; +- IssmDouble viscosity; +- IssmDouble epsilon[6]; + IssmDouble thickness; + IssmDouble *xyz_list = NULL; + +@@ -3188,11 +3186,10 @@ + IssmDouble* viscousheating = xNew(numvertices); + + /*Retrieve all inputs and parameters*/ +- this->GetVerticesCoordinatesBase(&xyz_list); ++ this->GetVerticesCoordinates(&xyz_list); + Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input* vz_input = this->GetInput(VzEnum); _assert_(vz_input); +- Input* thickness_input = this->GetInput(ThicknessEnum); _assert_(thickness_input); + + /*loop over vertices: */ + Gauss* gauss=this->NewGauss(); +@@ -3199,13 +3196,9 @@ + for (int iv=0;ivGaussVertex(iv); + +- thickness_input->GetInputValue(&thickness,gauss); ++ this->ViscousHeating(&phi,xyz_list,gauss,vx_input,vy_input,vz_input); + +- this->StrainRateFS(&epsilon[0],xyz_list,gauss,vx_input,vy_input,vz_input); +- this->material->ViscosityFS(&viscosity,3,xyz_list,gauss,vx_input,vy_input,vz_input); +- this->GetPhi(&phi,&epsilon[0],viscosity); +- +- viscousheating[iv]=phi*thickness; ++ viscousheating[iv]=phi; + } + + /*Create PentaVertex input, which will hold the basal friction:*/ +Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21778) ++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21779) +@@ -1073,8 +1073,8 @@ + + xDelete(watercolumn); + xDelete(drainage_int); ++ xDelete(basalnodeindices); + } +- xDelete(basalnodeindices); + }/*}}}*/ + void EnthalpyAnalysis::DrainageUpdateEnthalpy(FemModel* femmodel){/*{{{*/ + Index: /issm/oecreview/Archive/21724-22754/ISSM-21779-21780.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21779-21780.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21779-21780.diff (revision 22755) @@ -0,0 +1,73 @@ +Index: ../trunk-jpl/src/m/exp/expcoarsen.m +=================================================================== +--- ../trunk-jpl/src/m/exp/expcoarsen.m (revision 21779) ++++ ../trunk-jpl/src/m/exp/expcoarsen.m (revision 21780) +@@ -1,4 +1,4 @@ +-function expcoarsen(newfile,oldfile,resolution) ++function expcoarsen(newfile,varargin) + %EXPCOARSEN - coarsen an exp contour + % + % This routine read an Argus file and remove points with respect to +@@ -6,15 +6,24 @@ + % + % Usage: + % expcoarsen(newfile,oldfile,resolution) ++% expcoarsen(file,resolution) + % + % Example: + % expcoarsen('DomainOutline.exp','Antarctica.exp',4000) + + %Some checks +-if nargin~=3 | nargout +- error('expcoarsen usage: expcoarsen(newfile,oldfile,resolution)') +-elseif ~exist(oldfile) +- error(['expcut error message: the file ' oldfile ' does not exist']) ++if nargin==2, ++ resolution = varargin{1}; ++ oldfile= newfile; ++elseif nargin==3, ++ oldfile = varargin{1}; ++ resolution = varargin{2}; ++else ++ error('bad usage'); ++end ++ ++if ~exist(oldfile) ++ error(['expcoarsen error message: file ''' oldfile ''' does not exist']) + elseif exist(newfile), + choice=input(['A file ' newfile ' already exists, do you want to modify it? (y/n)'],'s'); + if ~strcmpi(choice,'y'), +Index: ../trunk-jpl/src/m/exp/expread.m +=================================================================== +--- ../trunk-jpl/src/m/exp/expread.m (revision 21779) ++++ ../trunk-jpl/src/m/exp/expread.m (revision 21780) +@@ -64,6 +64,9 @@ + A=fscanf(fid,'%f %f',[2 Struct(count).nods]); + Struct(count).x=A(1,:)'; + Struct(count).y=A(2,:)'; ++ if any(isnan(A)) ++ warning('NaNs found in coordinates, note that some tools like exptool will not work properly with NaNs'); ++ end + + if(Struct(count).nods~=length(Struct(count).x))error(['Profile ' num2str(count) ' reports incorrect length']); end; + +@@ -77,5 +80,6 @@ + end + end + ++ + %close file + fclose(fid); +Index: ../trunk-jpl/src/m/exp/exptool.m +=================================================================== +--- ../trunk-jpl/src/m/exp/exptool.m (revision 21779) ++++ ../trunk-jpl/src/m/exp/exptool.m (revision 21780) +@@ -98,7 +98,7 @@ + [path root ext]=fileparts(newfile); + + %get current figure +-nofigurecopy=getfieldvalue(options,'nofigurecopy',1); ++nofigurecopy=getfieldvalue(options,'nofigurecopy',0); + if ~nofigurecopy, + if ~isempty(get(0,'children')),%if there is already a figure (return the number of opened figures) + set(gcf,'Renderer','zbuffer'); %fixes a bug on Mac OS X (not needed in future Matlab version) Index: /issm/oecreview/Archive/21724-22754/ISSM-21780-21781.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21780-21781.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21780-21781.diff (revision 22755) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/src/m/shp/shp2exp.m +=================================================================== +--- ../trunk-jpl/src/m/shp/shp2exp.m (revision 21780) ++++ ../trunk-jpl/src/m/shp/shp2exp.m (revision 21781) +@@ -36,7 +36,15 @@ + expstruct(end).nods=length(x); + expstruct(end).density=1; + expstruct(end).closed=1; +- expstruct(end).name=num2str(shp(i).id); ++ if isfield(shp(i),'id'), ++ expstruct(end).name=num2str(shp(i).id); ++ elseif isfield(shp(i),'NAME'), ++ expstruct(end).name=num2str(shp(i).SUBREGION1); ++ elseif isfield(shp(i),'SUBREGION1'), ++ expstruct(end).name=num2str(shp(i).SUBREGION1); ++ else ++ expstruct(end).name='unknown'; ++ end + elseif strcmpi(shp(i).Geometry,'Point'), + x=shp(i).X; y=shp(i).Y; + expstruct(end+1).x=x; Index: /issm/oecreview/Archive/21724-22754/ISSM-21781-21782.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21781-21782.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21781-21782.diff (revision 22755) @@ -0,0 +1,48 @@ +Index: ../trunk-jpl/src/m/plot/kmlgroundoverlay.m +=================================================================== +--- ../trunk-jpl/src/m/plot/kmlgroundoverlay.m (revision 21781) ++++ ../trunk-jpl/src/m/plot/kmlgroundoverlay.m (revision 21782) +@@ -27,13 +27,24 @@ + kmlgroundoverlaydescription=getfieldvalue(options,'kmlgroundoverlaydescription',''); + + %figure out min and max for lat and long of this image: +-west=min(md.mesh.long); +-east=max(md.mesh.long); +-south=min(md.mesh.lat); +-north=max(md.mesh.lat); ++if strcmpi(getfieldvalue(options,'coord',''),'latlon'), ++ %need to plot with option 'coord','latlon' ++ XLIM=xlim(); ++ YLIM=ylim(); ++ west=XLIM(1); ++ east=XLIM(2); ++ south=YLIM(1); ++ north=YLIM(2); ++else ++ west=min(md.mesh.long); ++ east=max(md.mesh.long); ++ south=min(md.mesh.lat); ++ north=max(md.mesh.lat); ++end + + %print image at high resolution +-export_fig([kmlroot '/' kmlimagename],'-transparent','-zbuffer'); %zbuffer to avoid "Bad data returned by HARDCOPY. Not calling IMWRITE" ++%export_fig([kmlroot '/' kmlimagename],'-transparent','-zbuffer'); %zbuffer to avoid "Bad data returned by HARDCOPY. Not calling IMWRITE" ++export_fig([kmlroot '/' kmlimagename],'-transparent'); + %printmodel([kmlroot '/' kmlimagename],kmlimagetype,'trim','on','resolution',kmlresolution,'margin','off','frame','off'); + + %now write kml file +@@ -60,3 +71,13 @@ + fprintf(fid,'%s\n',''); + + fclose(fid); ++ ++if strcmpi(getfieldvalue(options,'kmz','on'),'on') ++ disp('Converting to kmz...'); ++ system(['cat ' kmlroot '/' kmlfilename '| sed -e "s/' kmlimagename '\.png/files\/' kmlimagename '.png/g" > doc.kml']); ++ system('mkdir files'); ++ system(['mv ' kmlroot '/' kmlimagename '.png files/']); ++ system(['zip -r ' kmlfilename '.zip files doc.kml']); ++ system(['mv ' kmlfilename '.zip ' kmlfilename]); ++ system(['rm -rf files doc.kml']); ++end Index: /issm/oecreview/Archive/21724-22754/ISSM-21782-21783.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21782-21783.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21782-21783.diff (revision 22755) @@ -0,0 +1,43 @@ +Index: ../trunk-jpl/src/m/plot/plot_overlay.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_overlay.m (revision 21782) ++++ ../trunk-jpl/src/m/plot/plot_overlay.m (revision 21783) +@@ -40,12 +40,18 @@ + md=radarpower(md,options); + end + contrast = getfieldvalue(options,'contrast',1); +-radar = (md.radaroverlay.pwr).^(contrast); +-radar = radar./max(radar(:)); ++radar = md.radaroverlay.pwr; + if size(radar,3)>1, + disp('WARNING: color image converted to greyscale intensity image'); +- radar=sum(radar,3)/3; ++ if strcmp(class(radar),'uint8'), ++ radar=double(sum(radar,3))/(255*3); ++ else ++ radar=sum(radar,3)/3; ++ end + end ++radar = radar.^(contrast); ++radar = radar./max(radar(:)); ++ + if getfieldvalue(options,'backgroundbtw',0) + radar(find(radar==0))=1; %Change background from black to white + end +@@ -53,8 +59,14 @@ + %InterpFromMeshToGrid + xmin=min(md.radaroverlay.x); + ymax=max(md.radaroverlay.y); +-xspacing=(max(md.radaroverlay.x)-min(md.radaroverlay.x))/(length(md.radaroverlay.x)); +-yspacing=(max(md.radaroverlay.y)-min(md.radaroverlay.y))/(length(md.radaroverlay.y)); ++xspacing=(max(md.radaroverlay.x)-min(md.radaroverlay.x))/(length(md.radaroverlay.x) -1); ++yspacing=(max(md.radaroverlay.y)-min(md.radaroverlay.y))/(length(md.radaroverlay.y) -1); ++if(md.radaroverlay.x(end)-md.radaroverlay.x(1)<0) ++ xspacing= -xspacing; ++end ++if(md.radaroverlay.y(end)-md.radaroverlay.y(1)<0) ++ yspacing= -yspacing; ++end + nlines=length(md.radaroverlay.y); + ncols =length(md.radaroverlay.x); + disp('Interpolating data on grid...'); Index: /issm/oecreview/Archive/21724-22754/ISSM-21783-21784.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21783-21784.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21783-21784.diff (revision 22755) @@ -0,0 +1,24 @@ +Index: ../trunk-jpl/src/m/plot/googlemaps.m +=================================================================== +--- ../trunk-jpl/src/m/plot/googlemaps.m (revision 21783) ++++ ../trunk-jpl/src/m/plot/googlemaps.m (revision 21784) +@@ -140,6 +140,9 @@ + [X Y]=ll2xy(LAT,LON,+1,45,70); + elseif md.mesh.epsg==3031, + [X Y]=ll2xy(LAT,LON,-1,0,71); ++ elseif md.mesh.epsg==4326, ++ X=LON; ++ Y=LAT; + else + error('EPSG code not supported yet'); + end +@@ -164,6 +167,9 @@ + [X Y]=ll2xy(LAT,LON,+1,45,70); + elseif md.mesh.epsg==3031, + [X Y]=ll2xy(LAT,LON,-1,0,71); ++ elseif md.mesh.epsg==4326, ++ X=LON; ++ Y=LAT; + else + error('EPSG code not supported yet'); + end Index: /issm/oecreview/Archive/21724-22754/ISSM-21784-21785.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21784-21785.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21784-21785.diff (revision 22755) @@ -0,0 +1,85 @@ +Index: ../trunk-jpl/test/NightlyRun/test430.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test430.m (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test430.m (revision 21785) +@@ -0,0 +1,76 @@ ++%Test Name: MISMIP3D ++md=triangle(model(),'../Exp/Square.exp',100000.); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md.initialization.vx(:)=1.; ++md.initialization.vy(:)=1.; ++md.geometry.thickness(:)=500-md.mesh.x/10000; ++md.geometry.bed =-100-md.mesh.x/1000; ++md.geometry.base=-md.geometry.thickness*md.materials.rho_ice/md.materials.rho_water; ++md.mask.groundedice_levelset=md.geometry.thickness+md.materials.rho_water/md.materials.rho_ice*md.geometry.bed; ++pos=find(md.mask.groundedice_levelset>=0); ++md.geometry.base(pos)=md.geometry.bed(pos); ++md.geometry.surface=md.geometry.base+md.geometry.thickness; ++md=setflowequation(md,'SSA','all'); ++ ++%Boundary conditions: ++md.mask.ice_levelset=-ones(md.mesh.numberofvertices,1); ++md.mask.ice_levelset(find(md.mesh.x==max(md.mesh.x)))=0; ++md.stressbalance.spcvx(:)=NaN; ++md.stressbalance.spcvy(:)=NaN; ++md.stressbalance.spcvz(:)=NaN; ++pos=find((md.mesh.y<1000000.1 & md.mesh.y>999999.9) | (md.mesh.y<0.1 & md.mesh.y>-0.1)); ++md.stressbalance.spcvy(pos)=0; ++pos2=find(md.mesh.x<0.1 & md.mesh.x>-0.1); ++md.stressbalance.spcvx(pos2)=0; ++md.stressbalance.spcvy(pos2)=0; ++ ++md.materials.rheology_B=1/((10^-25)^(1/3))*ones(md.mesh.numberofvertices,1); ++md.materials.rheology_law='None'; ++md.friction.coefficient(:)=sqrt(10^7)*ones(md.mesh.numberofvertices,1); ++md.friction.p=3*ones(md.mesh.numberofelements,1); ++md.smb.mass_balance(:)=1; ++md.basalforcings.groundedice_melting_rate(:)=0; ++md.basalforcings.floatingice_melting_rate(:)=0; ++md.transient.isthermal=0; ++md.transient.isstressbalance=1; ++md.transient.isgroundingline=1; ++md.transient.ismasstransport=1; ++md.transient.issmb=1; ++md.groundingline.migration='SubelementMigration'; ++md.timestepping.final_time=30; ++md.timestepping.time_step=10; ++ ++md.cluster=generic('name',oshostname(),'np',3); ++md=solve(md,'Transient'); ++ ++%Fields and tolerances to track changes ++field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Pressure1',... ++ 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Pressure2',... ++ 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Pressure3'}; ++field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,... ++ 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-09,1e-10,... ++ 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-09,1e-10}; ++field_values={... ++ (md.results.TransientSolution(1).Base),... ++ (md.results.TransientSolution(1).Surface),... ++ (md.results.TransientSolution(1).Thickness),... ++ (md.results.TransientSolution(1).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(1).Vx),... ++ (md.results.TransientSolution(1).Vy),... ++ (md.results.TransientSolution(1).Pressure),... ++ (md.results.TransientSolution(2).Base),... ++ (md.results.TransientSolution(2).Surface),... ++ (md.results.TransientSolution(2).Thickness),... ++ (md.results.TransientSolution(2).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(2).Vx),... ++ (md.results.TransientSolution(2).Vy),... ++ (md.results.TransientSolution(2).Pressure),... ++ (md.results.TransientSolution(3).Base),... ++ (md.results.TransientSolution(3).Surface),... ++ (md.results.TransientSolution(3).Thickness),... ++ (md.results.TransientSolution(3).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(3).Vx),... ++ (md.results.TransientSolution(3).Vy),... ++ (md.results.TransientSolution(3).Pressure),... ++ }; +Index: ../trunk-jpl/test/Archives/Archive430.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21785-21786.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21785-21786.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21785-21786.diff (revision 22755) @@ -0,0 +1,114 @@ +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21785) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21786) +@@ -38,6 +38,7 @@ + md.transient.isgroundingline=1; + md.transient.ismasstransport=1; + md.transient.issmb=1; ++md.transient.requested_outputs={'default','BasalforcingsFloatingiceMeltingRate'}; + md.groundingline.migration='SubelementMigration'; + md.timestepping.final_time=30; + md.timestepping.time_step=10; +@@ -46,12 +47,12 @@ + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Vz1','Pressure1',... +- 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2',... +- 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3'}; +-field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-09,1e-10,... +- 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-09,1e-10}; ++field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Vz1','Pressure1','FloatingiceMeltingrate1',... ++ 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... ++ 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; ++field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... ++ 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-09,1e-10,1e-13,... ++ 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +@@ -61,6 +62,7 @@ + (md.results.TransientSolution(1).Vy),... + (md.results.TransientSolution(1).Vz),... + (md.results.TransientSolution(1).Pressure),... ++ (md.results.TransientSolution(1).BasalforcingsFloatingiceMeltingRate),... + (md.results.TransientSolution(2).Base),... + (md.results.TransientSolution(2).Surface),... + (md.results.TransientSolution(2).Thickness),... +@@ -69,6 +71,7 @@ + (md.results.TransientSolution(2).Vy),... + (md.results.TransientSolution(2).Vz),... + (md.results.TransientSolution(2).Pressure),... ++ (md.results.TransientSolution(2).BasalforcingsFloatingiceMeltingRate),... + (md.results.TransientSolution(3).Base),... + (md.results.TransientSolution(3).Surface),... + (md.results.TransientSolution(3).Thickness),... +@@ -77,4 +80,5 @@ + (md.results.TransientSolution(3).Vy),... + (md.results.TransientSolution(3).Vz),... + (md.results.TransientSolution(3).Pressure),... ++ (md.results.TransientSolution(3).BasalforcingsFloatingiceMeltingRate),... + }; +Index: ../trunk-jpl/test/NightlyRun/test430.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test430.m (revision 21785) ++++ ../trunk-jpl/test/NightlyRun/test430.m (revision 21786) +@@ -37,6 +37,7 @@ + md.transient.isgroundingline=1; + md.transient.ismasstransport=1; + md.transient.issmb=1; ++md.transient.requested_outputs={'default','BasalforcingsFloatingiceMeltingRate'}; + md.groundingline.migration='SubelementMigration'; + md.timestepping.final_time=30; + md.timestepping.time_step=10; +@@ -45,12 +46,12 @@ + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Pressure1',... +- 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Pressure2',... +- 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Pressure3'}; +-field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-09,1e-10,... +- 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-09,1e-10}; ++field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Pressure1','FloatingiceMeltingrate1',... ++ 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Pressure2','FloatingiceMeltingrate2',... ++ 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Pressure3','FloatingiceMeltingrate3'}; ++field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,1e-13,1e-13,... ++ 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-10,1e-13,... ++ 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +@@ -59,6 +60,7 @@ + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... + (md.results.TransientSolution(1).Pressure),... ++ (md.results.TransientSolution(1).BasalforcingsFloatingiceMeltingRate),... + (md.results.TransientSolution(2).Base),... + (md.results.TransientSolution(2).Surface),... + (md.results.TransientSolution(2).Thickness),... +@@ -66,6 +68,7 @@ + (md.results.TransientSolution(2).Vx),... + (md.results.TransientSolution(2).Vy),... + (md.results.TransientSolution(2).Pressure),... ++ (md.results.TransientSolution(2).BasalforcingsFloatingiceMeltingRate),... + (md.results.TransientSolution(3).Base),... + (md.results.TransientSolution(3).Surface),... + (md.results.TransientSolution(3).Thickness),... +@@ -73,4 +76,5 @@ + (md.results.TransientSolution(3).Vx),... + (md.results.TransientSolution(3).Vy),... + (md.results.TransientSolution(3).Pressure),... ++ (md.results.TransientSolution(3).BasalforcingsFloatingiceMeltingRate),... + }; +Index: ../trunk-jpl/test/Archives/Archive435.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive430.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21786-21787.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21786-21787.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21786-21787.diff (revision 22755) @@ -0,0 +1,908 @@ +Index: ../trunk-jpl/test/NightlyRun/test323.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test323.m (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test323.m (revision 21787) +@@ -4,7 +4,8 @@ + md=parameterize(md,'../Par/SquareSheetConstrained.par'); + md=setflowequation(md,'SSA','all'); + md.cluster=generic('name',oshostname(),'np',3); +-md.timestepping.time_adapt=1; ++md.timestepping = timesteppingadaptive(md.timestepping); ++md.timestepping.time_step_max = 10000.; + md.timestepping.final_time=1120.; + md=solve(md,'Transient'); + +Index: ../trunk-jpl/test/NightlyRun/test324.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test324.m (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test324.m (revision 21787) +@@ -5,7 +5,8 @@ + md=extrude(md,5,1.2); + md=setflowequation(md,'SIA','all'); + md.cluster=generic('name',oshostname(),'np',3); +-md.timestepping.time_adapt=1; ++md.timestepping = timesteppingadaptive(md.timestepping); ++md.timestepping.time_step_max = 10000.; + md.timestepping.final_time=16000.; + md=solve(md,'Transient'); + +Index: ../trunk-jpl/test/NightlyRun/test226.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test226.m (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test226.m (revision 21787) +@@ -4,7 +4,7 @@ + md=parameterize(md,'../Par/SquareShelf.par'); + md=setflowequation(md,'SSA','all'); + md.cluster=generic('name',oshostname(),'np',3); +-md.timestepping.time_adapt=1.; ++md.timestepping = timesteppingadaptive(md.timestepping); + md.timestepping.final_time=15.; + md=solve(md,'Transient'); + +Index: ../trunk-jpl/test/NightlyRun/test226.js +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test226.js (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test226.js (revision 21787) +@@ -5,7 +5,7 @@ + parameterize(md); + setflowequation(md,'SSA','all'); + //md.cluster=generic('name',oshostname(),'np',3); +-md.timestepping.time_adapt=1.; ++md.timestepping = timesteppingadaptive(md.timestepping); + md.timestepping.final_time=15.; + md=solve(md,'Transient'); + +Index: ../trunk-jpl/test/NightlyRun/test227.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test227.m (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test227.m (revision 21787) +@@ -5,7 +5,7 @@ + md=extrude(md,3,1.); + md=setflowequation(md,'HO','all'); + md.cluster=generic('name',oshostname(),'np',3); +-md.timestepping.time_adapt=1.; ++md.timestepping = timesteppingadaptive(md.timestepping); + md.timestepping.final_time=20.; + md=solve(md,'Transient'); + +Index: ../trunk-jpl/test/NightlyRun/test323.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test323.py (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test323.py (revision 21787) +@@ -14,7 +14,8 @@ + md=parameterize(md,'../Par/SquareSheetConstrained.py') + md=setflowequation(md,'SSA','all') + md.cluster=generic('name',gethostname(),'np',3) +-md.timestepping.time_adapt=1 ++md.timestepping = timesteppingadaptive(md.timestepping); ++md.timestepping.time_step_max = 10000.; + md.timestepping.final_time=1120. + md=solve(md,'Transient') + +Index: ../trunk-jpl/test/NightlyRun/test227.js +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test227.js (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test227.js (revision 21787) +@@ -6,7 +6,7 @@ + md.extrude(md,3,1.); + setflowequation(md,'HO','all'); + //md.cluster=generic('name',oshostname(),'np',3); +-md.timestepping.time_adapt=1.; ++md.timestepping = timesteppingadaptive(md.timestepping); + md.timestepping.final_time=20.; + md=solve(md,'Transient'); + +Index: ../trunk-jpl/test/NightlyRun/test324.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test324.py (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test324.py (revision 21787) +@@ -15,7 +15,8 @@ + md.extrude(5,1.2) + md=setflowequation(md,'SIA','all') + md.cluster=generic('name',gethostname(),'np',3) +-md.timestepping.time_adapt=1 ++md.timestepping = timesteppingadaptive(md.timestepping); ++md.timestepping.time_step_max = 10000.; + md.timestepping.final_time=16000. + md=solve(md,'Transient') + +Index: ../trunk-jpl/test/NightlyRun/test226.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test226.py (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test226.py (revision 21787) +@@ -13,7 +13,7 @@ + md=parameterize(md,'../Par/SquareShelf.py') + md=setflowequation(md,'SSA','all') + md.cluster=generic('name',gethostname(),'np',3) +-md.timestepping.time_adapt=1. ++md.timestepping = timesteppingadaptive(md.timestepping); + md.timestepping.final_time=15. + md=solve(md,'Transient') + +Index: ../trunk-jpl/test/NightlyRun/test227.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test227.py (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test227.py (revision 21787) +@@ -14,7 +14,7 @@ + md.extrude(3,1.) + md=setflowequation(md,'HO','all') + md.cluster=generic('name',gethostname(),'np',3) +-md.timestepping.time_adapt=1. ++md.timestepping = timesteppingadaptive(md.timestepping) + md.timestepping.final_time=20. + md=solve(md,'Transient') + +Index: ../trunk-jpl/test/NightlyRun/test4001.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test4001.m (revision 21786) ++++ ../trunk-jpl/test/NightlyRun/test4001.m (revision 21787) +@@ -538,7 +538,6 @@ + %timestepping: + md.timestepping.final_time=final_time; + md.timestepping.time_step=time_step; +- md.timestepping.time_adapt=0; + md.transient.isgroundingline=1; + md.transient.isthermal=0; + md.groundingline.migration='SubelementMigration2'; +@@ -652,7 +651,6 @@ + md.timestepping.start_time=start_time; + md.timestepping.final_time=final_time; + md.timestepping.time_step=time_step; +- md.timestepping.time_adapt=0; + md.cluster=generic('name',oshostname(),'np',2); + md.results.TransientSolution.Base=md.geometry.base; + md.transient.isgroundingline=1; +Index: ../trunk-jpl/src/m/classes/timeadaptation.m +=================================================================== +--- ../trunk-jpl/src/m/classes/timeadaptation.m (revision 21786) ++++ ../trunk-jpl/src/m/classes/timeadaptation.m (nonexistent) +@@ -1,90 +0,0 @@ +-%TIMESTEPPING Class definition +-% +-% Usage: +-% timeadaptation=timeadaptation(); +- +-classdef timeadaptation +- properties (SetAccess=public) +- start_time = 0.; +- final_time = 0.; +- time_step_min = 0.; +- time_step_max = 0.; +- cfl_coefficient = 0.; +- interp_forcings = 1; +- end +- methods +- function self = timeadaptation(varargin) % {{{ +- switch nargin +- case 0 +- self=setdefaultparameters(self); +- case 1 +- self=structtoobj(timeadaptation(),varargin{1}); +- otherwise +- error('constructor not supported'); +- end +- end % }}} +- function self = setdefaultparameters(self) % {{{ +- +- %time between 2 time steps +- self.time_step_min = 0.01; +- self.time_step_max = 1.; +- +- %final time +- self.final_time=10.*self.time_step_max; +- +- %default CFL coefficient +- self.cfl_coefficient=0.5; +- +- %should we interpolate forcings between timesteps? +- self.interp_forcings=1; +- end % }}} +- function md = checkconsistency(self,md,solution,analyses) % {{{ +- +- md = checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1); +- md = checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1); +- md = checkfield(md,'fieldname','timestepping.time_step_min','numel',[1],'>=',0,'NaN',1,'Inf',1); +- md = checkfield(md,'fieldname','timestepping.time_step_max','numel',[1],'>=',0,'NaN',1,'Inf',1); +- if (self.time_step_min>self.time_step_max) +- md = checkmessage(md,['base not equal to bed on grounded ice!']); +- end +- md = checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1); +- md = checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0 1]); +- if self.final_time-self.start_time<0, +- md = checkmessage(md,'timestepping.final_time should be larger than timestepping.start_time'); +- end +- end % }}} +- function disp(self) % {{{ +- disp(sprintf(' timeadaptation parameters:')); +- +- unit = 'yr'; +- fielddisplay(self,'start_time',['simulation starting time [' unit ']']); +- fielddisplay(self,'final_time',['final time to stop the simulation [' unit ']']); +- fielddisplay(self,'time_step_min',['minimum length of time step [' unit ']']); +- fielddisplay(self,'time_step_max',['maximum length of time step [' unit ']']); +- fielddisplay(self,'cfl_coefficient','coefficient applied to cfl condition'); +- fielddisplay(self,'interp_forcings','interpolate in time between requested forcing values ? (0 or 1)'); +- +- end % }}} +- function marshall(self,prefix,md,fid) % {{{ +- +- scale = md.constants.yts; +- WriteData(fid,prefix,'name','md.timestepping.type','data',2,'format','Integer'); +- WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','start_time','format','Double','scale',scale); +- WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','final_time','format','Double','scale',scale); +- WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','time_step_min','format','Double','scale',scale); +- WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','time_step_max','format','Double','scale',scale); +- WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','cfl_coefficient','format','Double'); +- WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','interp_forcings','format','Boolean'); +- end % }}} +- function savemodeljs(self,fid,modelname) % {{{ +- +- writejsdouble(fid,[modelname '.timeadaptation.start_time'],self.start_time); +- writejsdouble(fid,[modelname '.timeadaptation.final_time'],self.final_time); +- writejsdouble(fid,[modelname '.timeadaptation.time_step_min'],self.time_step_min); +- writejsdouble(fid,[modelname '.timeadaptation.time_step_max'],self.time_step_max); +- writejsdouble(fid,[modelname '.timeadaptation.cfl_coefficient'],self.cfl_coefficient); +- writejsdouble(fid,[modelname '.timeadaptation.interp_forcings'],self.interp_forcings); +- +- end % }}} +- end +-end +Index: ../trunk-jpl/src/m/classes/timesteppingadaptive.py +=================================================================== +--- ../trunk-jpl/src/m/classes/timesteppingadaptive.py (nonexistent) ++++ ../trunk-jpl/src/m/classes/timesteppingadaptive.py (revision 21787) +@@ -0,0 +1,86 @@ ++from fielddisplay import fielddisplay ++from checkfield import checkfield ++from WriteData import WriteData ++ ++class timesteppingadaptive(object): ++ """ ++ TIMESTEPPINGADAPTIVE Class definition ++ ++ Usage: ++ timesteppingadaptive=timesteppingadaptive(); ++ """ ++ ++ def __init__(self,*args): # {{{ ++ if not len(args): ++ self.start_time = 0. ++ self.final_time = 0. ++ self.time_step_min = 0. ++ self.time_step_max = 0. ++ self.cfl_coefficient = 0. ++ self.interp_forcings = 1 ++ ++ #set defaults ++ self.setdefaultparameters() ++ ++ elif len(args)==1 and args[0].__module__=='timestepping': ++ old=args[0] ++ #first call setdefaultparameters: ++ self.setdefaultparameters() ++ self.start_time = old.start_time ++ self.final_time = old.final_time ++ self.interp_forcings = old.interp_forcings ++ ++ else: ++ raise Exception('constructor not supported') ++ #}}} ++ def __repr__(self): # {{{ ++ string=" timesteppingadaptive parameters:" ++ string="%s\n%s"%(string,fielddisplay(self,"start_time","simulation starting time [yr]")) ++ string="%s\n%s"%(string,fielddisplay(self,"final_time","final time to stop the simulation [yr]")) ++ string="%s\n%s"%(string,fielddisplay(self,"time_step_min","minimum length of time steps [yr]")) ++ string="%s\n%s"%(string,fielddisplay(self,"time_step_max","maximum length of time steps [yr]")) ++ string="%s\n%s"%(string,fielddisplay(self,"cfl_coefficient","coefficient applied to cfl condition")) ++ string="%s\n%s"%(string,fielddisplay(self,"interp_forcings","interpolate in time between requested forcing values ? (0 or 1)")) ++ return string ++ #}}} ++ def setdefaultparameters(self): # {{{ ++ ++ #time between 2 time steps ++ self.time_step_min=0.01 ++ self.time_step_max=10. ++ ++ #final time ++ self.final_time=10.*self.time_step_max ++ ++ #time adaptation? ++ self.cfl_coefficient=0.5 ++ ++ #should we interpolate forcings between timesteps? ++ self.interp_forcings=1 ++ ++ return self ++ #}}} ++ def checkconsistency(self,md,solution,analyses): # {{{ ++ ++ md = checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1) ++ md = checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1) ++ md = checkfield(md,'fieldname','timestepping.time_step_min','numel',[1],'>=',0,'NaN',1,'Inf',1) ++ md = checkfield(md,'fieldname','timestepping.time_step_max','numel',[1],'>=',md.timestepping.time_step_min,'NaN',1,'Inf',1) ++ md = checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1) ++ if self.final_time-self.start_time<0: ++ md.checkmessage("timestepping.final_time should be larger than timestepping.start_time") ++ md = checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0,1]) ++ ++ return md ++ # }}} ++ def marshall(self,prefix,md,fid): # {{{ ++ ++ yts=md.constants.yts ++ WriteData(fid,prefix,'name','md.timestepping.type','data',2,'format','Integer'); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','start_time','format','Double','scale',yts) ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','final_time','format','Double','scale',yts) ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','time_step_min','format','Double','scale',yts) ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','time_step_max','format','Double','scale',yts) ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','cfl_coefficient','format','Double') ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','interp_forcings','format','Boolean') ++ # }}} +Index: ../trunk-jpl/src/m/classes/timesteppingadaptive.js +=================================================================== +--- ../trunk-jpl/src/m/classes/timesteppingadaptive.js (nonexistent) ++++ ../trunk-jpl/src/m/classes/timesteppingadaptive.js (revision 21787) +@@ -0,0 +1,78 @@ ++//TIMESTEPPINGADAPTIVE class definition ++// ++// Usage: ++// timesteppingadaptive=new timesteppingadaptive(); ++ ++function timesteppingadaptive (){ ++ //methods ++ this.setdefaultparameters = function(){// {{{ ++ //time between 2 time steps ++ this.time_step_min=0.01; ++ this.time_step_max=10.; ++ ++ //final time ++ this.final_time=10.*this.time_step_max; ++ ++ //time adaptation? ++ this.cfl_coefficient=0.5; ++ ++ //should we interpolate forcings between timesteps? ++ this.interp_forcings=1; ++ }// }}} ++ this.disp= function(){// {{{ ++ ++ var unit; ++ console.log(sprintf(' timesteppingadaptive parameters:')); ++ unit = 'yr'; ++ fielddisplay(this,'start_time','simulation starting time ['+ unit + ']'); ++ fielddisplay(this,'final_time','final time to stop the simulation ['+ unit + ']'); ++ fielddisplay(this,'time_step_min','minimum length of time steps [' +unit+ ']'); ++ fielddisplay(this,'time_step_max','maximum length of time steps [' +unit+ ']'); ++ fielddisplay(this,'cfl_coefficient','coefficient applied to cfl condition'); ++ fielddisplay(this,'interp_forcings','interpolate in time between requested forcing values ? (0 or 1)'); ++ ++ }// }}} ++ this.classname= function(){// {{{ ++ return "timesteppingadaptive"; ++ ++ }// }}} ++ this.checkconsistency = function(md,solution,analyses) { //{{{ ++ ++ checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1); ++ checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1); ++ checkfield(md,'fieldname','timestepping.time_step_min','numel',[1],'>=',0,'NaN',1,'Inf',1); ++ checkfield(md,'fieldname','timestepping.time_step_max','numel',[1],'>=',md.timestepping.time_step_max,'NaN',1,'Inf',1); ++ checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1); ++ checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0,1]); ++ if (this.final_time-this.start_time<0){ ++ md.checkmessage('timestepping.final_time should be larger than timestepping.start_time'); ++ } ++ } // }}} ++ this.marshall=function(md,prefix,fid) { //{{{ ++ ++ var scale; ++ scale = md.constants.yts; ++ ++ WriteData(fid,prefix,'name','md.timestepping.type','data',2,'format','Integer'); ++ WriteData(fid,prefix,'object',this,'class','timestepping','fieldname','start_time','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',this,'class','timestepping','fieldname','final_time','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',this,'class','timestepping','fieldname','time_step_min','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',this,'class','timestepping','fieldname','time_step_max','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',this,'class','timestepping','fieldname','cfl_coefficient','format','Double'); ++ WriteData(fid,prefix,'object',this,'class','timestepping','fieldname','interp_forcings','format','Boolean'); ++ ++ }//}}} ++ this.fix=function() { //{{{ ++ }//}}} ++ //properties ++ // {{{ ++ this.start_time = 0.; ++ this.final_time = 0.; ++ this.time_step_min = 0.; ++ this.time_step_max = 0.; ++ this.cfl_coefficient = 0.; ++ this.interp_forcings = 1; ++ ++ this.setdefaultparameters(); ++ //}}} ++} +Index: ../trunk-jpl/src/m/classes/timesteppingadaptive.m +=================================================================== +--- ../trunk-jpl/src/m/classes/timesteppingadaptive.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/timesteppingadaptive.m (revision 21787) +@@ -0,0 +1,87 @@ ++%TIMESTEPPINGADAPTIVE Class definition ++% ++% Usage: ++% timesteppingadaptive=timesteppingadaptive(); ++ ++classdef timesteppingadaptive ++ properties (SetAccess=public) ++ start_time = 0.; ++ final_time = 0.; ++ time_step_min = 0.; ++ time_step_max = 0.; ++ cfl_coefficient = 0.; ++ interp_forcings = 1; ++ end ++ methods ++ function self = timesteppingadaptive(varargin) % {{{ ++ switch nargin ++ case 0 ++ self=setdefaultparameters(self); ++ case 1 ++ self=structtoobj(timesteppingadaptive(),varargin{1}); ++ otherwise ++ error('constructor not supported'); ++ end ++ end % }}} ++ function self = setdefaultparameters(self) % {{{ ++ ++ %time between 2 time steps ++ self.time_step_min = 0.01; ++ self.time_step_max = 10.; ++ ++ %final time ++ self.final_time=10.*self.time_step_max; ++ ++ %default CFL coefficient ++ self.cfl_coefficient=0.5; ++ ++ %should we interpolate forcings between timesteps? ++ self.interp_forcings=1; ++ end % }}} ++ function md = checkconsistency(self,md,solution,analyses) % {{{ ++ ++ md = checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','timestepping.time_step_min','numel',[1],'>=',0,'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','timestepping.time_step_max','numel',[1],'>=',md.timestepping.time_step_min,'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1); ++ md = checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0 1]); ++ if self.final_time-self.start_time<0, ++ md = checkmessage(md,'timestepping.final_time should be larger than timestepping.start_time'); ++ end ++ end % }}} ++ function disp(self) % {{{ ++ disp(sprintf(' timesteppingadaptive parameters:')); ++ ++ unit = 'yr'; ++ fielddisplay(self,'start_time',['simulation starting time [' unit ']']); ++ fielddisplay(self,'final_time',['final time to stop the simulation [' unit ']']); ++ fielddisplay(self,'time_step_min',['minimum length of time step [' unit ']']); ++ fielddisplay(self,'time_step_max',['maximum length of time step [' unit ']']); ++ fielddisplay(self,'cfl_coefficient','coefficient applied to cfl condition'); ++ fielddisplay(self,'interp_forcings','interpolate in time between requested forcing values ? (0 or 1)'); ++ ++ end % }}} ++ function marshall(self,prefix,md,fid) % {{{ ++ ++ scale = md.constants.yts; ++ WriteData(fid,prefix,'name','md.timestepping.type','data',2,'format','Integer'); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','start_time','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','final_time','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','time_step_min','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','time_step_max','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','cfl_coefficient','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','timestepping','fieldname','interp_forcings','format','Boolean'); ++ end % }}} ++ function savemodeljs(self,fid,modelname) % {{{ ++ ++ writejsdouble(fid,[modelname '.timesteppingadaptive.start_time'],self.start_time); ++ writejsdouble(fid,[modelname '.timesteppingadaptive.final_time'],self.final_time); ++ writejsdouble(fid,[modelname '.timesteppingadaptive.time_step_min'],self.time_step_min); ++ writejsdouble(fid,[modelname '.timesteppingadaptive.time_step_max'],self.time_step_max); ++ writejsdouble(fid,[modelname '.timesteppingadaptive.cfl_coefficient'],self.cfl_coefficient); ++ writejsdouble(fid,[modelname '.timesteppingadaptive.interp_forcings'],self.interp_forcings); ++ ++ end % }}} ++ end ++end +Index: ../trunk-jpl/src/m/classes/timestepping.py +=================================================================== +--- ../trunk-jpl/src/m/classes/timestepping.py (revision 21786) ++++ ../trunk-jpl/src/m/classes/timestepping.py (revision 21787) +@@ -14,8 +14,6 @@ + self.start_time = 0. + self.final_time = 0. + self.time_step = 0. +- self.time_adapt = 0 +- self.cfl_coefficient = 0. + self.interp_forcings = 1 + + #set defaults +@@ -27,8 +25,6 @@ + string="%s\n%s"%(string,fielddisplay(self,"start_time","simulation starting time [yr]")) + string="%s\n%s"%(string,fielddisplay(self,"final_time","final time to stop the simulation [yr]")) + string="%s\n%s"%(string,fielddisplay(self,"time_step","length of time steps [yr]")) +- string="%s\n%s"%(string,fielddisplay(self,"time_adapt","use cfl condition to define time step ? (0 or 1) ")) +- string="%s\n%s"%(string,fielddisplay(self,"cfl_coefficient","coefficient applied to cfl condition")) + string="%s\n%s"%(string,fielddisplay(self,"interp_forcings","interpolate in time between requested forcing values ? (0 or 1)")) + return string + #}}} +@@ -40,10 +36,6 @@ + #final time + self.final_time=10.*self.time_step + +- #time adaptation? +- self.time_adapt=0 +- self.cfl_coefficient=0.5 +- + #should we interpolate forcings between timesteps? + self.interp_forcings=1 + +@@ -54,8 +46,6 @@ + md = checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','timestepping.time_step','numel',[1],'>=',0,'NaN',1,'Inf',1) +- md = checkfield(md,'fieldname','timestepping.time_adapt','numel',[1],'values',[0,1]) +- md = checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1) + if self.final_time-self.start_time<0: + md.checkmessage("timestepping.final_time should be larger than timestepping.start_time") + md = checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0,1]) +@@ -69,7 +59,5 @@ + WriteData(fid,prefix,'object',self,'fieldname','start_time','format','Double','scale',yts) + WriteData(fid,prefix,'object',self,'fieldname','final_time','format','Double','scale',yts) + WriteData(fid,prefix,'object',self,'fieldname','time_step','format','Double','scale',yts) +- WriteData(fid,prefix,'object',self,'fieldname','time_adapt','format','Boolean') +- WriteData(fid,prefix,'object',self,'fieldname','cfl_coefficient','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','interp_forcings','format','Boolean') + # }}} +Index: ../trunk-jpl/src/m/classes/timestepping.m +=================================================================== +--- ../trunk-jpl/src/m/classes/timestepping.m (revision 21786) ++++ ../trunk-jpl/src/m/classes/timestepping.m (revision 21787) +@@ -8,8 +8,6 @@ + start_time = 0.; + final_time = 0.; + time_step = 0.; +- time_adapt = 0; +- cfl_coefficient = 0.; + interp_forcings = 1; + end + methods +@@ -29,10 +27,6 @@ + %final time + self.final_time=10.*self.time_step; + +- %time adaptation? +- self.time_adapt=0; +- self.cfl_coefficient=0.5; +- + %should we interpolate forcings between timesteps? + self.interp_forcings=1; + end % }}} +@@ -41,8 +35,6 @@ + md = checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','timestepping.time_step','numel',[1],'>=',0,'NaN',1,'Inf',1); +- md = checkfield(md,'fieldname','timestepping.time_adapt','numel',[1],'values',[0 1]); +- md = checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1); + md = checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0 1]); + if self.final_time-self.start_time<0, + md = checkmessage(md,'timestepping.final_time should be larger than timestepping.start_time'); +@@ -55,8 +47,6 @@ + fielddisplay(self,'start_time',['simulation starting time [' unit ']']); + fielddisplay(self,'final_time',['final time to stop the simulation [' unit ']']); + fielddisplay(self,'time_step',['length of time steps [' unit ']']); +- fielddisplay(self,'time_adapt','use cfl condition to define time step ? (0 or 1) '); +- fielddisplay(self,'cfl_coefficient','coefficient applied to cfl condition'); + fielddisplay(self,'interp_forcings','interpolate in time between requested forcing values ? (0 or 1)'); + + end % }}} +@@ -67,8 +57,6 @@ + WriteData(fid,prefix,'object',self,'fieldname','start_time','format','Double','scale',scale); + WriteData(fid,prefix,'object',self,'fieldname','final_time','format','Double','scale',scale); + WriteData(fid,prefix,'object',self,'fieldname','time_step','format','Double','scale',scale); +- WriteData(fid,prefix,'object',self,'fieldname','time_adapt','format','Boolean'); +- WriteData(fid,prefix,'object',self,'fieldname','cfl_coefficient','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','interp_forcings','format','Boolean'); + end % }}} + function savemodeljs(self,fid,modelname) % {{{ +@@ -76,8 +64,6 @@ + writejsdouble(fid,[modelname '.timestepping.start_time'],self.start_time); + writejsdouble(fid,[modelname '.timestepping.final_time'],self.final_time); + writejsdouble(fid,[modelname '.timestepping.time_step'],self.time_step); +- writejsdouble(fid,[modelname '.timestepping.time_adapt'],self.time_adapt); +- writejsdouble(fid,[modelname '.timestepping.cfl_coefficient'],self.cfl_coefficient); + writejsdouble(fid,[modelname '.timestepping.interp_forcings'],self.interp_forcings); + + end % }}} +Index: ../trunk-jpl/src/m/classes/timestepping.js +=================================================================== +--- ../trunk-jpl/src/m/classes/timestepping.js (revision 21786) ++++ ../trunk-jpl/src/m/classes/timestepping.js (revision 21787) +@@ -12,10 +12,6 @@ + //final time + this.final_time=10.*this.time_step; + +- //time adaptation? +- this.time_adapt=0; +- this.cfl_coefficient=0.5; +- + //should we interpolate forcings between timesteps? + this.interp_forcings=1; + }// }}} +@@ -27,8 +23,6 @@ + fielddisplay(this,'start_time','simulation starting time ['+ unit + ']'); + fielddisplay(this,'final_time','final time to stop the simulation ['+ unit + ']'); + fielddisplay(this,'time_step','length of time steps [' +unit+ ']'); +- fielddisplay(this,'time_adapt','use cfl condition to define time step ? (0 or 1) '); +- fielddisplay(this,'cfl_coefficient','coefficient applied to cfl condition'); + fielddisplay(this,'interp_forcings','interpolate in time between requested forcing values ? (0 or 1)'); + + }// }}} +@@ -36,41 +30,35 @@ + return "timestepping"; + + }// }}} +- this.checkconsistency = function(md,solution,analyses) { //{{{ +- +- checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1); +- checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1); +- checkfield(md,'fieldname','timestepping.time_step','numel',[1],'>=',0,'NaN',1,'Inf',1); +- checkfield(md,'fieldname','timestepping.time_adapt','numel',[1],'values',[0,1]); +- checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1); +- checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0,1]); +- if (this.final_time-this.start_time<0){ +- md.checkmessage('timestepping.final_time should be larger than timestepping.start_time'); +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ ++ this.checkconsistency = function(md,solution,analyses) { //{{{ + +- var scale; +- scale = md.constants.yts; +- +- WriteData(fid,prefix,'name','md.timestepping.type','data',1,'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','start_time','format','Double','scale',scale); +- WriteData(fid,prefix,'object',this,'fieldname','final_time','format','Double','scale',scale); +- WriteData(fid,prefix,'object',this,'fieldname','time_step','format','Double','scale',scale); +- WriteData(fid,prefix,'object',this,'fieldname','time_adapt','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','cfl_coefficient','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','interp_forcings','format','Boolean'); ++ checkfield(md,'fieldname','timestepping.start_time','numel',[1],'NaN',1,'Inf',1); ++ checkfield(md,'fieldname','timestepping.final_time','numel',[1],'NaN',1,'Inf',1); ++ checkfield(md,'fieldname','timestepping.time_step','numel',[1],'>=',0,'NaN',1,'Inf',1); ++ checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0,1]); ++ if (this.final_time-this.start_time<0){ ++ md.checkmessage('timestepping.final_time should be larger than timestepping.start_time'); ++ } ++ } // }}} ++ this.marshall=function(md,prefix,fid) { //{{{ + +- }//}}} +- this.fix=function() { //{{{ +- }//}}} ++ var scale; ++ scale = md.constants.yts; ++ ++ WriteData(fid,prefix,'name','md.timestepping.type','data',1,'format','Integer'); ++ WriteData(fid,prefix,'object',this,'fieldname','start_time','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',this,'fieldname','final_time','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',this,'fieldname','time_step','format','Double','scale',scale); ++ WriteData(fid,prefix,'object',this,'fieldname','interp_forcings','format','Boolean'); ++ ++ }//}}} ++ this.fix=function() { //{{{ ++ }//}}} + //properties + // {{{ + this.start_time = 0.; + this.final_time = 0.; + this.time_step = 0.; +- this.time_adapt = 0; +- this.cfl_coefficient = 0.; + this.interp_forcings = 1; + + this.setdefaultparameters(); +Index: ../trunk-jpl/src/m/classes/model.py +=================================================================== +--- ../trunk-jpl/src/m/classes/model.py (revision 21786) ++++ ../trunk-jpl/src/m/classes/model.py (revision 21787) +@@ -23,6 +23,7 @@ + from friction import friction + from flowequation import flowequation + from timestepping import timestepping ++from timesteppingadaptive import timesteppingadaptive + from initialization import initialization + from rifts import rifts + from slr import slr +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21786) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21787) +@@ -31,7 +31,7 @@ + LevelsetStabilizationEnum, + TimesteppingTypeEnum, + FixedTimesteppingEnum, +- TimeAdaptationEnum, ++ AdaptiveTimesteppingEnum, + TimesteppingTimeStepMinEnum, + TimesteppingTimeStepMaxEnum, + /*}}}*/ +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21786) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21787) +@@ -39,7 +39,7 @@ + case LevelsetStabilizationEnum : return "LevelsetStabilization"; + case TimesteppingTypeEnum : return "TimesteppingType"; + case FixedTimesteppingEnum : return "FixedTimestepping"; +- case TimeAdaptationEnum : return "TimeAdaptation"; ++ case AdaptiveTimesteppingEnum : return "AdaptiveTimestepping"; + case TimesteppingTimeStepMinEnum : return "TimesteppingTimeStepMin"; + case TimesteppingTimeStepMaxEnum : return "TimesteppingTimeStepMax"; + case AutodiffIsautodiffEnum : return "AutodiffIsautodiff"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21786) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21787) +@@ -39,7 +39,7 @@ + else if (strcmp(name,"LevelsetStabilization")==0) return LevelsetStabilizationEnum; + else if (strcmp(name,"TimesteppingType")==0) return TimesteppingTypeEnum; + else if (strcmp(name,"FixedTimestepping")==0) return FixedTimesteppingEnum; +- else if (strcmp(name,"TimeAdaptation")==0) return TimeAdaptationEnum; ++ else if (strcmp(name,"AdaptiveTimestepping")==0) return AdaptiveTimesteppingEnum; + else if (strcmp(name,"TimesteppingTimeStepMin")==0) return TimesteppingTimeStepMinEnum; + else if (strcmp(name,"TimesteppingTimeStepMax")==0) return TimesteppingTimeStepMaxEnum; + else if (strcmp(name,"AutodiffIsautodiff")==0) return AutodiffIsautodiffEnum; +Index: ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 21786) ++++ ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 21787) +@@ -123,7 +123,7 @@ + int IoCodeToEnumTimestepping(int enum_in){/*{{{*/ + switch(enum_in){ + case 1: return FixedTimesteppingEnum; +- case 2: return TimeAdaptationEnum; ++ case 2: return AdaptiveTimesteppingEnum; + default: _error_("Marshalled materials code \""<AddObject(iomodel->CopyConstantObject("md.timestepping.start_time",TimesteppingStartTimeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.final_time",TimesteppingFinalTimeEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_adapt",TimesteppingTimeAdaptEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_step",TimesteppingTimeStepEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.cfl_coefficient",TimesteppingCflCoefficientEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.interp_forcings",TimesteppingInterpForcingsEnum)); + break; +- case TimeAdaptationEnum: +- parameters->AddObject(new BoolParam(TimesteppingTimeAdaptEnum,true)); ++ case AdaptiveTimesteppingEnum: + parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.start_time",TimesteppingStartTimeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.final_time",TimesteppingFinalTimeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.time_step_min",TimesteppingTimeStepMinEnum)); +@@ -157,7 +154,7 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.timestepping.interp_forcings",TimesteppingInterpForcingsEnum)); + break; + default: +- _error_(EnumToStringx(timestepping_type) <<" not supported yet"); ++ _error_("Time stepping \""<FindConstant(&time,"md.timestepping.start_time"); + parameters->AddObject(new DoubleParam(TimeEnum,time)); +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21786) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21787) +@@ -22,7 +22,7 @@ + IssmDouble finaltime,dt,yts; + bool isstressbalance,ismasstransport,issmb,isFS,isthermal,isgroundingline,isgia,isslr,iscoupler,ismovingfront,isdamageevolution,ishydrology; + bool save_results,dakota_analysis; +- bool time_adapt; ++ int timestepping; + int output_frequency; + int recording_frequency; + int domaintype,groundingline_migration,smb_model,amr_frequency; +@@ -46,7 +46,7 @@ + femmodel->parameters->FindParam(&yts,ConstantsYtsEnum); + femmodel->parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); + femmodel->parameters->FindParam(&output_frequency,SettingsOutputFrequencyEnum); +- femmodel->parameters->FindParam(&time_adapt,TimesteppingTimeAdaptEnum); ++ femmodel->parameters->FindParam(×tepping,TimesteppingTypeEnum); + femmodel->parameters->FindParam(&isstressbalance,TransientIsstressbalanceEnum); + femmodel->parameters->FindParam(&ismasstransport,TransientIsmasstransportEnum); + femmodel->parameters->FindParam(&issmb,TransientIssmbEnum); +@@ -70,15 +70,20 @@ + #endif + + while(time < finaltime - (yts*DBL_EPSILON)){ //make sure we run up to finaltime. +- /*Increment*/ +- if(time_adapt){ +- femmodel->TimeAdaptx(&dt); +- if(time+dt>finaltime) dt=finaltime-time; +- femmodel->parameters->SetParam(dt,TimesteppingTimeStepEnum); ++ ++ /*Time Increment*/ ++ switch(timestepping){ ++ case AdaptiveTimesteppingEnum: ++ femmodel->TimeAdaptx(&dt); ++ if(time+dt>finaltime) dt=finaltime-time; ++ femmodel->parameters->SetParam(dt,TimesteppingTimeStepEnum); ++ break; ++ case FixedTimesteppingEnum: ++ femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); ++ break; ++ default: ++ _error_("Time stepping \""<parameters->FindParam(&dt,TimesteppingTimeStepEnum); +- } + step+=1; + time+=dt; + femmodel->parameters->SetParam(time,TimeEnum); +@@ -182,7 +187,6 @@ + if(step%amr_frequency==0 && timeReMesh();//Do not refine the last step + } + #endif +- + } + + femmodel->RequestedDependentsx(); +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21786) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21787) +@@ -2064,8 +2064,6 @@ + /*}}}*/ + void FemModel::TimeAdaptx(IssmDouble* pdt){/*{{{*/ + +- int i; +- + /*output: */ + IssmDouble dt; + +@@ -2076,7 +2074,7 @@ + /*Go through elements, and figure out the minimum of the time steps for each element (using CFL criterion): */ + Element* element=(Element*)elements->GetObjectByOffset(0); min_dt=element->TimeAdapt(); + +- for (i=1;iSize();i++){ ++ for(int i=1;iSize();i++){ + element=xDynamicCast(elements->GetObjectByOffset(i)); + dt=element->TimeAdapt(); + if(dtFindParam(×tepping_type,TimesteppingTypeEnum); +- if(timestepping_type==TimeAdaptationEnum){ +- parameters->FindParam(&dt_low,TimesteppingTimeStepMinEnum); +- parameters->FindParam(&dt_high,TimesteppingTimeStepMaxEnum); +- if(min_dtdt_high) min_dt = dt_high; +- } ++ parameters->FindParam(&dt_low,TimesteppingTimeStepMinEnum); ++ parameters->FindParam(&dt_high,TimesteppingTimeStepMaxEnum); ++ if(min_dtdt_high) min_dt = dt_high; + + /*Assign output pointers:*/ + *pdt=min_dt; Index: /issm/oecreview/Archive/21724-22754/ISSM-21787-21788.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21787-21788.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21787-21788.diff (revision 22755) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/m/classes/mask.m +=================================================================== +--- ../trunk-jpl/src/m/classes/mask.m (revision 21787) ++++ ../trunk-jpl/src/m/classes/mask.m (revision 21788) +@@ -44,9 +44,6 @@ + if sum(isice)==0, + warning('no ice present in the domain'); + end +- if max(md.mask.ice_levelset)<0, +- disp('WARNING: no ice front provided'); +- end + end % }}} + function disp(self) % {{{ + disp(sprintf(' masks:')); Index: /issm/oecreview/Archive/21724-22754/ISSM-21788-21789.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21788-21789.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21788-21789.diff (revision 22755) @@ -0,0 +1,25 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 21788) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 21789) +@@ -45,7 +45,7 @@ + /*Fetch segments and names: */ + iomodel->FetchMultipleData(&gatenames,&numgates, "md.massfluxatgate.name"); + iomodel->FetchMultipleData(&gatedefinitionstrings,&temp, "md.massfluxatgate.definitionstring"); _assert_(temp==numgates); +- iomodel->FetchMultipleData(&gatesegments,&gatesegments_M,NULL,&temp, "md.massfluxatgate.segments"); _assert_(temp==numgates); ++ iomodel->FetchMultipleData(&gatesegments,&gatesegments_M,NULL,&temp, "md.massfluxatgate.segments"); _assert_(temp==numgates); + + for(j=0;jAddObject(new Massfluxatgate(gatenames[j],StringToEnumx(gatedefinitionstrings[j]),gatesegments_M[j],gatesegments[j])); +@@ -52,8 +52,9 @@ + } + /*Free ressources:*/ + for(j=0;j(string); +- IssmDouble* gate = gatesegments[j]; xDelete(gate); ++ char* string = gatenames[j]; xDelete(string); ++ char* string2 = gatedefinitionstrings[j]; xDelete(string2); ++ IssmDouble* gate = gatesegments[j]; xDelete(gate); + } + xDelete(gatenames); + xDelete(gatesegments); Index: /issm/oecreview/Archive/21724-22754/ISSM-21789-21790.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21789-21790.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21789-21790.diff (revision 22755) @@ -0,0 +1,204 @@ +Index: ../trunk-jpl/test/NightlyRun/test441.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test441.m (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test441.m (revision 21790) +@@ -0,0 +1,80 @@ ++%Test Name: MISMIP3D ++md=triangle(model(),'../Exp/Square.exp',100000.); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md.initialization.vx(:)=1.; ++md.initialization.vy(:)=1.; ++md.geometry.thickness(:)=500-md.mesh.x/10000; ++md.geometry.bed =-100-md.mesh.x/1000; ++md.geometry.base=-md.geometry.thickness*md.materials.rho_ice/md.materials.rho_water; ++md.mask.groundedice_levelset=md.geometry.thickness+md.materials.rho_water/md.materials.rho_ice*md.geometry.bed; ++pos=find(md.mask.groundedice_levelset>=0); ++md.geometry.base(pos)=md.geometry.bed(pos); ++md.geometry.surface=md.geometry.base+md.geometry.thickness; ++md=setflowequation(md,'SSA','all'); ++ ++%Boundary conditions: ++md.mask.ice_levelset=-ones(md.mesh.numberofvertices,1); ++md.mask.ice_levelset(find(md.mesh.x==max(md.mesh.x)))=0; ++md.stressbalance.spcvx(:)=NaN; ++md.stressbalance.spcvy(:)=NaN; ++md.stressbalance.spcvz(:)=NaN; ++pos=find((md.mesh.y<1000000.1 & md.mesh.y>999999.9) | (md.mesh.y<0.1 & md.mesh.y>-0.1)); ++md.stressbalance.spcvy(pos)=0; ++pos2=find(md.mesh.x<0.1 & md.mesh.x>-0.1); ++md.stressbalance.spcvx(pos2)=0; ++md.stressbalance.spcvy(pos2)=0; ++ ++md.materials.rheology_B=1/((10^-25)^(1/3))*ones(md.mesh.numberofvertices,1); ++md.materials.rheology_law='None'; ++md.friction.coefficient(:)=sqrt(10^7)*ones(md.mesh.numberofvertices,1); ++md.friction.p=3*ones(md.mesh.numberofelements,1); ++md.smb.mass_balance(:)=1; ++md.basalforcings.groundedice_melting_rate(:)=0; ++md.basalforcings.floatingice_melting_rate(:)=30; ++md.transient.isthermal=0; ++md.transient.isstressbalance=1; ++md.transient.isgroundingline=1; ++md.transient.ismasstransport=1; ++md.transient.issmb=1; ++md.transient.requested_outputs={'default','BasalforcingsFloatingiceMeltingRate'}; ++md.groundingline.migration='SubelementMigration2'; ++md.timestepping.final_time=30; ++md.timestepping.time_step=10; ++ ++md.cluster=generic('name',oshostname(),'np',3); ++md=solve(md,'Transient'); ++ ++%Fields and tolerances to track changes ++field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Pressure1','FloatingiceMeltingrate1',... ++ 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Pressure2','FloatingiceMeltingrate2',... ++ 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Pressure3','FloatingiceMeltingrate3'}; ++field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,1e-13,1e-13,... ++ 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-10,1e-13,... ++ 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-10,1e-13}; ++field_values={... ++ (md.results.TransientSolution(1).Base),... ++ (md.results.TransientSolution(1).Surface),... ++ (md.results.TransientSolution(1).Thickness),... ++ (md.results.TransientSolution(1).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(1).Vx),... ++ (md.results.TransientSolution(1).Vy),... ++ (md.results.TransientSolution(1).Pressure),... ++ (md.results.TransientSolution(1).BasalforcingsFloatingiceMeltingRate),... ++ (md.results.TransientSolution(2).Base),... ++ (md.results.TransientSolution(2).Surface),... ++ (md.results.TransientSolution(2).Thickness),... ++ (md.results.TransientSolution(2).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(2).Vx),... ++ (md.results.TransientSolution(2).Vy),... ++ (md.results.TransientSolution(2).Pressure),... ++ (md.results.TransientSolution(2).BasalforcingsFloatingiceMeltingRate),... ++ (md.results.TransientSolution(3).Base),... ++ (md.results.TransientSolution(3).Surface),... ++ (md.results.TransientSolution(3).Thickness),... ++ (md.results.TransientSolution(3).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(3).Vx),... ++ (md.results.TransientSolution(3).Vy),... ++ (md.results.TransientSolution(3).Pressure),... ++ (md.results.TransientSolution(3).BasalforcingsFloatingiceMeltingRate),... ++ }; +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21790) +@@ -0,0 +1,84 @@ ++%Test Name: MISMIP3DHO ++md=triangle(model(),'../Exp/Square.exp',100000.); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md.initialization.vx(:)=1.; ++md.initialization.vy(:)=1.; ++md.geometry.thickness(:)=500-md.mesh.x/10000; ++md.geometry.bed =-100-md.mesh.x/1000; ++md.geometry.base=-md.geometry.thickness*md.materials.rho_ice/md.materials.rho_water; ++md.mask.groundedice_levelset=md.geometry.thickness+md.materials.rho_water/md.materials.rho_ice*md.geometry.bed; ++pos=find(md.mask.groundedice_levelset>=0); ++md.geometry.base(pos)=md.geometry.bed(pos); ++md.geometry.surface=md.geometry.base+md.geometry.thickness; ++md=extrude(md,4,1.); ++md=setflowequation(md,'HO','all'); ++ ++%Boundary conditions: ++md.mask.ice_levelset=-ones(md.mesh.numberofvertices,1); ++md.mask.ice_levelset(find(md.mesh.x==max(md.mesh.x)))=0; ++md.stressbalance.spcvx(:)=NaN; ++md.stressbalance.spcvy(:)=NaN; ++md.stressbalance.spcvz(:)=NaN; ++pos=find((md.mesh.y<1000000.1 & md.mesh.y>999999.9) | (md.mesh.y<0.1 & md.mesh.y>-0.1)); ++md.stressbalance.spcvy(pos)=0; ++pos2=find(md.mesh.x<0.1 & md.mesh.x>-0.1); ++md.stressbalance.spcvx(pos2)=0; ++md.stressbalance.spcvy(pos2)=0; ++ ++md.materials.rheology_B=1/((10^-25)^(1/3))*ones(md.mesh.numberofvertices,1); ++md.materials.rheology_law='None'; ++md.friction.coefficient(:)=sqrt(10^7)*ones(md.mesh.numberofvertices,1); ++md.friction.p=3*ones(md.mesh.numberofelements,1); ++md.smb.mass_balance(:)=1; ++md.basalforcings.groundedice_melting_rate(:)=0; ++md.basalforcings.floatingice_melting_rate(:)=30; ++md.transient.isthermal=0; ++md.transient.isstressbalance=1; ++md.transient.isgroundingline=1; ++md.transient.ismasstransport=1; ++md.transient.issmb=1; ++md.transient.requested_outputs={'default','BasalforcingsFloatingiceMeltingRate'}; ++md.groundingline.migration='SubelementMigration2'; ++md.timestepping.final_time=30; ++md.timestepping.time_step=10; ++ ++md.cluster=generic('name',oshostname(),'np',3); ++md=solve(md,'Transient'); ++ ++%Fields and tolerances to track changes ++field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Vz1','Pressure1','FloatingiceMeltingrate1',... ++ 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... ++ 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; ++field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... ++ 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-09,1e-10,1e-13,... ++ 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-09,1e-10,1e-13}; ++field_values={... ++ (md.results.TransientSolution(1).Base),... ++ (md.results.TransientSolution(1).Surface),... ++ (md.results.TransientSolution(1).Thickness),... ++ (md.results.TransientSolution(1).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(1).Vx),... ++ (md.results.TransientSolution(1).Vy),... ++ (md.results.TransientSolution(1).Vz),... ++ (md.results.TransientSolution(1).Pressure),... ++ (md.results.TransientSolution(1).BasalforcingsFloatingiceMeltingRate),... ++ (md.results.TransientSolution(2).Base),... ++ (md.results.TransientSolution(2).Surface),... ++ (md.results.TransientSolution(2).Thickness),... ++ (md.results.TransientSolution(2).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(2).Vx),... ++ (md.results.TransientSolution(2).Vy),... ++ (md.results.TransientSolution(2).Vz),... ++ (md.results.TransientSolution(2).Pressure),... ++ (md.results.TransientSolution(2).BasalforcingsFloatingiceMeltingRate),... ++ (md.results.TransientSolution(3).Base),... ++ (md.results.TransientSolution(3).Surface),... ++ (md.results.TransientSolution(3).Thickness),... ++ (md.results.TransientSolution(3).MaskGroundediceLevelset),... ++ (md.results.TransientSolution(3).Vx),... ++ (md.results.TransientSolution(3).Vy),... ++ (md.results.TransientSolution(3).Vz),... ++ (md.results.TransientSolution(3).Pressure),... ++ (md.results.TransientSolution(3).BasalforcingsFloatingiceMeltingRate),... ++ }; +Index: ../trunk-jpl/test/Archives/Archive442.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive442.arch +=================================================================== +--- ../trunk-jpl/test/Archives/Archive442.arch (nonexistent) ++++ ../trunk-jpl/test/Archives/Archive442.arch (revision 21790) + +Property changes on: ../trunk-jpl/test/Archives/Archive442.arch +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +\ No newline at end of property +Index: ../trunk-jpl/test/Archives/Archive441.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive441.arch +=================================================================== +--- ../trunk-jpl/test/Archives/Archive441.arch (nonexistent) ++++ ../trunk-jpl/test/Archives/Archive441.arch (revision 21790) + +Property changes on: ../trunk-jpl/test/Archives/Archive441.arch +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +\ No newline at end of property Index: /issm/oecreview/Archive/21724-22754/ISSM-21790-21791.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21790-21791.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21790-21791.diff (revision 22755) @@ -0,0 +1,369 @@ +Index: ../trunk-jpl/src/c/bamg/typedefs.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/typedefs.h (revision 21790) ++++ ../trunk-jpl/src/c/bamg/typedefs.h (revision 21791) +@@ -6,11 +6,9 @@ + namespace bamg { + + /*Integer coordinates types*/ +- typedef int Icoor1; +- typedef long long Icoor2; + + /*I2 and R2*/ +- typedef P2 I2; ++ typedef P2 I2; + typedef P2 R2; + } + +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21790) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21791) +@@ -1048,7 +1048,7 @@ + } + } + /*}}}*/ +- void Mesh::AddVertex( BamgVertex &s,Triangle* t, Icoor2* det3){/*{{{*/ ++ void Mesh::AddVertex( BamgVertex &s,Triangle* t, long long* det3){/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/Add)*/ + // ------------------------------- + // s2 +@@ -1067,7 +1067,7 @@ + + /*Intermediaries*/ + Triangle* tt[3]; //the three triangles +- Icoor2 det3local[3]; //three determinants (integer) ++ long long det3local[3]; //three determinants (integer) + int nbzerodet =0; //number of zeros in det3 + int izerodet=-1; //egde containing the vertex s + int iedge; +@@ -1078,7 +1078,7 @@ + BamgVertex* s2=t->GetVertex(2); + + //determinant of t +- Icoor2 detOld=t->det; ++ long long detOld=t->det; + + /* infvertexindex = index of the infinite vertex (NULL) + if no infinite vertex (NULL) infvertexindex=-1 +@@ -2804,7 +2804,7 @@ + BamgVertex *newvertex=orderedvertices[icount]; + + //Find the triangle in which newvertex is located +- Icoor2 det3[3]; ++ long long det3[3]; + Triangle* tcvi = TriangleFindFromCoord(newvertex->i,det3); //(newvertex->i = integer coordinates) + + //Add newvertex to the quadtree +@@ -2831,7 +2831,7 @@ + double seuil= 1.414/2 ;// for two close point + long i; + long NbSwap=0; +- Icoor2 det3[3]; ++ long long det3[3]; + + //number of new points + const long nbvnew=nbv-nbvold; +@@ -3016,7 +3016,7 @@ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MetricAt)*/ + + I2 a = R2ToI2(A); +- Icoor2 deta[3]; ++ long long deta[3]; + Triangle * t =TriangleFindFromCoord(a,deta); + if (t->det <0) { // outside + double ba,bb; +@@ -3475,7 +3475,7 @@ + long NbSwap=0; + for (int icount=2; icounti,det3); + quadtree->Add(*vi); + AddVertex(*vi,tcvi,det3); +@@ -3892,7 +3892,7 @@ + if (nbvold!=nbv){ + long iv = nbvold; + long NbSwap = 0; +- Icoor2 det3[3]; ++ long long det3[3]; + for (int i=nbvold;i (BAMG v1.01, Mesh2.cpp/FindTriangleContening)*/ + + Triangle * t=0; +@@ -3962,7 +3962,7 @@ + _assert_(t>=triangles && t0 ? Next(Adj(Next(edge))) : Previous(Adj(Previous(edge)))) { + kkk++; +@@ -4791,7 +4791,7 @@ + BamgVertex *v1, *v2 = tta.EdgeVertex(0),*vbegin =v2; + // we turn around a in the direct direction + +- Icoor2 det2 = v2 ? det(*v2,a,b): -1 , det1; ++ long long det2 = v2 ? det(*v2,a,b): -1 , det1; + if(v2) // normal case + det2 = det(*v2,a,b); + else { // no chance infini vertex try the next +@@ -4818,7 +4818,7 @@ + if (!v1 || !v2){ + _error_("!v1 || !v2"); + } +- Icoor2 detss = 0,l=0; ++ long long detss = 0,l=0; + while ((SwapForForcingEdge( va, vb, tc, detss, det1,det2,NbSwap))) + if(l++ > 10000000) { + _error_("Loop in forcing Egde, nb de swap=" << NbSwap << ", nb of try swap (" << l << ") too big"); +@@ -4852,7 +4852,7 @@ + return NbSwap; + } + /*}}}*/ +- void swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,Icoor2 det1,Icoor2 det2){ /*{{{*/ ++ void swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,long long det1,long long det2){ /*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/swap)*/ + // -------------------------------------------------------------- + // short a2=aa[a];// les 2 numero de l arete dans les 2 triangles +@@ -4896,7 +4896,7 @@ + t2->SetSingleVertexToTriangleConnectivity(); + } // end swap + /*}}}*/ +- int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb ,AdjacentTriangle & tt1,Icoor2 & dets1, Icoor2 & detsa,Icoor2 & detsb, int & NbSwap) {/*{{{*/ ++ int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb ,AdjacentTriangle & tt1,long long & dets1, long long & detsa,long long & detsb, int & NbSwap) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/SwapForForcingEdge)*/ + // l'arete ta coupe l'arete pva pvb + // de cas apres le swap sa coupe toujours +@@ -4917,9 +4917,9 @@ + BamgVertex & s1= (*t1)[OppositeVertex[a1]]; + BamgVertex & s2= (*t2)[OppositeVertex[a2]]; + +- Icoor2 dets2 = det(*pva,*pvb,s2); +- Icoor2 det1=t1->det , det2=t2->det ; +- Icoor2 detT = det1+det2; ++ long long dets2 = det(*pva,*pvb,s2); ++ long long det1=t1->det , det2=t2->det ; ++ long long detT = det1+det2; + if ((det1<=0 ) || (det2<=0)){ + _error_("(det1<=0 ) || (det2<=0)"); + } +@@ -4926,8 +4926,8 @@ + if ( (detsa>=0) || (detsb<=0) ){ // [a,b] cut infinite line va,bb + _error_("(detsa>=0) || (detsb<=0)"); + } +- Icoor2 ndet1 = bamg::det(s1,sa,s2); +- Icoor2 ndet2 = detT - ndet1; ++ long long ndet1 = bamg::det(s1,sa,s2); ++ long long ndet2 = detT - ndet1; + + int ToSwap =0; //pas de swap + if ((ndet1 >0) && (ndet2 >0)) +Index: ../trunk-jpl/src/c/bamg/AdjacentTriangle.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/AdjacentTriangle.h (revision 21790) ++++ ../trunk-jpl/src/c/bamg/AdjacentTriangle.h (revision 21791) +@@ -36,7 +36,7 @@ + int swap(); + AdjacentTriangle Adj() const; + BamgVertex* EdgeVertex(const int & i) const; +- Icoor2& det() const; ++ long long& det() const; + }; + } + #endif +Index: ../trunk-jpl/src/c/bamg/Triangle.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Triangle.cpp (revision 21790) ++++ ../trunk-jpl/src/c/bamg/Triangle.cpp (revision 21791) +@@ -237,10 +237,10 @@ + BamgVertex *s1=t1->vertices[OppositeVertex[a1]]; + BamgVertex *s2=t2->vertices[OppositeVertex[a2]]; + +- Icoor2 det1=t1->det , det2=t2->det ; +- Icoor2 detT = det1+det2; +- Icoor2 detA = Abs(det1) + Abs(det2); +- Icoor2 detMin = Min(det1,det2); ++ long long det1=t1->det , det2=t2->det ; ++ long long detT = det1+det2; ++ long long detA = Abs(det1) + Abs(det2); ++ long long detMin = Min(det1,det2); + + int OnSwap = 0; + // si 2 triangle infini (bord) => detT = -2; +@@ -255,7 +255,7 @@ + det2 = detT - det1; + OnSwap = (Abs(det1) + Abs(det2)) < detA; + +- Icoor2 detMinNew=Min(det1,det2); ++ long long detMinNew=Min(det1,det2); + // if (detMin<0 && (Abs(det1) + Abs(det2) == detA)) OnSwap=BinaryRand();// just for test + if (! OnSwap &&(detMinNew>0)) { + OnSwap = detMin ==0; +@@ -264,7 +264,7 @@ + while (1) + if(kopt) { + // critere de Delaunay pure isotrope +- Icoor2 xb1 = sb->i.x - s1->i.x, ++ long long xb1 = sb->i.x - s1->i.x, + x21 = s2->i.x - s1->i.x, + yb1 = sb->i.y - s1->i.y, + y21 = s2->i.y - s1->i.y, +Index: ../trunk-jpl/src/c/bamg/det.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/det.h (revision 21790) ++++ ../trunk-jpl/src/c/bamg/det.h (revision 21791) +@@ -5,9 +5,9 @@ + + namespace bamg { + +- Icoor2 inline det(const I2 &a,const I2 & b,const I2 &c){ +- Icoor2 bax = b.x - a.x ,bay = b.y - a.y; +- Icoor2 cax = c.x - a.x ,cay = c.y - a.y; ++ long long inline det(const I2 &a,const I2 & b,const I2 &c){ ++ long long bax = b.x - a.x ,bay = b.y - a.y; ++ long long cax = c.x - a.x ,cay = c.y - a.y; + return bax*cay - bay*cax; + } + +Index: ../trunk-jpl/src/c/bamg/AdjacentTriangle.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/AdjacentTriangle.cpp (revision 21790) ++++ ../trunk-jpl/src/c/bamg/AdjacentTriangle.cpp (revision 21791) +@@ -33,7 +33,7 @@ + return t->vertices[VerticesOfTriangularEdge[a][i]]; + } + /*}}}*/ +- Icoor2 & AdjacentTriangle::det() const {/*{{{*/ ++ long long & AdjacentTriangle::det() const {/*{{{*/ + return t->det; + } + /*}}}*/ +Index: ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.cpp (revision 21790) ++++ ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.cpp (revision 21791) +@@ -192,13 +192,13 @@ + + Triangle *tbegin, *t; + +- Icoor2 deta[3], deti,detj; ++ long long deta[3], deti,detj; + double ba[3]; + int ifirst=-1,ilast; + int i0,i1,i2; + int ocut,i,j,k=-1; + // int OnAVertices =0; +- Icoor2 dt[3]; ++ long long dt[3]; + I2 a = Bh.R2ToI2(A) ,b= Bh.R2ToI2(B);// compute the Icoor a,b + I2 vi,vj; + int iedge =-1;// not a edge +@@ -355,7 +355,7 @@ + + k = OppositeVertex[ocut]; + +- Icoor2 detbij = bamg::det((*t)[i],(*t)[j],b); ++ long long detbij = bamg::det((*t)[i],(*t)[j],b); + + if (detbij >= 0) { //we find the triangle contening b + dt[0]=bamg::det((*t)[1],(*t)[2],b); +Index: ../trunk-jpl/src/c/bamg/Mesh.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.h (revision 21790) ++++ ../trunk-jpl/src/c/bamg/Mesh.h (revision 21791) +@@ -37,7 +37,7 @@ + long nbtout; // Nb of oudeside triangle + + R2 pmin,pmax; // extrema +- double coefIcoor; // coef to integer Icoor1; ++ double coefIcoor; // coef to integer + ListofIntersectionTriangles lIntTria; + + long NbVerticesOnGeomVertex; +@@ -75,7 +75,7 @@ + double MaximalHmax(); + I2 R2ToI2(const R2 & P) const; + R2 I2ToR2(const I2 & P) const; +- void AddVertex(BamgVertex & s,Triangle * t,Icoor2 * =0) ; ++ void AddVertex(BamgVertex & s,Triangle * t,long long * =0) ; + void Insert(bool random); + void Echo(void); + void ForceBoundary(); +@@ -102,7 +102,7 @@ + long GetId(const Edge & t) const; + long GetId(const Edge * t) const; + BamgVertex* NearestVertex(int i,int j) ; +- Triangle* TriangleFindFromCoord(const I2 & ,Icoor2 [3],Triangle *tstart=0) const; ++ Triangle* TriangleFindFromCoord(const I2 & ,long long [3],Triangle *tstart=0) const; + void ReadMesh(int* index,double* x,double* y,int nods,int nels); + void ReadMesh(BamgMesh* bamgmesh, BamgOpts* bamgopts); + void WriteMesh(BamgMesh* bamgmesh,BamgOpts* bamgopts); +@@ -148,10 +148,10 @@ + AdjacentTriangle CloseBoundaryEdge(I2 ,Triangle *, double &,double &) ; + void swap(Triangle *t1,short a1, + Triangle *t2,short a2, +- BamgVertex *s1,BamgVertex *s2,Icoor2 det1,Icoor2 det2); ++ BamgVertex *s1,BamgVertex *s2,long long det1,long long det2); + int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb , +- AdjacentTriangle & tt1,Icoor2 & dets1, +- Icoor2 & detsa,Icoor2 & detsb, int & nbswap); ++ AdjacentTriangle & tt1,long long & dets1, ++ long long & detsa,long long & detsb, int & nbswap); + int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) ; + inline AdjacentTriangle Previous(const AdjacentTriangle & ta){ + return AdjacentTriangle(ta.t,PreviousEdge[ta.a]); +@@ -169,7 +169,7 @@ + double ret; + I2 ia=va,ib=vb,ic=vc; + I2 ab=ib-ia,bc=ic-ib,ac=ic-ia; +- Icoor2 deta=Det(ab,ac); ++ long long deta=Det(ab,ac); + if (deta <=0) ret = -1; + else { + double a = sqrt((double) (ac,ac)), +Index: ../trunk-jpl/src/c/bamg/BamgVertex.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgVertex.cpp (revision 21790) ++++ ../trunk-jpl/src/c/bamg/BamgVertex.cpp (revision 21791) +@@ -156,7 +156,7 @@ + PNew = P+Xmove; + double delta=Norme2_2(Xmove); + +- Icoor2 deta[3]; ++ long long deta[3]; + I2 IBTh = BTh.R2ToI2(PNew); + + tstart=BTh.TriangleFindFromCoord(IBTh,deta,tstart); +Index: ../trunk-jpl/src/c/bamg/Triangle.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Triangle.h (revision 21790) ++++ ../trunk-jpl/src/c/bamg/Triangle.h (revision 21791) +@@ -20,7 +20,7 @@ + short AdjEdgeIndex[3]; // edge id in the adjacent triangles. The edge number 1 is the edge number AdjEdgeIndex[1] in the Adjacent triangle 1 + + public: +- Icoor2 det; //Integer determinant (twice its area) ++ long long det; //Integer determinant (twice its area) + union { + Triangle *link; + long color; Index: /issm/oecreview/Archive/21724-22754/ISSM-21791-21792.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21791-21792.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21791-21792.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 21791) ++++ ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 21792) +@@ -28,7 +28,7 @@ + int i0,i1,i2; + double areacoord[3]; + double aa,bb; +- Icoor2 dete[3]; ++ long long dete[3]; + + /*Checks*/ + if (M_data!=nods_data && M_data!=nels_data){ Index: /issm/oecreview/Archive/21724-22754/ISSM-21792-21793.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21792-21793.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21792-21793.diff (revision 22755) @@ -0,0 +1,78 @@ +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21792) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21793) +@@ -720,6 +720,7 @@ + SoftMigrationEnum, + SubelementMigrationEnum, + SubelementMigration2Enum, ++ SubelementMigration3Enum, + ContactEnum, + GroundingOnlyEnum, + MaskGroundediceLevelsetEnum, +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21792) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21793) +@@ -710,6 +710,7 @@ + case SoftMigrationEnum : return "SoftMigration"; + case SubelementMigrationEnum : return "SubelementMigration"; + case SubelementMigration2Enum : return "SubelementMigration2"; ++ case SubelementMigration3Enum : return "SubelementMigration3"; + case ContactEnum : return "Contact"; + case GroundingOnlyEnum : return "GroundingOnly"; + case MaskGroundediceLevelsetEnum : return "MaskGroundediceLevelset"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21792) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21793) +@@ -725,6 +725,7 @@ + else if (strcmp(name,"SoftMigration")==0) return SoftMigrationEnum; + else if (strcmp(name,"SubelementMigration")==0) return SubelementMigrationEnum; + else if (strcmp(name,"SubelementMigration2")==0) return SubelementMigration2Enum; ++ else if (strcmp(name,"SubelementMigration3")==0) return SubelementMigration3Enum; + else if (strcmp(name,"Contact")==0) return ContactEnum; + else if (strcmp(name,"GroundingOnly")==0) return GroundingOnlyEnum; + else if (strcmp(name,"MaskGroundediceLevelset")==0) return MaskGroundediceLevelsetEnum; +@@ -750,11 +751,11 @@ + else if (strcmp(name,"RootPath")==0) return RootPathEnum; + else if (strcmp(name,"OutputFileName")==0) return OutputFileNameEnum; + else if (strcmp(name,"InputFileName")==0) return InputFileNameEnum; +- else if (strcmp(name,"LockFileName")==0) return LockFileNameEnum; + else stage=7; + } + if(stage==7){ +- if (strcmp(name,"RestartFileName")==0) return RestartFileNameEnum; ++ if (strcmp(name,"LockFileName")==0) return LockFileNameEnum; ++ else if (strcmp(name,"RestartFileName")==0) return RestartFileNameEnum; + else if (strcmp(name,"ToolkitsOptionsAnalyses")==0) return ToolkitsOptionsAnalysesEnum; + else if (strcmp(name,"ToolkitsOptionsStrings")==0) return ToolkitsOptionsStringsEnum; + else if (strcmp(name,"QmuErrName")==0) return QmuErrNameEnum; +@@ -873,11 +874,11 @@ + else if (strcmp(name,"Massconaxpby")==0) return MassconaxpbyEnum; + else if (strcmp(name,"NodeSId")==0) return NodeSIdEnum; + else if (strcmp(name,"ElementSId")==0) return ElementSIdEnum; +- else if (strcmp(name,"VectorParam")==0) return VectorParamEnum; + else stage=8; + } + if(stage==8){ +- if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; ++ if (strcmp(name,"VectorParam")==0) return VectorParamEnum; ++ else if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; + else if (strcmp(name,"Segment")==0) return SegmentEnum; + else if (strcmp(name,"SegmentRiftfront")==0) return SegmentRiftfrontEnum; + else if (strcmp(name,"SpcDynamic")==0) return SpcDynamicEnum; +@@ -996,11 +997,11 @@ + else if (strcmp(name,"P1bubble")==0) return P1bubbleEnum; + else if (strcmp(name,"P1bubblecondensed")==0) return P1bubblecondensedEnum; + else if (strcmp(name,"P2")==0) return P2Enum; +- else if (strcmp(name,"P2bubble")==0) return P2bubbleEnum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"P2bubblecondensed")==0) return P2bubblecondensedEnum; ++ if (strcmp(name,"P2bubble")==0) return P2bubbleEnum; ++ else if (strcmp(name,"P2bubblecondensed")==0) return P2bubblecondensedEnum; + else if (strcmp(name,"P2xP1")==0) return P2xP1Enum; + else if (strcmp(name,"P1xP2")==0) return P1xP2Enum; + else if (strcmp(name,"P1xP3")==0) return P1xP3Enum; Index: /issm/oecreview/Archive/21724-22754/ISSM-21793-21794.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21793-21794.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21793-21794.diff (revision 22755) @@ -0,0 +1,100 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21793) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21794) +@@ -469,7 +469,8 @@ + + /*Intermediaries */ + IssmDouble Jdet,dt; +- IssmDouble ms,mb,gmb,fmb,thickness,phi; ++ IssmDouble ms,mb,gmb,fmb,thickness; ++ IssmDouble gllevelset,phi=1.; + IssmDouble* xyz_list = NULL; + + /*Fetch number of nodes and dof for this finite element*/ +@@ -484,7 +485,7 @@ + element->FindParam(&dt,TimesteppingTimeStepEnum); + Input* gmb_input = element->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(gmb_input); + Input* fmb_input = element->GetInput(BasalforcingsFloatingiceMeltingRateEnum); _assert_(fmb_input); +- Input* groundedice_input = element->GetInput(MaskGroundediceLevelsetEnum); _assert_(groundedice_input); ++ Input* gllevelset_input = element->GetInput(MaskGroundediceLevelsetEnum); _assert_(gllevelset_input); + Input* ms_input = element->GetInput(SmbMassBalanceEnum); _assert_(ms_input); + Input* thickness_input = element->GetInput(ThicknessEnum); _assert_(thickness_input); + +@@ -499,7 +500,7 @@ + ms_input->GetInputValue(&ms,gauss); + gmb_input->GetInputValue(&gmb,gauss); + fmb_input->GetInputValue(&fmb,gauss); +- groundedice_input->GetInputValue(&phi,gauss); ++ gllevelset_input->GetInputValue(&phi,gauss); + thickness_input->GetInputValue(&thickness,gauss); + if(phi>0.) mb=gmb; + else mb=fmb; +@@ -519,9 +520,13 @@ + if(!element->IsIceInElement()) return NULL; + + /*Intermediaries */ +- IssmDouble Jdet,dt; +- IssmDouble ms,mb,gmb,fmb,thickness,phi; ++ int migration_style,point1; ++ bool mainlyfloating; ++ IssmDouble Jdet,fraction1,fraction2; ++ IssmDouble dt,gllevelset; ++ IssmDouble ms,mb,gmb,fmb,thickness,phi=1.; + IssmDouble* xyz_list = NULL; ++ Gauss* gauss = NULL; + + /*Fetch number of nodes and dof for this finite element*/ + int numnodes = element->GetNumberOfNodes(); +@@ -536,11 +541,21 @@ + Input* gmb_input = element->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(gmb_input); + Input* fmb_input = element->GetInput(BasalforcingsFloatingiceMeltingRateEnum); _assert_(fmb_input); + Input* ms_input = element->GetInput(SmbMassBalanceEnum); _assert_(ms_input); +- Input* groundedice_input = element->GetInput(MaskGroundediceLevelsetEnum); _assert_(groundedice_input); ++ Input* gllevelset_input = element->GetInput(MaskGroundediceLevelsetEnum); _assert_(gllevelset_input); + Input* thickness_input = element->GetInput(ThicknessEnum); _assert_(thickness_input); + ++ /*Recover portion of element that is grounded*/ ++ phi=element->GetGroundedPortion(xyz_list); ++ if(migration_style==SubelementMigration2Enum){ ++ gllevelset_input=element->GetInput(MaskGroundediceLevelsetEnum); _assert_(gllevelset_input); ++ element->GetGroundedPart(&point1,&fraction1,&fraction2,&mainlyfloating); ++ gauss = element->NewGauss(point1,fraction1,fraction2,mainlyfloating,3); ++ } ++ else{ ++ gauss = element->NewGauss(3); ++ } ++ + /* Start looping on the number of gaussian points: */ +- Gauss* gauss=element->NewGauss(2); + for(int ig=gauss->begin();igend();ig++){ + gauss->GaussPoint(ig); + +@@ -550,10 +565,24 @@ + ms_input->GetInputValue(&ms,gauss); + gmb_input->GetInputValue(&gmb,gauss); + fmb_input->GetInputValue(&fmb,gauss); +- groundedice_input->GetInputValue(&phi,gauss); ++ gllevelset_input->GetInputValue(&gllevelset,gauss); + thickness_input->GetInputValue(&thickness,gauss); +- if(phi>0) mb=gmb; +- else mb=fmb; ++ if(migration_style==SubelementMigrationEnum){ ++ if (phi<0.00000001) mb=gmb; ++ else mb=(1-phi)*fmb+phi*gmb; // phi is the fraction of grounded ice so (1-phi) is floating ++ } ++ else if(migration_style==SubelementMigration2Enum){ ++ if(gllevelset>0.) mb=gmb; ++ else mb=fmb; ++ } ++ else if(migration_style==SubelementMigration3Enum){ ++ if (phi<0.00000001) mb=gmb; ++ else mb=gmb; ++ } ++ else{ ++ if(gllevelset>0) mb=gmb; ++ else mb=fmb; ++ } + + for(int i=0;ivalues[i]+=Jdet*gauss->weight*(thickness+dt*(ms-mb))*basis[i]; + } Index: /issm/oecreview/Archive/21724-22754/ISSM-21794-21795.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21794-21795.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21794-21795.diff (revision 22755) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21794) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21795) +@@ -51,8 +51,8 @@ + 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-09,1e-10,1e-13,... +- 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-09,1e-10,1e-13}; ++ 3e-11,3e-11,9e-10,7e-11,2e-09,5e-08,1e-09,1e-10,1e-13,... ++ 3e-10,4e-11,3e-10,2e-10,7e-05,9e-05,1e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21795-21796.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21795-21796.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21795-21796.diff (revision 22755) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21795) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21796) +@@ -51,8 +51,8 @@ + 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,2e-09,5e-08,1e-09,1e-10,1e-13,... +- 3e-10,4e-11,3e-10,2e-10,7e-05,9e-05,1e-09,1e-10,1e-13}; ++ 3e-11,3e-11,9e-10,7e-11,3e-09,5e-08,1e-09,1e-10,1e-13,... ++ 4e-10,4e-10,3e-10,2e-10,7e-05,9e-05,1e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21796-21797.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21796-21797.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21796-21797.diff (revision 22755) @@ -0,0 +1,134 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21796) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21797) +@@ -468,10 +468,14 @@ + if(!element->IsIceInElement()) return NULL; + + /*Intermediaries */ ++ int migration_style,point1; ++ bool mainlyfloating; ++ IssmDouble fraction1,fraction2; + IssmDouble Jdet,dt; + IssmDouble ms,mb,gmb,fmb,thickness; + IssmDouble gllevelset,phi=1.; + IssmDouble* xyz_list = NULL; ++ Gauss* gauss = NULL; + + /*Fetch number of nodes and dof for this finite element*/ + int numnodes = element->GetNumberOfNodes(); +@@ -489,8 +493,18 @@ + Input* ms_input = element->GetInput(SmbMassBalanceEnum); _assert_(ms_input); + Input* thickness_input = element->GetInput(ThicknessEnum); _assert_(thickness_input); + ++ /*Recover portion of element that is grounded*/ ++ phi=element->GetGroundedPortion(xyz_list); ++ if(migration_style==SubelementMigration2Enum){ ++ gllevelset_input=element->GetInput(MaskGroundediceLevelsetEnum); _assert_(gllevelset_input); ++ element->GetGroundedPart(&point1,&fraction1,&fraction2,&mainlyfloating); ++ gauss = element->NewGauss(point1,fraction1,fraction2,mainlyfloating,3); ++ } ++ else{ ++ gauss = element->NewGauss(3); ++ } ++ + /* Start looping on the number of gaussian points: */ +- Gauss* gauss=element->NewGauss(2); + for(int ig=gauss->begin();igend();ig++){ + gauss->GaussPoint(ig); + +@@ -500,11 +514,26 @@ + ms_input->GetInputValue(&ms,gauss); + gmb_input->GetInputValue(&gmb,gauss); + fmb_input->GetInputValue(&fmb,gauss); +- gllevelset_input->GetInputValue(&phi,gauss); ++ gllevelset_input->GetInputValue(&gllevelset,gauss); + thickness_input->GetInputValue(&thickness,gauss); +- if(phi>0.) mb=gmb; +- else mb=fmb; + ++ if(migration_style==SubelementMigrationEnum){ ++ if (phi<0.00000001) mb=gmb; ++ else mb=(1-phi)*fmb+phi*gmb; // phi is the fraction of grounded ice so (1-phi) is floating ++ } ++ else if(migration_style==SubelementMigration2Enum){ ++ if(gllevelset>0.) mb=gmb; ++ else mb=fmb; ++ } ++ else if(migration_style==SubelementMigration3Enum){ ++ if (phi<0.00000001) mb=gmb; ++ else mb=gmb; ++ } ++ else{ ++ if(gllevelset>0) mb=gmb; ++ else mb=fmb; ++ } ++ + for(int i=0;ivalues[i]+=Jdet*gauss->weight*(thickness+dt*(ms-mb))*basis[i]; + } + +@@ -520,13 +549,9 @@ + if(!element->IsIceInElement()) return NULL; + + /*Intermediaries */ +- int migration_style,point1; +- bool mainlyfloating; +- IssmDouble Jdet,fraction1,fraction2; +- IssmDouble dt,gllevelset; ++ IssmDouble Jdet,dt; + IssmDouble ms,mb,gmb,fmb,thickness,phi=1.; + IssmDouble* xyz_list = NULL; +- Gauss* gauss = NULL; + + /*Fetch number of nodes and dof for this finite element*/ + int numnodes = element->GetNumberOfNodes(); +@@ -544,18 +569,8 @@ + Input* gllevelset_input = element->GetInput(MaskGroundediceLevelsetEnum); _assert_(gllevelset_input); + Input* thickness_input = element->GetInput(ThicknessEnum); _assert_(thickness_input); + +- /*Recover portion of element that is grounded*/ +- phi=element->GetGroundedPortion(xyz_list); +- if(migration_style==SubelementMigration2Enum){ +- gllevelset_input=element->GetInput(MaskGroundediceLevelsetEnum); _assert_(gllevelset_input); +- element->GetGroundedPart(&point1,&fraction1,&fraction2,&mainlyfloating); +- gauss = element->NewGauss(point1,fraction1,fraction2,mainlyfloating,3); +- } +- else{ +- gauss = element->NewGauss(3); +- } +- + /* Start looping on the number of gaussian points: */ ++ Gauss* gauss=element->NewGauss(2); + for(int ig=gauss->begin();igend();ig++){ + gauss->GaussPoint(ig); + +@@ -565,25 +580,12 @@ + ms_input->GetInputValue(&ms,gauss); + gmb_input->GetInputValue(&gmb,gauss); + fmb_input->GetInputValue(&fmb,gauss); +- gllevelset_input->GetInputValue(&gllevelset,gauss); ++ gllevelset_input->GetInputValue(&phi,gauss); + thickness_input->GetInputValue(&thickness,gauss); +- if(migration_style==SubelementMigrationEnum){ +- if (phi<0.00000001) mb=gmb; +- else mb=(1-phi)*fmb+phi*gmb; // phi is the fraction of grounded ice so (1-phi) is floating +- } +- else if(migration_style==SubelementMigration2Enum){ +- if(gllevelset>0.) mb=gmb; +- else mb=fmb; +- } +- else if(migration_style==SubelementMigration3Enum){ +- if (phi<0.00000001) mb=gmb; +- else mb=gmb; +- } +- else{ +- if(gllevelset>0) mb=gmb; +- else mb=fmb; +- } + ++ if(phi>0.) mb=gmb; ++ else mb=fmb; ++ + for(int i=0;ivalues[i]+=Jdet*gauss->weight*(thickness+dt*(ms-mb))*basis[i]; + } + Index: /issm/oecreview/Archive/21724-22754/ISSM-21797-21798.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21797-21798.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21797-21798.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21797) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21798) +@@ -526,7 +526,7 @@ + else mb=fmb; + } + else if(migration_style==SubelementMigration3Enum){ +- if (phi<0.00000001) mb=gmb; ++ if (phi<0.00000001) mb=fmb; + else mb=gmb; + } + else{ Index: /issm/oecreview/Archive/21724-22754/ISSM-21798-21799.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21798-21799.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21798-21799.diff (revision 22755) @@ -0,0 +1,58 @@ +Index: ../trunk-jpl/src/c/cores/extrudefrombase_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/extrudefrombase_core.cpp (revision 21798) ++++ ../trunk-jpl/src/c/cores/extrudefrombase_core.cpp (revision 21799) +@@ -14,7 +14,7 @@ + /*Intermediaries*/ + int elementtype,domaintype; + +- if(VerboseSolution()) _printf0_("extruding solution from base...\n"); ++ if(VerboseSolution()) _printf0_(" extruding solution from base...\n"); + + /*Get parameters*/ + femmodel->parameters->FindParam(&domaintype,DomainTypeEnum); +Index: ../trunk-jpl/src/c/cores/depthaverage_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/depthaverage_core.cpp (revision 21798) ++++ ../trunk-jpl/src/c/cores/depthaverage_core.cpp (revision 21799) +@@ -15,7 +15,7 @@ + int domaintype,elementtype; + int inputenum,input_average_enum; + +- if(VerboseSolution()) _printf0_("depth averaging solution...\n"); ++ if(VerboseSolution()) _printf0_(" depth averaging solution...\n"); + + /*Get parameters*/ + femmodel->parameters->FindParam(&domaintype,DomainTypeEnum); +Index: ../trunk-jpl/src/c/cores/extrudefromtop_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/extrudefromtop_core.cpp (revision 21798) ++++ ../trunk-jpl/src/c/cores/extrudefromtop_core.cpp (revision 21799) +@@ -14,7 +14,7 @@ + /*Intermediaries*/ + int elementtype,domaintype; + +- if(VerboseSolution()) _printf0_("extruding solution from top...\n"); ++ if(VerboseSolution()) _printf0_(" extruding solution from top...\n"); + + /*Get parameters*/ + femmodel->parameters->FindParam(&domaintype,DomainTypeEnum); +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21798) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21799) +@@ -1689,7 +1689,13 @@ + } + vector_result->Assemble(); + +- if(save_results)results->AddResult(new GenericExternalResult*>(results->Size()+1,output_enum,vector_result,step,time)); ++ if(save_results){ ++ results->AddResult(new GenericExternalResult*>(results->Size()+1,output_enum,vector_result,step,time)); ++ /*We do not do a copy for Vectors, so don't delete*/ ++ } ++ else{ ++ delete vector_result; ++ } + } + else{ + IssmDouble* values = xNewZeroInit(nlines*ncols); Index: /issm/oecreview/Archive/21724-22754/ISSM-21799-21800.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21799-21800.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21799-21800.diff (revision 22755) @@ -0,0 +1,82 @@ +Index: ../trunk-jpl/test/NightlyRun/test430.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test430.m (revision 21799) ++++ ../trunk-jpl/test/NightlyRun/test430.m (revision 21800) +@@ -31,7 +31,7 @@ + md.friction.p=3*ones(md.mesh.numberofelements,1); + md.smb.mass_balance(:)=1; + md.basalforcings.groundedice_melting_rate(:)=0; +-md.basalforcings.floatingice_melting_rate(:)=0; ++md.basalforcings.floatingice_melting_rate(:)=30; + md.transient.isthermal=0; + md.transient.isstressbalance=1; + md.transient.isgroundingline=1; +Index: ../trunk-jpl/test/Archives/Archive441.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive439.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive505.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive442.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive506.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive802.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive426.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive507.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive803.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive435.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive409.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive427.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive430.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive805.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21799) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21800) +@@ -32,7 +32,7 @@ + md.friction.p=3*ones(md.mesh.numberofelements,1); + md.smb.mass_balance(:)=1; + md.basalforcings.groundedice_melting_rate(:)=0; +-md.basalforcings.floatingice_melting_rate(:)=0; ++md.basalforcings.floatingice_melting_rate(:)=30; + md.transient.isthermal=0; + md.transient.isstressbalance=1; + md.transient.isgroundingline=1; Index: /issm/oecreview/Archive/21724-22754/ISSM-21800-21801.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21800-21801.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21800-21801.diff (revision 22755) @@ -0,0 +1,30 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21800) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21801) +@@ -51,8 +51,8 @@ + 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,3e-09,5e-08,1e-09,1e-10,1e-13,... +- 4e-10,4e-10,3e-10,2e-10,7e-05,9e-05,1e-09,1e-10,1e-13}; ++ 3e-11,3e-11,9e-10,7e-11,6e-09,5e-08,1e-09,1e-10,1e-13,... ++ 4e-10,1e-09,1e-09,1e-09,2e-04,2e-04,1e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21800) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21801) +@@ -51,8 +51,8 @@ + 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,1e-09,5e-08,1e-09,1e-10,1e-13,... +- 1e-10,3e-11,1e-10,7e-11,1e-09,5e-08,1e-09,1e-10,1e-13}; ++ 3e-11,3e-11,9e-10,7e-11,4e-09,5e-08,1e-09,1e-10,1e-13,... ++ 1e-10,4e-09,2e-09,2e-09,4e-04,4e-04,1e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21801-21802.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21801-21802.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21801-21802.diff (revision 22755) @@ -0,0 +1,3287 @@ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 21801) ++++ ../trunk-jpl/src/c/Makefile.am (revision 21802) +@@ -46,6 +46,7 @@ + ./bamg/VertexOnVertex.cpp\ + ./bamg/Mesh.cpp\ + ./shared/Bamg/BigPrimeNumber.cpp\ ++ ./classes/AmrBamg.cpp\ + ./modules/Bamgx/Bamgx.cpp\ + ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\ + ./modules/BamgTriangulatex/BamgTriangulatex.cpp +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 21801) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 21802) +@@ -604,6 +604,7 @@ + if(strcmp(record_name,"md.hydrology.model")==0) integer = IoCodeToEnumHydrology(integer); + if(strcmp(record_name,"md.materials.type")==0) integer = IoCodeToEnumMaterials(integer); + if(strcmp(record_name,"md.timestepping.type")==0) integer = IoCodeToEnumTimestepping(integer); ++ if(strcmp(record_name,"md.amr.type")==0) integer = IoCodeToEnumAmr(integer); + + /*Broadcast to other cpus*/ + ISSM_MPI_Bcast(&integer,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21801) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21802) +@@ -697,7 +697,7 @@ + bamgmesh->SubDomains=xNew(4*nbsubdomains); + for (i=0;iSubDomains[i*4+0]=3; +- bamgmesh->SubDomains[i*4+1]=reft[GetId(subdomains[i].head)]; ++ bamgmesh->SubDomains[i*4+1]=reft[GetId(subdomains[i].head)]+1;//MATLAB indexing + bamgmesh->SubDomains[i*4+2]=1; + bamgmesh->SubDomains[i*4+3]=subdomains[i].ReferenceNumber; + } +@@ -3075,10 +3075,10 @@ + - ((*tcvj)(0)->r.y -(*tcvj)(2)->r.y)*(bv.r.x -(*tcvj)(2)->r.x)); + IssmDouble area_3 =((bv.r.x -(*tcvj)(1)->r.x)*((*tcvj)(0)->r.y-(*tcvj)(1)->r.y) + - (bv.r.y -(*tcvj)(1)->r.y)*((*tcvj)(0)->r.x-(*tcvj)(1)->r.x)); +- if(area_1<0 || area_2<0 || area_3<0){ +- pointsoutside = true; +- continue; +- } ++ // if(area_1<0 || area_2<0 || area_3<0){ ++ // pointsoutside = true; ++ // continue; ++ // } + if(!bv.GeomEdgeHook){ + vertices[nbv].r = bv.r; + vertices[nbv].PreviousNumber = i+1; +@@ -3085,7 +3085,7 @@ + vertices[nbv++].m = bv.m; + } + } +- if(pointsoutside) _printf_("WARNING: One or more points of the initial mesh fall outside of the geometric boundary\n"); ++ //if(pointsoutside) _printf_("WARNING: One or more points of the initial mesh fall outside of the geometric boundary\n"); + Bh.CreateSingleVertexToTriangleConnectivity(); + InsertNewPoints(nbvold,NbTSwap,bamgopts->random); + } +Index: ../trunk-jpl/src/c/bamg/BamgOpts.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgOpts.cpp (revision 21801) ++++ ../trunk-jpl/src/c/bamg/BamgOpts.cpp (revision 21802) +@@ -4,30 +4,30 @@ + /*Constructors/Destructors*/ + BamgOpts::BamgOpts(){/*{{{*/ + +- this->anisomax=0; +- this->cutoff=0; +- this->coeff=0; +- this->errg=0; +- this->gradation=0; +- this->Hessiantype=0; +- this->MaxCornerAngle=0; +- this->maxnbv=0; +- this->maxsubdiv=0; +- this->Metrictype=0; +- this->nbjacobi=0; +- this->nbsmooth=0; +- this->omega=0; +- this->power=0; +- this->random=0; +- this->verbose=0; ++ this->anisomax = 0; ++ this->cutoff = 0; ++ this->coeff = 0; ++ this->errg = 0; ++ this->gradation = 0; ++ this->Hessiantype = 0; ++ this->MaxCornerAngle = 0; ++ this->maxnbv = 0; ++ this->maxsubdiv = 0; ++ this->Metrictype = 0; ++ this->nbjacobi = 0; ++ this->nbsmooth = 0; ++ this->omega = 0; ++ this->power = 0; ++ this->random = 0; ++ this->verbose = 0; + +- this->Crack=0; +- this->geometricalmetric=0; +- this->KeepVertices=0; +- this->splitcorners=0; ++ this->Crack = 0; ++ this->geometricalmetric = 0; ++ this->KeepVertices = 0; ++ this->splitcorners = 0; + +- this->hmin=0; +- this->hmax=0; ++ this->hmin = 0; ++ this->hmax = 0; + this->hminVertices=NULL; this->hminVerticesSize[0]=this->hminVerticesSize[1]=0; + this->hmaxVertices=NULL; this->hmaxVerticesSize[0]=this->hmaxVerticesSize[1]=0; + this->hVertices=NULL; this->hVerticesSize[0]=this->hVerticesSize[1]=0; +Index: ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.h (revision 21801) ++++ ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.h (revision 21802) +@@ -9,6 +9,7 @@ + int IoCodeToEnumHydrology(int enum_in); + int IoCodeToEnumMaterials(int enum_in); + int IoCodeToEnumTimestepping(int enum_in); ++int IoCodeToEnumAmr(int enum_in); + + int IoCodeToEnumVertexEquation(int enum_in); + int IoCodeToEnumElementEquation(int enum_in); +Index: ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 21801) ++++ ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 21802) +@@ -127,6 +127,13 @@ + default: _error_("Marshalled materials code \""<ymax) ymax=y_data[i]; + } + ++ /*Create Single vertex to element connectivity*/ ++ int* connectivity = xNew(nods_data); ++ for(i=0;i=0 & k=0 & i0=0 && it=nels_data){ + _error_("Triangle number " << it << " not in [0 " << nels_data + << "], report bug to developers (interpolation point: " <(reft); ++ xDelete(connectivity); + *pdata_interp=data_interp; + return 1; + } +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21801) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21802) +@@ -20,6 +20,7 @@ + int i,j,m,k; + int numoutputs,materialtype,smb_model,basalforcing_model,timestepping_type; + char** requestedoutputs = NULL; ++ char* fieldname = NULL; + IssmDouble time; + + /*parameters for mass flux:*/ +@@ -59,7 +60,7 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.inversion.iscontrol",InversionIscontrolEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.inversion.type",InversionTypeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.law",CalvingLawEnum)); +- {/*This is specific to ice...*/ ++ {/*This is specific to ice...*/ + parameters->AddObject(iomodel->CopyConstantObject("md.mesh.elementtype",MeshElementtypeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.steadystate.reltol",SteadystateReltolEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.steadystate.maxiter",SteadystateMaxiterEnum)); +@@ -80,10 +81,6 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.transient.amr_frequency",TransientAmrFrequencyEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.materials.rheology_law",MaterialsRheologyLawEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.gia.cross_section_shape",GiaCrossSectionShapeEnum)); +- /*amr properties*/ +- parameters->AddObject(iomodel->CopyConstantObject("md.amr.level_max",AmrLevelMaxEnum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.amr.region_level_1",AmrRegionLevel1Enum)); +- parameters->AddObject(iomodel->CopyConstantObject("md.amr.region_level_max",AmrRegionLevelMaxEnum)); + + /*For stress balance only*/ + parameters->AddObject(iomodel->CopyConstantObject("md.flowequation.isFS",FlowequationIsFSEnum)); +@@ -94,9 +91,40 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.stressbalance.abstol",StressbalanceAbstolEnum)); + if(iomodel->domaintype==Domain3DEnum) + parameters->AddObject(iomodel->CopyConstantObject("md.mesh.numberoflayers",MeshNumberoflayersEnum)); ++ } ++ ++ /*amr properties*/ ++ int amrtype,amr_frequency; ++ iomodel->FindConstant(&amr_frequency,"md.transient.amr_frequency"); ++ if(solution_type==TransientSolutionEnum && amr_frequency){ ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.type",AmrTypeEnum)); ++ iomodel->FindConstant(&amrtype,"md.amr.type"); ++ switch(amrtype){ ++ #ifdef _HAVE_NEOPZ_ ++ case AmrNeopzEnum: ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.level_max",AmrLevelMaxEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.region_level_1",AmrRegionLevel1Enum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.region_level_max",AmrRegionLevelMaxEnum)); ++ break; ++ #endif ++ ++ #ifdef _HAVE_BAMG_ ++ case AmrBamgEnum: ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.hmin",AmrHminEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.hmax",AmrHmaxEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.err",AmrErrEnum)); ++ /*Convert fieldname to enum and put it in params*/ ++ iomodel->FindConstant(&fieldname,"md.amr.fieldname"); ++ parameters->AddObject(new IntParam(AmrFieldEnum,StringToEnumx(fieldname))); ++ xDelete(fieldname); ++ break; ++ #endif ++ ++ default: ++ _error_("Adaptive mesh refinement "<AddObject(iomodel->CopyConstantObject("md.basalforcings.model",BasalforcingsEnum)); + iomodel->FindConstant(&basalforcing_model,"md.basalforcings.model"); +@@ -254,7 +282,7 @@ + /*Now, deal with toolkits options, which need to be put into the parameters dataset: */ + ParseToolkitsOptionsx(parameters,toolkitsoptionsfid); + +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_ADOLC_ + if(VerboseMProcessor()) _printf0_(" starting autodiff parameters \n"); + CreateParametersAutodiff(parameters,iomodel); + if(VerboseMProcessor()) _printf0_(" ending autodiff parameters \n"); +Index: ../trunk-jpl/src/m/classes/amr.m +=================================================================== +--- ../trunk-jpl/src/m/classes/amr.m (revision 21801) ++++ ../trunk-jpl/src/m/classes/amr.m (revision 21802) +@@ -49,7 +49,7 @@ + end % }}} + function marshall(self,prefix,md,fid) % {{{ + +- scale = md.constants.yts; ++ WriteData(fid,prefix,'name','md.amr.type','data',2,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','level_max','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','region_level_1','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','region_level_max','format','Double'); +Index: ../trunk-jpl/src/m/classes/trans.js +=================================================================== +--- ../trunk-jpl/src/m/classes/trans.js (revision 21801) ++++ ../trunk-jpl/src/m/classes/trans.js (revision 21802) +@@ -8,18 +8,18 @@ + this.setdefaultparameters = function(){// {{{ + + //full analysis: Stressbalance, Masstransport and Thermal but no groundingline migration for now +- this.issmb = 1; +- this.ismasstransport = 1; +- this.isstressbalance = 1; +- this.isthermal = 1; +- this.isgroundingline = 0; +- this.isgia = 0; ++ this.issmb = 1; ++ this.ismasstransport = 1; ++ this.isstressbalance = 1; ++ this.isthermal = 1; ++ this.isgroundingline = 0; ++ this.isgia = 0; + this.isdamageevolution = 0; +- this.ismovingfront = 0; +- this.ishydrology = 0; +- this.isslr = 0; +- this.iscoupler = 0; +- this.amr_frequency = 1; ++ this.ismovingfront = 0; ++ this.ishydrology = 0; ++ this.isslr = 0; ++ this.iscoupler = 0; ++ this.amr_frequency = 0; + + //default output + this.requested_outputs=['default']; +Index: ../trunk-jpl/src/m/classes/transient.py +=================================================================== +--- ../trunk-jpl/src/m/classes/transient.py (revision 21801) ++++ ../trunk-jpl/src/m/classes/transient.py (revision 21802) +@@ -83,20 +83,20 @@ + def setdefaultparameters(self): # {{{ + + #full analysis: Stressbalance, Masstransport and Thermal but no groundingline migration for now +- self.issmb = True +- self.ismasstransport = True +- self.isstressbalance = True +- self.isthermal = True +- self.isgroundingline = False +- self.isgia = False +- self.isesa = False ++ self.issmb = True ++ self.ismasstransport = True ++ self.isstressbalance = True ++ self.isthermal = True ++ self.isgroundingline = False ++ self.isgia = False ++ self.isesa = False + self.isdamageevolution = False +- self.ismovingfront = False +- self.ishydrology = False +- self.isslr = False +- self.isoceancoupling = False +- self.iscoupler = False +- self.amr_frequency = 1 ++ self.ismovingfront = False ++ self.ishydrology = False ++ self.isslr = False ++ self.isoceancoupling = False ++ self.iscoupler = False ++ self.amr_frequency = 0 + + #default output + self.requested_outputs=['default'] +Index: ../trunk-jpl/src/m/classes/amrbamg.m +=================================================================== +--- ../trunk-jpl/src/m/classes/amrbamg.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/amrbamg.m (revision 21802) +@@ -0,0 +1,57 @@ ++%AMRBAMG Class definition ++% ++% Usage: ++% amrbamg=amrbamg(); ++ ++classdef amrbamg ++ properties (SetAccess=public) ++ hmin = 0.; ++ hmax = 0.; ++ fieldname = ''; ++ err = 0.; ++ end ++ methods ++ function self = amrbamg(varargin) % {{{ ++ switch nargin ++ case 0 ++ self=setdefaultparameters(self); ++ otherwise ++ error('constructor not supported'); ++ end ++ end % }}} ++ function self = setdefaultparameters(self) % {{{ ++ ++ %hmin and hmax ++ self.hmin=100.; ++ self.hmax=100.e3; ++ ++ %fields ++ self.fieldname ='Vel'; ++ self.err=3.; ++ ++ end % }}} ++ function md = checkconsistency(self,md,solution,analyses) % {{{ ++ ++ md = checkfield(md,'fieldname','amr.hmax','numel',[1],'>',0,'NaN',1); ++ md = checkfield(md,'fieldname','amr.hmin','numel',[1],'>',0,'<',self.hmax,'NaN',1); ++ %md = checkfield(md,'fieldname','amr.fieldname','string',[1]); ++ end % }}} ++ function disp(self) % {{{ ++ disp(sprintf(' amrbamg parameters:')); ++ ++ fielddisplay(self,'hmin',['minimum element length']); ++ fielddisplay(self,'hmax',['maximum element length']); ++ fielddisplay(self,'fieldname',['name of input that will be used to compute the metric (should be an input of FemModel)']); ++ ++ end % }}} ++ function marshall(self,prefix,md,fid) % {{{ ++ ++ WriteData(fid,prefix,'name','md.amr.type','data',1,'format','Integer'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','hmin','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','hmax','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','fieldname','format','String'); ++ WriteData(fid,prefix,'object',self,'class','err','fieldname','err','format','Double'); ++ ++ end % }}} ++ end ++end +Index: ../trunk-jpl/src/m/classes/transient.m +=================================================================== +--- ../trunk-jpl/src/m/classes/transient.m (revision 21801) ++++ ../trunk-jpl/src/m/classes/transient.m (revision 21802) +@@ -67,7 +67,7 @@ + self.isslr = 0; + self.isoceancoupling = 0; + self.iscoupler = 0; +- self.amr_frequency = 1; ++ self.amr_frequency = 0; + + %default output + self.requested_outputs={'default'}; +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21801) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21802) +@@ -110,7 +110,6 @@ + if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); + } + } +- if(VerboseSolution()) _printf0_(" computing thermal regime\n"); + thermal_core(femmodel); + } + +@@ -181,12 +180,18 @@ + } + + /*Adaptive mesh refinement*/ +- #ifdef _HAVE_NEOPZ_ + if(amr_frequency){ + if(save_results) femmodel->WriteMeshInResults(); +- if(step%amr_frequency==0 && timeReMesh();//Do not refine the last step ++ if(step%amr_frequency==0 && timeReMesh();//Do not refine the last step ++ } ++ //if(save_results){ ++ // printf("-------------- file: transient_core.cpp line: %i\n",__LINE__); ++ // femmodel->WriteMeshInResults(); ++ // OutputResultsx(femmodel); ++ //} + } +- #endif + } + + femmodel->RequestedDependentsx(); +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 21801) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 21802) +@@ -22,6 +22,9 @@ + #ifdef _HAVE_NEOPZ_ + #include "./AdaptiveMeshRefinement.h" + #endif ++#ifdef _HAVE_BAMG_ ++#include "./AmrBamg.h" ++#endif + /*}}}*/ + + class FemModel { +@@ -46,10 +49,15 @@ + Results *results; //results that cannot be fit into the elements + Vertices *vertices; //one set of vertices + ++ //FIXME: do we want only one class and have virtual functions? or keep 2 classes, at least rename AdaptiveMeshRefinement -> AmrNeopz + #ifdef _HAVE_NEOPZ_ + AdaptiveMeshRefinement *amr; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process + #endif + ++ #ifdef _HAVE_BAMG_ ++ AmrBamg *amrbamg; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process ++ #endif ++ + /*constructors, destructors: */ + FemModel(int argc,char** argv,ISSM_MPI_Comm comm_init,bool trace=false); + FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* toolkitsfilename, char* lockfilename, char* restartfilename, ISSM_MPI_Comm incomm, int solution_type,IssmPDouble* X); +@@ -60,9 +68,11 @@ + void CleanUp(void); + FemModel* copy(); + void Echo(); ++ int GetElementsWidth(){return 3;};//just tria elements in this first version + void InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, char* restartfilename, const int solution_type,bool trace,IssmPDouble* X=NULL); + void InitFromFids(char* rootpath, FILE* IOMODEL, FILE* toolkitsoptionsfid, int in_solution_type, bool trace, IssmPDouble* X=NULL); + void Marshall(char** pmarshalled_data, int* pmarshalled_data_size, int marshall_direction); ++ void ReMesh(void); + void Restart(void); + void SetCurrentConfiguration(int configuration_type); + void SetCurrentConfiguration(int configuration_type,int analysis_type); +@@ -145,15 +155,10 @@ + void InitFromBuffers(char* buffer, int buffersize, char* toolkits, int solution_type,bool trace,IssmPDouble* X=NULL); + #endif + +- #ifdef _HAVE_NEOPZ_ +- /*Adaptive mesh refinement methods*/ +- void InitializeAdaptiveRefinement(void); +- void ReMesh(void); ++ /*AMR*/ + void BedrockFromMismipPlus(void); + void AdjustBaseThicknessAndMask(void); + void GetMesh(Vertices* femmodel_vertices,Elements* femmodel_elements,IssmDouble** px, IssmDouble** py, IssmDouble** pz, int** pelementslist); +- int GetElementsWidth(){return 3;};//just tria elements in this first version +- void ExecuteRefinement(int &numberofvertices,int &numberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist); + void GetGroundediceLevelSet(IssmDouble** pmasklevelset); + void CreateVertices(int newnumberofvertices,int newnumberofelements,int elementswidth,int* newelementslist,int* my_vertices,IssmDouble* newx,IssmDouble* newy,IssmDouble* newz,Vertices* vertices); + void CreateElements(int newnumberofelements,int elementswidth,int* newelementslist,bool* my_elements,Elements* elements); +@@ -167,8 +172,17 @@ + void SetRefPatterns(void); + void SmoothedDeviatoricStressTensor(IssmDouble** ptauxx,IssmDouble** ptauyy,IssmDouble** ptauxy); //nodal values, just for SSA-P1: TauXX, TauYY, TauXY + void ZZErrorEstimator(IssmDouble** pelementerror); ++ ++ #ifdef _HAVE_BAMG_ ++ void ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); ++ void InitializeAdaptiveRefinementBamg(void); + #endif ++ ++ #ifdef _HAVE_NEOPZ_ ++ /*Adaptive mesh refinement methods*/ ++ void ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); ++ void InitializeAdaptiveRefinementNeopz(void); ++ #endif + }; +- + + #endif +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (nonexistent) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21802) +@@ -0,0 +1,131 @@ ++/*!\file AmrBamg.cpp ++ * \brief: implementation of the adaptive mesh refinement tool based on bamg ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "./AmrBamg.h" ++#include "../bamg/bamgobjects.h" ++#include "../modules/Bamgx/Bamgx.h" ++ ++using namespace bamg; ++using namespace std; ++ ++/*Constructor, copy, clean up and destructor*/ ++AmrBamg::AmrBamg(IssmDouble hmin, IssmDouble hmax){/*{{{*/ ++ ++ this->geometry = NULL; ++ this->fathermesh = NULL; ++ this->previousmesh = NULL; ++ ++ /*Only initialize options for now (same as bamg.m)*/ ++ this->options = new BamgOpts(); ++ this->options->anisomax = 10.e30; ++ this->options->cutoff = 10.e-5; ++ this->options->coeff = 1; ++ this->options->errg = 0.1; ++ this->options->gradation = 1.5; ++ this->options->Hessiantype = 0; ++ this->options->MaxCornerAngle = 10; ++ this->options->maxnbv = 1e6; ++ this->options->maxsubdiv = 10; ++ this->options->Metrictype = 0; ++ this->options->nbjacobi = 1; ++ this->options->nbsmooth = 3; ++ this->options->omega = 1.8; ++ this->options->power = 1; ++ this->options->random = 0; ++ this->options->verbose = 0; ++ this->options->Crack = 0; ++ this->options->geometricalmetric = 0; ++ this->options->KeepVertices = 1; /*!!!!! VERY IMPORTANT !!!!!*/ ++ this->options->splitcorners = 1; ++ this->options->hmin = hmin; ++ this->options->hmax = hmax; ++} ++/*}}}*/ ++AmrBamg::~AmrBamg(){/*{{{*/ ++ ++ if(this->geometry) delete this->geometry; ++ if(this->fathermesh) delete this->fathermesh; ++ if(this->previousmesh) delete this->previousmesh; ++ if(this->options) delete this->options; ++ ++} ++/*}}}*/ ++ ++/*Methods*/ ++void AmrBamg::Initialize(int* elements,IssmDouble* x,IssmDouble* y,int numberofvertices,int numberofelements){/*{{{*/ ++ ++ /*Check options*/ ++ _assert_(this->options); ++ this->options->Check(); ++ ++ /*Read father mesh and create geometry*/ ++ Mesh* Th=new Mesh(elements,x,y,numberofvertices,numberofelements); ++ ++ /*Write geometry*/ ++ this->geometry = new BamgGeom(); ++ Th->Gh.WriteGeometry(this->geometry,this->options); ++ ++ /*Write father mesh*/ ++ this->fathermesh = new BamgMesh(); ++ Th->WriteMesh(this->fathermesh,this->options); ++ ++ /*Cleanup and return*/ ++ delete Th; ++}/*}}}*/ ++void AmrBamg::ExecuteRefinementBamg(int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ ++ ++ /*Intermediaries*/ ++ BamgGeom* geomout=new BamgGeom(); ++ BamgMesh* meshout=new BamgMesh(); ++ ++ /*Some checks*/ ++ _assert_(this->geometry); ++ _assert_(this->options); ++ _assert_(this->fathermesh); ++ ++ /*remesh*/ ++ if(this->previousmesh){ ++ Bamgx(meshout,geomout,this->previousmesh,this->geometry,this->options); ++ } ++ else{ ++ Bamgx(meshout,geomout,this->fathermesh,this->geometry,this->options); ++ } ++ ++ /*Change previous mesh*/ ++ if(this->previousmesh) delete this->previousmesh; ++ this->previousmesh = meshout; ++ ++ /*Prepare output*/ ++ int nbv = meshout->VerticesSize[0]; ++ int nbt = meshout->TrianglesSize[0]; ++ IssmDouble *x = xNew(nbv); ++ IssmDouble *y = xNew(nbv); ++ IssmDouble *z = xNew(nbv); ++ for(int i=0;iVertices[i*2+0]; ++ y[i] = meshout->Vertices[i*2+1]; ++ z[i] = 0.; ++ } ++ int* elementslist= xNew(nbt*3); ++ for(int i=0;i(meshout->Triangles[4*i+0]); ++ elementslist[3*i+1] = reCast(meshout->Triangles[4*i+1]); ++ elementslist[3*i+2] = reCast(meshout->Triangles[4*i+2]); ++ } ++ ++ /*Cleanup and return*/ ++ delete geomout; ++ *pnewnumberofvertices = nbv; ++ *pnewnumberofelements = nbt; ++ *px = x; ++ *py = y; ++ *pz = z; ++ *pelementslist = elementslist; ++}/*}}}*/ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21801) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21802) +@@ -44,7 +44,7 @@ + FemModel::FemModel(int argc,char** argv,ISSM_MPI_Comm incomm,bool trace){/*{{{*/ + + /*configuration: */ +- int solution_type; ++ int solution_type,amrtype,amr_frequency; + int ierr; + + /*File names*/ +@@ -79,10 +79,24 @@ + /*Save communicator in the parameters dataset: */ + this->parameters->AddObject(new GenericParam(incomm,FemModelCommEnum)); + +- #ifdef _HAVE_NEOPZ_ +- this->InitializeAdaptiveRefinement(); +- #endif ++ /*AMR stuff*/ ++ this->parameters->FindParam(&amr_frequency,TransientAmrFrequencyEnum); ++ if(amr_frequency){ ++ this->parameters->FindParam(&amrtype,AmrTypeEnum); ++ switch(amrtype){ + ++ #ifdef _HAVE_NEOPZ_ ++ case AmrNeopzEnum: this->InitializeAdaptiveRefinementNeopz(); break; ++ #endif ++ ++ #ifdef _HAVE_BAMG_ ++ case AmrBamgEnum: this->InitializeAdaptiveRefinementBamg(); break; ++ #endif ++ ++ default: _error_("not implemented yet"); ++ } ++ } ++ + /*Free resources */ + xDelete(lockfilename); + xDelete(binfilename); +@@ -141,6 +155,10 @@ + if(amr)delete amr; + #endif + ++ #ifdef _HAVE_BAMG_ ++ if(amrbamg)delete amrbamg; ++ #endif ++ + /*Now delete: */ + if(profiler)delete profiler; + +@@ -1501,6 +1519,150 @@ + xDelete(control_type); + } + /*}}}*/ ++void FemModel::ReMesh(void){/*{{{*/ ++ ++ /*Intermediaries*/ ++ IssmDouble *newx = NULL; ++ IssmDouble *newy = NULL; ++ IssmDouble *newz = NULL; ++ int *newelementslist = NULL; ++ int newnumberofvertices = -1; ++ int newnumberofelements = -1; ++ bool* my_elements = NULL; ++ int* my_vertices = NULL; ++ int elementswidth = this->GetElementsWidth();//just tria elements in this version ++ int amrtype; ++ ++ /*Branch to specific amr depending on requested method*/ ++ parameters->FindParam(&amrtype,AmrTypeEnum); ++ switch(amrtype){ ++ #ifdef _HAVE_NEOPZ_ ++ case AmrNeopzEnum: this->ReMeshNeopz(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; ++ #endif ++ ++ #ifdef _HAVE_BAMG_ ++ case AmrBamgEnum: this->ReMeshBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; ++ #endif ++ ++ default: _error_("not implemented yet"); ++ } ++ ++ /*Partitioning the new mesh. Maybe ElementsAndVerticesPartitioning.cpp could be modified to set this without iomodel.*/ ++ this->ElementsAndVerticesPartitioning(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,&my_elements,&my_vertices); ++ ++ if(this->loads->Size()!=0) _error_("not supported yet"); ++ ++ /*Create vertices*/ ++ Vertices* new_vertices=new Vertices(); ++ this->CreateVertices(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,my_vertices,newx,newy,newz,new_vertices); ++ ++ /*Creating elements*/ ++ /*Just Tria in this version*/ ++ Elements* new_elements=new Elements(); ++ this->CreateElements(newnumberofelements,elementswidth,newelementslist,my_elements,new_elements); ++ ++ /*Creating materials*/ ++ Materials* new_materials=new Materials(); ++ this->CreateMaterials(newnumberofelements,my_elements,new_materials); ++ ++ /*Creating nodes and constraints*/ ++ /*Just SSA (2D) and P1 in this version*/ ++ Nodes* new_nodes=new Nodes(); ++ Constraints* new_constraints=new Constraints(); ++ ++ int nodecounter=0; ++ int constraintcounter=0; ++ for(int i=0;inummodels;i++){//create nodes for each analysis in analysis_type_list ++ ++ int analysis_enum = this->analysis_type_list[i]; ++ ++ /*As the domain is 2D, it is not necessary to create nodes for this analysis*/ ++ /*itapopo must verify if domain is not 3D. Only 2D in this version!*/ ++ if(analysis_enum==StressbalanceVerticalAnalysisEnum) continue; ++ ++ this->CreateNodes(newnumberofvertices,my_vertices,nodecounter,analysis_enum,new_nodes); ++ if(analysis_enum==StressbalanceAnalysisEnum) this->CreateConstraints(newnumberofvertices,newnumberofelements,nodecounter,constraintcounter,newx,newy,my_vertices,new_constraints); ++ this->UpdateElements(newnumberofelements,newelementslist,my_elements,nodecounter,i,new_elements); ++ ++ if(new_nodes->Size()) nodecounter=new_nodes->MaximumId(); ++ constraintcounter = new_constraints->NumberOfConstraints(); ++ /*Make sure nodecounter is at least 0 (if no node exists, maxid will be -1*/ ++ _assert_(nodecounter>=0); ++ } ++ ++ new_elements->Presort(); ++ new_nodes->Presort(); ++ new_vertices->Presort(); ++ this->loads->Presort(); ++ new_materials->Presort(); ++ new_constraints->Presort(); ++ ++ /*reset hooks for elements, loads and nodes: */ ++ new_elements->ResetHooks(); ++ this->loads->ResetHooks(); ++ new_materials->ResetHooks(); ++ ++ /*do the post-processing of the datasets to get an FemModel that can actually run analyses: */ ++ int analysis_type; ++ for(int i=0;inummodels;i++){ ++ analysis_type=this->analysis_type_list[i]; ++ //SetCurrentConfiguration(analysis_type); ++ ++ this->analysis_counter=i; ++ /*Now, plug analysis_counter and analysis_type inside the parameters: */ ++ this->parameters->SetParam(this->analysis_counter,AnalysisCounterEnum); ++ this->parameters->SetParam(analysis_type,AnalysisTypeEnum); ++ this->parameters->SetParam(analysis_type,ConfigurationTypeEnum); ++ ++ /*configure elements, loads and nodes, for this new analysis: */ ++ new_elements->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); ++ this->loads->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); ++ ++ /*take care of toolkits options, that depend on this analysis type (present only after model processor)*/ ++ if(this->parameters->Exist(ToolkitsOptionsStringsEnum)){ ++ ToolkitsOptionsFromAnalysis(this->parameters,analysis_type); ++ if(VerboseSolver()) _printf0_(" toolkits Options set for analysis type: " << EnumToStringx(analysis_type) << "\n"); ++ } ++ ++ ConfigureObjectsx(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); ++ if(i==0){ ++ VerticesDofx(new_vertices,this->parameters); //only call once, we only have one set of vertices ++ } ++ SpcNodesx(new_nodes,new_constraints,this->parameters,analysis_type); ++ NodesDofx(new_nodes,this->parameters,analysis_type); ++ } ++ ++ /*Finally: interpolate all inputs and insert them into the new elements.*/ ++ this->InterpolateInputs(new_vertices,new_elements); ++ ++ /*Delete old structure and set new pointers*/ ++ delete this->vertices; this->vertices = new_vertices; ++ delete this->elements; this->elements = new_elements; ++ delete this->nodes; this->nodes = new_nodes; ++ delete this->constraints; this->constraints = new_constraints; ++ delete this->materials; this->materials = new_materials; ++ ++ GetMaskOfIceVerticesLSMx(this); ++ ++ /*Insert MISMIP+ bed topography*/ ++ if(false) this->BedrockFromMismipPlus(); ++ ++ /*Adjust base, thickness and mask grounded ice leve set*/ ++ if(true) this->AdjustBaseThicknessAndMask(); ++ ++ /*Reset current configuration: */ ++ analysis_type=this->analysis_type_list[this->analysis_counter]; ++ SetCurrentConfiguration(analysis_type); ++ ++ /*Cleanup*/ ++ xDelete(newx); ++ xDelete(newy); ++ xDelete(newz); ++ xDelete(newelementslist); ++ xDelete(my_vertices); ++ xDelete(my_elements); ++} ++/*}}}*/ + void FemModel::RequestedDependentsx(void){/*{{{*/ + + bool isautodiff = false; +@@ -2233,949 +2395,8 @@ + return 1; + } + /*}}}*/ +-#ifdef _HAVE_DAKOTA_ +-void FemModel::DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses){/*{{{*/ + +- int i,j; +- int my_rank; +- +- /*intermediary: */ +- char root[50]; +- int index; +- int npart; +- double femmodel_response; +- int flag; +- double *vertex_response = NULL; +- double *qmu_response = NULL; +- double *responses_pointer = NULL; +- +- /*retrieve npart: */ +- parameters->FindParam(&npart,QmuNumberofpartitionsEnum); +- my_rank=IssmComm::GetRank(); +- +- /*save the d_responses pointer: */ +- responses_pointer=d_responses; +- +- //watch out, we have more d_numresponses than numresponsedescriptors, because the responses have been expanded if they were scaled. +- //because we don't know the d_responses descriptors (the scaled ones) we can't key off them, so we will key off the responses_descriptors: */ +- +- for(i=0;i(vertex_response); +- xDelete(qmu_response); +- +- } +- else if (flag==IndexedEnum){ +- +- /*indexed response: plug index into parameters and call response module: */ +- parameters->SetParam(index,IndexEnum); +- +- this->Responsex(&femmodel_response,root); +- +- if(my_rank==0){ +- /*plug response: */ +- responses_pointer[0]=femmodel_response; +- +- /*increment response_pointer :*/ +- responses_pointer++; +- } +- } +- else if (flag==NodalEnum){ +- _error_("nodal response functions not supported yet!"); +- +- /*increment response_pointer :*/ +- responses_pointer++; +- } +- else if (flag==RegularEnum){ +- +- /*perfectly normal response function: */ +- this->Responsex(&femmodel_response,root); +- +- if(my_rank==0){ +- /*plug response: */ +- responses_pointer[0]=femmodel_response; +- +- /*increment response_pointer :*/ +- responses_pointer++; +- } +- } +- else _error_("flag type " << flag << " not supported yet for response analysis"); +- } +- +- /*Synthesize echo: {{{*/ +- if(my_rank==0){ +- _printf_(" responses: " << d_numresponses << ": "); +- for(i=0;i* wg,Vector* dwgdt, IssmDouble* x, IssmDouble* y){ /*{{{*/ +- +- /*Go through elements, and add contribution from each element to the deflection vector wg:*/ +- for(int i=0;iSize();i++){ +- Element* element=xDynamicCast(elements->GetObjectByOffset(i)); +- element->GiaDeflection(wg,dwgdt, x,y); +- } +-} +-/*}}}*/ +-#endif +-#ifdef _HAVE_ESA_ +-void FemModel::EsaGeodetic2D(Vector* pUp, Vector* pNorth, Vector* pEast, IssmDouble* xx, IssmDouble* yy){/*{{{*/ +- +- int ns,nsmax; +- +- /*Go through elements, and add contribution from each element to the deflection vector wg:*/ +- ns = elements->Size(); +- +- /*Figure out max of ns: */ +- ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- +- /*Call the esa geodetic core: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- element->EsaGeodetic2D(pUp,pNorth,pEast,xx,yy); +- } +- if(i%100==0){ +- pUp->Assemble(); +- pNorth->Assemble(); +- pEast->Assemble(); +- } +- } +- +- /*One last time: */ +- pUp->Assemble(); +- pNorth->Assemble(); +- pEast->Assemble(); +- +- /*Free ressources:*/ +- xDelete(xx); +- xDelete(yy); +-} +-/*}}}*/ +-void FemModel::EsaGeodetic3D(Vector* pUp, Vector* pNorth, Vector* pEast, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius, IssmDouble* xx, IssmDouble* yy, IssmDouble* zz){/*{{{*/ +- +- IssmDouble eartharea=0; +- IssmDouble eartharea_cpu=0; +- +- int ns,nsmax; +- +- /*Go through elements, and add contribution from each element to the deflection vector wg:*/ +- ns = elements->Size(); +- +- /*First, figure out the surface area of Earth: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- eartharea_cpu += element->GetAreaSpherical(); +- } +- ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- +- /*Figure out max of ns: */ +- ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- +- /*Call the esa geodetic core: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- element->EsaGeodetic3D(pUp,pNorth,pEast,latitude,longitude,radius,xx,yy,zz,eartharea); +- } +- if(i%100==0){ +- pUp->Assemble(); +- pNorth->Assemble(); +- pEast->Assemble(); +- } +- } +- +- /*One last time: */ +- pUp->Assemble(); +- pNorth->Assemble(); +- pEast->Assemble(); +- +- /*Free ressources:*/ +- xDelete(latitude); +- xDelete(longitude); +- xDelete(radius); +- xDelete(xx); +- xDelete(yy); +- xDelete(zz); +-} +-/*}}}*/ +-#endif +-#ifdef _HAVE_SEALEVELRISE_ +-void FemModel::SealevelriseEustatic(Vector* pSgi, IssmDouble* peustatic, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius) { /*{{{*/ +- +- /*serialized vectors:*/ +- IssmDouble eustatic = 0.; +- IssmDouble eustatic_cpu = 0.; +- IssmDouble eustatic_cpu_e = 0.; +- IssmDouble oceanarea = 0.; +- IssmDouble oceanarea_cpu = 0.; +- IssmDouble eartharea = 0.; +- IssmDouble eartharea_cpu = 0.; +- int ns,nsmax; +- +- /*Go through elements, and add contribution from each element to the deflection vector wg:*/ +- ns = elements->Size(); +- +- /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- oceanarea_cpu += element->OceanArea(); +- eartharea_cpu += element->GetAreaSpherical(); +- } +- ISSM_MPI_Reduce (&oceanarea_cpu,&oceanarea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&oceanarea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- _assert_(oceanarea>0.); +- +- ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- +- /*Figure out max of ns: */ +- ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- +- /*Call the sea level rise core: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- element->SealevelriseEustatic(pSgi,&eustatic_cpu_e,latitude,longitude,radius,oceanarea,eartharea); +- eustatic_cpu+=eustatic_cpu_e; +- } +- if(i%100==0)pSgi->Assemble(); +- } +- if(VerboseConvergence())_printf0_("\n"); +- +- /*One last time: */ +- pSgi->Assemble(); +- +- /*Sum all eustatic components from all cpus:*/ +- ISSM_MPI_Reduce (&eustatic_cpu,&eustatic,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&eustatic,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- _assert_(!xIsNan(eustatic)); +- +- /*Assign output pointers:*/ +- *peustatic=eustatic; +- +-} +-/*}}}*/ +-void FemModel::SealevelriseNonEustatic(Vector* pSgo, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius, bool verboseconvolution){/*{{{*/ +- +- /*serialized vectors:*/ +- IssmDouble* Sg_old=NULL; +- +- IssmDouble eartharea=0; +- IssmDouble eartharea_cpu=0; +- +- int ns,nsmax; +- +- /*Serialize vectors from previous iteration:*/ +- Sg_old=pSg_old->ToMPISerial(); +- +- /*Go through elements, and add contribution from each element to the deflection vector wg:*/ +- ns = elements->Size(); +- +- /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- eartharea_cpu += element->GetAreaSpherical(); +- } +- +- ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- +- /*Figure out max of ns: */ +- ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- +- /*Call the sea level rise core: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- element->SealevelriseNonEustatic(pSgo,Sg_old,latitude,longitude,radius,eartharea); +- } +- if(i%100==0)pSgo->Assemble(); +- } +- if(verboseconvolution)if(VerboseConvergence())_printf_("\n"); +- +- /*Free ressources:*/ +- xDelete(Sg_old); +-} +-/*}}}*/ +-void FemModel::SealevelriseRotationalFeedback(Vector* pSgo_rot, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius){/*{{{*/ +- +- /*serialized vectors:*/ +- IssmDouble* Sg_old=NULL; +- IssmDouble eartharea=0; +- IssmDouble eartharea_cpu=0; +- IssmDouble tide_love_h, tide_love_k, fluid_love, moi_e, moi_p, omega, g; +- IssmDouble load_love_k2 = -0.30922675; //degree 2 load Love number +- IssmDouble m1, m2, m3; +- IssmDouble lati, longi, radi, value; +- +- /*Serialize vectors from previous iteration:*/ +- Sg_old=pSg_old->ToMPISerial(); +- +- /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ +- for(int i=0;iSize();i++){ +- Element* element=xDynamicCast(elements->GetObjectByOffset(i)); +- eartharea_cpu += element->GetAreaSpherical(); +- } +- ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- +- IssmDouble moi_list[3]={0,0,0}; +- IssmDouble moi_list_cpu[3]={0,0,0}; +- for(int i=0;iSize();i++){ +- Element* element=xDynamicCast(elements->GetObjectByOffset(i)); +- element->SealevelriseMomentOfInertia(&moi_list[0],Sg_old,eartharea); +- moi_list_cpu[0] += moi_list[0]; +- moi_list_cpu[1] += moi_list[1]; +- moi_list_cpu[2] += moi_list[2]; +- } +- ISSM_MPI_Reduce (&moi_list_cpu[0],&moi_list[0],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&moi_list[0],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- // +- ISSM_MPI_Reduce (&moi_list_cpu[1],&moi_list[1],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&moi_list[1],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- // +- ISSM_MPI_Reduce (&moi_list_cpu[2],&moi_list[2],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&moi_list[2],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- +- /*pull out some useful parameters: */ +- parameters->FindParam(&tide_love_h,SealevelriseTidalLoveHEnum); +- parameters->FindParam(&tide_love_k,SealevelriseTidalLoveKEnum); +- parameters->FindParam(&fluid_love,SealevelriseFluidLoveEnum); +- parameters->FindParam(&moi_e,SealevelriseEquatorialMoiEnum); +- parameters->FindParam(&moi_p,SealevelrisePolarMoiEnum); +- parameters->FindParam(&omega,SealevelriseAngularVelocityEnum); +- +- /*compute perturbation terms for angular velocity vector: */ +- m1 = 1/(1-tide_love_k/fluid_love) * (1+load_love_k2)/(moi_p-moi_e) * moi_list[0]; +- m2 = 1/(1-tide_love_k/fluid_love) * (1+load_love_k2)/(moi_p-moi_e) * moi_list[1]; +- m3 = -(1+load_love_k2)/moi_p * moi_list[2]; // term associated with fluid number (3-order-of-magnitude smaller) is negelected +- +- /* Green's function (1+k_2-h_2/g): checked against Glenn Milne's thesis Chapter 3 (eqs: 3.3-4, 3.10-11) +- * Perturbation terms for angular velocity vector (m1, m2, m3): checked against Mitrovica (2005 Appendix) & Jensen et al (2013 Appendix A3) +- * Sea level rotational feedback: checked against GMD eqs 8-9 (only first order terms, i.e., degree 2 order 0 & 1 considered) +- * all DONE in Geographic coordinates: theta \in [-90,90], lambda \in [-180 180] +- */ +- for(int i=0;iSize();i++){ +- int sid; +- //Vertex* vertex=(Vertex*)vertices->GetObjectByOffset(i); +- Vertex* vertex=xDynamicCast(vertices->GetObjectByOffset(i)); +- sid=vertex->Sid(); +- +- lati=latitude[sid]/180*PI; longi=longitude[sid]/180*PI; radi=radius[sid]; +- +- /*only first order terms are considered now: */ +- value=((1.0+tide_love_k-tide_love_h)/9.81)*pow(omega*radi,2.0)* +- (-m3/6.0 + 0.5*m3*cos(2.0*lati) - 0.5*sin(2.*lati)*(m1*cos(longi)+m2*sin(longi))); +- +- pSgo_rot->SetValue(sid,value,INS_VAL); //INS_VAL ensures that you don't add several times +- } +- +- /*Assemble mesh velocity*/ +- pSgo_rot->Assemble(); +- +- /*Free ressources:*/ +- xDelete(Sg_old); +- +-} +-/*}}}*/ +-void FemModel::SealevelriseGeodetic(Vector* pUp, Vector* pNorth, Vector* pEast, Vector* pSg, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius, IssmDouble* xx, IssmDouble* yy, IssmDouble* zz){/*{{{*/ +- +- /*serialized vectors:*/ +- IssmDouble* Sg=NULL; +- +- IssmDouble eartharea=0; +- IssmDouble eartharea_cpu=0; +- +- int ns,nsmax; +- +- /*Serialize vectors from previous iteration:*/ +- Sg=pSg->ToMPISerial(); +- +- /*Go through elements, and add contribution from each element to the deflection vector wg:*/ +- ns = elements->Size(); +- +- /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- eartharea_cpu += element->GetAreaSpherical(); +- } +- ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- +- /*Figure out max of ns: */ +- ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- +- /*Call the sea level rise core: */ +- for(int i=0;i(elements->GetObjectByOffset(i)); +- element->SealevelriseGeodetic(pUp,pNorth,pEast,Sg,latitude,longitude,radius,xx,yy,zz,eartharea); +- } +- if(i%100==0){ +- pUp->Assemble(); +- pNorth->Assemble(); +- pEast->Assemble(); +- } +- } +- +- /*One last time: */ +- pUp->Assemble(); +- pNorth->Assemble(); +- pEast->Assemble(); +- +- /*Free ressources:*/ +- xDelete(Sg); +- xDelete(latitude); +- xDelete(longitude); +- xDelete(radius); +- xDelete(xx); +- xDelete(yy); +- xDelete(zz); +-} +-/*}}}*/ +-IssmDouble FemModel::SealevelriseOceanAverage(Vector* Sg) { /*{{{*/ +- +- IssmDouble* Sg_serial=NULL; +- IssmDouble oceanvalue,oceanvalue_cpu; +- IssmDouble oceanarea,oceanarea_cpu; +- +- /*Serialize vectors from previous iteration:*/ +- Sg_serial=Sg->ToMPISerial(); +- +- /*Initialize:*/ +- oceanvalue_cpu=0; +- oceanarea_cpu=0; +- +- /*Go through elements, and add contribution from each element and divide by overall ocean area:*/ +- for(int i=0;iSize();i++){ +- Element* element=xDynamicCast(elements->GetObjectByOffset(i)); +- oceanarea_cpu += element->OceanArea(); +- oceanvalue_cpu += element->OceanAverage(Sg_serial); +- } +- ISSM_MPI_Reduce (&oceanarea_cpu,&oceanarea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&oceanarea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- +- ISSM_MPI_Reduce (&oceanvalue_cpu,&oceanvalue,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&oceanvalue,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- +- /*Free ressources:*/ +- xDelete(Sg_serial); +- +- return oceanvalue/oceanarea; +-} +-/*}}}*/ +-#endif +-void FemModel::HydrologyEPLupdateDomainx(IssmDouble* pEplcount){ /*{{{*/ +- +- Vector* mask = NULL; +- Vector* recurence = NULL; +- Vector* active = NULL; +- IssmDouble* serial_mask = NULL; +- IssmDouble* serial_rec = NULL; +- IssmDouble* serial_active = NULL; +- IssmDouble* old_active = NULL; +- int* eplzigzag_counter = NULL; +- int eplflip_lock; +- +- HydrologyDCEfficientAnalysis* effanalysis = new HydrologyDCEfficientAnalysis(); +- HydrologyDCInefficientAnalysis* inefanalysis = new HydrologyDCInefficientAnalysis(); +- +- /*Step 1: update mask, the mask might be extended by residual and/or using downstream sediment head*/ +- mask=new Vector(this->nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum)); +- recurence=new Vector(this->nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum)); +- this->parameters->FindParam(&eplzigzag_counter,NULL,EplZigZagCounterEnum); +- this->parameters->FindParam(&eplflip_lock,HydrologydcEplflipLockEnum); +- GetVectorFromInputsx(&old_active,this,HydrologydcMaskEplactiveNodeEnum,NodeSIdEnum); +- +- for (int i=0;iSize();i++){ +- Element* element=xDynamicCast(elements->GetObjectByOffset(i)); +- effanalysis->HydrologyEPLGetMask(mask,recurence,eplzigzag_counter,element); +- } +- /*check for changes and increment zigzag counter, change the mask if necessary*/ +- recurence->Assemble(); +- serial_rec=recurence->ToMPISerial(); +- for (int i=0;iSize();i++){ +- Node* node=xDynamicCast(nodes->GetObjectByOffset(i)); +- if(serial_rec[node->Sid()]==1.)eplzigzag_counter[node->Lid()] ++; +- if(eplzigzag_counter[node->Lid()]>eplflip_lock & eplflip_lock!=0){ +- mask->SetValue(node->Sid(),old_active[node->Sid()],INS_VAL); +- } +- } +- this->parameters->SetParam(eplzigzag_counter,this->nodes->Size(),EplZigZagCounterEnum); +- /*Assemble and serialize*/ +- mask->Assemble(); +- serial_mask=mask->ToMPISerial(); +- +- xDelete(eplzigzag_counter); +- xDelete(serial_rec); +- xDelete(old_active); +- delete mask; +- delete recurence; +- +- /*Update Mask*/ +- InputUpdateFromVectorx(this,serial_mask,HydrologydcMaskEplactiveNodeEnum,NodeSIdEnum); +- xDelete(serial_mask); +- inefanalysis->ElementizeEplMask(this); +- /*Step 2: update node activity. If one element is connected to mask=1, all nodes are active*/ +- active=new Vector(nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum)); +- for (int i=0;iSize();i++){ +- Element* element=xDynamicCast(elements->GetObjectByOffset(i)); +- effanalysis->HydrologyEPLGetActive(active,element); +- } +- +- /*Assemble and serialize*/ +- active->Assemble(); +- serial_active=active->ToMPISerial(); +- delete active; +- +- /*Update node activation accordingly*/ +- int counter =0; +- for (int i=0;iSize();i++){ +- Node* node=xDynamicCast(nodes->GetObjectByOffset(i)); +- if(node->InAnalysis(HydrologyDCEfficientAnalysisEnum)){ +- if(serial_active[node->Sid()]==1.){ +- node->Activate(); +- if(!node->IsClone()) counter++; +- } +- else{ +- node->Deactivate(); +- } +- } +- } +- xDelete(serial_active); +- delete effanalysis; +- delete inefanalysis; +- int sum_counter; +- ISSM_MPI_Reduce(&counter,&sum_counter,1,ISSM_MPI_INT,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&sum_counter,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- counter=sum_counter; +- *pEplcount = counter; +- if(VerboseSolution()) _printf0_(" Number of active nodes in EPL layer: "<< counter <<"\n"); +- +- /*Update dof indexings*/ +- this->UpdateConstraintsx(); +- +-} +-/*}}}*/ +-void FemModel::UpdateConstraintsL2ProjectionEPLx(IssmDouble* pL2count){ /*{{{*/ +- +- Vector* active = NULL; +- IssmDouble* serial_active = NULL; +- HydrologyDCEfficientAnalysis* effanalysis = new HydrologyDCEfficientAnalysis(); +- +- /*update node activity. If one element is connected to mask=1, all nodes are active*/ +- active=new Vector(nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum)); +- for (int i=0;iSize();i++){ +- Element* element=xDynamicCast(elements->GetObjectByOffset(i)); +- effanalysis->HydrologyEPLGetActive(active,element); +- } +- +- /*Assemble and serialize*/ +- active->Assemble(); +- serial_active=active->ToMPISerial(); +- delete active; +- delete effanalysis; +- +- /*Update node activation accordingly*/ +- int counter =0; +- for (int i=0;iSize();i++){ +- Node* node=xDynamicCast(nodes->GetObjectByOffset(i)); +- if(node->InAnalysis(L2ProjectionEPLAnalysisEnum)){ +- if(serial_active[node->Sid()]==1.){ +- node->Activate(); +- if(!node->IsClone()) counter++; +- } +- else{ +- node->Deactivate(); +- } +- } +- } +- xDelete(serial_active); +- int sum_counter; +- ISSM_MPI_Reduce(&counter,&sum_counter,1,ISSM_MPI_INT,ISSM_MPI_SUM,0,IssmComm::GetComm() ); +- ISSM_MPI_Bcast(&sum_counter,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- counter=sum_counter; +- *pL2count = counter; +- if(VerboseSolution()) _printf0_(" Number of active nodes L2 Projection: "<< counter <<"\n"); +-} +-/*}}}*/ +-#ifdef _HAVE_JAVASCRIPT_ +-FemModel::FemModel(IssmDouble* buffer, int buffersize, char* toolkits, char* solution, char* modelname,ISSM_MPI_Comm incomm, bool trace){ /*{{{*/ +- /*configuration: */ +- int solution_type; +- int ierr; +- +- /*First things first, store the communicator, and set it as a global variable: */ +- IssmComm::SetComm(incomm); +- +- /*Start profiler: */ +- this->profiler=new Profiler(); +- profiler->Tag(START); +- +- /*From command line arguments, retrieve different filenames needed to create the FemModel: */ +- solution_type=StringToEnumx(solution); +- +- /*Create femmodel from input files: */ +- profiler->Tag(STARTINIT); +- this->InitFromBuffers((char*)buffer,buffersize,toolkits, solution_type,trace,NULL); +- profiler->Tag(FINISHINIT); +- +- /*Save communicator in the parameters dataset: */ +- this->parameters->AddObject(new GenericParam(incomm,FemModelCommEnum)); +- +-} +-/*}}}*/ +-void FemModel::CleanUpJs(char** poutput, size_t* psize){/*{{{*/ +- +- /*Intermediary*/ +- FILE *output_fid; +- GenericParam* outputbufferparam=NULL; +- GenericParam* outputbuffersizeparam=NULL; +- char** poutputbuffer; +- size_t* poutputbuffersize; +- +- +- /*Before we delete the profiler, report statistics for this run: */ +- profiler->Tag(FINISH); //final tagging +- _printf0_("\n"); +- _printf0_(" "<DeltaTime(STARTINIT,FINISHINIT) << "\n"); +- _printf0_(" "<DeltaTime(STARTCORE,FINISHCORE) << "\n"); +- _printf0_("\n"); +- _printf0_(" Total elapsed time: " +- <DeltaTimeModHour(START,FINISH)<<" hrs " +- <DeltaTimeModMin(START,FINISH)<<" min " +- <DeltaTimeModSec(START,FINISH)<<" sec" +- ); +- _printf0_("\n"); +- +- /*Before we close the output file, recover the buffer and size:*/ +- outputbufferparam = xDynamicCast*>(this->parameters->FindParamObject(OutputBufferPointerEnum)); +- poutputbuffer=outputbufferparam->GetParameterValue(); +- outputbuffersizeparam = xDynamicCast*>(this->parameters->FindParamObject(OutputBufferSizePointerEnum)); +- poutputbuffersize=outputbuffersizeparam->GetParameterValue(); +- +- /*Assign output values: */ +- *poutput=*poutputbuffer; +- *psize=*poutputbuffersize; +-} +-/*}}}*/ +-void FemModel::InitFromBuffers(char* buffer, int buffersize, char* toolkits, int in_solution_type, bool trace, IssmPDouble* X){/*{{{*/ +- +- /*intermediary*/ +- FILE *IOMODEL = NULL; +- FILE *toolkitsoptionsfid = NULL; +- FILE *output_fid = NULL; +- int my_rank; +- size_t outputsize; +- char *outputbuffer; +- const char *rootpath = ""; //needed for Dakota runs only, which we won't do here. +- +- /*recover my_rank:*/ +- my_rank=IssmComm::GetRank(); +- +- /*Open input file descriptor on cpu 0: */ +- if(my_rank==0) IOMODEL = fmemopen((void*)buffer, buffersize, "rb"); +- +- /*Open toolkits file descriptor: */ +- toolkitsoptionsfid=fmemopen((void*)toolkits, strlen(toolkits)+1, "r"); +- +- /*Now, go create FemModel:*/ +- this->InitFromFids((char*)rootpath,IOMODEL,toolkitsoptionsfid,in_solution_type,trace,X); +- +- /*Close input file and toolkits file descriptors: */ +- if(my_rank==0) fclose(IOMODEL); +- fclose(toolkitsoptionsfid); +- +- /*Open output file once for all and add output file descriptor to parameters*/ +- output_fid=open_memstream(&outputbuffer,&outputsize); +- if(output_fid==NULL)_error_("could not initialize output stream"); +- this->parameters->SetParam(output_fid,OutputFilePointerEnum); +- this->parameters->AddObject(new GenericParam(&outputbuffer,OutputBufferPointerEnum)); +- this->parameters->AddObject(new GenericParam(&outputsize,OutputBufferSizePointerEnum)); +- +-}/*}}}*/ +-#endif +- +-#ifdef _HAVE_NEOPZ_ +-void FemModel::InitializeAdaptiveRefinement(void){/*{{{*/ +- +- /*Define variables*/ +- int my_rank = IssmComm::GetRank(); +- this->amr = NULL;//initialize amr as NULL +- int numberofvertices = this->vertices->NumberOfVertices(); +- int numberofelements = this->elements->NumberOfElements(); +- int numberofsegments = 0; //used on matlab +- IssmDouble* x = NULL; +- IssmDouble* y = NULL; +- IssmDouble* z = NULL; +- int* elements = NULL; +- int elementswidth = this->GetElementsWidth(); //just tria elements in this version. Itapopo: +- int levelmax = 0; +- IssmDouble regionlevel1 = 0.; +- IssmDouble regionlevelmax = 0.; +- +- /*Get vertices coordinates of the coarse mesh (father mesh)*/ +- /*elements comes in Matlab indexing*/ +- this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elements); +- +- /*Get amr parameters*/ +- this->parameters->FindParam(&levelmax,AmrLevelMaxEnum); +- this->parameters->FindParam(®ionlevel1,AmrRegionLevel1Enum); +- this->parameters->FindParam(®ionlevelmax,AmrRegionLevelMaxEnum); +- +- /*Create initial mesh (coarse mesh) in neopz data structure*/ +- /*Just CPU #0 should keep AMR object*/ +- this->SetRefPatterns(); +- if(my_rank==0){ +- bool ismisomip = false; +- if(ismisomip){//itapopo +- TPZFileStream fstr; +- std::stringstream ss; +- int frictionlaw; +- +- this->parameters->FindParam(&frictionlaw,FrictionLawEnum); +- +- ss << levelmax; +- if(frictionlaw==1){ +- ss << "_viscous/amr.txt"; +- }else if(frictionlaw==7){ +- ss << "_tsai/amr.txt"; +- }else{ +- _error_("friction law not supported here."); +- } +- +- std::string AMRfile = "/home/santos/Misomip2/L" + ss.str(); +- fstr.OpenRead(AMRfile.c_str()); +- +- TPZSaveable *sv = TPZSaveable::Restore(fstr,0); +- this->amr = dynamic_cast(sv); +- } +- else{ +- this->amr = new AdaptiveMeshRefinement(); +- //this->amr->SetLevelMax(levelmax); //Set max level of refinement +- //this->amr->SetRegions(regionlevel1,regionlevelmax); +- this->amr->CreateInitialMesh(numberofvertices,numberofelements,numberofsegments,elementswidth,x,y,z,elements,NULL); +- } +- this->amr->SetLevelMax(levelmax); //Set max level of refinement +- this->amr->SetRegions(regionlevel1,regionlevelmax); +- } +- +- /*Free the vectors*/ +- xDelete(x); +- xDelete(y); +- xDelete(z); +- xDelete(elements); +- +-} +-/*}}}*/ +-void FemModel::SetRefPatterns(){/*{{{*/ +- +- /*Initialize the global variable of refinement patterns*/ +- gRefDBase.InitializeUniformRefPattern(EOned); +- gRefDBase.InitializeUniformRefPattern(ETriangle); +- +- //gRefDBase.InitializeRefPatterns(); +- /*Insert specifics patterns to ISSM core*/ +- std::string filepath = REFPATTERNDIR; +- std::string filename1 = filepath + "/2D_Triang_Rib_3.rpt"; +- std::string filename2 = filepath + "/2D_Triang_Rib_4.rpt"; +- std::string filename3 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4.rpt"; +- std::string filename4 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4_permuted.rpt"; +- std::string filename5 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5.rpt"; +- std::string filename6 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5_permuted.rpt"; +- std::string filename7 = filepath + "/2D_Triang_Rib_5.rpt"; +- +- TPZAutoPointer refpat1 = new TPZRefPattern(filename1); +- TPZAutoPointer refpat2 = new TPZRefPattern(filename2); +- TPZAutoPointer refpat3 = new TPZRefPattern(filename3); +- TPZAutoPointer refpat4 = new TPZRefPattern(filename4); +- TPZAutoPointer refpat5 = new TPZRefPattern(filename5); +- TPZAutoPointer refpat6 = new TPZRefPattern(filename6); +- TPZAutoPointer refpat7 = new TPZRefPattern(filename7); +- +- if(!gRefDBase.FindRefPattern(refpat1)) gRefDBase.InsertRefPattern(refpat1); +- if(!gRefDBase.FindRefPattern(refpat2)) gRefDBase.InsertRefPattern(refpat2); +- if(!gRefDBase.FindRefPattern(refpat3)) gRefDBase.InsertRefPattern(refpat3); +- if(!gRefDBase.FindRefPattern(refpat4)) gRefDBase.InsertRefPattern(refpat4); +- if(!gRefDBase.FindRefPattern(refpat5)) gRefDBase.InsertRefPattern(refpat5); +- if(!gRefDBase.FindRefPattern(refpat6)) gRefDBase.InsertRefPattern(refpat6); +- if(!gRefDBase.FindRefPattern(refpat7)) gRefDBase.InsertRefPattern(refpat7); +-} +-/*}}}*/ +-void FemModel::ReMesh(void){/*{{{*/ +- +- /*Variables*/ +- IssmDouble *newx = NULL; +- IssmDouble *newy = NULL; +- IssmDouble *newz = NULL; +- int *newelementslist = NULL; +- int newnumberofvertices = -1; +- int newnumberofelements = -1; +- bool* my_elements = NULL; +- int* my_vertices = NULL; +- int elementswidth = this->GetElementsWidth();//just tria elements in this version +- +- /*Execute refinement and get the new mesh*/ +- /*newelementslist come in Matlab indexing*/ +- this->ExecuteRefinement(newnumberofvertices,newnumberofelements,&newx,&newy,&newz,&newelementslist); +- +- /*Partitioning the new mesh. Maybe ElementsAndVerticesPartitioning.cpp could be modified to set this without iomodel.*/ +- this->ElementsAndVerticesPartitioning(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,&my_elements,&my_vertices); +- +- if(this->loads->Size()!=0) _error_("not supported yet"); +- +- /*Create vertices*/ +- Vertices* new_vertices=new Vertices(); +- this->CreateVertices(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,my_vertices,newx,newy,newz,new_vertices); +- +- /*Creating elements*/ +- /*Just Tria in this version*/ +- Elements* new_elements=new Elements(); +- this->CreateElements(newnumberofelements,elementswidth,newelementslist,my_elements,new_elements); +- +- /*Creating materials*/ +- Materials* new_materials=new Materials(); +- this->CreateMaterials(newnumberofelements,my_elements,new_materials); +- +- /*Creating nodes and constraints*/ +- /*Just SSA (2D) and P1 in this version*/ +- Nodes* new_nodes=new Nodes(); +- Constraints* new_constraints=new Constraints(); +- +- int nodecounter=0; +- int constraintcounter=0; +- for(int i=0;inummodels;i++){//create nodes for each analysis in analysis_type_list +- +- int analysis_enum = this->analysis_type_list[i]; +- +- /*As the domain is 2D, it is not necessary to create nodes for this analysis*/ +- /*itapopo must verify if domain is not 3D. Only 2D in this version!*/ +- if(analysis_enum==StressbalanceVerticalAnalysisEnum) continue; +- +- this->CreateNodes(newnumberofvertices,my_vertices,nodecounter,analysis_enum,new_nodes); +- if(analysis_enum==StressbalanceAnalysisEnum) this->CreateConstraints(newnumberofvertices,newnumberofelements,nodecounter,constraintcounter,newx,newy,my_vertices,new_constraints); +- this->UpdateElements(newnumberofelements,newelementslist,my_elements,nodecounter,i,new_elements); +- +- if(new_nodes->Size()) nodecounter=new_nodes->MaximumId(); +- constraintcounter = new_constraints->NumberOfConstraints(); +- /*Make sure nodecounter is at least 0 (if no node exists, maxid will be -1*/ +- _assert_(nodecounter>=0); +- } +- +- new_elements->Presort(); +- new_nodes->Presort(); +- new_vertices->Presort(); +- this->loads->Presort(); +- new_materials->Presort(); +- new_constraints->Presort(); +- +- /*reset hooks for elements, loads and nodes: */ +- new_elements->ResetHooks(); +- this->loads->ResetHooks(); +- new_materials->ResetHooks(); +- +- /*do the post-processing of the datasets to get an FemModel that can actually run analyses: */ +- int analysis_type; +- for(int i=0;inummodels;i++){ +- analysis_type=this->analysis_type_list[i]; +- //SetCurrentConfiguration(analysis_type); +- +- this->analysis_counter=i; +- /*Now, plug analysis_counter and analysis_type inside the parameters: */ +- this->parameters->SetParam(this->analysis_counter,AnalysisCounterEnum); +- this->parameters->SetParam(analysis_type,AnalysisTypeEnum); +- this->parameters->SetParam(analysis_type,ConfigurationTypeEnum); +- +- /*configure elements, loads and nodes, for this new analysis: */ +- new_elements->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); +- this->loads->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); +- +- /*take care of toolkits options, that depend on this analysis type (present only after model processor)*/ +- if(this->parameters->Exist(ToolkitsOptionsStringsEnum)){ +- ToolkitsOptionsFromAnalysis(this->parameters,analysis_type); +- if(VerboseSolver()) _printf0_(" toolkits Options set for analysis type: " << EnumToStringx(analysis_type) << "\n"); +- } +- +- ConfigureObjectsx(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); +- if(i==0){ +- VerticesDofx(new_vertices,this->parameters); //only call once, we only have one set of vertices +- } +- SpcNodesx(new_nodes,new_constraints,this->parameters,analysis_type); +- NodesDofx(new_nodes,this->parameters,analysis_type); +- } +- +- /*Finally: interpolate all inputs and insert them into the new elements.*/ +- this->InterpolateInputs(new_vertices,new_elements); +- +- /*Delete old structure and set new pointers*/ +- delete this->vertices; this->vertices = new_vertices; +- delete this->elements; this->elements = new_elements; +- delete this->nodes; this->nodes = new_nodes; +- delete this->constraints; this->constraints = new_constraints; +- delete this->materials; this->materials = new_materials; +- +- GetMaskOfIceVerticesLSMx(this); +- +- /*Insert MISMIP+ bed topography*/ +- if(false) this->BedrockFromMismipPlus(); +- +- /*Adjust base, thickness and mask grounded ice leve set*/ +- if(true) this->AdjustBaseThicknessAndMask(); +- +- /*Reset current configuration: */ +- analysis_type=this->analysis_type_list[this->analysis_counter]; +- SetCurrentConfiguration(analysis_type); +- +- /*Cleanup*/ +- xDelete(newx); +- xDelete(newy); +- xDelete(newz); +- xDelete(newelementslist); +- xDelete(my_vertices); +- xDelete(my_elements); +- +- return; +- +-} +-/*}}}*/ ++/*AMR*/ + void FemModel::BedrockFromMismipPlus(void){/*{{{*/ + + /*Insert bedrock from mismip+ setup*/ +@@ -3244,7 +2465,7 @@ + b[i] = base_float; + } + +- if(abs(sl[i])>0) _error_("Sea level value not supported!"); ++ if(abs(sl[i])>0) _error_("Sea level value "<AddInput(MaskGroundediceLevelsetEnum,&phi[0],P1Enum); + element->AddInput(ThicknessEnum,&h[0],P1Enum); + element->AddInput(BaseEnum,&b[0],P1Enum); +- + } + + /*Delete*/ +@@ -3264,72 +2484,8 @@ + xDelete(b); + xDelete(r); + xDelete(sl); +- +- return; + } + /*}}}*/ +-void FemModel::WriteMeshInResults(void){/*{{{*/ +- +- int step = -1; +- int numberofelements = -1; +- int numberofvertices = -1; +- IssmDouble time = -1; +- IssmDouble* x = NULL; +- IssmDouble* y = NULL; +- IssmDouble* z = NULL; +- int* elementslist = NULL; +- +- if(!this->elements || !this->vertices || !this->results || !this->parameters) return; +- +- parameters->FindParam(&step,StepEnum); +- parameters->FindParam(&time,TimeEnum); +- numberofelements=this->elements->NumberOfElements(); +- numberofvertices=this->vertices->NumberOfVertices(); +- +- /*Get mesh. Elementslist comes in Matlab indexing*/ +- this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elementslist); +- +- /*Write mesh in Results*/ +- this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshElementsEnum, +- elementslist,numberofelements,this->GetElementsWidth(),step,time)); +- +- this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshXEnum, +- x,numberofvertices,1,step,time)); +- +- this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshYEnum, +- y,numberofvertices,1,step,time)); +- +- //itapopo +- if(IssmComm::GetRank()==0){ +- TPZFileStream fstr; +- std::stringstream ss; +- int frictionlaw,levelmax; +- this->parameters->FindParam(&frictionlaw,FrictionLawEnum); +- this->parameters->FindParam(&levelmax,AmrLevelMaxEnum); +- ss << levelmax; +- if(frictionlaw==1){ +- ss << "_viscous/amr.txt"; +- }else if(frictionlaw==7){ +- ss << "_tsai/amr.txt"; +- }else{ +- _error_("friction law not supported here."); +- } +- std::string AMRfile = "/home/santos/Misomip2/L" + ss.str(); +- fstr.OpenWrite(AMRfile.c_str()); +- int withclassid = 1; +- this->amr->Write(fstr,withclassid); +- } +- //itapopo +- +- /*Cleanup*/ +- xDelete(x); +- xDelete(y); +- xDelete(z); +- xDelete(elementslist); +- +- return; +-} +-/*}}}*/ + void FemModel::InterpolateInputs(Vertices* newfemmodel_vertices,Elements* newfemmodel_elements){/*{{{*/ + + int maxinputs = MaximumNumberOfDefinitionsEnum; +@@ -3341,7 +2497,7 @@ + element->GetInputsInterpolations(input_interpolations); + } + input_interpolations->Assemble(); +- ++ + /*Serialize and set output*/ + IssmDouble* input_interpolations_serial = input_interpolations->ToMPISerial(); + delete input_interpolations; +@@ -3373,7 +2529,7 @@ + P1input_enums[numP1inputs] = i; + P1input_interp[numP1inputs] = inputinterp; + } +- numP1inputs++; ++ numP1inputs++; + break; + case P0Enum: + case DoubleInputEnum: +@@ -3420,7 +2576,7 @@ + for(int j=0;j(vector); + } +- ++ + /*Old mesh coordinates*/ + IssmDouble *Xold = NULL; + IssmDouble *Yold = NULL; +@@ -3432,7 +2588,7 @@ + IssmDouble* XC_new = NULL; + IssmDouble* YC_new = NULL; + int *Indexnew = NULL; +- ++ + /*Get the old mesh*/ + this->GetMesh(this->vertices,this->elements,&Xold,&Yold,&Zold,&Indexold); + +@@ -3458,16 +2614,16 @@ + InterpFromMeshToMesh2dx(&P0inputsnew,Indexold,Xold,Yold,numverticesold,numelementsold, + P0inputsold,numelementsold,numP0inputs, + XC_new,YC_new,numelementsnew,NULL); +- ++ + /*Interpolate P1 inputs in the new mesh*/ + InterpFromMeshToMesh2dx(&P1inputsnew,Indexold,Xold,Yold,numverticesold,numelementsold, + P1inputsold,numverticesold,numP1inputs, + Xnew,Ynew,numverticesnew,NULL); +- ++ + /*Insert P0 inputs into the new elements.*/ + vector=NULL; + for(int i=0;i(numelementsnew); + for(int j=0;j(XC_new); + xDelete(YC_new); + xDelete(Indexnew); +- + } + /*}}}*/ +-void FemModel::ExecuteRefinement(int &numberofvertices,int &numberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ +- +- /*elements is in Matlab indexing*/ +- int my_rank = IssmComm::GetRank(); +- int numberofsegments = -1; +- IssmDouble* vx = NULL; //itapopo this is not being used +- IssmDouble* vy = NULL; //itapopo this is not being used +- IssmDouble* x = NULL; +- IssmDouble* y = NULL; +- IssmDouble* z = NULL; +- int* elementslist = NULL; +- int* segments = NULL; +- IssmDouble* masklevelset = NULL; +- IssmDouble* pelementerror = NULL; +- const int elementswidth = this->GetElementsWidth();//just 2D mesh, tria elements +- +- /*Solutions which will be used to refine the elements*/ +- this->GetGroundediceLevelSet(&masklevelset);//itapopo verificar se já existe um método igual a esse ++void FemModel::WriteMeshInResults(void){/*{{{*/ + +- //Compute the ZZ error estimator per element +- this->ZZErrorEstimator(&pelementerror); +- +- _printf0_("P Element error\n"); +- for(int i=0;ielements->NumberOfElements();i++) _printf0_(""<amr->ExecuteRefinement(type_process,vx,vy,masklevelset, +- numberofvertices,numberofelements,numberofsegments,&x,&y,&z,&elementslist,&segments); +- if(numberofvertices<=0 || numberofelements<=0 /*|| newnumberofsegments<=0*/) _error_("Error in the refinement process."); +- } +- else{ +- x=xNew(numberofvertices); +- y=xNew(numberofvertices); +- z=xNew(numberofvertices); +- elementslist=xNew(numberofelements*this->GetElementsWidth()); +- } ++ if(!this->elements || !this->vertices || !this->results || !this->parameters) return; ++ ++ parameters->FindParam(&step,StepEnum); ++ parameters->FindParam(&time,TimeEnum); ++ numberofelements=this->elements->NumberOfElements(); ++ numberofvertices=this->vertices->NumberOfVertices(); + +- /*Send new mesh to others CPU*/ +- ISSM_MPI_Bcast(&numberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(&numberofelements,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(x,numberofvertices,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(y,numberofvertices,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(z,numberofvertices,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(elementslist,numberofelements*this->GetElementsWidth(),ISSM_MPI_INT,0,IssmComm::GetComm()); ++ /*Get mesh. Elementslist comes in Matlab indexing*/ ++ this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elementslist); + +- /*Assign the pointers*/ +- (*pelementslist) = elementslist; //Matlab indexing +- (*px) = x; +- (*py) = y; +- (*pz) = z; ++ /*Write mesh in Results*/ ++ printf("-------------- file: FemModel.cpp line: %i\n",__LINE__); ++ this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshElementsEnum, ++ elementslist,numberofelements,this->GetElementsWidth(),step,time)); + ++ this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshXEnum, ++ x,numberofvertices,1,step,time)); ++ ++ this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshYEnum, ++ y,numberofvertices,1,step,time)); ++ ++ //itapopo ++ #ifdef _HAVE_NEOPZ_ ++ if(IssmComm::GetRank()==0){ ++ TPZFileStream fstr; ++ std::stringstream ss; ++ int frictionlaw,levelmax; ++ this->parameters->FindParam(&frictionlaw,FrictionLawEnum); ++ this->parameters->FindParam(&levelmax,AmrLevelMaxEnum); ++ ss << levelmax; ++ if(frictionlaw==1){ ++ ss << "_viscous/amr.txt"; ++ }else if(frictionlaw==7){ ++ ss << "_tsai/amr.txt"; ++ }else{ ++ _error_("friction law not supported here."); ++ } ++ std::string AMRfile = "/home/santos/Misomip2/L" + ss.str(); ++ fstr.OpenWrite(AMRfile.c_str()); ++ int withclassid = 1; ++ this->amr->Write(fstr,withclassid); ++ } ++ #endif ++ //itapopo ++ + /*Cleanup*/ +- if(segments) xDelete(segments); +- xDelete(masklevelset); +- xDelete(pelementerror); +- ++ xDelete(x); ++ xDelete(y); ++ xDelete(z); ++ xDelete(elementslist); + } + /*}}}*/ + void FemModel::GetGroundediceLevelSet(IssmDouble **pmasklevelset){/*{{{*/ +@@ -3634,8 +2792,8 @@ + int* connectivity=NULL; + connectivity=xNewZeroInit(newnumberofvertices); + +- for (int i=0;i0 && vertexid-1(this->materials->GetObjectByOffset(this->materials->Size()-1)->copy()); + newmatpar->SetMid(newnumberofelements+1); + materials->AddObject(newmatpar);//put it at the end of the materials +- + } + /*}}}*/ + void FemModel::CreateNodes(int newnumberofvertices,int* my_vertices,int nodecounter,int analysis_enum,Nodes* nodes){/*{{{*/ +@@ -3953,7 +3110,6 @@ + delete vspcvy; + delete vspcvxflag; + delete vspcvyflag; +- + } + /*}}}*/ + void FemModel::UpdateElements(int newnumberofelements,int* newelementslist,bool* my_elements,int nodecounter,int analysis_counter,Elements* newelements){/*{{{*/ +@@ -4052,7 +3208,6 @@ + xDelete(epart); + xDelete(npart); + xDelete(index); +- + } + /*}}}*/ + void FemModel::SmoothedDeviatoricStressTensor(IssmDouble** ptauxx,IssmDouble** ptauyy,IssmDouble** ptauxy){/*{{{*/ +@@ -4140,7 +3295,6 @@ + xDelete(deviatoricstressxy); + xDelete(totalweight); + xDelete(elem_vertices); +- + } + /*}}}*/ + void FemModel::ZZErrorEstimator(IssmDouble** pelementerror){/*{{{*/ +@@ -4214,7 +3368,965 @@ + xDelete(basis); + xDelete(elem_vertices); + delete velementerror; ++} ++/*}}}*/ + ++#ifdef _HAVE_DAKOTA_ ++void FemModel::DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses){/*{{{*/ ++ ++ int i,j; ++ int my_rank; ++ ++ /*intermediary: */ ++ char root[50]; ++ int index; ++ int npart; ++ double femmodel_response; ++ int flag; ++ double *vertex_response = NULL; ++ double *qmu_response = NULL; ++ double *responses_pointer = NULL; ++ ++ /*retrieve npart: */ ++ parameters->FindParam(&npart,QmuNumberofpartitionsEnum); ++ my_rank=IssmComm::GetRank(); ++ ++ /*save the d_responses pointer: */ ++ responses_pointer=d_responses; ++ ++ //watch out, we have more d_numresponses than numresponsedescriptors, because the responses have been expanded if they were scaled. ++ //because we don't know the d_responses descriptors (the scaled ones) we can't key off them, so we will key off the responses_descriptors: */ ++ ++ for(i=0;i(vertex_response); ++ xDelete(qmu_response); ++ ++ } ++ else if (flag==IndexedEnum){ ++ ++ /*indexed response: plug index into parameters and call response module: */ ++ parameters->SetParam(index,IndexEnum); ++ ++ this->Responsex(&femmodel_response,root); ++ ++ if(my_rank==0){ ++ /*plug response: */ ++ responses_pointer[0]=femmodel_response; ++ ++ /*increment response_pointer :*/ ++ responses_pointer++; ++ } ++ } ++ else if (flag==NodalEnum){ ++ _error_("nodal response functions not supported yet!"); ++ ++ /*increment response_pointer :*/ ++ responses_pointer++; ++ } ++ else if (flag==RegularEnum){ ++ ++ /*perfectly normal response function: */ ++ this->Responsex(&femmodel_response,root); ++ ++ if(my_rank==0){ ++ /*plug response: */ ++ responses_pointer[0]=femmodel_response; ++ ++ /*increment response_pointer :*/ ++ responses_pointer++; ++ } ++ } ++ else _error_("flag type " << flag << " not supported yet for response analysis"); ++ } ++ ++ /*Synthesize echo: {{{*/ ++ if(my_rank==0){ ++ _printf_(" responses: " << d_numresponses << ": "); ++ for(i=0;i* wg,Vector* dwgdt, IssmDouble* x, IssmDouble* y){ /*{{{*/ ++ ++ /*Go through elements, and add contribution from each element to the deflection vector wg:*/ ++ for(int i=0;iSize();i++){ ++ Element* element=xDynamicCast(elements->GetObjectByOffset(i)); ++ element->GiaDeflection(wg,dwgdt, x,y); ++ } ++} ++/*}}}*/ ++#endif ++#ifdef _HAVE_ESA_ ++void FemModel::EsaGeodetic2D(Vector* pUp, Vector* pNorth, Vector* pEast, IssmDouble* xx, IssmDouble* yy){/*{{{*/ ++ ++ int ns,nsmax; ++ ++ /*Go through elements, and add contribution from each element to the deflection vector wg:*/ ++ ns = elements->Size(); ++ ++ /*Figure out max of ns: */ ++ ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ++ /*Call the esa geodetic core: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ element->EsaGeodetic2D(pUp,pNorth,pEast,xx,yy); ++ } ++ if(i%100==0){ ++ pUp->Assemble(); ++ pNorth->Assemble(); ++ pEast->Assemble(); ++ } ++ } ++ ++ /*One last time: */ ++ pUp->Assemble(); ++ pNorth->Assemble(); ++ pEast->Assemble(); ++ ++ /*Free ressources:*/ ++ xDelete(xx); ++ xDelete(yy); ++} ++/*}}}*/ ++void FemModel::EsaGeodetic3D(Vector* pUp, Vector* pNorth, Vector* pEast, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius, IssmDouble* xx, IssmDouble* yy, IssmDouble* zz){/*{{{*/ ++ ++ IssmDouble eartharea=0; ++ IssmDouble eartharea_cpu=0; ++ ++ int ns,nsmax; ++ ++ /*Go through elements, and add contribution from each element to the deflection vector wg:*/ ++ ns = elements->Size(); ++ ++ /*First, figure out the surface area of Earth: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ eartharea_cpu += element->GetAreaSpherical(); ++ } ++ ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ++ /*Figure out max of ns: */ ++ ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ++ /*Call the esa geodetic core: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ element->EsaGeodetic3D(pUp,pNorth,pEast,latitude,longitude,radius,xx,yy,zz,eartharea); ++ } ++ if(i%100==0){ ++ pUp->Assemble(); ++ pNorth->Assemble(); ++ pEast->Assemble(); ++ } ++ } ++ ++ /*One last time: */ ++ pUp->Assemble(); ++ pNorth->Assemble(); ++ pEast->Assemble(); ++ ++ /*Free ressources:*/ ++ xDelete(latitude); ++ xDelete(longitude); ++ xDelete(radius); ++ xDelete(xx); ++ xDelete(yy); ++ xDelete(zz); ++} ++/*}}}*/ ++#endif ++#ifdef _HAVE_SEALEVELRISE_ ++void FemModel::SealevelriseEustatic(Vector* pSgi, IssmDouble* peustatic, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius) { /*{{{*/ ++ ++ /*serialized vectors:*/ ++ IssmDouble eustatic = 0.; ++ IssmDouble eustatic_cpu = 0.; ++ IssmDouble eustatic_cpu_e = 0.; ++ IssmDouble oceanarea = 0.; ++ IssmDouble oceanarea_cpu = 0.; ++ IssmDouble eartharea = 0.; ++ IssmDouble eartharea_cpu = 0.; ++ int ns,nsmax; ++ ++ /*Go through elements, and add contribution from each element to the deflection vector wg:*/ ++ ns = elements->Size(); ++ ++ /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ oceanarea_cpu += element->OceanArea(); ++ eartharea_cpu += element->GetAreaSpherical(); ++ } ++ ISSM_MPI_Reduce (&oceanarea_cpu,&oceanarea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&oceanarea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ _assert_(oceanarea>0.); ++ ++ ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ++ /*Figure out max of ns: */ ++ ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ++ /*Call the sea level rise core: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ element->SealevelriseEustatic(pSgi,&eustatic_cpu_e,latitude,longitude,radius,oceanarea,eartharea); ++ eustatic_cpu+=eustatic_cpu_e; ++ } ++ if(i%100==0)pSgi->Assemble(); ++ } ++ if(VerboseConvergence())_printf0_("\n"); ++ ++ /*One last time: */ ++ pSgi->Assemble(); ++ ++ /*Sum all eustatic components from all cpus:*/ ++ ISSM_MPI_Reduce (&eustatic_cpu,&eustatic,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&eustatic,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ _assert_(!xIsNan(eustatic)); ++ ++ /*Assign output pointers:*/ ++ *peustatic=eustatic; ++ ++} ++/*}}}*/ ++void FemModel::SealevelriseNonEustatic(Vector* pSgo, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius, bool verboseconvolution){/*{{{*/ ++ ++ /*serialized vectors:*/ ++ IssmDouble* Sg_old=NULL; ++ ++ IssmDouble eartharea=0; ++ IssmDouble eartharea_cpu=0; ++ ++ int ns,nsmax; ++ ++ /*Serialize vectors from previous iteration:*/ ++ Sg_old=pSg_old->ToMPISerial(); ++ ++ /*Go through elements, and add contribution from each element to the deflection vector wg:*/ ++ ns = elements->Size(); ++ ++ /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ eartharea_cpu += element->GetAreaSpherical(); ++ } ++ ++ ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ++ /*Figure out max of ns: */ ++ ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ++ /*Call the sea level rise core: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ element->SealevelriseNonEustatic(pSgo,Sg_old,latitude,longitude,radius,eartharea); ++ } ++ if(i%100==0)pSgo->Assemble(); ++ } ++ if(verboseconvolution)if(VerboseConvergence())_printf_("\n"); ++ ++ /*Free ressources:*/ ++ xDelete(Sg_old); ++} ++/*}}}*/ ++void FemModel::SealevelriseRotationalFeedback(Vector* pSgo_rot, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius){/*{{{*/ ++ ++ /*serialized vectors:*/ ++ IssmDouble* Sg_old=NULL; ++ IssmDouble eartharea=0; ++ IssmDouble eartharea_cpu=0; ++ IssmDouble tide_love_h, tide_love_k, fluid_love, moi_e, moi_p, omega, g; ++ IssmDouble load_love_k2 = -0.30922675; //degree 2 load Love number ++ IssmDouble m1, m2, m3; ++ IssmDouble lati, longi, radi, value; ++ ++ /*Serialize vectors from previous iteration:*/ ++ Sg_old=pSg_old->ToMPISerial(); ++ ++ /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ ++ for(int i=0;iSize();i++){ ++ Element* element=xDynamicCast(elements->GetObjectByOffset(i)); ++ eartharea_cpu += element->GetAreaSpherical(); ++ } ++ ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ++ IssmDouble moi_list[3]={0,0,0}; ++ IssmDouble moi_list_cpu[3]={0,0,0}; ++ for(int i=0;iSize();i++){ ++ Element* element=xDynamicCast(elements->GetObjectByOffset(i)); ++ element->SealevelriseMomentOfInertia(&moi_list[0],Sg_old,eartharea); ++ moi_list_cpu[0] += moi_list[0]; ++ moi_list_cpu[1] += moi_list[1]; ++ moi_list_cpu[2] += moi_list[2]; ++ } ++ ISSM_MPI_Reduce (&moi_list_cpu[0],&moi_list[0],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&moi_list[0],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ // ++ ISSM_MPI_Reduce (&moi_list_cpu[1],&moi_list[1],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&moi_list[1],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ // ++ ISSM_MPI_Reduce (&moi_list_cpu[2],&moi_list[2],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&moi_list[2],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ++ /*pull out some useful parameters: */ ++ parameters->FindParam(&tide_love_h,SealevelriseTidalLoveHEnum); ++ parameters->FindParam(&tide_love_k,SealevelriseTidalLoveKEnum); ++ parameters->FindParam(&fluid_love,SealevelriseFluidLoveEnum); ++ parameters->FindParam(&moi_e,SealevelriseEquatorialMoiEnum); ++ parameters->FindParam(&moi_p,SealevelrisePolarMoiEnum); ++ parameters->FindParam(&omega,SealevelriseAngularVelocityEnum); ++ ++ /*compute perturbation terms for angular velocity vector: */ ++ m1 = 1/(1-tide_love_k/fluid_love) * (1+load_love_k2)/(moi_p-moi_e) * moi_list[0]; ++ m2 = 1/(1-tide_love_k/fluid_love) * (1+load_love_k2)/(moi_p-moi_e) * moi_list[1]; ++ m3 = -(1+load_love_k2)/moi_p * moi_list[2]; // term associated with fluid number (3-order-of-magnitude smaller) is negelected ++ ++ /* Green's function (1+k_2-h_2/g): checked against Glenn Milne's thesis Chapter 3 (eqs: 3.3-4, 3.10-11) ++ * Perturbation terms for angular velocity vector (m1, m2, m3): checked against Mitrovica (2005 Appendix) & Jensen et al (2013 Appendix A3) ++ * Sea level rotational feedback: checked against GMD eqs 8-9 (only first order terms, i.e., degree 2 order 0 & 1 considered) ++ * all DONE in Geographic coordinates: theta \in [-90,90], lambda \in [-180 180] ++ */ ++ for(int i=0;iSize();i++){ ++ int sid; ++ //Vertex* vertex=(Vertex*)vertices->GetObjectByOffset(i); ++ Vertex* vertex=xDynamicCast(vertices->GetObjectByOffset(i)); ++ sid=vertex->Sid(); ++ ++ lati=latitude[sid]/180*PI; longi=longitude[sid]/180*PI; radi=radius[sid]; ++ ++ /*only first order terms are considered now: */ ++ value=((1.0+tide_love_k-tide_love_h)/9.81)*pow(omega*radi,2.0)* ++ (-m3/6.0 + 0.5*m3*cos(2.0*lati) - 0.5*sin(2.*lati)*(m1*cos(longi)+m2*sin(longi))); ++ ++ pSgo_rot->SetValue(sid,value,INS_VAL); //INS_VAL ensures that you don't add several times ++ } ++ ++ /*Assemble mesh velocity*/ ++ pSgo_rot->Assemble(); ++ ++ /*Free ressources:*/ ++ xDelete(Sg_old); ++ ++} ++/*}}}*/ ++void FemModel::SealevelriseGeodetic(Vector* pUp, Vector* pNorth, Vector* pEast, Vector* pSg, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius, IssmDouble* xx, IssmDouble* yy, IssmDouble* zz){/*{{{*/ ++ ++ /*serialized vectors:*/ ++ IssmDouble* Sg=NULL; ++ ++ IssmDouble eartharea=0; ++ IssmDouble eartharea_cpu=0; ++ ++ int ns,nsmax; ++ ++ /*Serialize vectors from previous iteration:*/ ++ Sg=pSg->ToMPISerial(); ++ ++ /*Go through elements, and add contribution from each element to the deflection vector wg:*/ ++ ns = elements->Size(); ++ ++ /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ eartharea_cpu += element->GetAreaSpherical(); ++ } ++ ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ++ /*Figure out max of ns: */ ++ ISSM_MPI_Reduce(&ns,&nsmax,1,ISSM_MPI_INT,ISSM_MPI_MAX,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&nsmax,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ++ /*Call the sea level rise core: */ ++ for(int i=0;i(elements->GetObjectByOffset(i)); ++ element->SealevelriseGeodetic(pUp,pNorth,pEast,Sg,latitude,longitude,radius,xx,yy,zz,eartharea); ++ } ++ if(i%100==0){ ++ pUp->Assemble(); ++ pNorth->Assemble(); ++ pEast->Assemble(); ++ } ++ } ++ ++ /*One last time: */ ++ pUp->Assemble(); ++ pNorth->Assemble(); ++ pEast->Assemble(); ++ ++ /*Free ressources:*/ ++ xDelete(Sg); ++ xDelete(latitude); ++ xDelete(longitude); ++ xDelete(radius); ++ xDelete(xx); ++ xDelete(yy); ++ xDelete(zz); ++} ++/*}}}*/ ++IssmDouble FemModel::SealevelriseOceanAverage(Vector* Sg) { /*{{{*/ ++ ++ IssmDouble* Sg_serial=NULL; ++ IssmDouble oceanvalue,oceanvalue_cpu; ++ IssmDouble oceanarea,oceanarea_cpu; ++ ++ /*Serialize vectors from previous iteration:*/ ++ Sg_serial=Sg->ToMPISerial(); ++ ++ /*Initialize:*/ ++ oceanvalue_cpu=0; ++ oceanarea_cpu=0; ++ ++ /*Go through elements, and add contribution from each element and divide by overall ocean area:*/ ++ for(int i=0;iSize();i++){ ++ Element* element=xDynamicCast(elements->GetObjectByOffset(i)); ++ oceanarea_cpu += element->OceanArea(); ++ oceanvalue_cpu += element->OceanAverage(Sg_serial); ++ } ++ ISSM_MPI_Reduce (&oceanarea_cpu,&oceanarea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&oceanarea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ++ ISSM_MPI_Reduce (&oceanvalue_cpu,&oceanvalue,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&oceanvalue,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ++ /*Free ressources:*/ ++ xDelete(Sg_serial); ++ ++ return oceanvalue/oceanarea; ++} ++/*}}}*/ ++#endif ++void FemModel::HydrologyEPLupdateDomainx(IssmDouble* pEplcount){ /*{{{*/ ++ ++ Vector* mask = NULL; ++ Vector* recurence = NULL; ++ Vector* active = NULL; ++ IssmDouble* serial_mask = NULL; ++ IssmDouble* serial_rec = NULL; ++ IssmDouble* serial_active = NULL; ++ IssmDouble* old_active = NULL; ++ int* eplzigzag_counter = NULL; ++ int eplflip_lock; ++ ++ HydrologyDCEfficientAnalysis* effanalysis = new HydrologyDCEfficientAnalysis(); ++ HydrologyDCInefficientAnalysis* inefanalysis = new HydrologyDCInefficientAnalysis(); ++ ++ /*Step 1: update mask, the mask might be extended by residual and/or using downstream sediment head*/ ++ mask=new Vector(this->nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum)); ++ recurence=new Vector(this->nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum)); ++ this->parameters->FindParam(&eplzigzag_counter,NULL,EplZigZagCounterEnum); ++ this->parameters->FindParam(&eplflip_lock,HydrologydcEplflipLockEnum); ++ GetVectorFromInputsx(&old_active,this,HydrologydcMaskEplactiveNodeEnum,NodeSIdEnum); ++ ++ for (int i=0;iSize();i++){ ++ Element* element=xDynamicCast(elements->GetObjectByOffset(i)); ++ effanalysis->HydrologyEPLGetMask(mask,recurence,eplzigzag_counter,element); ++ } ++ /*check for changes and increment zigzag counter, change the mask if necessary*/ ++ recurence->Assemble(); ++ serial_rec=recurence->ToMPISerial(); ++ for (int i=0;iSize();i++){ ++ Node* node=xDynamicCast(nodes->GetObjectByOffset(i)); ++ if(serial_rec[node->Sid()]==1.)eplzigzag_counter[node->Lid()] ++; ++ if(eplzigzag_counter[node->Lid()]>eplflip_lock & eplflip_lock!=0){ ++ mask->SetValue(node->Sid(),old_active[node->Sid()],INS_VAL); ++ } ++ } ++ this->parameters->SetParam(eplzigzag_counter,this->nodes->Size(),EplZigZagCounterEnum); ++ /*Assemble and serialize*/ ++ mask->Assemble(); ++ serial_mask=mask->ToMPISerial(); ++ ++ xDelete(eplzigzag_counter); ++ xDelete(serial_rec); ++ xDelete(old_active); ++ delete mask; ++ delete recurence; ++ ++ /*Update Mask*/ ++ InputUpdateFromVectorx(this,serial_mask,HydrologydcMaskEplactiveNodeEnum,NodeSIdEnum); ++ xDelete(serial_mask); ++ inefanalysis->ElementizeEplMask(this); ++ /*Step 2: update node activity. If one element is connected to mask=1, all nodes are active*/ ++ active=new Vector(nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum)); ++ for (int i=0;iSize();i++){ ++ Element* element=xDynamicCast(elements->GetObjectByOffset(i)); ++ effanalysis->HydrologyEPLGetActive(active,element); ++ } ++ ++ /*Assemble and serialize*/ ++ active->Assemble(); ++ serial_active=active->ToMPISerial(); ++ delete active; ++ ++ /*Update node activation accordingly*/ ++ int counter =0; ++ for (int i=0;iSize();i++){ ++ Node* node=xDynamicCast(nodes->GetObjectByOffset(i)); ++ if(node->InAnalysis(HydrologyDCEfficientAnalysisEnum)){ ++ if(serial_active[node->Sid()]==1.){ ++ node->Activate(); ++ if(!node->IsClone()) counter++; ++ } ++ else{ ++ node->Deactivate(); ++ } ++ } ++ } ++ xDelete(serial_active); ++ delete effanalysis; ++ delete inefanalysis; ++ int sum_counter; ++ ISSM_MPI_Reduce(&counter,&sum_counter,1,ISSM_MPI_INT,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&sum_counter,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ counter=sum_counter; ++ *pEplcount = counter; ++ if(VerboseSolution()) _printf0_(" Number of active nodes in EPL layer: "<< counter <<"\n"); ++ ++ /*Update dof indexings*/ ++ this->UpdateConstraintsx(); ++ ++} ++/*}}}*/ ++void FemModel::UpdateConstraintsL2ProjectionEPLx(IssmDouble* pL2count){ /*{{{*/ ++ ++ Vector* active = NULL; ++ IssmDouble* serial_active = NULL; ++ HydrologyDCEfficientAnalysis* effanalysis = new HydrologyDCEfficientAnalysis(); ++ ++ /*update node activity. If one element is connected to mask=1, all nodes are active*/ ++ active=new Vector(nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum)); ++ for (int i=0;iSize();i++){ ++ Element* element=xDynamicCast(elements->GetObjectByOffset(i)); ++ effanalysis->HydrologyEPLGetActive(active,element); ++ } ++ ++ /*Assemble and serialize*/ ++ active->Assemble(); ++ serial_active=active->ToMPISerial(); ++ delete active; ++ delete effanalysis; ++ ++ /*Update node activation accordingly*/ ++ int counter =0; ++ for (int i=0;iSize();i++){ ++ Node* node=xDynamicCast(nodes->GetObjectByOffset(i)); ++ if(node->InAnalysis(L2ProjectionEPLAnalysisEnum)){ ++ if(serial_active[node->Sid()]==1.){ ++ node->Activate(); ++ if(!node->IsClone()) counter++; ++ } ++ else{ ++ node->Deactivate(); ++ } ++ } ++ } ++ xDelete(serial_active); ++ int sum_counter; ++ ISSM_MPI_Reduce(&counter,&sum_counter,1,ISSM_MPI_INT,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ++ ISSM_MPI_Bcast(&sum_counter,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ counter=sum_counter; ++ *pL2count = counter; ++ if(VerboseSolution()) _printf0_(" Number of active nodes L2 Projection: "<< counter <<"\n"); ++} ++/*}}}*/ ++#ifdef _HAVE_JAVASCRIPT_ ++FemModel::FemModel(IssmDouble* buffer, int buffersize, char* toolkits, char* solution, char* modelname,ISSM_MPI_Comm incomm, bool trace){ /*{{{*/ ++ /*configuration: */ ++ int solution_type; ++ int ierr; ++ ++ /*First things first, store the communicator, and set it as a global variable: */ ++ IssmComm::SetComm(incomm); ++ ++ /*Start profiler: */ ++ this->profiler=new Profiler(); ++ profiler->Tag(START); ++ ++ /*From command line arguments, retrieve different filenames needed to create the FemModel: */ ++ solution_type=StringToEnumx(solution); ++ ++ /*Create femmodel from input files: */ ++ profiler->Tag(STARTINIT); ++ this->InitFromBuffers((char*)buffer,buffersize,toolkits, solution_type,trace,NULL); ++ profiler->Tag(FINISHINIT); ++ ++ /*Save communicator in the parameters dataset: */ ++ this->parameters->AddObject(new GenericParam(incomm,FemModelCommEnum)); ++ ++} ++/*}}}*/ ++void FemModel::CleanUpJs(char** poutput, size_t* psize){/*{{{*/ ++ ++ /*Intermediary*/ ++ FILE *output_fid; ++ GenericParam* outputbufferparam=NULL; ++ GenericParam* outputbuffersizeparam=NULL; ++ char** poutputbuffer; ++ size_t* poutputbuffersize; ++ ++ ++ /*Before we delete the profiler, report statistics for this run: */ ++ profiler->Tag(FINISH); //final tagging ++ _printf0_("\n"); ++ _printf0_(" "<DeltaTime(STARTINIT,FINISHINIT) << "\n"); ++ _printf0_(" "<DeltaTime(STARTCORE,FINISHCORE) << "\n"); ++ _printf0_("\n"); ++ _printf0_(" Total elapsed time: " ++ <DeltaTimeModHour(START,FINISH)<<" hrs " ++ <DeltaTimeModMin(START,FINISH)<<" min " ++ <DeltaTimeModSec(START,FINISH)<<" sec" ++ ); ++ _printf0_("\n"); ++ ++ /*Before we close the output file, recover the buffer and size:*/ ++ outputbufferparam = xDynamicCast*>(this->parameters->FindParamObject(OutputBufferPointerEnum)); ++ poutputbuffer=outputbufferparam->GetParameterValue(); ++ outputbuffersizeparam = xDynamicCast*>(this->parameters->FindParamObject(OutputBufferSizePointerEnum)); ++ poutputbuffersize=outputbuffersizeparam->GetParameterValue(); ++ ++ /*Assign output values: */ ++ *poutput=*poutputbuffer; ++ *psize=*poutputbuffersize; ++} ++/*}}}*/ ++void FemModel::InitFromBuffers(char* buffer, int buffersize, char* toolkits, int in_solution_type, bool trace, IssmPDouble* X){/*{{{*/ ++ ++ /*intermediary*/ ++ FILE *IOMODEL = NULL; ++ FILE *toolkitsoptionsfid = NULL; ++ FILE *output_fid = NULL; ++ int my_rank; ++ size_t outputsize; ++ char *outputbuffer; ++ const char *rootpath = ""; //needed for Dakota runs only, which we won't do here. ++ ++ /*recover my_rank:*/ ++ my_rank=IssmComm::GetRank(); ++ ++ /*Open input file descriptor on cpu 0: */ ++ if(my_rank==0) IOMODEL = fmemopen((void*)buffer, buffersize, "rb"); ++ ++ /*Open toolkits file descriptor: */ ++ toolkitsoptionsfid=fmemopen((void*)toolkits, strlen(toolkits)+1, "r"); ++ ++ /*Now, go create FemModel:*/ ++ this->InitFromFids((char*)rootpath,IOMODEL,toolkitsoptionsfid,in_solution_type,trace,X); ++ ++ /*Close input file and toolkits file descriptors: */ ++ if(my_rank==0) fclose(IOMODEL); ++ fclose(toolkitsoptionsfid); ++ ++ /*Open output file once for all and add output file descriptor to parameters*/ ++ output_fid=open_memstream(&outputbuffer,&outputsize); ++ if(output_fid==NULL)_error_("could not initialize output stream"); ++ this->parameters->SetParam(output_fid,OutputFilePointerEnum); ++ this->parameters->AddObject(new GenericParam(&outputbuffer,OutputBufferPointerEnum)); ++ this->parameters->AddObject(new GenericParam(&outputsize,OutputBufferSizePointerEnum)); ++ ++}/*}}}*/ ++#endif ++ ++#ifdef _HAVE_BAMG_ ++void FemModel::ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist){/*{{{*/ ++ ++ /*Output*/ ++ IssmDouble *newx = NULL; ++ IssmDouble *newy = NULL; ++ IssmDouble *newz = NULL; ++ int *newelementslist = NULL; ++ int newnumberofvertices = -1; ++ int newnumberofelements = -1; ++ ++ /*Get Rank*/ ++ int my_rank = IssmComm::GetRank(); ++ ++ if(my_rank==0){ ++ this->amrbamg->ExecuteRefinementBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); ++ if(newnumberofvertices<=0 || newnumberofelements<=0) _error_("Error in the refinement process."); ++ } ++ else{ ++ newx=xNew(newnumberofvertices); ++ newy=xNew(newnumberofvertices); ++ newz=xNew(newnumberofvertices); ++ newelementslist=xNew(newnumberofelements*this->GetElementsWidth()); ++ } ++ ++ /*Send new mesh to others CPU*/ ++ ISSM_MPI_Bcast(&newnumberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&newnumberofelements,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(newx,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(newy,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(newz,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(newelementslist,newnumberofelements*this->GetElementsWidth(),ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ++ /*Assign output pointers*/ ++ *pnewnumberofvertices = newnumberofvertices; ++ *pnewnumberofelements = newnumberofelements; ++ *pnewx = newx; ++ *pnewy = newy; ++ *pnewz = newz; ++ *pnewelementslist = newelementslist; ++} ++/*}}}*/ ++void FemModel::InitializeAdaptiveRefinementBamg(void){/*{{{*/ ++ ++ /*Define variables*/ ++ int numberofvertices = this->vertices->NumberOfVertices(); ++ int numberofelements = this->elements->NumberOfElements(); ++ int numberofsegments = 0; //used on matlab ++ IssmDouble* x = NULL; ++ IssmDouble* y = NULL; ++ IssmDouble* z = NULL; ++ int* elements = NULL; ++ int elementswidth = this->GetElementsWidth(); //just tria elements in this version. Itapopo: ++ IssmDouble hmin,hmax,err; ++ int fieldenum; ++ ++ /*Get rank*/ ++ int my_rank = IssmComm::GetRank(); ++ ++ /*Initialize field as NULL for now*/ ++ this->amrbamg = NULL; ++ ++ /*Get vertices coordinates of the coarse mesh (father mesh)*/ ++ this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elements); ++ ++ /*Get amr parameters*/ ++ this->parameters->FindParam(&hmin,AmrHminEnum); ++ this->parameters->FindParam(&hmax,AmrHmaxEnum); ++ this->parameters->FindParam(&fieldenum,AmrFieldEnum); ++ this->parameters->FindParam(&err,AmrErrEnum); ++ ++ /*Create bamg data structures for bamg (only cpu 0)*/ ++ if(my_rank==0){ ++ /*Re-create original mesh and put it in bamg structure*/ ++ this->amrbamg = new AmrBamg(hmin,hmax); ++ this->amrbamg->Initialize(elements,x,y,numberofvertices,numberofelements); ++ } ++ ++ /*Free the vectors*/ ++ xDelete(x); ++ xDelete(y); ++ xDelete(z); ++ xDelete(elements); ++} ++/*}}}*/ ++#endif ++ ++#ifdef _HAVE_NEOPZ_ ++void FemModel::ReMeshNeopz(int* pnumberofvertices,int* pnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ ++ ++ /*elements is in Matlab indexing*/ ++ int my_rank = IssmComm::GetRank(); ++ int numberofsegments = -1; ++ int numberofvertices,numberofelements; ++ IssmDouble* vx = NULL; //itapopo this is not being used ++ IssmDouble* vy = NULL; //itapopo this is not being used ++ IssmDouble* x = NULL; ++ IssmDouble* y = NULL; ++ IssmDouble* z = NULL; ++ int* elementslist = NULL; ++ int* segments = NULL; ++ IssmDouble* masklevelset = NULL; ++ IssmDouble* pelementerror = NULL; ++ const int elementswidth = this->GetElementsWidth();//just 2D mesh, tria elements ++ ++ /*Solutions which will be used to refine the elements*/ ++ this->GetGroundediceLevelSet(&masklevelset);//itapopo verificar se já existe um método igual a esse ++ ++ //Compute the ZZ error estimator per element ++ this->ZZErrorEstimator(&pelementerror); ++ ++ _printf0_("P Element error\n"); ++ for(int i=0;ielements->NumberOfElements();i++) _printf0_(""<amr->ExecuteRefinement(type_process,vx,vy,masklevelset, ++ numberofvertices,numberofelements,numberofsegments,&x,&y,&z,&elementslist,&segments); ++ if(numberofvertices<=0 || numberofelements<=0 /*|| newnumberofsegments<=0*/) _error_("Error in the refinement process."); ++ } ++ else{ ++ x=xNew(numberofvertices); ++ y=xNew(numberofvertices); ++ z=xNew(numberofvertices); ++ elementslist=xNew(numberofelements*this->GetElementsWidth()); ++ } ++ ++ /*Send new mesh to others CPU*/ ++ ISSM_MPI_Bcast(&numberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&numberofelements,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(x,numberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(y,numberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(z,numberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(elementslist,numberofelements*this->GetElementsWidth(),ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ++ /*Assign the pointers*/ ++ (*pelementslist) = elementslist; //Matlab indexing ++ (*px) = x; ++ (*py) = y; ++ (*pz) = z; ++ *pnumberofelements = numberofelements; ++ *pnumberofvertices = numberofvertices; ++ ++ /*Cleanup*/ ++ if(segments) xDelete(segments); ++ xDelete(masklevelset); ++ xDelete(pelementerror); ++ ++} ++/*}}}*/ ++void FemModel::InitializeAdaptiveRefinementNeopz(void){/*{{{*/ ++ ++ /*Define variables*/ ++ int my_rank = IssmComm::GetRank(); ++ int numberofvertices = this->vertices->NumberOfVertices(); ++ int numberofelements = this->elements->NumberOfElements(); ++ int numberofsegments = 0; //used on matlab ++ IssmDouble* x = NULL; ++ IssmDouble* y = NULL; ++ IssmDouble* z = NULL; ++ int* elements = NULL; ++ int elementswidth = this->GetElementsWidth(); //just tria elements in this version. Itapopo: ++ int levelmax = 0; ++ IssmDouble regionlevel1 = 0.; ++ IssmDouble regionlevelmax = 0.; ++ ++ /*Initialize field as NULL for now*/ ++ this->amr = NULL; ++ ++ /*Get vertices coordinates of the coarse mesh (father mesh)*/ ++ /*elements comes in Matlab indexing*/ ++ this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elements); ++ ++ /*Get amr parameters*/ ++ this->parameters->FindParam(&levelmax,AmrLevelMaxEnum); ++ this->parameters->FindParam(®ionlevel1,AmrRegionLevel1Enum); ++ this->parameters->FindParam(®ionlevelmax,AmrRegionLevelMaxEnum); ++ ++ /*Create initial mesh (coarse mesh) in neopz data structure*/ ++ /*Just CPU #0 should keep AMR object*/ ++ this->SetRefPatterns(); ++ if(my_rank==0){ ++ bool ismisomip = false; ++ if(ismisomip){//itapopo ++ TPZFileStream fstr; ++ std::stringstream ss; ++ int frictionlaw; ++ ++ this->parameters->FindParam(&frictionlaw,FrictionLawEnum); ++ ++ ss << levelmax; ++ if(frictionlaw==1){ ++ ss << "_viscous/amr.txt"; ++ }else if(frictionlaw==7){ ++ ss << "_tsai/amr.txt"; ++ }else{ ++ _error_("friction law not supported here."); ++ } ++ ++ std::string AMRfile = "/home/santos/Misomip2/L" + ss.str(); ++ fstr.OpenRead(AMRfile.c_str()); ++ ++ TPZSaveable *sv = TPZSaveable::Restore(fstr,0); ++ this->amr = dynamic_cast(sv); ++ } ++ else{ ++ this->amr = new AdaptiveMeshRefinement(); ++ //this->amr->SetLevelMax(levelmax); //Set max level of refinement ++ //this->amr->SetRegions(regionlevel1,regionlevelmax); ++ this->amr->CreateInitialMesh(numberofvertices,numberofelements,numberofsegments,elementswidth,x,y,z,elements,NULL); ++ } ++ this->amr->SetLevelMax(levelmax); //Set max level of refinement ++ this->amr->SetRegions(regionlevel1,regionlevelmax); ++ } ++ ++ /*Free the vectors*/ ++ xDelete(x); ++ xDelete(y); ++ xDelete(z); ++ xDelete(elements); ++} ++/*}}}*/ ++void FemModel::SetRefPatterns(){/*{{{*/ ++ ++ /*Initialize the global variable of refinement patterns*/ ++ gRefDBase.InitializeUniformRefPattern(EOned); ++ gRefDBase.InitializeUniformRefPattern(ETriangle); ++ ++ //gRefDBase.InitializeRefPatterns(); ++ /*Insert specifics patterns to ISSM core*/ ++ std::string filepath = REFPATTERNDIR; ++ std::string filename1 = filepath + "/2D_Triang_Rib_3.rpt"; ++ std::string filename2 = filepath + "/2D_Triang_Rib_4.rpt"; ++ std::string filename3 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4.rpt"; ++ std::string filename4 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4_permuted.rpt"; ++ std::string filename5 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5.rpt"; ++ std::string filename6 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5_permuted.rpt"; ++ std::string filename7 = filepath + "/2D_Triang_Rib_5.rpt"; ++ ++ TPZAutoPointer refpat1 = new TPZRefPattern(filename1); ++ TPZAutoPointer refpat2 = new TPZRefPattern(filename2); ++ TPZAutoPointer refpat3 = new TPZRefPattern(filename3); ++ TPZAutoPointer refpat4 = new TPZRefPattern(filename4); ++ TPZAutoPointer refpat5 = new TPZRefPattern(filename5); ++ TPZAutoPointer refpat6 = new TPZRefPattern(filename6); ++ TPZAutoPointer refpat7 = new TPZRefPattern(filename7); ++ ++ if(!gRefDBase.FindRefPattern(refpat1)) gRefDBase.InsertRefPattern(refpat1); ++ if(!gRefDBase.FindRefPattern(refpat2)) gRefDBase.InsertRefPattern(refpat2); ++ if(!gRefDBase.FindRefPattern(refpat3)) gRefDBase.InsertRefPattern(refpat3); ++ if(!gRefDBase.FindRefPattern(refpat4)) gRefDBase.InsertRefPattern(refpat4); ++ if(!gRefDBase.FindRefPattern(refpat5)) gRefDBase.InsertRefPattern(refpat5); ++ if(!gRefDBase.FindRefPattern(refpat6)) gRefDBase.InsertRefPattern(refpat6); ++ if(!gRefDBase.FindRefPattern(refpat7)) gRefDBase.InsertRefPattern(refpat7); ++} ++/*}}}*/ ++#endif +Index: ../trunk-jpl/src/c/classes/AmrBamg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.h (nonexistent) ++++ ../trunk-jpl/src/c/classes/AmrBamg.h (revision 21802) +@@ -0,0 +1,30 @@ ++#ifndef AMRBAMG ++#define AMRBAMG ++ ++/*Includes*/ ++#include "../shared/shared.h" ++#include "../toolkits/toolkits.h" ++ ++#include "../bamg/BamgMesh.h" ++#include "../bamg/BamgGeom.h" ++#include "../bamg/BamgOpts.h" ++ ++class AmrBamg{ ++ ++ public: ++ /* Constructor, destructor etc*/ ++ AmrBamg(IssmDouble hmin, IssmDouble hmax); ++ ~AmrBamg(); ++ ++ /*General methods*/ ++ void Initialize(int* elements,IssmDouble* x,IssmDouble* y,int numberofvertices,int numberofelements); ++ void ExecuteRefinementBamg(int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist); ++ ++ private: ++ BamgGeom* geometry; ++ BamgMesh* fathermesh; ++ BamgMesh* previousmesh; ++ BamgOpts* options; ++}; ++ ++#endif +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21801) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21802) +@@ -832,10 +832,17 @@ + EsaNumRequestedOutputsEnum, + /*}}}*/ + /*Adaptive mesh refinement (AMR){{{*/ ++ TransientAmrFrequencyEnum, ++ AmrTypeEnum, ++ AmrNeopzEnum, + AmrLevelMaxEnum, + AmrRegionLevel1Enum, + AmrRegionLevelMaxEnum, +- TransientAmrFrequencyEnum, ++ AmrBamgEnum, ++ AmrHminEnum, ++ AmrHmaxEnum, ++ AmrFieldEnum, ++ AmrErrEnum, + /*}}}*/ + ParametersENDEnum, + /*Coordinate Systems{{{*/ +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21801) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21802) +@@ -808,10 +808,17 @@ + case EsaTransitionsEnum : return "EsaTransitions"; + case EsaRequestedOutputsEnum : return "EsaRequestedOutputs"; + case EsaNumRequestedOutputsEnum : return "EsaNumRequestedOutputs"; ++ case TransientAmrFrequencyEnum : return "TransientAmrFrequency"; ++ case AmrTypeEnum : return "AmrType"; ++ case AmrNeopzEnum : return "AmrNeopz"; + case AmrLevelMaxEnum : return "AmrLevelMax"; + case AmrRegionLevel1Enum : return "AmrRegionLevel1"; + case AmrRegionLevelMaxEnum : return "AmrRegionLevelMax"; +- case TransientAmrFrequencyEnum : return "TransientAmrFrequency"; ++ case AmrBamgEnum : return "AmrBamg"; ++ case AmrHminEnum : return "AmrHmin"; ++ case AmrHmaxEnum : return "AmrHmax"; ++ case AmrFieldEnum : return "AmrField"; ++ case AmrErrEnum : return "AmrErr"; + case ParametersENDEnum : return "ParametersEND"; + case XYEnum : return "XY"; + case XYZEnum : return "XYZ"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21801) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21802) +@@ -826,10 +826,17 @@ + else if (strcmp(name,"EsaTransitions")==0) return EsaTransitionsEnum; + else if (strcmp(name,"EsaRequestedOutputs")==0) return EsaRequestedOutputsEnum; + else if (strcmp(name,"EsaNumRequestedOutputs")==0) return EsaNumRequestedOutputsEnum; ++ else if (strcmp(name,"TransientAmrFrequency")==0) return TransientAmrFrequencyEnum; ++ else if (strcmp(name,"AmrType")==0) return AmrTypeEnum; ++ else if (strcmp(name,"AmrNeopz")==0) return AmrNeopzEnum; + else if (strcmp(name,"AmrLevelMax")==0) return AmrLevelMaxEnum; + else if (strcmp(name,"AmrRegionLevel1")==0) return AmrRegionLevel1Enum; + else if (strcmp(name,"AmrRegionLevelMax")==0) return AmrRegionLevelMaxEnum; +- else if (strcmp(name,"TransientAmrFrequency")==0) return TransientAmrFrequencyEnum; ++ else if (strcmp(name,"AmrBamg")==0) return AmrBamgEnum; ++ else if (strcmp(name,"AmrHmin")==0) return AmrHminEnum; ++ else if (strcmp(name,"AmrHmax")==0) return AmrHmaxEnum; ++ else if (strcmp(name,"AmrField")==0) return AmrFieldEnum; ++ else if (strcmp(name,"AmrErr")==0) return AmrErrEnum; + else if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; + else if (strcmp(name,"XY")==0) return XYEnum; + else if (strcmp(name,"XYZ")==0) return XYZEnum; +@@ -867,7 +874,10 @@ + else if (strcmp(name,"Param")==0) return ParamEnum; + else if (strcmp(name,"Moulin")==0) return MoulinEnum; + else if (strcmp(name,"Pengrid")==0) return PengridEnum; +- else if (strcmp(name,"Penpair")==0) return PenpairEnum; ++ else stage=8; ++ } ++ if(stage==8){ ++ if (strcmp(name,"Penpair")==0) return PenpairEnum; + else if (strcmp(name,"Profiler")==0) return ProfilerEnum; + else if (strcmp(name,"MatrixParam")==0) return MatrixParamEnum; + else if (strcmp(name,"Masscon")==0) return MassconEnum; +@@ -874,10 +884,7 @@ + else if (strcmp(name,"Massconaxpby")==0) return MassconaxpbyEnum; + else if (strcmp(name,"NodeSId")==0) return NodeSIdEnum; + else if (strcmp(name,"ElementSId")==0) return ElementSIdEnum; +- else stage=8; +- } +- if(stage==8){ +- if (strcmp(name,"VectorParam")==0) return VectorParamEnum; ++ else if (strcmp(name,"VectorParam")==0) return VectorParamEnum; + else if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; + else if (strcmp(name,"Segment")==0) return SegmentEnum; + else if (strcmp(name,"SegmentRiftfront")==0) return SegmentRiftfrontEnum; +@@ -990,7 +997,10 @@ + else if (strcmp(name,"TotalFloatingBmb")==0) return TotalFloatingBmbEnum; + else if (strcmp(name,"TotalGroundedBmb")==0) return TotalGroundedBmbEnum; + else if (strcmp(name,"TotalSmb")==0) return TotalSmbEnum; +- else if (strcmp(name,"P0")==0) return P0Enum; ++ else stage=9; ++ } ++ if(stage==9){ ++ if (strcmp(name,"P0")==0) return P0Enum; + else if (strcmp(name,"P0Array")==0) return P0ArrayEnum; + else if (strcmp(name,"P1")==0) return P1Enum; + else if (strcmp(name,"P1DG")==0) return P1DGEnum; +@@ -997,10 +1007,7 @@ + else if (strcmp(name,"P1bubble")==0) return P1bubbleEnum; + else if (strcmp(name,"P1bubblecondensed")==0) return P1bubblecondensedEnum; + else if (strcmp(name,"P2")==0) return P2Enum; +- else stage=9; +- } +- if(stage==9){ +- if (strcmp(name,"P2bubble")==0) return P2bubbleEnum; ++ else if (strcmp(name,"P2bubble")==0) return P2bubbleEnum; + else if (strcmp(name,"P2bubblecondensed")==0) return P2bubblecondensedEnum; + else if (strcmp(name,"P2xP1")==0) return P2xP1Enum; + else if (strcmp(name,"P1xP2")==0) return P1xP2Enum; Index: /issm/oecreview/Archive/21724-22754/ISSM-21802-21803.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21802-21803.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21802-21803.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21802) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21803) +@@ -2712,7 +2712,6 @@ + this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elementslist); + + /*Write mesh in Results*/ +- printf("-------------- file: FemModel.cpp line: %i\n",__LINE__); + this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshElementsEnum, + elementslist,numberofelements,this->GetElementsWidth(),step,time)); + Index: /issm/oecreview/Archive/21724-22754/ISSM-21803-21804.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21803-21804.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21803-21804.diff (revision 22755) @@ -0,0 +1,31 @@ +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21803) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21804) +@@ -186,11 +186,6 @@ + if(VerboseSolution()) _printf0_(" refining mesh\n"); + femmodel->ReMesh();//Do not refine the last step + } +- //if(save_results){ +- // printf("-------------- file: transient_core.cpp line: %i\n",__LINE__); +- // femmodel->WriteMeshInResults(); +- // OutputResultsx(femmodel); +- //} + } + } + +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21803) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21804) +@@ -109,8 +109,8 @@ + IssmDouble *y = xNew(nbv); + IssmDouble *z = xNew(nbv); + for(int i=0;iVertices[i*2+0]; +- y[i] = meshout->Vertices[i*2+1]; ++ x[i] = meshout->Vertices[i*3+0]; ++ y[i] = meshout->Vertices[i*3+1]; + z[i] = 0.; + } + int* elementslist= xNew(nbt*3); Index: /issm/oecreview/Archive/21724-22754/ISSM-21804-21805.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21804-21805.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21804-21805.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/plot/plotmodel.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plotmodel.m (revision 21804) ++++ ../trunk-jpl/src/m/plot/plotmodel.m (revision 21805) +@@ -47,6 +47,8 @@ + set(gcf,'Position',[756 62 827 504]); + elseif strcmpi(figposition,'mathieu'), + set(gcf,'Position',[300 1 1580 1150]); ++ elseif strcmpi(figposition,'byron'), ++ set(gcf,'Position',[40 1580 560*1.25 420*1.25]); %left, bottom, width, height; W=560 H=420 is default + elseif strcmpi(figposition,'fullscreen'), + set(gcf,'Position',get(0,'ScreenSize')); + elseif strcmpi(figposition,'halfright'), Index: /issm/oecreview/Archive/21724-22754/ISSM-21805-21806.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21805-21806.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21805-21806.diff (revision 22755) @@ -0,0 +1,1617 @@ +Index: ../trunk-jpl/src/m/contrib/tsantos/AMRexportVTK.m +=================================================================== +--- ../trunk-jpl/src/m/contrib/tsantos/AMRexportVTK.m (revision 21805) ++++ ../trunk-jpl/src/m/contrib/tsantos/AMRexportVTK.m (revision 21806) +@@ -36,7 +36,7 @@ + error('Your Element definition is not taken into account \n'); + end + +-%this is the result structure ++%this is the result structure (just the Transient solution) + res_struct=model.results; + %checking for results + if (length(fields(res_struct))>0); +@@ -50,7 +50,7 @@ + %looking for multiple time steps + if(size(sol_struct{i},2)>num_of_timesteps); + num_of_timesteps=size(sol_struct{i},2); +- outstep=model.timestepping.time_step*model.settings.output_frequency; ++ outstep=model.timestepping.time_step*model.settings.output_frequency; + end + end + else +@@ -100,7 +100,7 @@ + timestep = step; + else + timestep = size(sol_struct{j},2); +- end ++ end + + %getting the number of fields in the solution + fieldnames=fields(sol_struct{j}(timestep)); +@@ -119,8 +119,23 @@ + fprintf(fid,'LOOKUP_TABLE default\n'); + s='%e\n'; + fprintf(fid,s,sol_struct{j}(timestep).(fieldnames{k})); +- end +- end ++ end ++ end ++ fprintf(fid,'CELL_DATA %s \n',num2str(num_of_elt)); ++ for k=1:num_of_fields ++ if ((numel(sol_struct{j}(timestep).(fieldnames{k})))==num_of_elt); ++ %paraview does not like NaN, replacing ++ nanval=find(isnan(sol_struct{j}(timestep).(fieldnames{k}))); ++ sol_struct{j}(timestep).(fieldnames{k})(nanval)=-9999; ++ %also checking for verry small value that mess up ++ smallval=(abs(sol_struct{j}(timestep).(fieldnames{k}))<1.0e-20); ++ sol_struct{j}(timestep).(fieldnames{k})(smallval)=0.0; ++ fprintf(fid,'SCALARS %s float 1 \n',fieldnames{k}); ++ fprintf(fid,'LOOKUP_TABLE default\n'); ++ s='%e\n'; ++ fprintf(fid,s,sol_struct{j}(timestep).(fieldnames{k})); ++ end ++ end + end + end + %loop on arguments, if something other than result is asked, do +Index: ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.h +=================================================================== +--- ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.h (revision 21805) ++++ ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.h (revision 21806) +@@ -44,48 +44,47 @@ + + /*Public methods*/ + /* Constructor, destructor etc*/ +- AdaptiveMeshRefinement(); // Default constructor +- AdaptiveMeshRefinement(const AdaptiveMeshRefinement &cp); // Copy constructor +- AdaptiveMeshRefinement & operator= (const AdaptiveMeshRefinement &cp); // Operator of copy +- virtual ~AdaptiveMeshRefinement(); // Destructor ++ AdaptiveMeshRefinement(); ++ AdaptiveMeshRefinement(const AdaptiveMeshRefinement &cp); ++ AdaptiveMeshRefinement & operator= (const AdaptiveMeshRefinement &cp); ++ virtual ~AdaptiveMeshRefinement(); + + /*Savable methods*/ +- virtual int ClassId() const; // ClassId to save the class +- virtual void Read(TPZStream &buf, void *context); // Read this class +- virtual void Write(TPZStream &buf, int withclassid); // Write this class, using ClassId to identify ++ virtual int ClassId() const; ++ virtual void Read(TPZStream &buf,void *context); ++ virtual void Write(TPZStream &buf,int withclassid); + + /*General methods*/ +- void CleanUp(); // Clean all attributes +- void Initialize(); // Initialize the attributes with NULL and values out of usually range +- void SetLevelMax(int &h); // Define the max level of refinement +- void SetRegions(double &D1,double Dhmax); // Define the regions which will be refined +- void SetElementWidth(int &width); // Define elements width +- void ExecuteRefinement(int &type_process,double *vx,double *vy,double *masklevelset,int &nvertices,int &nelements,int &nsegments,double** px,double** py,double** pz,int** pelements,int** psegments=NULL); // A new mesh will be created and refined. This returns the new mesh +- void CreateInitialMesh(int &nvertices,int &nelements,int &nsegments,int &width,double* x,double* y,double* z,int* elements,int* segments=NULL); // Create a NeoPZ geometric mesh by coords and elements ++ void CleanUp(); ++ void Initialize(); ++ void SetLevelMax(int &h); ++ void SetRegions(double &D1,double Dhmax); ++ void SetElementWidth(int &width); ++ void Execute(bool &amr_verbose,int &numberofelements, ++ double* partiallyfloatedelements,double *masklevelset,double* deviatorictensorerror,double* thicknesserror, ++ int &newnumberofvertices,int &newnumberofelements,double** x,double** y,int** elementslist); ++ void CreateInitialMesh(int &nvertices,int &nelements,int &width,double* x,double* y,int* elements); + TPZGeoMesh* CreateRefPatternMesh(TPZGeoMesh* gmesh); +- void CheckMesh(int &nvertices,int &nelements,int &nsegments,int &width,double** px,double** py,double** pz,int** pelements,int** psegments=NULL); // Check the consistency of the mesh ++ void CheckMesh(int &nvertices,int &nelements,int &width,double** px,double** py,int** pelements); + + private: +- + /*Private attributes*/ +- int elementswidth; // Geometric nodes for element: 3 == Tria, 4 == Tetra, 6 == Penta +- int levelmax; // Max level of refinement +- double regionlevel1; // Region which will be refined with level 1 +- double regionlevelmax; // Region which will be refined with level max +- TPZGeoMesh *fathermesh; // Father Mesh is the entire mesh without refinement +- TPZGeoMesh *previousmesh; // Previous mesh is a refined mesh of last step ++ int elementswidth; // Geometric nodes for element: 3 == Tria, 4 == Tetra, 6 == Penta ++ int levelmax; // Max level of refinement ++ double regionlevel1; // Region which will be refined with level 1 ++ double regionlevelmax; // Region which will be refined with level max ++ std::vector sid2index; // Vector that keeps index of PZGeoMesh elements used in the ISSM mesh (sid) ++ TPZGeoMesh *fathermesh; // Father Mesh is the entire mesh without refinement ++ TPZGeoMesh *currentmesh; // Current Mesh is the refined mesh + + /*Private methods*/ +- void RefinementProcess(TPZGeoMesh *gmesh,std::vector > &GLvec); // Start the refinement process +- void RefineMesh(TPZGeoMesh *gmesh, std::vector &ElemVec); // Refine the elements in ElemVec +- void RefineMeshToAvoidHangingNodes(TPZGeoMesh *gmesh); // Refine the elements to avoid hanging nodes +- void SetElementsToRefine(TPZGeoMesh *gmesh,std::vector > &GLvec,int &hlevel, std::vector &ElemVec); //Define wich elements will be refined +- void TagAllElements(TPZGeoMesh *gmesh,std::vector &ElemVec); // This tag all elements to be refined, that is, refine all elements +- void TagElementsNearGroundingLine(TPZGeoMesh *gmesh,std::vector > &GLvec,int &hlevel,std::vector &ElemVec); // This tag elements near the grounding line +- void CalcGroundingLinePosition(double *masklevelset,std::vector > &GLvec); // Calculate the grounding line position using previous mesh +- void GetMesh(TPZGeoMesh *gmesh,int &nvertices,int &nelements,int &nsegments,double** px,double** py,double** pz,int** pelements,int** psegments=NULL); // Return coords and elements in ISSM data structure +- inline int GetElemMaterialID(){return 1;} // Return element material ID +- inline int GetBoundaryMaterialID(){return 2;} // Return segment (2D boundary) material ID ++ void RefinementProcess(bool &amr_verbose,double* partiallyfloatedelements,double* masklevelset,double* deviatorictensorerror,double* thicknesserror); ++ void RefineMesh(TPZGeoMesh *gmesh,std::vector &elements); ++ void RefineMeshToAvoidHangingNodes(TPZGeoMesh *gmesh); ++ void GetMesh(int &nvertices,int &nelements,double** px,double** py,int** pelements); ++ void FindElements(int &numberofpoints,double* xp,double* yp,TPZGeoMesh *gmesh,int &hlevel,std::vector &elements); ++ void AllElements(TPZGeoMesh *gmesh,std::vector &elements); ++ inline int GetElemMaterialID(){return 1;} + }; + + #endif +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 21805) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 21806) +@@ -169,9 +169,12 @@ + void UpdateElements(int newnumberofelements,int* newelementslist,bool* my_elements,int nodecounter,int analysis_counter,Elements* newelements); + void ElementsAndVerticesPartitioning(int& newnumberofvertices,int& newnumberofelements,int& elementswidth,int* newelementslist,bool** pmy_elements,int** pmy_vertices); + void WriteMeshInResults(void); +- void SetRefPatterns(void); ++ void WriteErrorEstimatorsInResults(void); + void SmoothedDeviatoricStressTensor(IssmDouble** ptauxx,IssmDouble** ptauyy,IssmDouble** ptauxy); //nodal values, just for SSA-P1: TauXX, TauYY, TauXY + void ZZErrorEstimator(IssmDouble** pelementerror); ++ void SmoothedGradThickness(IssmDouble** pdHdx,IssmDouble** pdHdy); ++ void ThicknessZZErrorEstimator(IssmDouble** pelementerror); ++ void MeanGroundedIceLevelSet(IssmDouble** pmasklevelset); + + #ifdef _HAVE_BAMG_ + void ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); +@@ -182,6 +185,7 @@ + /*Adaptive mesh refinement methods*/ + void ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); + void InitializeAdaptiveRefinementNeopz(void); ++ void SetRefPatterns(void); + #endif + }; + +Index: ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.cpp (revision 21805) ++++ ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.cpp (revision 21806) +@@ -9,6 +9,11 @@ + #endif + + #include "./AdaptiveMeshRefinement.h" ++#include "TPZVTKGeoMesh.h" ++#include "../shared/shared.h" ++#include "pzgeotriangle.h" ++#include "pzreftriangle.h" ++using namespace pzgeom; + + /*Constructor, copy, clean up and destructor*/ + AdaptiveMeshRefinement::AdaptiveMeshRefinement(){/*{{{*/ +@@ -16,7 +21,7 @@ + } + /*}}}*/ + AdaptiveMeshRefinement::AdaptiveMeshRefinement(const AdaptiveMeshRefinement &cp){/*{{{*/ +- this->Initialize(); ++ this->Initialize(); + this->operator =(cp); + } + /*}}}*/ +@@ -24,14 +29,17 @@ + + /*Clean all attributes*/ + this->CleanUp(); +- + /*Copy all data*/ +- this->fathermesh = new TPZGeoMesh(*cp.fathermesh); +- this->previousmesh = new TPZGeoMesh(*cp.previousmesh); +- this->levelmax = cp.levelmax; +- this->elementswidth = cp.elementswidth; +- this->regionlevel1 = cp.regionlevel1; +- this->regionlevelmax = cp.regionlevelmax; ++ this->fathermesh = new TPZGeoMesh(*cp.fathermesh); ++ this->currentmesh = new TPZGeoMesh(*cp.currentmesh); ++ this->levelmax = cp.levelmax; ++ this->elementswidth = cp.elementswidth; ++ this->regionlevel1 = cp.regionlevel1; ++ this->regionlevelmax = cp.regionlevelmax; ++ this->sid2index.clear(); ++ this->sid2index.resize(cp.sid2index.size()); ++ for(int i=0;isid2index[i]=cp.sid2index[i]; ++ + return *this; + + } +@@ -38,18 +46,18 @@ + /*}}}*/ + AdaptiveMeshRefinement::~AdaptiveMeshRefinement(){/*{{{*/ + +- //bool ismismip = false; +- //if(ismismip){//itapopo +- // TPZFileStream fstr; +- // std::stringstream ss; ++ bool ismismip = false; ++ if(ismismip){//itapopo ++ TPZFileStream fstr; ++ std::stringstream ss; + +- // ss << this->levelmax; +- // std::string AMRfile = "/home/santos/Misomip2/L" + ss.str() + "_tsai/amr.txt"; ++ ss << this->levelmax; ++ std::string AMRfile = "/home/santos/L" + ss.str() + "_amr.txt"; + +- // fstr.OpenWrite(AMRfile.c_str()); +- // int withclassid = 1; +- // this->Write(fstr,withclassid); +- //} ++ fstr.OpenWrite(AMRfile.c_str()); ++ int withclassid = 1; ++ this->Write(fstr,withclassid); ++ } + this->CleanUp(); + gRefDBase.clear(); + } +@@ -56,24 +64,26 @@ + /*}}}*/ + void AdaptiveMeshRefinement::CleanUp(){/*{{{*/ + +- /*Verify and delete all data*/ ++ /*Verify and delete all data*/ + if(this->fathermesh) delete this->fathermesh; +- if(this->previousmesh) delete this->previousmesh; +- this->levelmax = -1; +- this->elementswidth = -1; +- this->regionlevel1 = -1; +- this->regionlevelmax = -1; ++ if(this->currentmesh) delete this->currentmesh; ++ this->levelmax = -1; ++ this->elementswidth = -1; ++ this->regionlevel1 = -1; ++ this->regionlevelmax = -1; ++ this->sid2index.clear(); + } + /*}}}*/ + void AdaptiveMeshRefinement::Initialize(){/*{{{*/ + + /*Set pointers to NULL*/ +- this->fathermesh = NULL; +- this->previousmesh = NULL; +- this->levelmax = -1; +- this->elementswidth = -1; +- this->regionlevel1 = -1; +- this->regionlevelmax = -1; ++ this->fathermesh = NULL; ++ this->currentmesh = NULL; ++ this->levelmax = -1; ++ this->elementswidth = -1; ++ this->regionlevel1 = -1; ++ this->regionlevelmax = -1; ++ this->sid2index.clear(); + } + /*}}}*/ + int AdaptiveMeshRefinement::ClassId() const{/*{{{*/ +@@ -80,428 +90,347 @@ + return 13829430; //Antartic area with ice shelves (km^2) + } + /*}}}*/ +-void AdaptiveMeshRefinement::Read(TPZStream &buf, void *context){/*{{{*/ ++void AdaptiveMeshRefinement::Read(TPZStream &buf,void *context){/*{{{*/ + +- try +- { +- /* Read the id context*/ +- TPZSaveable::Read(buf,context); ++ try ++ { ++ /* Read the id context*/ ++ TPZSaveable::Read(buf,context); ++ /* Read class id*/ ++ int classid; ++ buf.Read(&classid,1); ++ /* Verify the class id*/ ++ if(classid!=this->ClassId()) _error_("AdaptiveMeshRefinement::Read: Error in restoring AdaptiveMeshRefinement!\n"); ++ /* Read simple attributes */ ++ buf.Read(&this->levelmax,1); ++ buf.Read(&this->elementswidth,1); ++ buf.Read(&this->regionlevel1,1); ++ buf.Read(&this->regionlevelmax,1); ++ /* Read vector attributes*/ ++ int size; ++ buf.Read(&size,1); ++ int* psid2index=xNew(size); ++ buf.Read(psid2index,size); ++ this->sid2index.clear(); ++ this->sid2index.assign(psid2index,psid2index+size); ++ /* Read geometric mesh (father)*/ ++ TPZSaveable *sv1 = TPZSaveable::Restore(buf,0); ++ this->fathermesh = dynamic_cast(sv1); ++ /* Read geometric mesh (current)*/ ++ TPZSaveable *sv2 = TPZSaveable::Restore(buf,0); ++ this->currentmesh = dynamic_cast(sv2); ++ /* Cleanup*/ ++ xDelete(psid2index); ++ } ++ catch(const std::exception& e) ++ { ++ _error_("AdaptiveMeshRefinement::Read: Exception catched!\n"); ++ } + +- /* Read class id*/ +- int classid; +- buf.Read(&classid,1); +- +- /* Verify the class id*/ +- if (classid != this->ClassId() ) +- { +- std::cout << "Error in restoring AdaptiveMeshRefinement!\n"; +- std::cout.flush(); +- DebugStop(); +- } +- +- /* Read simple attributes */ +- buf.Read(&this->levelmax,1); +- buf.Read(&this->elementswidth,1); +- buf.Read(&this->regionlevel1,1); +- buf.Read(&this->regionlevelmax,1); +- +- /* Read geometric mesh*/ +- TPZSaveable *sv1 = TPZSaveable::Restore(buf,0); +- this->fathermesh = dynamic_cast(sv1); +- +- TPZSaveable *sv2 = TPZSaveable::Restore(buf,0); +- this->previousmesh = dynamic_cast(sv2); +- } +- catch(const std::exception& e) +- { +- std::cout << "Exception catched! " << e.what() << std::endl; +- std::cout.flush(); +- DebugStop(); +- } + } + /*}}}*/ + template class TPZRestoreClass;/*{{{*/ + /*}}}*/ +-void AdaptiveMeshRefinement::Write(TPZStream &buf, int withclassid){/*{{{*/ ++void AdaptiveMeshRefinement::Write(TPZStream &buf,int withclassid){/*{{{*/ + +- try +- { +- /* Write context (this class) class ID*/ +- TPZSaveable::Write(buf,withclassid); +- +- /* Write this class id*/ +- int classid = ClassId(); +- buf.Write(&classid,1); +- +- /* Write simple attributes */ +- buf.Write(&this->levelmax,1); +- buf.Write(&this->elementswidth,1); +- buf.Write(&this->regionlevel1,1); +- buf.Write(&this->regionlevelmax,1); +- +- /* Write the geometric mesh*/ +- this->fathermesh->Write(buf, this->ClassId()); +- this->previousmesh->Write(buf, this->ClassId()); ++ try ++ { ++ /* Write context (this class) class ID*/ ++ TPZSaveable::Write(buf,withclassid); ++ /* Write this class id*/ ++ int classid = this->ClassId(); ++ buf.Write(&classid,1); ++ /* Write simple attributes */ ++ buf.Write(&this->levelmax,1); ++ buf.Write(&this->elementswidth,1); ++ buf.Write(&this->regionlevel1,1); ++ buf.Write(&this->regionlevelmax,1); ++ /* Write vector attributes*/ ++ int size=this->sid2index.size(); ++ int* psid2index=&this->sid2index[0]; ++ buf.Write(&size,1);//vector size ++ buf.Write(psid2index,this->sid2index.size()); ++ /* Write the geometric mesh*/ ++ this->fathermesh->Write(buf,this->ClassId()); ++ this->currentmesh->Write(buf,this->ClassId()); + } + catch(const std::exception& e) + { +- std::cout << "Exception catched! " << e.what() << std::endl; +- std::cout.flush(); +- DebugStop(); ++ _error_("AdaptiveMeshRefinement::Write: Exception catched!\n"); + } + } + /*}}}*/ + + /*Mesh refinement methods*/ +-#include "TPZVTKGeoMesh.h" //itapopo +-#include "../shared/shared.h" //itapopo +-void AdaptiveMeshRefinement::ExecuteRefinement(int &type_process,double *vx, double *vy, double *masklevelset, int &nvertices, int &nelements, int &nsegments, double** px, double** py, double** pz, int** pelements, int** psegments){/*{{{*/ ++void AdaptiveMeshRefinement::Execute(bool &amr_verbose, ++ int &numberofelements, ++ double* partiallyfloatedelements, ++ double *masklevelset, ++ double* deviatorictensorerror, ++ double* thicknesserror, ++ int &newnumberofvertices,int &newnumberofelements,double** x,double** y,int** elementslist){/*{{{*/ + +- /*IMPORTANT! pelements (and psegments) are in Matlab indexing*/ ++ /*IMPORTANT! newelements are in Matlab indexing*/ + /*NEOPZ works only in C indexing*/ ++ if(!this->fathermesh || !this->currentmesh) _error_("Impossible to execute refinement: fathermesh or currentmesh is NULL!\n"); ++ if(numberofelements!=this->sid2index.size()) _error_("Impossible to execute refinement: sid2index.size is not equal to numberofelements!\n"); + +- _assert_(this->fathermesh); +- _assert_(this->previousmesh); ++ /*Execute the refinement.*/ ++ this->RefinementProcess(amr_verbose,partiallyfloatedelements,masklevelset,deviatorictensorerror,thicknesserror); + +- /*Calculate the position of the grounding line using previous mesh*/ +- std::vector > GLvec; +- this->CalcGroundingLinePosition(masklevelset, GLvec); +- +- // std::ofstream file1("/home/santos/mesh0.vtk"); +- // TPZVTKGeoMesh::PrintGMeshVTK(this->fathermesh,file1 ); +- +- /*run refinement or unrefinement process*/ +- TPZGeoMesh *newmesh; +- switch (type_process) { +- case 0: newmesh = this->previousmesh; break; // refine previous mesh +- case 1: newmesh = new TPZGeoMesh(*this->fathermesh); break; // refine mesh 0 (unrefine process) +- default: DebugStop(); break;//itapopo verificar se irá usar _assert_ +- } +- +- this->RefinementProcess(newmesh,GLvec); ++ /*Get new geometric mesh in ISSM data structure*/ ++ this->GetMesh(newnumberofvertices,newnumberofelements,x,y,elementslist); + +- //std::ofstream file2("/home/santos/mesh1.vtk"); +- //TPZVTKGeoMesh::PrintGMeshVTK(this->previousmesh,file2 ); +- +- /*Set new mesh pointer. Previous mesh just have uniform elements*/ +- if(type_process==1){ +- if(this->previousmesh) delete this->previousmesh; +- this->previousmesh = newmesh; +- } +- +- /*Refine elements to avoid hanging nodes*/ +- //TPZGeoMesh *nohangingnodesmesh = new TPZGeoMesh(*newmesh);//itapopo testando, este era o original +- TPZGeoMesh *nohangingnodesmesh = this->CreateRefPatternMesh(newmesh);//itapopo testando, este eh novo metodo +- +- //std::ofstream file3("/home/santos/mesh2.vtk"); +- //TPZVTKGeoMesh::PrintGMeshVTK(this->previousmesh,file3); +- +- this->RefineMeshToAvoidHangingNodes(nohangingnodesmesh); +- +- //std::ofstream file4("/home/santos/mesh3.vtk"); +- //TPZVTKGeoMesh::PrintGMeshVTK(nohangingnodesmesh,file4); +- +- /*Get new geometric mesh in ISSM data structure*/ +- this->GetMesh(nohangingnodesmesh,nvertices,nelements,nsegments,px,py,pz,pelements,psegments); +- +- /*Verify the new geometry*/ +- this->CheckMesh(nvertices,nelements,nsegments,this->elementswidth,px,py,pz,pelements,psegments); ++ /*Verify the new geometry*/ ++ this->CheckMesh(newnumberofvertices,newnumberofelements,this->elementswidth,x,y,elementslist); + +- _printf_("\trefinement process done!\n\n"); +- +- delete nohangingnodesmesh; + } + /*}}}*/ +-void AdaptiveMeshRefinement::RefinementProcess(TPZGeoMesh *gmesh,std::vector > &GLvec){/*{{{*/ +- +- /*Refine mesh levelmax times*/ +- _printf_("\n\trefinement process (level max = " << this->levelmax << ")\n"); +- _printf_("\tprogress: "); +- for(int hlevel=1;hlevel<=this->levelmax;hlevel++){ +- +- /*Set elements to be refined using some criteria*/ +- std::vector ElemVec; //elements without children +- this->SetElementsToRefine(gmesh,GLvec,hlevel,ElemVec); +- +- /*Refine the mesh*/ +- this->RefineMesh(gmesh, ElemVec); +- +- _printf_("* "); +- } +- _printf_("\n"); ++void AdaptiveMeshRefinement::RefinementProcess(bool &amr_verbose,double* partiallyfloatedelements,double* masklevelset, ++ double* deviatorictensorerror,double* thicknesserror){/*{{{*/ ++ ++ if(amr_verbose) _printf_("\n\trefinement process started (level max = " << this->levelmax << ")\n"); ++ ++ /*Intermediaries*/ ++ TPZGeoMesh* nohangingnodesmesh=NULL; ++ double mean_mask = 0; ++ double mean_tauerror = 0; ++ double mean_Herror = 0; ++ double group_error = 0; ++ ++ /*Calculate mean values*/ ++ for(int i=0;isid2index.size();i++){ ++ mean_mask += masklevelset[i]; ++ mean_tauerror += deviatorictensorerror[i]; ++ mean_Herror += thicknesserror[i]; ++ } ++ mean_mask /= this->sid2index.size(); ++ mean_tauerror /= this->sid2index.size(); ++ mean_Herror /= this->sid2index.size(); ++ ++ if(amr_verbose) _printf_("\t\tuniform refinement...\n"); ++ for(int i=0;isid2index.size();i++){ ++ TPZGeoEl* geoel=this->currentmesh->Element(this->sid2index[i]); ++ if(geoel->HasSubElement()) _error_("Impossible to refine: geoel (index) "<sid2index[i]<<" has subelements!\n"); ++ if(geoel->MaterialId()!=this->GetElemMaterialID()) _error_("Impossible to refine: geoel->MaterialId is not GetElemMaterialID!\n"); ++ /*Refine*/ ++ if(thicknesserror[i]>mean_Herror){ ++ TPZVec sons; ++ if(geoel->Level()levelmax) geoel->Divide(sons); ++ } ++ else if(geoel->Level()>0){ /*try to unrefine*/ ++ TPZVec sons; ++ geoel->Father()->GetHigherSubElements(sons); ++ group_error=0; ++ for(int j=0;jIndex(); ++ } ++ } ++ } ++ this->currentmesh->BuildConnectivity(); ++ ++ if(amr_verbose) _printf_("\t\trefine to avoid hanging nodes...\n"); ++ this->RefineMeshToAvoidHangingNodes(this->currentmesh); ++ this->currentmesh->BuildConnectivity(); ++ ++ //nohangingnodesmesh = this->CreateRefPatternMesh(newmesh); itapopo tentar otimizar ++ ++ if(amr_verbose) _printf_("\trefinement process done!\n"); + } + /*}}}*/ +-void AdaptiveMeshRefinement::RefineMesh(TPZGeoMesh *gmesh, std::vector &ElemVec){/*{{{*/ ++void AdaptiveMeshRefinement::RefineMesh(TPZGeoMesh *gmesh,std::vector &elements){/*{{{*/ + +- /*Refine elements in ElemVec: uniform pattern refinement*/ +- for(int i = 0; i < ElemVec.size(); i++){ +- +- /*Get geometric element and verify if it has already been refined*/ +- int index = ElemVec[i]; +- TPZGeoEl * geoel = gmesh->Element(index); +- if(geoel->HasSubElement()) DebugStop(); //itapopo _assert_(!geoel->HasSubElement()); +- if(geoel->MaterialId() != this->GetElemMaterialID()) DebugStop(); //itapopo verificar se usará _assert_ +- +- /*Divide geoel*/ +- TPZVec Sons; +- geoel->Divide(Sons); +- +- /*If a 1D segment is neighbor, it must be divided too*/ +- if(this->elementswidth != 3) DebugStop(); //itapopo verificar o segment para malha 3D +- +- std::vector sides(3); +- sides[0] = 3; sides[1] = 4; sides[2] = 5; +- for(int j = 0; j < sides.size(); j++ ){ +- +- TPZGeoElSide Neighbour = geoel->Neighbour(sides[j]); +- +- if( Neighbour.Element()->MaterialId() == this->GetBoundaryMaterialID() && !Neighbour.Element()->HasSubElement() ){ +- TPZVec pv2; +- Neighbour.Element()->Divide(pv2); +- } +- } ++ /*Refine elements: uniform pattern refinement*/ ++ for(int i=0;iElement(index); ++ if(geoel->HasSubElement()) _error_("Impossible to refine: geoel (index) " << index << " has subelements!\n"); ++ if(geoel->MaterialId()!=this->GetElemMaterialID()) _error_("Impossible to refine: geoel->MaterialId is not GetElemMaterialID!\n"); ++ /*Divide geoel*/ ++ TPZVec Sons; ++ geoel->Divide(Sons); + } +- +- gmesh->BuildConnectivity(); +- ++ gmesh->BuildConnectivity(); + } + /*}}}*/ + void AdaptiveMeshRefinement::RefineMeshToAvoidHangingNodes(TPZGeoMesh *gmesh){/*{{{*/ + +- _printf_("\trefine to avoid hanging nodes...\n"); +- /*Refine elements to avoid hanging nodes: non-uniform refinement*/ +- const int NElem = gmesh->NElements(); +- for(int i = 0; i < NElem; i++){ +- +- /*Get geometric element and verify if it has already been refined. Geoel may not have been previously refined*/ +- TPZGeoEl * geoel = gmesh->Element(i); +- if(!geoel) continue; +- if(geoel->HasSubElement()) continue; +- if(geoel->MaterialId() != this->GetElemMaterialID()) continue; +- +- /*Get the refinement pattern for this element and refine it*/ +- TPZAutoPointer refp = TPZRefPatternTools::PerfectMatchRefPattern(geoel); +- if(refp){ +- TPZVec Sons; +- geoel->SetRefPattern(refp); +- geoel->Divide(Sons); +- } +- +- } ++ /*Refine elements to avoid hanging nodes: non-uniform refinement*/ ++ const int NElem = gmesh->NElements(); ++ for(int i=0;iElement(i); ++ if(!geoel) continue; ++ if(geoel->HasSubElement()) continue; ++ if(geoel->MaterialId() != this->GetElemMaterialID()) continue; ++ /*Get the refinement pattern for this element and refine it*/ ++ TPZAutoPointer refp=TPZRefPatternTools::PerfectMatchRefPattern(geoel); ++ if(refp){ ++ TPZVec Sons; ++ geoel->SetRefPattern(refp); ++ geoel->Divide(Sons); ++ } ++ } ++ gmesh->BuildConnectivity(); + +- gmesh->BuildConnectivity(); +- + } + /*}}}*/ +-void AdaptiveMeshRefinement::GetMesh(TPZGeoMesh *gmesh,int &nvertices,int &nelements,int &nsegments,double** px,double** py,double** pz, int** pelements, int** psegments){/*{{{*/ ++void AdaptiveMeshRefinement::GetMesh(int &nvertices,int &nelements,double** px,double** py, int** pelements){/*{{{*/ + +- /*IMPORTANT! pelements (and psegments) are in Matlab indexing*/ +- /*NEOPZ works only in C indexing*/ ++ /* IMPORTANT! pelements are in Matlab indexing ++ NEOPZ works only in C indexing. ++ This method cleans up and updated the this->sid2index ++ and fills in it with the new mesh. ++ Avoid to call this method before Refinement Process.*/ + +- /* vertices */ +- int ntotalvertices = gmesh->NNodes();//total +- +- /* mesh coords */ +- double* newmeshX = xNew(ntotalvertices); +- double* newmeshY = xNew(ntotalvertices); +- double* newmeshZ = xNew(ntotalvertices); +- +- /* getting mesh coords */ +- for(int i = 0; i < ntotalvertices; i++ ){ +- TPZVec coords(3,0.); +- gmesh->NodeVec()[i].GetCoordinates(coords); +- newmeshX[i] = coords[0]; +- newmeshY[i] = coords[1]; +- newmeshZ[i] = coords[2]; +- } +- +- /* elements */ +- std::vector GeoVec; GeoVec.clear(); +- for(int i = 0; i < gmesh->NElements(); i++){ +- if( gmesh->ElementVec()[i]->HasSubElement() ) continue; +- if( gmesh->ElementVec()[i]->MaterialId() != this->GetElemMaterialID() ) continue; +- GeoVec.push_back( gmesh->ElementVec()[i]); +- } +- +- int ntotalelements = (int)GeoVec.size(); +- int* newelements = xNew(ntotalelements*this->elementswidth); ++ /*Intermediaries */ ++ TPZGeoMesh* gmesh = this->currentmesh;//itapopo confirmar ++ ++ long sid,nodeindex; ++ int nconformelements,nconformvertices; ++ int* newelements = NULL; ++ double* newmeshX = NULL;//xNew(ntotalvertices); ++ double* newmeshY = NULL;//xNew(ntotalvertices); ++ TPZGeoEl* geoel = NULL; ++ long* vertex_index2sid = xNew(gmesh->NNodes()); ++ this->sid2index.clear(); ++ ++ /*Get mesh coords */ ++ //for(int i=0;i coords(3,0.); ++ // gmesh->NodeVec()[i].GetCoordinates(coords); ++ // newmeshX[i] = coords[0]; ++ // newmeshY[i] = coords[1]; ++ //} + +- if ( !(this->elementswidth == 3) && !(this->elementswidth == 4) && !(this->elementswidth == 6) ) DebugStop(); ++ /*Fill in the vertex_index2sid vector with non usual index value*/ ++ for(int i=0;iNNodes();i++) vertex_index2sid[i]=-1; ++ ++ /*Get elements without sons and fill in the vertex_index2sid with used vertices (indexes) */ ++ sid=0; ++ for(int i=0;iNElements();i++){//over gmesh elements index ++ geoel=gmesh->ElementVec()[i]; ++ if(!geoel) continue; ++ if(geoel->HasSubElement()) continue; ++ if(geoel->MaterialId() != this->GetElemMaterialID()) continue; ++ this->sid2index.push_back(i);//keep the element index ++ for(int j=0;jelementswidth;j++){ ++ nodeindex=geoel->NodeIndex(j); ++ if(vertex_index2sid[nodeindex]==-1){ ++ vertex_index2sid[nodeindex]=sid; ++ sid++; ++ } ++ } ++ } + +- for(int i=0;ielementswidth;j++) newelements[i*this->elementswidth+j]=(int)GeoVec[i]->NodeIndex(j)+1;//C to Matlab indexing +- } +- +- /* segments */ +- std::vector SegVec; SegVec.clear(); +- for(int i = 0; i < gmesh->NElements(); i++){ +- if( gmesh->ElementVec()[i]->HasSubElement() ) continue; +- if( gmesh->ElementVec()[i]->MaterialId() != this->GetBoundaryMaterialID() ) continue; +- SegVec.push_back( gmesh->ElementVec()[i]); +- } +- +- int ntotalsegments = (int)SegVec.size(); +- int *newsegments=NULL; +- if(ntotalsegments>0) newsegments=xNew(ntotalsegments*3); +- +- for(int i=0;iNodeIndex(j)+1;//C to Matlab indexing +- +- int neighborindex = SegVec[i]->Neighbour(2).Element()->Index(); +- int neighbourid = -1; +- +- for(int j = 0; j < GeoVec.size(); j++){ +- if( GeoVec[j]->Index() == neighborindex || GeoVec[j]->FatherIndex() == neighborindex){ +- neighbourid = j; +- break; +- } +- } +- +- if(neighbourid==-1) DebugStop(); //itapopo talvez passar para _assert_ +- newsegments[i*3+2] = neighbourid+1;//C to Matlab indexing +- } +- +- //setting outputs +- nvertices = ntotalvertices; +- nelements = ntotalelements; +- nsegments = ntotalsegments; +- *px = newmeshX; +- *py = newmeshY; +- *pz = newmeshZ; +- *pelements = newelements; +- *psegments = newsegments; +- ++ nconformelements = (int)this->sid2index.size(); ++ nconformvertices = (int)sid; ++ newelements = xNew(nconformelements*this->elementswidth); ++ newmeshX = xNew(nconformvertices); ++ newmeshY = xNew(nconformvertices); ++ ++ for(int i=0;i coords(3,0.); ++ gmesh->NodeVec()[i].GetCoordinates(coords); ++ newmeshX[sid] = coords[0]; ++ newmeshY[sid] = coords[1]; ++ } ++ } ++ ++ for(int i=0;isid2index.size();i++){//over the sid (fill the ISSM elements) ++ for(int j=0;jelementswidth;j++) { ++ geoel = gmesh->ElementVec()[this->sid2index[i]]; ++ sid = vertex_index2sid[geoel->NodeIndex(j)]; ++ newelements[i*this->elementswidth+j]=(int)sid+1;//C to Matlab indexing ++ } ++ } ++ ++ /*Setting outputs*/ ++ nvertices = nconformvertices; ++ nelements = nconformelements; ++ *px = newmeshX; ++ *py = newmeshY; ++ *pelements = newelements; ++ ++ /*Cleanup*/ ++ xDelete(vertex_index2sid); ++ + } + /*}}}*/ +-void AdaptiveMeshRefinement::CalcGroundingLinePosition(double *masklevelset,std::vector > &GLvec){/*{{{*/ +- +- /* Find grounding line using elments center point */ +- GLvec.clear(); +- for(int i=0;ipreviousmesh->NElements();i++){ +- +- if(this->previousmesh->Element(i)->MaterialId()!=this->GetElemMaterialID()) continue; +- if(this->previousmesh->Element(i)->HasSubElement()) continue; +- +- //itapopo apenas malha 2D triangular! +- int vertex0 = this->previousmesh->Element(i)->NodeIndex(0); +- int vertex1 = this->previousmesh->Element(i)->NodeIndex(1); +- int vertex2 = this->previousmesh->Element(i)->NodeIndex(2); +- +- //itapopo inserir uma verificação para não acessar fora da memória +- double mls0 = masklevelset[vertex0]; +- double mls1 = masklevelset[vertex1]; +- double mls2 = masklevelset[vertex2]; +- +- if( mls0*mls1 < 0. || mls1*mls2 < 0. ){ +- const int side = 6; +- TPZVec qsi(2,0.); +- TPZVec X(3,0.); +- this->previousmesh->Element(i)->CenterPoint(side, qsi); +- this->previousmesh->Element(i)->X(qsi, X); +- GLvec.push_back(X); +- } +- } +- +-// itapopo apenas para debugar +-// std::ofstream fileGL("/Users/santos/Desktop/gl.nb"); +-// fileGL << "ListPlot[{"; +-// for(int i = 0; i < GLvec.size(); i++){ +-// fileGL << "{" << GLvec[i][0] << "," << GLvec[i][1] << /*"," << 0. << */"}"; +-// if(i != GLvec.size()-1) fileGL << ","; +-// } +-// fileGL << "}]"; +-// fileGL.flush(); +-// fileGL.close(); +- +-} +-/*}}}*/ +-void AdaptiveMeshRefinement::SetElementsToRefine(TPZGeoMesh *gmesh,std::vector > &GLvec,int &hlevel,std::vector &ElemVec){/*{{{*/ ++void AdaptiveMeshRefinement::FindElements(int &numberofpoints,double* xp,double* yp,TPZGeoMesh *gmesh,int &hlevel,std::vector &elements){/*{{{*/ + +- if(!gmesh) DebugStop(); //itapopo verificar se usará _assert_ ++ if(!gmesh) _error_("Impossible to set elements: gmesh is NULL!\n"); + +- ElemVec.clear(); ++ if(false){ ++ this->AllElements(gmesh,elements); //uniform, refine all elements! ++ return; ++ } ++ ++ /*Intermediaries*/ ++ elements.clear(); ++ double D1 = this->regionlevel1; ++ double Dhmax = this->regionlevelmax; ++ int hmax = this->levelmax; ++ double alpha = (hmax==1) ? 0. : log(D1/Dhmax)/(hmax-1.); ++ double Di = D1/exp(alpha*(hlevel-1)); ++ int side2D = 6; ++ double distance,value; + +- // itapopo inserir modo de encontrar criterio TESTING!!!! Come to false! +- if(false) this->TagAllElements(gmesh,ElemVec); //uniform, refine all elements! ++ /*Find elements near the points */ ++ for(int i=0;iNElements();i++){ ++ if(gmesh->Element(i)->MaterialId()!=this->GetElemMaterialID()) continue; ++ if(gmesh->Element(i)->HasSubElement()) continue; ++ if(gmesh->Element(i)->Level()>=hlevel) continue; ++ TPZVec qsi(2,0.); ++ TPZVec centerPoint(3,0.); ++ gmesh->Element(i)->CenterPoint(side2D, qsi); ++ gmesh->Element(i)->X(qsi, centerPoint); ++ distance = Di; ++ for (int j=0;jTagElementsNearGroundingLine(gmesh, GLvec, hlevel, ElemVec); +- + } + /*}}}*/ +-void AdaptiveMeshRefinement::TagAllElements(TPZGeoMesh *gmesh,std::vector &ElemVec){/*{{{*/ +- ++void AdaptiveMeshRefinement::AllElements(TPZGeoMesh *gmesh,std::vector &elements){/*{{{*/ + /* Uniform refinement. This refines the entire mesh */ + int nelements = gmesh->NElements(); ++ elements.clear(); + for(int i=0;iElement(i)->MaterialId()!=this->GetElemMaterialID()) continue; + if(gmesh->Element(i)->HasSubElement()) continue; +- ElemVec.push_back(i); ++ elements.push_back(i); + } + } + /*}}}*/ +-void AdaptiveMeshRefinement::TagElementsNearGroundingLine(TPZGeoMesh *gmesh,std::vector > &GLvec,int &hlevel,std::vector &ElemVec){/*{{{*/ +- +- /* Tag elements near grounding line */ +- double D1 = this->regionlevel1; +- double Dhmax = this->regionlevelmax; +- int hmax = this->levelmax; +- double alpha = (hmax==1) ? 0. : log(D1/Dhmax)/(hmax-1.); +- double Di = D1/exp(alpha*(hlevel-1)); +- +- for(int i=0;iNElements();i++){ +- +- if(gmesh->Element(i)->MaterialId()!=this->GetElemMaterialID()) continue; +- if(gmesh->Element(i)->HasSubElement()) continue; +- if(gmesh->Element(i)->Level()>=hlevel) continue; +- +- const int side2D = 6; +- TPZVec qsi(2,0.); +- TPZVec centerPoint(3,0.); +- gmesh->Element(i)->CenterPoint(side2D, qsi); +- gmesh->Element(i)->X(qsi, centerPoint); +- +- REAL distance = Di; +- +- for (int j = 0; j < GLvec.size(); j++) { +- +- REAL value = ( GLvec[j][0] - centerPoint[0] ) * ( GLvec[j][0] - centerPoint[0] ); // (x2-x1)^2 +- value += ( GLvec[j][1] - centerPoint[1] ) * ( GLvec[j][1] - centerPoint[1] );// (y2-y1)^2 +- value = std::sqrt(value); //Radius +- +- //finding the min distance to the grounding line +- if(value < distance) distance = value; +- +- } +- +- if(distance < Di) ElemVec.push_back(i); +- } +- +-} +-/*}}}*/ +-void AdaptiveMeshRefinement::CreateInitialMesh(int &nvertices,int &nelements,int &nsegments,int &width,double* x,double* y,double* z,int* elements,int* segments){/*{{{*/ ++void AdaptiveMeshRefinement::CreateInitialMesh(int &nvertices,int &nelements,int &width,double* x,double* y,int* elements){/*{{{*/ + +- /*IMPORTANT! elements come in Matlab indexing*/ +- /*NEOPZ works only in C indexing*/ ++ /* IMPORTANT! elements come in Matlab indexing ++ NEOPZ works only in C indexing*/ + +- _assert_(nvertices>0); +- _assert_(nelements>0); ++ if(nvertices<=0) _error_("Impossible to create initial mesh: nvertices is <= 0!\n"); ++ if(nelements<=0) _error_("Impossible to create initial mesh: nelements is <= 0!\n"); + this->SetElementWidth(width); + + /*Verify and creating initial mesh*/ +- if(this->fathermesh) _error_("Initial mesh already exists!"); ++ if(this->fathermesh || this->currentmesh) _error_("Initial mesh already exists!"); + + this->fathermesh = new TPZGeoMesh(); +- this->fathermesh->NodeVec().Resize( nvertices ); ++ this->fathermesh->NodeVec().Resize(nvertices); + +- /*Set the vertices (geometric nodes in NeoPZ context)*/ ++ /*Set the vertices (geometric nodes in NeoPZ context)*/ + for(int i=0;i coord(3,0.); + coord[0]= x[i]; + coord[1]= y[i]; +- coord[2]= z[i]; ++ coord[2]= 0.; + /*Insert in the mesh*/ + this->fathermesh->NodeVec()[i].SetCoord(coord); + this->fathermesh->NodeVec()[i].SetNodeId(i); +@@ -511,48 +440,27 @@ + long index; + const int mat = this->GetElemMaterialID(); + TPZManVector elem(this->elementswidth,0); +- +- for(int iel=0;ielsid2index.clear(); + +- for(int jel=0;jelelementswidth;jel++) elem[jel]=elements[iel*this->elementswidth+jel]-1;//Convert Matlab to C indexing +- ++ for(int i=0;ielementswidth;j++) elem[j]=elements[i*this->elementswidth+j]-1;//Convert Matlab to C indexing + /*reftype = 0: uniform, fast / reftype = 1: uniform and non-uniform (avoid hanging nodes), it is not too fast */ +- const int reftype = 0; ++ const int reftype = 1; + switch(this->elementswidth){ +- case 3: this->fathermesh->CreateGeoElement(ETriangle, elem, mat, index, reftype); break; +- case 4: this->fathermesh->CreateGeoElement(ETetraedro, elem, mat, index, reftype); DebugStop(); break; +- case 6: this->fathermesh->CreateGeoElement(EPrisma, elem, mat, index, reftype); DebugStop(); break; +- default: DebugStop();//itapopo _error_("mesh not supported yet"); ++ case 3: this->fathermesh->CreateGeoElement(ETriangle,elem,mat,index,reftype); break; ++ default: _error_("mesh not supported yet"); + } +- + /*Define the element ID*/ +- this->fathermesh->ElementVec()[index]->SetId(iel); ++ this->fathermesh->ElementVec()[index]->SetId(i); ++ /*Initialize sid2index*/ ++ this->sid2index.push_back((int)index); + } +- +- /*Generate the 1D segments elements (boundary)*/ +- const int matboundary = this->GetBoundaryMaterialID(); +- TPZManVector boundary(2,0.); +- +- for(int iel=nelements;ielfathermesh->CreateGeoElement(EOned, boundary, matboundary, index, reftype);//cria elemento unidimensional +- this->fathermesh->ElementVec()[index]->SetId(iel); +- } +- + /*Build element and node connectivities*/ + this->fathermesh->BuildConnectivity(); +- +- /*Create previous mesh as a copy of father mesh*/ +- this->previousmesh = new TPZGeoMesh(*this->fathermesh); +- ++ /*Set current mesh*/ ++ this->currentmesh=new TPZGeoMesh(*this->fathermesh); + } + /*}}}*/ +-#include "pzgeotriangle.h" //itapopo +-#include "pzreftriangle.h" //itapopo +-using namespace pzgeom; + TPZGeoMesh* AdaptiveMeshRefinement::CreateRefPatternMesh(TPZGeoMesh* gmesh){/*{{{*/ + + TPZGeoMesh *newgmesh = new TPZGeoMesh(); +@@ -645,39 +553,40 @@ + } + /*}}}*/ + void AdaptiveMeshRefinement::SetElementWidth(int &width){/*{{{*/ +- this->elementswidth = width; ++ if(width!=3) _error_("elementswidth not supported yet!"); ++ this->elementswidth = width; + } + /*}}}*/ +-void AdaptiveMeshRefinement::CheckMesh(int &nvertices,int &nelements,int &nsegments,int &width,double** px,double** py,double** pz,int** pelements, int** psegments){/*{{{*/ ++void AdaptiveMeshRefinement::CheckMesh(int &nvertices,int &nelements,int &width,double** px,double** py,int** pelements){/*{{{*/ + +- /*Basic verification*/ +- if( !(nvertices > 0) || !(nelements > 0) ) DebugStop(); //itapopo verificar se irá usar o _assert_ +- +- if ( !(width == 3) && !(width == 4) && !(width == 6) ) DebugStop(); // itapopo verifcar se irá usar o _assert_ +- +- if( !px || !py || !pz || !pelements ) DebugStop(); // itapopo verifcar se irá usar o _assert_ +- +- /*Verify if there are orphan nodes*/ +- std::set elemvertices; +- elemvertices.clear(); +- for(int i = 0; i < nelements; i++){ +- for(int j = 0; j < width; j++) { +- elemvertices.insert((*pelements)[i*width+j]); +- } +- } +- +- if( elemvertices.size() != nvertices ) DebugStop();//itapopo verificar se irá usar o _assert_ ++ /*Basic verification*/ ++ if(nvertices<=0) _error_("Impossible to continue: nvertices <=0!\n"); ++ if(nelements<=0) _error_("Impossible to continue: nelements <=0!\n"); ++ if(width!=3) _error_("Impossible to continue: width !=3!\n"); ++ if(!px) _error_("Impossible to continue: px is NULL!\n"); ++ if(!py) _error_("Impossible to continue: py is NULL!\n"); ++ if(!pelements) _error_("Impossible to continue: pelements is NULL!\n"); ++ ++ /*Verify if there are orphan nodes*/ ++ std::set elemvertices; ++ elemvertices.clear(); ++ for(int i=0;iWriteErrorEstimatorsInResults(); ++ #endif ++ //itapopo ++ + int step = -1; + int numberofelements = -1; + int numberofvertices = -1; +@@ -2752,6 +2758,39 @@ + xDelete(elementslist); + } + /*}}}*/ ++void FemModel::WriteErrorEstimatorsInResults(void){/*{{{*/ ++ ++ int step = -1; ++ int numberofelements = -1; ++ IssmDouble time = -1; ++ IssmDouble* stresserror = NULL; ++ IssmDouble* thicknesserror = NULL; ++ ++ if(!this->elements || !this->vertices || !this->results || !this->parameters) return; ++ ++ parameters->FindParam(&step,StepEnum); ++ parameters->FindParam(&time,TimeEnum); ++ numberofelements=this->elements->NumberOfElements(); ++ ++ /*Compute the deviatoric stress tensor*/ ++ this->ZZErrorEstimator(&stresserror); ++ ++ /*Compute the thickness error*/ ++ this->ThicknessZZErrorEstimator(&thicknesserror); ++ ++ /*Write error estimators in Results*/ ++ this->results->AddResult(new GenericExternalResult(this->results->Size()+1,DeviatoricStressErrorEstimatorEnum, ++ stresserror,numberofelements,1,step,time)); ++ ++ this->results->AddResult(new GenericExternalResult(this->results->Size()+1,ThicknessErrorEstimatorEnum, ++ thicknesserror,numberofelements,1,step,time)); ++ /*Cleanup*/ ++ xDelete(stresserror); ++ xDelete(thicknesserror); ++ ++ return; ++} ++/*}}}*/ + void FemModel::GetGroundediceLevelSet(IssmDouble **pmasklevelset){/*{{{*/ + + int elementswidth = this->GetElementsWidth();//just 2D mesh, tria elements +@@ -3211,11 +3250,8 @@ + /*}}}*/ + void FemModel::SmoothedDeviatoricStressTensor(IssmDouble** ptauxx,IssmDouble** ptauyy,IssmDouble** ptauxy){/*{{{*/ + +- this->DeviatoricStressx();//itapopo +- + int elementswidth = this->GetElementsWidth();//just 2D mesh, tria elements + int numberofvertices = this->vertices->NumberOfVertices(); +- + IssmDouble weight = 0.; + IssmDouble* tauxx = NULL; + IssmDouble* tauyy = NULL; +@@ -3230,7 +3266,11 @@ + Vector* vectauxy = new Vector(numberofvertices); + Vector* vectotalweight = new Vector(numberofvertices); + +- for(int i=0;ielements->Size();i++){ ++ /*Update the Deviatoric Stress tensor over the elements*/ ++ this->DeviatoricStressx(); ++ ++ /*Calculate the Smoothed Deviatoric Stress tensor*/ ++ for(int i=0;ielements->Size();i++){ + Element* element=xDynamicCast(this->elements->GetObjectByOffset(i)); + element->GetInputListOnVertices(deviatoricstressxx,DeviatoricStressxxEnum); + element->GetInputListOnVertices(deviatoricstressyy,DeviatoricStressyyEnum); +@@ -3298,7 +3338,7 @@ + /*}}}*/ + void FemModel::ZZErrorEstimator(IssmDouble** pelementerror){/*{{{*/ + +- /*Compute the Zienkiewicz and Zhu (ZZ) error estimator. ++ /*Compute the Zienkiewicz and Zhu (ZZ) error estimator for the deviatoric stress tensor. + * Ref.: Zienkiewicz and Zhu, A Simple Error Estimator and Adaptive Procedure for Practical Engineering Analysis, Int. J. Numer. Meth. Eng, 1987*/ + + IssmDouble Jdet,error,ftxx,ftyy,ftxy; +@@ -3341,11 +3381,11 @@ + ftyy+=(tauyy[n]-smoothedtauyy[elem_vertices[n]])*basis[n]; + ftxy+=(tauxy[n]-smoothedtauxy[elem_vertices[n]])*basis[n]; + } +- error+=Jdet*gauss->weight*( std::pow(ftxx,2)+std::pow(ftyy,2)+std::pow(ftxy,2) ); ++ error+=Jdet*gauss->weight*( std::pow(ftxx,2)+std::pow(ftyy,2)+std::pow(ftxy,2) ); //e^2 + } + /*Set the error in the global vector*/ + sid=element->Sid(); +- velementerror->SetValue(sid,error,INS_VAL); ++ velementerror->SetValue(sid,std::sqrt(error),INS_VAL);//sqrt( e^2 ) + /*Cleanup intermediaries*/ + xDelete(xyz_list); + delete gauss; +@@ -3369,7 +3409,182 @@ + delete velementerror; + } + /*}}}*/ ++void FemModel::SmoothedGradThickness(IssmDouble** pdHdx,IssmDouble** pdHdy){/*{{{*/ + ++ int elementswidth = this->GetElementsWidth();//just 2D mesh, tria elements ++ int numberofvertices = this->vertices->NumberOfVertices(); ++ ++ IssmDouble weight = 0.; ++ IssmDouble* dHdx = NULL; ++ IssmDouble* dHdy = NULL; ++ IssmDouble* totalweight = NULL; ++ IssmDouble* xyz_list = NULL; ++ IssmDouble* H = xNew(elementswidth); ++ IssmDouble* GradH = xNew(2); ++ int* elem_vertices = xNew(elementswidth); ++ Vector* vecdHdx = new Vector(numberofvertices); ++ Vector* vecdHdy = new Vector(numberofvertices); ++ Vector* vectotalweight = new Vector(numberofvertices); ++ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=xDynamicCast(this->elements->GetObjectByOffset(i)); ++ element->GetInputListOnVertices(H,ThicknessEnum); ++ element->GetVerticesSidList(elem_vertices); ++ element->GetVerticesCoordinates(&xyz_list); ++ ++ /*Get the gradient of thickness at the center point (in fact, GradH is constante over the element)*/ ++ Gauss* gauss=element->NewGauss(1); ++ gauss->GaussPoint(gauss->begin()); ++ element->ValueP1DerivativesOnGauss(GradH,H,xyz_list,gauss); ++ ++ /*weight to calculate the smoothed grad H*/ ++ Tria* triaelement = xDynamicCast(element); ++ weight = triaelement->GetArea();//the tria area is a choice for the weight ++ ++ /*dH/dx*/ ++ vecdHdx->SetValue(elem_vertices[0],weight*GradH[0],ADD_VAL); ++ vecdHdx->SetValue(elem_vertices[1],weight*GradH[0],ADD_VAL); ++ vecdHdx->SetValue(elem_vertices[2],weight*GradH[0],ADD_VAL); ++ /*dH/dy*/ ++ vecdHdy->SetValue(elem_vertices[0],weight*GradH[1],ADD_VAL); ++ vecdHdy->SetValue(elem_vertices[1],weight*GradH[1],ADD_VAL); ++ vecdHdy->SetValue(elem_vertices[2],weight*GradH[1],ADD_VAL); ++ /*total weight*/ ++ vectotalweight->SetValue(elem_vertices[0],weight,ADD_VAL); ++ vectotalweight->SetValue(elem_vertices[1],weight,ADD_VAL); ++ vectotalweight->SetValue(elem_vertices[2],weight,ADD_VAL); ++ /*Cleanup intermediaries*/ ++ xDelete(xyz_list); ++ delete gauss; ++ } ++ ++ /*Assemble*/ ++ vecdHdx->Assemble(); ++ vecdHdy->Assemble(); ++ vectotalweight->Assemble(); ++ ++ /*Serialize*/ ++ dHdx = vecdHdx->ToMPISerial(); ++ dHdy = vecdHdy->ToMPISerial(); ++ totalweight = vectotalweight->ToMPISerial(); ++ ++ /*Divide for the total weight*/ ++ for(int i=0;i0); ++ dHdx[i] = dHdx[i]/totalweight[i]; ++ dHdy[i] = dHdy[i]/totalweight[i]; ++ } ++ ++ /*Set output*/ ++ (*pdHdx) = dHdx; ++ (*pdHdy) = dHdy; ++ ++ /*Cleanup*/ ++ delete vecdHdx; ++ delete vecdHdy; ++ delete vectotalweight; ++ xDelete(H); ++ xDelete(GradH); ++ xDelete(totalweight); ++ xDelete(elem_vertices); ++} ++/*}}}*/ ++void FemModel::ThicknessZZErrorEstimator(IssmDouble** pelementerror){/*{{{*/ ++ /*Compute the Zienkiewicz and Zhu (ZZ) error estimator for the thickness ++ * Ref.: Zienkiewicz and Zhu, A Simple Error Estimator and Adaptive Procedure for Practical Engineering Analysis, Int. J. Numer. Meth. Eng, 1987*/ ++ ++ IssmDouble Jdet,error,fdHdx,fdHdy; ++ int sid; ++ int numnodes = this->GetElementsWidth();//just 2D mesh, tria elements, P1 ++ int numberofelements = this->elements->NumberOfElements(); ++ IssmDouble* xyz_list = NULL; ++ IssmDouble* smoothed_dHdx = NULL; ++ IssmDouble* smoothed_dHdy = NULL; ++ IssmDouble* H = xNew(numnodes); ++ IssmDouble* GradH = xNew(2); ++ IssmDouble* basis = xNew(numnodes); ++ int* elem_vertices = xNew(numnodes); ++ Vector* velementerror= new Vector(numberofelements); ++ ++ /*Get smoothed deviatoric stress tensor*/ ++ this->SmoothedGradThickness(&smoothed_dHdx,&smoothed_dHdy); ++ ++ /*Integrate the error over elements*/ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=xDynamicCast(this->elements->GetObjectByOffset(i)); ++ element->GetInputListOnVertices(H,ThicknessEnum); ++ element->GetVerticesSidList(elem_vertices); ++ element->GetVerticesCoordinates(&xyz_list); ++ /*Get the gradient of thickness*/ ++ Gauss* gaussH=element->NewGauss(1); ++ gaussH->GaussPoint(gaussH->begin()); ++ element->ValueP1DerivativesOnGauss(GradH,H,xyz_list,gaussH); ++ /*Integrate*/ ++ Gauss* gauss=element->NewGauss(2); ++ error=0.; ++ for(int ig=gauss->begin();igend();ig++){ ++ gauss->GaussPoint(ig); ++ element->JacobianDeterminant(&Jdet,xyz_list,gauss); ++ element->NodalFunctions(basis,gauss); ++ fdHdx=0;fdHdy=0; ++ for(int n=0;nweight*( std::pow(fdHdx,2)+std::pow(fdHdy,2) ); //e^2 ++ } ++ /*Set the error in the global vector*/ ++ sid=element->Sid(); ++ velementerror->SetValue(sid,std::sqrt(error),INS_VAL);//sqrt( e^2 ) ++ /*Cleanup intermediaries*/ ++ xDelete(xyz_list); ++ delete gaussH; ++ delete gauss; ++ } ++ ++ /*Assemble*/ ++ velementerror->Assemble(); ++ ++ /*Serialize and set output*/ ++ (*pelementerror)=velementerror->ToMPISerial(); ++ ++ /*Cleanup*/ ++ xDelete(smoothed_dHdx); ++ xDelete(smoothed_dHdy); ++ xDelete(H); ++ xDelete(GradH); ++ xDelete(basis); ++ xDelete(elem_vertices); ++ delete velementerror; ++} ++/*}}}*/ ++void FemModel::MeanGroundedIceLevelSet(IssmDouble** pmasklevelset){/*{{{*/ ++ ++ int elementswidth = this->GetElementsWidth(); ++ int numberofelements = this->elements->NumberOfElements(); ++ IssmDouble* elementlevelset = xNew(elementswidth); ++ Vector* vmasklevelset = new Vector(numberofelements); ++ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=xDynamicCast(this->elements->GetObjectByOffset(i)); ++ element->GetInputListOnVertices(elementlevelset,MaskGroundediceLevelsetEnum); ++ int sid = element->Sid(); ++ vmasklevelset->SetValue(sid,(elementlevelset[0]+elementlevelset[1]+elementlevelset[2])/3.,INS_VAL); ++ } ++ ++ /*Assemble*/ ++ vmasklevelset->Assemble(); ++ ++ /*Serialize and set output*/ ++ (*pmasklevelset)=vmasklevelset->ToMPISerial(); ++ ++ /*Cleanup*/ ++ xDelete(elementlevelset); ++ delete vmasklevelset; ++ ++} ++/*}}}*/ ++ + #ifdef _HAVE_DAKOTA_ + void FemModel::DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses){/*{{{*/ + +@@ -4159,66 +4374,65 @@ + #endif + + #ifdef _HAVE_NEOPZ_ +-void FemModel::ReMeshNeopz(int* pnumberofvertices,int* pnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ ++void FemModel::ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist){/*{{{*/ + +- /*elements is in Matlab indexing*/ +- int my_rank = IssmComm::GetRank(); +- int numberofsegments = -1; +- int numberofvertices,numberofelements; +- IssmDouble* vx = NULL; //itapopo this is not being used +- IssmDouble* vy = NULL; //itapopo this is not being used +- IssmDouble* x = NULL; +- IssmDouble* y = NULL; +- IssmDouble* z = NULL; +- int* elementslist = NULL; +- int* segments = NULL; +- IssmDouble* masklevelset = NULL; +- IssmDouble* pelementerror = NULL; +- const int elementswidth = this->GetElementsWidth();//just 2D mesh, tria elements ++ /*pnewelementslist keep vertices in Matlab indexing*/ ++ int my_rank = IssmComm::GetRank(); ++ bool amr_verbose = true; //itapopo ++ IssmDouble* x = NULL; ++ IssmDouble* y = NULL; ++ IssmDouble* z = NULL; ++ int* elementslist = NULL; ++ int oldnumberofelements = this->elements->NumberOfElements(); ++ int newnumberofvertices = -1; ++ int newnumberofelements = -1; ++ IssmDouble* partiallyfloatedelements= NULL;//itapopo verify if it will be used ++ IssmDouble* masklevelset = NULL; ++ IssmDouble* deviatorictensorerror = NULL; ++ IssmDouble* thicknesserror = NULL; + +- /*Solutions which will be used to refine the elements*/ +- this->GetGroundediceLevelSet(&masklevelset);//itapopo verificar se já existe um método igual a esse ++ /*Get the elements in which grounding line goes through*/ ++ //itapopo verificar se irá usar esse this->GetPartiallyFloatedElements(&partiallyfloatedelements); ++ /*Get mean mask level set over each element*/ ++ this->MeanGroundedIceLevelSet(&masklevelset); ++ /*Get the deviatoric error estimator*/ ++ this->ZZErrorEstimator(&deviatorictensorerror); ++ /*Get the thickness error estimator*/ ++ this->ThicknessZZErrorEstimator(&thicknesserror); + +- //Compute the ZZ error estimator per element +- this->ZZErrorEstimator(&pelementerror); +- +- _printf0_("P Element error\n"); +- for(int i=0;ielements->NumberOfElements();i++) _printf0_(""<amr->ExecuteRefinement(type_process,vx,vy,masklevelset, +- numberofvertices,numberofelements,numberofsegments,&x,&y,&z,&elementslist,&segments); +- if(numberofvertices<=0 || numberofelements<=0 /*|| newnumberofsegments<=0*/) _error_("Error in the refinement process."); ++ this->amr->Execute(amr_verbose,oldnumberofelements,partiallyfloatedelements,masklevelset,deviatorictensorerror,thicknesserror, ++ newnumberofvertices,newnumberofelements,&x,&y,&elementslist); ++ z=xNewZeroInit(newnumberofvertices); ++ if(newnumberofvertices<=0 || newnumberofelements<=0) _error_("Error in the ReMeshNeopz."); + } + else{ +- x=xNew(numberofvertices); +- y=xNew(numberofvertices); +- z=xNew(numberofvertices); +- elementslist=xNew(numberofelements*this->GetElementsWidth()); ++ x=xNew(newnumberofvertices); ++ y=xNew(newnumberofvertices); ++ z=xNew(newnumberofvertices); ++ elementslist=xNew(newnumberofelements*this->GetElementsWidth()); + } + + /*Send new mesh to others CPU*/ +- ISSM_MPI_Bcast(&numberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(&numberofelements,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(x,numberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(y,numberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(z,numberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(elementslist,numberofelements*this->GetElementsWidth(),ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&newnumberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&newnumberofelements,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(x,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(y,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(z,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(elementslist,newnumberofelements*this->GetElementsWidth(),ISSM_MPI_INT,0,IssmComm::GetComm()); + + /*Assign the pointers*/ +- (*pelementslist) = elementslist; //Matlab indexing +- (*px) = x; +- (*py) = y; +- (*pz) = z; +- *pnumberofelements = numberofelements; +- *pnumberofvertices = numberofvertices; ++ (*pnewelementslist) = elementslist; //Matlab indexing ++ (*pnewx) = x; ++ (*pnewy) = y; ++ (*pnewz) = z; ++ *pnewnumberofvertices= newnumberofvertices; ++ *pnewnumberofelements= newnumberofelements; + + /*Cleanup*/ +- if(segments) xDelete(segments); + xDelete(masklevelset); +- xDelete(pelementerror); ++ xDelete(deviatorictensorerror); ++ xDelete(thicknesserror); + + } + /*}}}*/ +@@ -4228,7 +4442,6 @@ + int my_rank = IssmComm::GetRank(); + int numberofvertices = this->vertices->NumberOfVertices(); + int numberofelements = this->elements->NumberOfElements(); +- int numberofsegments = 0; //used on matlab + IssmDouble* x = NULL; + IssmDouble* y = NULL; + IssmDouble* z = NULL; +@@ -4281,7 +4494,7 @@ + this->amr = new AdaptiveMeshRefinement(); + //this->amr->SetLevelMax(levelmax); //Set max level of refinement + //this->amr->SetRegions(regionlevel1,regionlevelmax); +- this->amr->CreateInitialMesh(numberofvertices,numberofelements,numberofsegments,elementswidth,x,y,z,elements,NULL); ++ this->amr->CreateInitialMesh(numberofvertices,numberofelements,elementswidth,x,y,elements); + } + this->amr->SetLevelMax(levelmax); //Set max level of refinement + this->amr->SetRegions(regionlevel1,regionlevelmax); +@@ -4297,10 +4510,8 @@ + void FemModel::SetRefPatterns(){/*{{{*/ + + /*Initialize the global variable of refinement patterns*/ +- gRefDBase.InitializeUniformRefPattern(EOned); + gRefDBase.InitializeUniformRefPattern(ETriangle); + +- //gRefDBase.InitializeRefPatterns(); + /*Insert specifics patterns to ISSM core*/ + std::string filepath = REFPATTERNDIR; + std::string filename1 = filepath + "/2D_Triang_Rib_3.rpt"; +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21805) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21806) +@@ -843,6 +843,8 @@ + AmrHmaxEnum, + AmrFieldEnum, + AmrErrEnum, ++ DeviatoricStressErrorEstimatorEnum, ++ ThicknessErrorEstimatorEnum, + /*}}}*/ + ParametersENDEnum, + /*Coordinate Systems{{{*/ +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21805) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21806) +@@ -819,6 +819,8 @@ + case AmrHmaxEnum : return "AmrHmax"; + case AmrFieldEnum : return "AmrField"; + case AmrErrEnum : return "AmrErr"; ++ case DeviatoricStressErrorEstimatorEnum : return "DeviatoricStressErrorEstimator"; ++ case ThicknessErrorEstimatorEnum : return "ThicknessErrorEstimator"; + case ParametersENDEnum : return "ParametersEND"; + case XYEnum : return "XY"; + case XYZEnum : return "XYZ"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21805) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21806) +@@ -837,6 +837,8 @@ + else if (strcmp(name,"AmrHmax")==0) return AmrHmaxEnum; + else if (strcmp(name,"AmrField")==0) return AmrFieldEnum; + else if (strcmp(name,"AmrErr")==0) return AmrErrEnum; ++ else if (strcmp(name,"DeviatoricStressErrorEstimator")==0) return DeviatoricStressErrorEstimatorEnum; ++ else if (strcmp(name,"ThicknessErrorEstimator")==0) return ThicknessErrorEstimatorEnum; + else if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; + else if (strcmp(name,"XY")==0) return XYEnum; + else if (strcmp(name,"XYZ")==0) return XYZEnum; +@@ -872,12 +874,12 @@ + else if (strcmp(name,"Numericalflux")==0) return NumericalfluxEnum; + else if (strcmp(name,"Neumannflux")==0) return NeumannfluxEnum; + else if (strcmp(name,"Param")==0) return ParamEnum; +- else if (strcmp(name,"Moulin")==0) return MoulinEnum; +- else if (strcmp(name,"Pengrid")==0) return PengridEnum; + else stage=8; + } + if(stage==8){ +- if (strcmp(name,"Penpair")==0) return PenpairEnum; ++ if (strcmp(name,"Moulin")==0) return MoulinEnum; ++ else if (strcmp(name,"Pengrid")==0) return PengridEnum; ++ else if (strcmp(name,"Penpair")==0) return PenpairEnum; + else if (strcmp(name,"Profiler")==0) return ProfilerEnum; + else if (strcmp(name,"MatrixParam")==0) return MatrixParamEnum; + else if (strcmp(name,"Masscon")==0) return MassconEnum; +@@ -995,12 +997,12 @@ + else if (strcmp(name,"IceVolume")==0) return IceVolumeEnum; + else if (strcmp(name,"IceVolumeAboveFloatation")==0) return IceVolumeAboveFloatationEnum; + else if (strcmp(name,"TotalFloatingBmb")==0) return TotalFloatingBmbEnum; +- else if (strcmp(name,"TotalGroundedBmb")==0) return TotalGroundedBmbEnum; +- else if (strcmp(name,"TotalSmb")==0) return TotalSmbEnum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"P0")==0) return P0Enum; ++ if (strcmp(name,"TotalGroundedBmb")==0) return TotalGroundedBmbEnum; ++ else if (strcmp(name,"TotalSmb")==0) return TotalSmbEnum; ++ else if (strcmp(name,"P0")==0) return P0Enum; + else if (strcmp(name,"P0Array")==0) return P0ArrayEnum; + else if (strcmp(name,"P1")==0) return P1Enum; + else if (strcmp(name,"P1DG")==0) return P1DGEnum; Index: /issm/oecreview/Archive/21724-22754/ISSM-21806-21807.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21806-21807.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21806-21807.diff (revision 22755) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21806) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21807) +@@ -52,7 +52,7 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,6e-09,5e-08,1e-09,1e-10,1e-13,... +- 4e-10,1e-09,1e-09,1e-09,2e-04,2e-04,1e-09,1e-10,1e-13}; ++ 4e-10,9e-09,5e-09,1e-09,6e-04,3e-04,1e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21806) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21807) +@@ -52,7 +52,7 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,4e-09,5e-08,1e-09,1e-10,1e-13,... +- 1e-10,4e-09,2e-09,2e-09,4e-04,4e-04,1e-09,1e-10,1e-13}; ++ 1e-10,5e-09,3e-09,2e-7,4e-04,4e-04,1e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21807-21808.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21807-21808.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21807-21808.diff (revision 22755) @@ -0,0 +1,1187 @@ +Index: ../trunk-jpl/src/m/classes/regionaloutput.m +=================================================================== +--- ../trunk-jpl/src/m/classes/regionaloutput.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/regionaloutput.m (revision 21808) +@@ -0,0 +1,106 @@ ++%REGIONALOUTPUT class definition ++% ++% Usage: ++% regionaloutput=regionaloutput(); ++% regionaloutput=regionaloutput('name','Volume1','definitionstring','Outputdefinition1','outputnamestring','IceVolume',... ++% 'mask',mask); ++% regionaloutput=regionaloutput('name','Volume1','definitionstring','Outputdefinition1','outputnamestring','IceVolume',... ++% 'maskexpstring','Exp/Mask.exp','model',md) ++% ++% where mask is a vectorial field of size md.mesh.numberofvertices,1 : where vertices with values > 1 are to be included in the calculated region. ++% Alternatively, the user can pass in an Argus file and model object instead of a mask, and mask will be calculated for the user ++% ++% See also: MISFIT, MASSCON, MASSCONAXPBY ++ ++classdef regionaloutput ++ properties (SetAccess=public) ++ %regionaloutput ++ name = ''; ++ definitionstring = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-100]' ++ outputnamestring = ''; %string that identifies the type of output you want, eg. IceVolume, TotalSmb, GroudedArea ++ mask = NaN; %mask vectorial field which identifies the region of interest (value > 0 will be included) ++ maskexpstring = ''; ++ end ++ ++ methods ++ function self = extrude(self,md) % {{{ ++ if ~isnan(self.mask) ++ self.mask=project3d(md,'vector',self.mask,'type','node'); ++ end ++ end % }}} ++ function self = regionaloutput(varargin) % {{{ ++ if nargin==0, ++ self=setdefaultparameters(self); ++ else ++ %use provided options to change fields ++ options=pairoptions(varargin{:}); ++ ++ %get name ++ self.name=getfieldvalue(options,'name',''); ++ if nargin==8 ++ self.mask=getfieldvalue(options,'mask',NaN); ++ if isnan(self.mask) ++ error('regionaloutput error message: ''mask'' field or ''maskexpstring'' and ''model'' fields should be defined!'); ++ end ++ elseif nargin==10 ++ modelname=getfieldvalue(options,'model'); ++ self.maskexpstring=getfieldvalue(options,'maskexpstring'); ++ self=setmaskfromexp(self,modelname); ++ else ++ error('regionaloutput error message: ''mask'' field or ''maskexpstring'' and ''model'' fields should be defined!'); ++ end ++ ++ self.definitionstring=getfieldvalue(options,'definitionstring'); ++ self.outputnamestring=getfieldvalue(options,'outputnamestring'); ++ ++ end ++ end % }}} ++ function self = setdefaultparameters(self) % {{{ ++ end % }}} ++ function self = setmaskfromexp(self,md) % {{{ ++ ++ if length(self.maskexpstring)>0 ++ self.mask=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,self.maskexpstring,'node',1); ++ end ++ end % }}} ++ function md = checkconsistency(self,md,solution,analyses) % {{{ ++ ++ if ~ischar(self.name), ++ error('regionaloutput error message: ''name'' field should be a string!'); ++ end ++ if ~ischar(self.outputnamestring), ++ error('regionaloutput error message: ''outputnamestring'' field should be a string!'); ++ end ++ ++ OutputdefinitionStringArray={}; ++ for i=1:100 ++ OutputdefinitionStringArray{i}=strcat('Outputdefinition',num2str(i)); ++ end ++ self=setmaskfromexp(self,md); ++ ++ md = checkfield(md,'fieldname','self.definitionstring','field',self.definitionstring,'values',OutputdefinitionStringArray); ++ md = checkfield(md,'fieldname','self.mask','field',self.mask,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); ++ ++ end % }}} ++ function md = disp(self) % {{{ ++ ++ disp(sprintf(' Regionaloutput:\n')); ++ ++ fielddisplay(self,'name','identifier for this regional response'); ++ fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from ''Outputdefinition[1-100]'''); ++ fielddisplay(self,'outputnamestring','string that identifies the type of output you want, eg. IceVolume, TotalSmb, GroudedArea'); ++ fielddisplay(self,'mask','mask vectorial field which identifies the region of interest (value > 0 will be included)'); ++ fielddisplay(self,'maskexpstring','name of Argus file that can be passed in to define the regional mask'); ++ ++ end % }}} ++ function md = marshall(self,prefix,md,fid) % {{{ ++ ++ self=setmaskfromexp(self,md); ++ WriteData(fid,prefix,'data',self.name,'name','md.regionaloutput.name','format','String'); ++ WriteData(fid,prefix,'data',self.definitionstring,'name','md.regionaloutput.definitionstring','format','String'); ++ WriteData(fid,prefix,'data',self.outputnamestring,'name','md.regionaloutput.outputnamestring','format','String'); ++ WriteData(fid,prefix,'data',self.mask,'name','md.regionaloutput.mask','format','DoubleMat','mattype',1); ++ ++ end % }}} ++ end ++end +Index: ../trunk-jpl/src/m/classes/massfluxatgate.py +=================================================================== +--- ../trunk-jpl/src/m/classes/massfluxatgate.py (revision 21807) ++++ ../trunk-jpl/src/m/classes/massfluxatgate.py (revision 21808) +@@ -34,10 +34,13 @@ + + string=" Massfluxatgate:" + string="%s\n%s"%(string,fielddisplay(self,'name','identifier for this massfluxatgate response')) +- string="%s\n%s"%(string,fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from Outputdefinition[1-10]')) ++ string="%s\n%s"%(string,fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from Outputdefinition[1-100]')) + string="%s\n%s"%(string,fielddisplay(self,'profilename','name of file (shapefile or argus file) defining a profile (or gate)')) + return string + #}}} ++ def extrude(self,md): # {{{ ++ return self ++ #}}} + def setdefaultparameters(self): # {{{ + return self + #}}} +@@ -48,9 +51,14 @@ + + if not isinstance(self.profilename, basestring): + raise RuntimeError("massfluxatgate error message: 'profilename' field should be a string!") +- +- md = checkfield(md,'field',self.definitionstring,'values',['Outputdefinition1','Outputdefinition2','Outputdefinition3','Outputdefinition4','Outputdefinition5','Outputdefinition6','Outputdefinition7','Outputdefinition8','Outputdefinition9','Outputdefinition10']) + ++ OutputdefinitionStringArray=[] ++ for i in range(1,100): ++ x='Outputdefinition'+str(i) ++ OutputdefinitionStringArray.append(x) ++ ++ md = checkfield(md,'field',self.definitionstring,'values',OutputdefinitionStringArray) ++ + #check the profilename points to a file!: + if not os.path.isfile(self.profilename): + raise RuntimeError("massfluxatgate error message: file name for profile corresponding to gate does not point to a legitimate file on disk!") +Index: ../trunk-jpl/src/m/classes/outputdefinition.py +=================================================================== +--- ../trunk-jpl/src/m/classes/outputdefinition.py (revision 21807) ++++ ../trunk-jpl/src/m/classes/outputdefinition.py (revision 21808) +@@ -21,6 +21,12 @@ + + return string + #}}} ++ def extrude(self,md): # {{{ ++ for definition in self.definitions: ++ definition.extrude(md); ++ ++ return self ++ #}}} + def setdefaultparameters(self): # {{{ + return self + #}}} +Index: ../trunk-jpl/src/m/classes/massconaxpby.m +=================================================================== +--- ../trunk-jpl/src/m/classes/massconaxpby.m (revision 21807) ++++ ../trunk-jpl/src/m/classes/massconaxpby.m (revision 21808) +@@ -2,26 +2,28 @@ + % + % Usage: + % massconaxpby=massconaxpby(); +-% massconaxpby=massconaxpby('name','MassCon58+35','namex','MassCon58','alpha',.5,'namey','MassCon35','beta',.5); ++% massconaxpby=massconaxpby('name','MassCon58+35','namex','MassCon58','alpha',.5,'namey','MassCon35','beta',.5,'definitionstring','Outputdefinition1'); + % + % where name is the name of the massconaxpby object, namex is the name of the first masscon, namey the name of the second masscon and alpha,beta the + % multiplicators. The meaning of axpby here is: resulting masscon is the linear combination (alpha *x + beta * y) + % of two masscons. + % +-% See also: MASSCON ++% See also: MASSCON, REGIONALOUTPUT + + classdef massconaxpby + properties (SetAccess=public) + %masscon axpby +- name = ''; ++ name = ''; + definitionstring = ''; %String that identifies this output definition uniquely, from 'Outputdefinition[1-10]' + namex = ''; + namey = ''; + alpha = NaN; +- beta = NaN; ++ beta = NaN; + end + + methods ++ function self = extrude(self,md) % {{{ ++ end % }}} + function self = massconaxpby(varargin) % {{{ + if nargin==0, + self=setdefaultparameters(self); +@@ -64,7 +66,7 @@ + end % }}} + function md = disp(self) % {{{ + +- disp(sprintf(' Misfit:\n')); ++ disp(sprintf(' Massconaxpby:\n')); + + fielddisplay(self,'name','name'); + fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from Outputdefinition[1-10]'); +@@ -76,12 +78,13 @@ + end % }}} + function md = marshall(self,prefix,md,fid) % {{{ + +- WriteData(fid,prefix,'data',self.name,'name','md.massconaxpby.name','format','String'); +- WriteData(fid,prefix,'data',self.definitionstring,'name','md.massconaxpby.definitionstring','format','String'); +- WriteData(fid,prefix,'data',self.namex,'name','md.massconaxpby.namex','format','String'); +- WriteData(fid,prefix,'data',self.namey,'name','md.massconaxpby.namey','format','String'); +- WriteData(fid,prefix,'data',self.alpha,'name','md.massconaxpby.alpha','format','Double'); +- WriteData(fid,prefix,'data',self.beta,'name','md.massconaxpby.beta','format','Double'); ++ WriteData(fid,prefix,'data',self.name,'name','md.massconaxpby.name','format','String'); ++ WriteData(fid,prefix,'data',self.definitionstring,'name','md.massconaxpby.definitionstring','format','String'); ++ WriteData(fid,prefix,'data',self.namex,'name','md.massconaxpby.namex','format','String'); ++ WriteData(fid,prefix,'data',self.namey,'name','md.massconaxpby.namey','format','String'); ++ WriteData(fid,prefix,'data',self.alpha,'name','md.massconaxpby.alpha','format','Double'); ++ WriteData(fid,prefix,'data',self.beta,'name','md.massconaxpby.beta','format','Double'); ++ + end % }}} + end + end +Index: ../trunk-jpl/src/m/classes/regionaloutput.py +=================================================================== +--- ../trunk-jpl/src/m/classes/regionaloutput.py (nonexistent) ++++ ../trunk-jpl/src/m/classes/regionaloutput.py (revision 21808) +@@ -0,0 +1,103 @@ ++from fielddisplay import fielddisplay ++from pairoptions import pairoptions ++from checkfield import checkfield ++from WriteData import WriteData ++from MeshProfileIntersection import MeshProfileIntersection ++import os ++ ++class regionaloutput(object): ++ """ ++ REGIONALOUTPUT class definition ++ ++ Usage: ++ regionaloutput=regionaloutput(); ++ regionaloutput=regionaloutput('name','Volume1','definitionstring','Outputdefinition1','outputnamestring','IceVolume','mask',mask); ++ regionaloutput=regionaloutput('name','Volume1','definitionstring','Outputdefinition1','outputnamestring','IceVolume','maskexpstring','Exp/Mask.exp','model',md) ++ ++ where mask is a vectorial field of size md.mesh.numberofvertices,1 : where vertices with values > 1 are to be included in the calculated region. ++ Alternatively, the user can pass in an Argus file and model object instead of a mask, and mask will be calculated for the user ++ """ ++ ++ def __init__(self,*args): # {{{ ++ ++ self.name = '' ++ self.definitionstring = '' ++ self.outputnamestring = '' ++ self.mask = float('NaN') ++ self.maskexpstring = '' ++ ++ #set defaults ++ self.setdefaultparameters() ++ ++ #use provided options to change fields ++ options=pairoptions(*args) ++ ++ #OK get other fields ++ self=options.AssignObjectFields(self) ++ ++ #get name ++ modelname=getfieldvalue(options,'model'); ++ self.maskexpstring=getfieldvalue(options,'maskexpstring'); ++ self.setmaskfromexp(self,md) ++ error('regionaloutput error message: ''mask'' field or ''maskexpstring'' and ''model'' fields should be defined!'); ++ ++ #}}} ++ def __repr__(self): # {{{ ++ ++ string=" Regionaloutput:" ++ string="%s\n%s"%(string,fielddisplay(self,'name','identifier for this regional response')) ++ string="%s\n%s"%(string,fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from Outputdefinition[1-100]')) ++ string="%s\n%s"%(string,fielddisplay(self,'outputnamestring','string that identifies the type of output you want, eg. IceVolume, TotalSmb, GroudedArea')) ++ string="%s\n%s"%(string,fielddisplay(self,'mask','mask vectorial field which identifies the region of interest (value > 0 will be included)')) ++ string="%s\n%s"%(string,fielddisplay(self,'maskexpstring','name of Argus file that can be passed in to define the regional mask')) ++ return string ++ #}}} ++ def extrude(self,md): # {{{ ++ self.mask=project3d(md,'vector',self.mask,'type','node') ++ return self ++ #}}} ++ def setdefaultparameters(self): # {{{ ++ return self ++ #}}} ++ def setmaskfromexp(self,md): # {{{ ++ if len(self.maskexpstring,0) > 0: ++ self.mask=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,self.maskexpstring,'node',1) ++ ++ return self ++ # }}} ++ def checkconsistency(self,md,solution,analyses): # {{{ ++ ++ if not isinstance(self.name, basestring): ++ raise RuntimeError("regionaloutput error message: 'name' field should be a string!") ++ ++ if not isinstance(self.outputnamestring, basestring): ++ raise RuntimeError("regionaloutput error message: 'outputnamestring' field should be a string!") ++ ++ if len(self.maskexpstring,0) > 0: ++ if not os.path.isfile(self.profilename): ++ raise RuntimeError("regionaloutput error message: file name for mask exp does not point to a legitimate file on disk!") ++ else: ++ self.setmaskfromexp(self,md) ++ ++ OutputdefinitionStringArray=[] ++ for i in range(1,100): ++ x='Outputdefinition'+str(i) ++ OutputdefinitionStringArray.append(x) ++ ++ md = checkfield(md,'field',self.definitionstring,'values',OutputdefinitionStringArray]) ++ md = checkfield(md,'field',self.mask,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1) ++ ++ return md ++ # }}} ++ def marshall(self,prefix,md,fid): # {{{ ++ ++ #before marshalling, make sure mask is set: ++ self.setmaskfromexp(self,md) ++ ++ #ok, marshall strings and mask: ++ WriteData(fid,prefix,'data',self.name,'name','md.regionaloutput.name','format','String') ++ WriteData(fid,prefix,'data',self.definitionstring,'name','md.regionaloutput.definitionstring','format','String') ++ WriteData(fid,prefix,'data',self.outputnamestring,'name','md.regionaloutput.outputnamestring','format','String'); ++ WriteData(fid,prefix,'data',self.mask,'name','md.regionaloutput.mask','format','DoubleMat','mattype',1); ++ ++ # }}} + +Property changes on: ../trunk-jpl/src/m/classes/regionaloutput.py +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property +Index: ../trunk-jpl/src/m/classes/model.py +=================================================================== +--- ../trunk-jpl/src/m/classes/model.py (revision 21807) ++++ ../trunk-jpl/src/m/classes/model.py (revision 21808) +@@ -466,6 +466,23 @@ + else: + setattr(fieldr,solutionsubfield,subfield) + ++ #OutputDefinitions fields ++ if md1.outputdefinition.definitions: ++ for solutionfield,field in md1.outputdefinition.__dict__.iteritems(): ++ if isinstance(field,list): ++ #get each definition ++ for i,fieldi in enumerate(field): ++ if fieldi: ++ fieldr=getattr(md2.outputdefinition,solutionfield)[i] ++ #get subfields ++ for solutionsubfield,subfield in fieldi.__dict__.iteritems(): ++ if np.size(subfield)==numberofvertices1: ++ setattr(fieldr,solutionsubfield,subfield[pos_node]) ++ elif np.size(subfield)==numberofelements1: ++ setattr(fieldr,solutionsubfield,subfield[pos_elem]) ++ else: ++ setattr(fieldr,solutionsubfield,subfield) ++ + #Keep track of pos_node and pos_elem + md2.mesh.extractedvertices=pos_node+1 + md2.mesh.extractedelements=pos_elem+1 +@@ -648,6 +665,7 @@ + md.mask.extrude(md) + md.qmu.extrude(md) + md.basalforcings.extrude(md) ++ md.outputdefinition.extrude(md) + + #increase connectivity if less than 25: + if md.mesh.average_vertex_connectivity<=25: +@@ -713,14 +731,14 @@ + md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1) + + +- # Hydrologydc variables +- if hasattr(md.hydrology,'hydrologydc'): +- md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1) +- md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1) +- md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1) +- md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1) +- if md.hydrology.isefficientlayer == 1: +- md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1) ++ # Hydrologydc variables ++ if hasattr(md.hydrology,'hydrologydc'): ++ md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1) ++ md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1) ++ md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1) ++ md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1) ++ if md.hydrology.isefficientlayer == 1: ++ md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1) + + #boundary conditions + md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers) +@@ -761,6 +779,23 @@ + md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1) + md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1) + ++ #OutputDefinitions ++ if md.outputdefinition.definitions: ++ for solutionfield,field in md.outputdefinition.__dict__.iteritems(): ++ if isinstance(field,list): ++ #get each definition ++ for i,fieldi in enumerate(field): ++ if fieldi: ++ fieldr=getattr(md.outputdefinition,solutionfield)[i] ++ #get subfields ++ for solutionsubfield,subfield in fieldi.__dict__.iteritems(): ++ if np.size(subfield)==md.mesh.numberofvertices: ++ setattr(fieldr,solutionsubfield,project2d(md,subfield,1)) ++ elif np.size(subfield)==md.mesh.numberofelements: ++ setattr(fieldr,solutionsubfield,project2d(md,subfield,1)) ++ else: ++ setattr(fieldr,solutionsubfield,subfield) ++ + #Initialize with the 2d mesh + mesh=mesh2d() + mesh.x=md.mesh.x2d +Index: ../trunk-jpl/src/m/classes/masscon.m +=================================================================== +--- ../trunk-jpl/src/m/classes/masscon.m (revision 21807) ++++ ../trunk-jpl/src/m/classes/masscon.m (revision 21808) +@@ -2,22 +2,27 @@ + % + % Usage: + % masscon=masscon(); +-% masscon=masscon('name','MassCon58',... %name of a North-East Greenland JPL MassCon ++% masscon=masscon('name','MassCon58','definitionstring','Outputdefinition1',... %name of a North-East Greenland JPL MassCon + % 'levelset',level); + % + % where level is a levelset vectorial field. + % +-% See also: MISFIT ++% See also: MISFIT, MASSCONAXPBY, REGIONALOUTPUT + + classdef masscon + properties (SetAccess=public) + %masscon + name = ''; +- definitionstring = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-10]' ++ definitionstring = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-10]' + levelset = NaN; %levelset vectorial field which identifies the boundaries of the masscon + end + + methods ++ function self = extrude(self,md) % {{{ ++ if ~isnan(self.levelset) ++ self.levelset=project3d(md,'vector',self.levelset,'type','node'); ++ end ++ end % }}} + function self = masscon(varargin) % {{{ + if nargin==0, + self=setdefaultparameters(self); +@@ -39,20 +44,20 @@ + if ~ischar(self.name), + error('masscon error message: ''name'' field should be a string!'); + end +- ++ + OutputdefinitionStringArray={}; + for i=1:100 + OutputdefinitionStringArray{i}=strcat('Outputdefinition',num2str(i)); + end + +- md = checkfield(md,'fieldname','self.definitionstring','field',self.definitionstring,'values','Outputdefinition'); ++ md = checkfield(md,'fieldname','self.definitionstring','field',self.definitionstring,'values',OutputdefinitionStringArray); + md = checkfield(md,'fieldname','self.levelset','field',self.levelset,'timeseries',1,'NaN',1,'Inf',1); + + end % }}} + function md = disp(self) % {{{ +- +- disp(sprintf(' Misfit:\n')); + ++ disp(sprintf(' Masscon:\n')); ++ + fielddisplay(self,'name','identifier for this masscon response'); + fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from ''Outputdefinition[1-10]'''); + fielddisplay(self,'levelset','levelset vectorial field which identifies the boundaries of the masscon'); +@@ -60,9 +65,9 @@ + end % }}} + function md = marshall(self,prefix,md,fid) % {{{ + +- WriteData(fid,prefix,'object',self,'fieldname','name','format','String'); +- WriteData(fid,prefix,'object',self,'fieldname','definitionstring','format','String'); +- WriteData(fid,prefix,'object',self,'fieldname','levelset','format','DoubleMat','mattype',1); ++ WriteData(fid,prefix,'data',self.name,'name','md.masscon.name','format','String'); ++ WriteData(fid,prefix,'data',self.definitionstring,'name','md.masscon.definitionstring','format','String'); ++ WriteData(fid,prefix,'data',self.levelset,'name','md.masscon.levelset','format','DoubleMat','mattype',1); + + end % }}} + end +Index: ../trunk-jpl/src/m/classes/outputdefinition.m +=================================================================== +--- ../trunk-jpl/src/m/classes/outputdefinition.m (revision 21807) ++++ ../trunk-jpl/src/m/classes/outputdefinition.m (revision 21808) +@@ -8,6 +8,11 @@ + definitions = {}; + end + methods ++ function self = extrude(self,md) % {{{ ++ for i=1:length(self.definitions) ++ self.definitions{i}=extrude(self.definitions{i},md); ++ end ++ end % }}} + function self = outputdefinition(varargin) % {{{ + switch nargin + case 0 +Index: ../trunk-jpl/src/m/classes/massfluxatgate.m +=================================================================== +--- ../trunk-jpl/src/m/classes/massfluxatgate.m (revision 21807) ++++ ../trunk-jpl/src/m/classes/massfluxatgate.m (revision 21808) +@@ -15,6 +15,8 @@ + segments = NaN; + end + methods ++ function self = extrude(self,md) % {{{ ++ end % }}} + function self = massfluxatgate(varargin) % {{{ + if nargin==0, + self=setdefaultparameters(self); +@@ -55,7 +57,7 @@ + + fielddisplay(self,'name','identifier for this massfluxatgate response'); + fielddisplay(self,'profilename','name of file (shapefile or argus file) defining a profile (or gate)'); +- fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from ''Outputdefinition[1-10]'''); ++ fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from ''Outputdefinition[1-100]'''); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21807) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21808) +@@ -702,6 +702,7 @@ + OutputdefinitionListEnum, + MassfluxatgateEnum, + NodalvalueEnum, ++ RegionaloutputEnum, + VxObsEnum, + VyObsEnum, + /*}}}*/ +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21807) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21808) +@@ -696,6 +696,7 @@ + case OutputdefinitionListEnum : return "OutputdefinitionList"; + case MassfluxatgateEnum : return "Massfluxatgate"; + case NodalvalueEnum : return "Nodalvalue"; ++ case RegionaloutputEnum : return "Regionaloutput"; + case VxObsEnum : return "VxObs"; + case VyObsEnum : return "VyObs"; + case AbsoluteEnum : return "Absolute"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21807) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21808) +@@ -711,6 +711,7 @@ + else if (strcmp(name,"OutputdefinitionList")==0) return OutputdefinitionListEnum; + else if (strcmp(name,"Massfluxatgate")==0) return MassfluxatgateEnum; + else if (strcmp(name,"Nodalvalue")==0) return NodalvalueEnum; ++ else if (strcmp(name,"Regionaloutput")==0) return RegionaloutputEnum; + else if (strcmp(name,"VxObs")==0) return VxObsEnum; + else if (strcmp(name,"VyObs")==0) return VyObsEnum; + else if (strcmp(name,"Absolute")==0) return AbsoluteEnum; +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 21807) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 21808) +@@ -182,20 +182,21 @@ + + /*masscon variables: */ + int nummasscons; +- char** masscon_name_s = NULL; +- int* masscon_definitionenum_s = NULL; ++ char** masscon_name_s = NULL; ++ char** masscon_definitionstring_s = NULL; + IssmDouble** masscon_levelset_s = NULL; +- int* masscon_levelset_M_s = NULL; +- int* masscon_levelset_N_s = NULL; ++ int* masscon_levelset_M_s = NULL; ++ int* masscon_levelset_N_s = NULL; + + /*Fetch name and levelset, etc ... (see src/m/classes/masscon.m): */ + iomodel->FetchMultipleData(&masscon_name_s,&nummasscons, "md.masscon.name"); +- iomodel->FetchMultipleData(&masscon_definitionenum_s,&nummasscons, "md.masscon.definitionenum"); ++ iomodel->FetchMultipleData(&masscon_definitionstring_s,&nummasscons, "md.masscon.definitionstring"); + iomodel->FetchMultipleData(&masscon_levelset_s,&masscon_levelset_M_s,&masscon_levelset_N_s,&nummasscons,"md.masscon.levelset"); ++ + for(j=0;jAddObject(new Masscon(masscon_name_s[j],masscon_definitionenum_s[j],masscon_levelset_s[j],masscon_levelset_M_s[j])); ++ output_definitions->AddObject(new Masscon(masscon_name_s[j],StringToEnumx(masscon_definitionstring_s[j]),masscon_levelset_s[j],masscon_levelset_M_s[j])); + + } + +@@ -205,6 +206,7 @@ + IssmDouble* matrix = NULL; + + string = masscon_name_s[j]; xDelete(string); ++ string = masscon_definitionstring_s[j]; xDelete(string); + matrix = masscon_levelset_s[j]; xDelete(matrix); + } + xDelete(masscon_name_s); +@@ -211,7 +213,8 @@ + xDelete(masscon_levelset_s); + xDelete(masscon_levelset_M_s); + xDelete(masscon_levelset_N_s); +- xDelete(masscon_definitionenum_s); ++ xDelete(masscon_definitionstring_s); ++ + /*}}}*/ + } + else if (output_definition_enums[i]==MassconaxpbyEnum){ +@@ -256,6 +259,48 @@ + xDelete(masscon_beta_s); + /*}}}*/ + } ++ else if (output_definition_enums[i]==RegionaloutputEnum){ ++ /*Deal with regional output: {{{*/ ++ ++ /*masscon variables: */ ++ int numout; ++ char** reg_name_s = NULL; ++ char** reg_definitionstring_s = NULL; ++ char** reg_outputnamestring_s = NULL; ++ IssmDouble** reg_mask_s = NULL; ++ int* reg_mask_M_s = NULL; ++ int* reg_mask_N_s = NULL; ++ ++ /*Fetch name and mask, etc ... (see src/m/classes/regionaloutput.m): */ ++ iomodel->FetchMultipleData(®_name_s,&numout, "md.regionaloutput.name"); ++ iomodel->FetchMultipleData(®_definitionstring_s,&numout, "md.regionaloutput.definitionstring"); ++ iomodel->FetchMultipleData(®_outputnamestring_s,&numout, "md.regionaloutput.outputnamestring"); ++ iomodel->FetchMultipleData(®_mask_s,®_mask_M_s,®_mask_N_s,&numout, "md.regionaloutput.mask"); ++ for(j=0;jAddObject(new Regionaloutput(reg_name_s[j],StringToEnumx(reg_definitionstring_s[j]),reg_outputnamestring_s[j],reg_mask_s[j],reg_mask_M_s[j])); ++ ++ } ++ ++ /*Free ressources:*/ ++ for(j=0;j(string); ++ string = reg_definitionstring_s[j]; xDelete(string); ++ string = reg_outputnamestring_s[j]; xDelete(string); ++ matrix = reg_mask_s[j]; xDelete(matrix); ++ } ++ xDelete(reg_name_s); ++ xDelete(reg_mask_s); ++ xDelete(reg_mask_M_s); ++ xDelete(reg_mask_N_s); ++ xDelete(reg_outputnamestring_s); ++ xDelete(reg_definitionstring_s); ++ } ++ /*}}}*/ + else _error_("output definition enum " << output_definition_enums[i] << " not supported yet!"); + } + } +Index: ../trunk-jpl/src/c/classes/Massfluxatgate.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Massfluxatgate.h (revision 21807) ++++ ../trunk-jpl/src/c/classes/Massfluxatgate.h (revision 21808) +@@ -83,11 +83,13 @@ + } + /*}}}*/ + ~Massfluxatgate(){/*{{{*/ +- xDelete(this->x1); +- xDelete(this->y1); +- xDelete(this->x2); +- xDelete(this->y2); +- xDelete(this->elements); ++ if(this->numsegments){ ++ xDelete(this->x1); ++ xDelete(this->y1); ++ xDelete(this->x2); ++ xDelete(this->y2); ++ xDelete(this->elements); ++ } + xDelete(this->name); + } + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/classes.h +=================================================================== +--- ../trunk-jpl/src/c/classes/classes.h (revision 21807) ++++ ../trunk-jpl/src/c/classes/classes.h (revision 21808) +@@ -20,6 +20,7 @@ + #include "./Nodalvalue.h" + #include "./Masscon.h" + #include "./Massconaxpby.h" ++#include "./Regionaloutput.h" + + /*Constraints: */ + #include "./Constraints/Constraints.h" +Index: ../trunk-jpl/src/c/classes/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21807) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21808) +@@ -1224,18 +1224,6 @@ + return phi*base_area; + } + /*}}}*/ +-IssmDouble Penta::IceMass(void){/*{{{*/ +- +- IssmDouble rho_ice; +- +- if(!IsIceInElement())return 0.; //do not contribute to the volume of the ice! +- +- /*recover ice density: */ +- rho_ice=matpar->GetMaterialParameter(MaterialsRhoIceEnum); +- +- return rho_ice*this->IceVolume(); +-} +-/*}}}*/ + IssmDouble Penta::IceVolume(void){/*{{{*/ + + /*The volume of a troncated prism is base * 1/3 sum(length of edges)*/ +Index: ../trunk-jpl/src/c/classes/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21807) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21808) +@@ -91,7 +91,6 @@ + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list); + void GetVerticesCoordinatesTop(IssmDouble** pxyz_list); + IssmDouble GroundedArea(void); +- IssmDouble IceMass(void); + IssmDouble IceVolume(void); + IssmDouble IceVolumeAboveFloatation(void); + void InputControlUpdate(IssmDouble scalar,bool save_parameter); +Index: ../trunk-jpl/src/c/classes/Elements/Seg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21807) ++++ ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21808) +@@ -78,7 +78,6 @@ + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list){_error_("not implemented yet");}; + void GetVerticesCoordinatesTop(IssmDouble** pxyz_list){_error_("not implemented yet");}; + IssmDouble GroundedArea(void){_error_("not implemented yet");}; +- IssmDouble IceMass(void){_error_("not implemented yet");}; + IssmDouble IceVolume(void){_error_("not implemented yet");}; + IssmDouble IceVolumeAboveFloatation(void){_error_("not implemented yet");}; + void InputControlUpdate(IssmDouble scalar,bool save_parameter){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Elements/Tetra.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21807) ++++ ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21808) +@@ -86,7 +86,6 @@ + IssmDouble GroundedArea(void){_error_("not implemented yet");}; + bool HasFaceOnBase(); + bool HasFaceOnSurface(); +- IssmDouble IceMass(void){_error_("not implemented yet");}; + IssmDouble IceVolume(void){_error_("not implemented yet");}; + IssmDouble IceVolumeAboveFloatation(void){_error_("not implemented yet");}; + bool IsFaceOnBoundary(void){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21807) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21808) +@@ -1589,18 +1589,6 @@ + } + } + /*}}}*/ +-IssmDouble Tria::IceMass(void){/*{{{*/ +- +- IssmDouble rho_ice; +- +- if(!IsIceInElement())return 0.; //do not contribute to the volume of the ice! +- +- /*recover ice density: */ +- rho_ice=matpar->GetMaterialParameter(MaterialsRhoIceEnum); +- +- return rho_ice*this->IceVolume(); +-} +-/*}}}*/ + IssmDouble Tria::IceVolume(void){/*{{{*/ + + /*The volume of a truncated prism is area_base * 1/numedges sum(length of edges)*/ +Index: ../trunk-jpl/src/c/classes/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21807) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21808) +@@ -90,7 +90,6 @@ + IssmDouble GroundedArea(void); + bool HasEdgeOnBase(); + bool HasEdgeOnSurface(); +- IssmDouble IceMass(void); + IssmDouble IceVolume(void); + IssmDouble IceVolumeAboveFloatation(void); + void InputControlUpdate(IssmDouble scalar,bool save_parameter); +Index: ../trunk-jpl/src/m/classes/model.m +=================================================================== +--- ../trunk-jpl/src/m/classes/model.m (revision 21807) ++++ ../trunk-jpl/src/m/classes/model.m (revision 21808) +@@ -259,8 +259,8 @@ + md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1); + if(md.hydrology.isefficientlayer==1) + md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1); +- end +- end ++ end ++ end + + %materials + md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B); +@@ -309,6 +309,20 @@ + md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1); + end + ++ %outputdefinitions ++ for i=1:length(md.outputdefinition.definitions) ++ if isobject(md.outputdefinition.definitions{i}) ++ %get subfields ++ solutionsubfields=fields(md.outputdefinition.definitions{i}); ++ for j=1:length(solutionsubfields), ++ field=md.outputdefinition.definitions{i}.(solutionsubfields{j}); ++ if length(field)==md.mesh.numberofvertices | length(field)==md.mesh.numberofelements, ++ md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1); ++ end ++ end ++ end ++ end ++ + %Initialize with the 2d mesh + mesh=mesh2d(); + mesh.x=md.mesh.x2d; +@@ -606,6 +620,22 @@ + end + end + ++ %OutputDefinitions fields ++ for i=1:length(md1.outputdefinition.definitions), ++ if isobject(md1.outputdefinition.definitions{i}) ++ %get subfields ++ solutionsubfields=fields(md1.outputdefinition.definitions{i}); ++ for j=1:length(solutionsubfields), ++ field=md1.outputdefinition.definitions{i}.(solutionsubfields{j}); ++ if length(field)==numberofvertices1, ++ md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node); ++ elseif length(field)==numberofelements1, ++ md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem); ++ end ++ end ++ end ++ end ++ + %Keep track of pos_node and pos_elem + md2.mesh.extractedvertices=pos_node; + md2.mesh.extractedelements=pos_elem; +@@ -792,6 +822,7 @@ + md.mask=extrude(md.mask,md); + md.qmu=extrude(md.qmu,md); + md.basalforcings=extrude(md.basalforcings,md); ++ md.outputdefinition=extrude(md.outputdefinition,md); + + %increase connectivity if less than 25: + if md.mesh.average_vertex_connectivity<=25, +Index: ../trunk-jpl/src/c/classes/Regionaloutput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Regionaloutput.h (nonexistent) ++++ ../trunk-jpl/src/c/classes/Regionaloutput.h (revision 21808) +@@ -0,0 +1,148 @@ ++/*!\file Regionaloutput.h ++ * \brief: header file for Regionaloutput object ++ */ ++ ++#ifndef _REGIONALOUTPUT_H_ ++#define _REGIONALOUTPUT_H_ ++ ++/*Headers:*/ ++/*{{{*/ ++#include "./Definition.h" ++#include "../datastructures/datastructures.h" ++#include "./Elements/Element.h" ++#include "./Elements/Elements.h" ++#include "./FemModel.h" ++#include "../classes/Params/Parameters.h" ++ ++/*}}}*/ ++ ++class Regionaloutput: public Object, public Definition{ ++ ++ public: ++ ++ int definitionenum; ++ char* outputname; ++ char* name; ++ IssmDouble* mask; ++ int M; ++ ++ /*Regionalicevolume: constructors, destructors :*/ ++ Regionaloutput(){/*{{{*/ ++ ++ this->definitionenum = -1; ++ this->outputname = NULL; ++ this->name = NULL; ++ this->mask=NULL; ++ this->M=0; ++ ++ } ++ /*}}}*/ ++ Regionaloutput(char* in_name, int in_definitionenum, char* in_outputname, IssmDouble* maskin, int Min){ /*{{{*/ ++ ++ this->definitionenum=in_definitionenum; ++ this->outputname = xNew(strlen(in_outputname)+1); ++ xMemCpy(this->outputname,in_outputname,strlen(in_outputname)+1); ++ this->name = xNew(strlen(in_name)+1); ++ xMemCpy(this->name,in_name,strlen(in_name)+1); ++ ++ this->mask = xNew(Min); ++ xMemCpy(this->mask, maskin, Min); ++ ++ this->M=Min; ++ ++ } ++ /*}}}*/ ++ ~Regionaloutput(){/*{{{*/ ++ if(this->name)xDelete(this->name); ++ if(this->outputname)xDelete(this->outputname); ++ if(this->mask)xDelete(this->mask); ++ } ++ /*}}}*/ ++ /*Object virtual function resolutoin: */ ++ Object* copy() {/*{{{*/ ++ Regionaloutput* mf = new Regionaloutput(this->name,this->definitionenum,this->outputname,this->mask,this->M); ++ return (Object*) mf; ++ } ++ /*}}}*/ ++ void DeepEcho(void){/*{{{*/ ++ this->Echo(); ++ } ++ /*}}}*/ ++ void Echo(void){/*{{{*/ ++ _printf_(" Regionaloutput: " << this->name << " " << this->definitionenum << "\n"); ++ _printf_(" outputname enum: " << this->outputname << "Enum\n"); ++ _printf_(" mask: " << this->mask << "\n"); ++ _printf_(" M: " << this->M << "\n"); ++ } ++ /*}}}*/ ++ int Id(void){/*{{{*/ ++ return -1; ++ } ++ /*}}}*/ ++ void Marshall(char** pmarshalled_data,int* pmarshalled_data_size, int marshall_direction){/*{{{*/ ++ _error_("not implemented yet!"); ++ } ++ /*}}}*/ ++ int ObjectEnum(void){/*{{{*/ ++ return RegionaloutputEnum; ++ } ++ /*}}}*/ ++ /*Definition virtual function resolutoin: */ ++ int DefinitionEnum(){/*{{{*/ ++ ++ return this->definitionenum; ++ } ++ /*}}}*/ ++ char* Name(){/*{{{*/ ++ ++ char* name2=xNew(strlen(this->name)+1); ++ xMemCpy(name2,this->name,strlen(this->name)+1); ++ ++ return name2; ++ } ++ /*}}}*/ ++ IssmDouble Response(FemModel* femmodel){/*{{{*/ ++ ++ int i; ++ IssmDouble val_t=0.; ++ IssmDouble all_val_t=0.; ++ int outputenum = StringToEnumx(this->outputname); ++ ++ for(i=0;ielements->Size();i++){ ++ Element* element=(Element*)femmodel->elements->GetObjectByOffset(i); ++ switch(outputenum){ ++ case GroundedAreaEnum: ++ val_t+=element->GroundedArea(this->mask); ++ break; ++ case IceMassEnum: ++ val_t+=element->IceMass(this->mask); ++ break; ++ case IceVolumeEnum: ++ val_t+=element->IceVolume(this->mask); ++ break; ++ case IceVolumeAboveFloatationEnum: ++ val_t+=element->IceVolumeAboveFloatation(this->mask); ++ break; ++ case TotalFloatingBmbEnum: ++ val_t+=element->TotalFloatingBmb(this->mask); ++ break; ++ case TotalGroundedBmbEnum: ++ val_t+=element->TotalGroundedBmb(this->mask); ++ break; ++ case TotalSmbEnum: ++ val_t+=element->TotalSmb(this->mask); ++ break; ++ default: ++ _error_("Regional output type " << this->outputname << " not supported yet!"); ++ } ++ } ++ ++ ISSM_MPI_Allreduce ( (void*)&val_t,(void*)&all_val_t,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); ++ val_t=all_val_t; ++ ++ return val_t; ++ } ++ /*}}}*/ ++}; ++ ++#endif /* _REGIONALOUTPUT_H_ */ +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21807) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21808) +@@ -1340,6 +1340,19 @@ + + } + /*}}}*/ ++IssmDouble Element::GroundedArea(IssmDouble* mask){/*{{{*/ ++ ++ /*Retrieve values of the mask defining the element: */ ++ for(int i=0;iGetNumberOfVertices();i++){ ++ if(mask[this->vertices[i]->Sid()]<=0.){ ++ return 0.; ++ } ++ } ++ ++ /*Return: */ ++ return this->GroundedArea(); ++} ++/*}}}*/ + bool Element::HasNodeOnBase(){/*{{{*/ + return (this->inputs->Max(MeshVertexonbaseEnum)>0.); + }/*}}}*/ +@@ -1346,6 +1359,57 @@ + bool Element::HasNodeOnSurface(){/*{{{*/ + return (this->inputs->Max(MeshVertexonsurfaceEnum)>0.); + }/*}}}*/ ++IssmDouble Element::IceMass(void){/*{{{*/ ++ ++ IssmDouble rho_ice; ++ ++ if(!IsIceInElement())return 0.; //do not contribute to the volume of the ice! ++ ++ /*recover ice density: */ ++ rho_ice=matpar->GetMaterialParameter(MaterialsRhoIceEnum); ++ ++ return rho_ice*this->IceVolume(); ++} ++/*}}}*/ ++IssmDouble Element::IceMass(IssmDouble* mask){/*{{{*/ ++ ++ /*Retrieve values of the mask defining the element: */ ++ for(int i=0;iGetNumberOfVertices();i++){ ++ if(mask[this->vertices[i]->Sid()]<=0.){ ++ return 0.; ++ } ++ } ++ ++ /*Return: */ ++ return this->IceMass(); ++} ++/*}}}*/ ++IssmDouble Element::IceVolume(IssmDouble* mask){/*{{{*/ ++ ++ /*Retrieve values of the mask defining the element: */ ++ for(int i=0;iGetNumberOfVertices();i++){ ++ if(mask[this->vertices[i]->Sid()]<=0.){ ++ return 0.; ++ } ++ } ++ ++ /*Return: */ ++ return this->IceVolume(); ++} ++/*}}}*/ ++IssmDouble Element::IceVolumeAboveFloatation(IssmDouble* mask){/*{{{*/ ++ ++ /*Retrieve values of the mask defining the element: */ ++ for(int i=0;iGetNumberOfVertices();i++){ ++ if(mask[this->vertices[i]->Sid()]<=0.){ ++ return 0.; ++ } ++ } ++ ++ /*Return: */ ++ return this->IceVolumeAboveFloatation(); ++} ++/*}}}*/ + int Element::Id(){/*{{{*/ + + return this->id; +@@ -2951,6 +3015,45 @@ + _assert_(matpar); + return this->matpar->TMeltingPoint(pressure); + }/*}}}*/ ++IssmDouble Element::TotalFloatingBmb(IssmDouble* mask){/*{{{*/ ++ ++ /*Retrieve values of the mask defining the element: */ ++ for(int i=0;iGetNumberOfVertices();i++){ ++ if(mask[this->vertices[i]->Sid()]<=0.){ ++ return 0.; ++ } ++ } ++ ++ /*Return: */ ++ return this->TotalFloatingBmb(); ++} ++/*}}}*/ ++IssmDouble Element::TotalGroundedBmb(IssmDouble* mask){/*{{{*/ ++ ++ /*Retrieve values of the mask defining the element: */ ++ for(int i=0;iGetNumberOfVertices();i++){ ++ if(mask[this->vertices[i]->Sid()]<=0.){ ++ return 0.; ++ } ++ } ++ ++ /*Return: */ ++ return this->TotalGroundedBmb(); ++} ++/*}}}*/ ++IssmDouble Element::TotalSmb(IssmDouble* mask){/*{{{*/ ++ ++ /*Retrieve values of the mask defining the element: */ ++ for(int i=0;iGetNumberOfVertices();i++){ ++ if(mask[this->vertices[i]->Sid()]<=0.){ ++ return 0.; ++ } ++ } ++ ++ /*Return: */ ++ return this->TotalSmb(); ++} ++/*}}}*/ + void Element::TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,int transformenum){/*{{{*/ + + /*All nodes have the same Coordinate System*/ +Index: ../trunk-jpl/src/c/classes/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21807) ++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21808) +@@ -108,8 +108,13 @@ + IssmDouble GetYcoord(IssmDouble* xyz_list,Gauss* gauss); + IssmDouble GetZcoord(IssmDouble* xyz_list,Gauss* gauss); + void GradientIndexing(int* indexing,int control_index,bool onsid=false); ++ IssmDouble GroundedArea(IssmDouble* mask); + bool HasNodeOnBase(); + bool HasNodeOnSurface(); ++ IssmDouble IceMass(); ++ IssmDouble IceMass(IssmDouble* mask); ++ IssmDouble IceVolume(IssmDouble* mask); ++ IssmDouble IceVolumeAboveFloatation(IssmDouble* mask); + int Id(); + void InputChangeName(int enum_type,int enum_type_old); + void InputCreate(IssmDouble* vector,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code); +@@ -149,6 +154,9 @@ + void StressMaxPrincipalCreateInput(void); + void ThermalToEnthalpy(IssmDouble* penthalpy,IssmDouble temperature,IssmDouble waterfraction,IssmDouble pressure); + IssmDouble TMeltingPoint(IssmDouble pressure); ++ IssmDouble TotalFloatingBmb(IssmDouble* mask); ++ IssmDouble TotalGroundedBmb(IssmDouble* mask); ++ IssmDouble TotalSmb(IssmDouble* mask); + void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,int cs_enum); + void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); + void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array); +@@ -211,7 +219,6 @@ + virtual void GetVerticesCoordinatesBase(IssmDouble** xyz_list)=0; + virtual void GetVerticesCoordinatesTop(IssmDouble** xyz_list)=0; + virtual IssmDouble GroundedArea(void)=0; +- virtual IssmDouble IceMass(void)=0; + virtual IssmDouble IceVolume(void)=0; + virtual IssmDouble IceVolumeAboveFloatation(void)=0; + virtual void InputControlUpdate(IssmDouble scalar,bool save_parameter)=0; Index: /issm/oecreview/Archive/21724-22754/ISSM-21808-21809.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21808-21809.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21808-21809.diff (revision 22755) @@ -0,0 +1,43 @@ +Index: ../trunk-jpl/src/m/classes/misfit.m +=================================================================== +--- ../trunk-jpl/src/m/classes/misfit.m (revision 21808) ++++ ../trunk-jpl/src/m/classes/misfit.m (revision 21809) +@@ -18,7 +18,7 @@ + properties (SetAccess=public) + %misfit + name = ''; +- definitionstring = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-10]' ++ definitionstring = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-100]' + model_string = ''; %string for field that is modeled + observation = NaN; %observed field that we compare the model against + observation_string = ''; %string for observed field. +@@ -30,6 +30,14 @@ + end + + methods ++ function self = extrude(self,md) % {{{ ++ if ~isnan(self.weights) ++ self.weights=project3d(md,'vector',self.weights,'type','node'); ++ end ++ if ~isnan(self.observation) ++ self.observation=project3d(md,'vector',self.observation,'type','node'); ++ end ++ end % }}} + function self = misfit(varargin) % {{{ + if nargin==0, + self=setdefaultparameters(self); +Index: ../trunk-jpl/src/m/classes/SMBforcing.m +=================================================================== +--- ../trunk-jpl/src/m/classes/SMBforcing.m (revision 21808) ++++ ../trunk-jpl/src/m/classes/SMBforcing.m (revision 21809) +@@ -67,8 +67,8 @@ + yts=md.constants.yts; + + WriteData(fid,prefix,'name','md.smb.model','data',1,'format','Integer'); +- WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); +- %WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','CompressedMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ %WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','CompressedMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + + %process requested outputs + outputs = self.requested_outputs; Index: /issm/oecreview/Archive/21724-22754/ISSM-21809-21810.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21809-21810.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21809-21810.diff (revision 22755) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/m/classes/SMBforcing.m +=================================================================== +--- ../trunk-jpl/src/m/classes/SMBforcing.m (revision 21809) ++++ ../trunk-jpl/src/m/classes/SMBforcing.m (revision 21810) +@@ -67,8 +67,8 @@ + yts=md.constants.yts; + + WriteData(fid,prefix,'name','md.smb.model','data',1,'format','Integer'); +- %WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); +- WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','CompressedMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ %WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','CompressedMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + + %process requested outputs + outputs = self.requested_outputs; Index: /issm/oecreview/Archive/21724-22754/ISSM-21810-21811.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21810-21811.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21810-21811.diff (revision 22755) @@ -0,0 +1,50 @@ +Index: ../trunk-jpl/src/c/classes/Regionaloutput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Regionaloutput.h (revision 21810) ++++ ../trunk-jpl/src/c/classes/Regionaloutput.h (revision 21811) +@@ -114,6 +114,9 @@ + case GroundedAreaEnum: + val_t+=element->GroundedArea(this->mask); + break; ++ case FloatingAreaEnum: ++ val_t+=element->FloatingArea(this->mask); ++ break; + case IceMassEnum: + val_t+=element->IceMass(this->mask); + break; +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21810) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21811) +@@ -842,6 +842,19 @@ + void Element::FindParam(int** pvalues,int* psize,int paramenum){/*{{{*/ + this->parameters->FindParam(pvalues,psize,paramenum); + }/*}}}*/ ++IssmDouble Element::FloatingArea(IssmDouble* mask){/*{{{*/ ++ ++ /*Retrieve values of the mask defining the element: */ ++ for(int i=0;iGetNumberOfVertices();i++){ ++ if(mask[this->vertices[i]->Sid()]<=0.){ ++ return 0.; ++ } ++ } ++ ++ /*Return: */ ++ return this->FloatingArea(); ++} ++/*}}}*/ + void Element::GetDofList(int** pdoflist,int approximation_enum,int setenum){/*{{{*/ + + /*Fetch number of nodes and dof for this finite element*/ +Index: ../trunk-jpl/src/c/classes/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21810) ++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21811) +@@ -80,6 +80,7 @@ + void FindParam(int* pvalue,int paramenum); + void FindParam(IssmDouble* pvalue,int paramenum); + void FindParam(int** pvalues,int* psize,int paramenum); ++ IssmDouble FloatingArea(IssmDouble* mask); + void GetDofList(int** pdoflist,int approximation_enum,int setenum); + void GetDofListPressure(int** pdoflist,int setenum); + void GetDofListVelocity(int** pdoflist,int setenum); Index: /issm/oecreview/Archive/21724-22754/ISSM-21811-21812.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21811-21812.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21811-21812.diff (revision 22755) @@ -0,0 +1,132 @@ +Index: ../trunk-jpl/src/c/classes/AmrBamg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.h (revision 21811) ++++ ../trunk-jpl/src/c/classes/AmrBamg.h (revision 21812) +@@ -12,13 +12,15 @@ + class AmrBamg{ + + public: ++ int fieldenum; ++ + /* Constructor, destructor etc*/ +- AmrBamg(IssmDouble hmin, IssmDouble hmax); ++ AmrBamg(IssmDouble hmin, IssmDouble hmax,int fieldenum_in,IssmDouble err_in); + ~AmrBamg(); + + /*General methods*/ + void Initialize(int* elements,IssmDouble* x,IssmDouble* y,int numberofvertices,int numberofelements); +- void ExecuteRefinementBamg(int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist); ++ void ExecuteRefinementBamg(IssmDouble* field,int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist); + + private: + BamgGeom* geometry; +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21811) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21812) +@@ -16,8 +16,9 @@ + using namespace std; + + /*Constructor, copy, clean up and destructor*/ +-AmrBamg::AmrBamg(IssmDouble hmin, IssmDouble hmax){/*{{{*/ ++AmrBamg::AmrBamg(IssmDouble hmin, IssmDouble hmax,int fieldenum_in,IssmDouble err){/*{{{*/ + ++ this->fieldenum = fieldenum_in; + this->geometry = NULL; + this->fathermesh = NULL; + this->previousmesh = NULL; +@@ -46,6 +47,11 @@ + this->options->splitcorners = 1; + this->options->hmin = hmin; + this->options->hmax = hmax; ++ ++ this->options->err=xNew(1); ++ this->options->errSize[0]=1; ++ this->options->errSize[1]=1; ++ this->options->err[0] = err; + } + /*}}}*/ + AmrBamg::~AmrBamg(){/*{{{*/ +@@ -79,7 +85,7 @@ + /*Cleanup and return*/ + delete Th; + }/*}}}*/ +-void AmrBamg::ExecuteRefinementBamg(int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ ++void AmrBamg::ExecuteRefinementBamg(IssmDouble* field,int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ + + /*Intermediaries*/ + BamgGeom* geomout=new BamgGeom(); +@@ -89,15 +95,28 @@ + _assert_(this->geometry); + _assert_(this->options); + _assert_(this->fathermesh); ++ _assert_(field); + ++ /*Prepare field for metric*/ ++ this->options->field = field; ++ + /*remesh*/ + if(this->previousmesh){ ++ this->options->fieldSize[0] = this->previousmesh->VerticesSize[0]; ++ this->options->fieldSize[1] = 1; + Bamgx(meshout,geomout,this->previousmesh,this->geometry,this->options); + } + else{ ++ this->options->fieldSize[0] = this->fathermesh->VerticesSize[0]; ++ this->options->fieldSize[1] = 1; + Bamgx(meshout,geomout,this->fathermesh,this->geometry,this->options); + } + ++ /*remove field for memory management (FemModel is taking care of deleting it)*/ ++ this->options->field = NULL; ++ this->options->fieldSize[0] = 0; ++ this->options->fieldSize[1] = 0; ++ + /*Change previous mesh*/ + if(this->previousmesh) delete this->previousmesh; + this->previousmesh = meshout; +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21811) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21812) +@@ -4300,8 +4300,16 @@ + /*Get Rank*/ + int my_rank = IssmComm::GetRank(); + ++ /*Get vector to create metric*/ ++ int numberofvertices = this->vertices->NumberOfVertices(); ++ Vector *vector = new Vector(numberofvertices); ++ GetVectorFromInputsx(&vector,this,this->amrbamg->fieldenum,VertexSIdEnum); ++ vector->Assemble(); ++ IssmDouble* vector_serial = vector->ToMPISerial(); ++ delete vector; ++ + if(my_rank==0){ +- this->amrbamg->ExecuteRefinementBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); ++ this->amrbamg->ExecuteRefinementBamg(vector_serial,&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); + if(newnumberofvertices<=0 || newnumberofelements<=0) _error_("Error in the refinement process."); + } + else{ +@@ -4310,6 +4318,7 @@ + newz=xNew(newnumberofvertices); + newelementslist=xNew(newnumberofelements*this->GetElementsWidth()); + } ++ xDelete(vector_serial); + + /*Send new mesh to others CPU*/ + ISSM_MPI_Bcast(&newnumberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +@@ -4357,10 +4366,11 @@ + this->parameters->FindParam(&fieldenum,AmrFieldEnum); + this->parameters->FindParam(&err,AmrErrEnum); + +- /*Create bamg data structures for bamg (only cpu 0)*/ ++ /*Create bamg data structures for bamg*/ ++ this->amrbamg = new AmrBamg(hmin,hmax,fieldenum,err); ++ ++ /*Re-create original mesh and put it in bamg structure (only cpu 0)*/ + if(my_rank==0){ +- /*Re-create original mesh and put it in bamg structure*/ +- this->amrbamg = new AmrBamg(hmin,hmax); + this->amrbamg->Initialize(elements,x,y,numberofvertices,numberofelements); + } + Index: /issm/oecreview/Archive/21724-22754/ISSM-21812-21813.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21812-21813.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21812-21813.diff (revision 22755) @@ -0,0 +1,64 @@ +Index: ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh +=================================================================== +--- ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh (nonexistent) ++++ ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh (revision 21813) +@@ -0,0 +1,52 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf install petsc-3.7.6 src ++mkdir install src ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' ++ ++#Untar and move petsc to install directory ++tar -zxvf petsc-3.7.6.tar.gz ++mv petsc-3.7.6/* src/ ++rm -rf petsc-3.7.6 ++ ++#configure ++cd src ++./config/configure.py \ ++ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ ++ --with-blas-lapack-dir="/opt/intel/compilers_and_libraries_2016.3.210/linux/mkl/lib/" \ ++ --with-mpi-dir="/opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/" \ ++ --known-mpi-shared-libraries=1 \ ++ --with-debugging=0 \ ++ --with-valgrind=0 \ ++ --with-x=0 \ ++ --with-ssl=0 \ ++ --with-batch=1 \ ++ --with-shared-libraries=1 \ ++ --download-metis=1 \ ++ --download-parmetis=1 \ ++ --download-mumps=1 \ ++ --download-scalapack=1 ++ ++#prepare script to reconfigure petsc ++cat > script.queue << EOF ++#PBS -A open ++#PBS -l nodes=1:ppn=1 ++#PBS -l walltime=200 ++ ++module load intel/16.0.3 ++module load impi/5.1.3 ++module load mkl/11.3.3 ++ ++export PATH="$PATH:." ++mpiexec -np 1 ./conftest-arch-linux2-c-opt ++EOF ++ ++#print instructions ++echo "== Now: cd src/ " ++echo "== qsub -q devel script.queue " ++echo "== Then run reconfigure script generated by PETSc and follow instructions" + +Property changes on: ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property Index: /issm/oecreview/Archive/21724-22754/ISSM-21813-21814.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21813-21814.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21813-21814.diff (revision 22755) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh +=================================================================== +--- ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh (revision 21813) ++++ ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh (revision 21814) +@@ -35,7 +35,7 @@ + #prepare script to reconfigure petsc + cat > script.queue << EOF + #PBS -A open +-#PBS -l nodes=1:ppn=1 ++#PBS -l nodes=1:ppn=1:stmem + #PBS -l walltime=200 + + module load intel/16.0.3 +@@ -48,5 +48,5 @@ + + #print instructions + echo "== Now: cd src/ " +-echo "== qsub -q devel script.queue " ++echo "== qsub script.queue " + echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/oecreview/Archive/21724-22754/ISSM-21814-21815.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21814-21815.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21814-21815.diff (revision 22755) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh +=================================================================== +--- ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh (revision 21814) ++++ ../trunk-jpl/externalpackages/petsc/install-3.7-aci.sh (revision 21815) +@@ -43,7 +43,8 @@ + module load mkl/11.3.3 + + export PATH="$PATH:." +-mpiexec -np 1 ./conftest-arch-linux2-c-opt ++cd $ISSM_DIR/externalpackages/petsc/src ++mpirun -np 1 ./conftest-arch-linux2-c-opt + EOF + + #print instructions Index: /issm/oecreview/Archive/21724-22754/ISSM-21815-21816.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21815-21816.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21815-21816.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/configure.ac +=================================================================== +--- ../trunk-jpl/configure.ac (revision 21815) ++++ ../trunk-jpl/configure.ac (revision 21816) +@@ -19,7 +19,7 @@ + AC_PROG_CPP + AC_PROG_CXX([icpc cl icl g++]) + AC_PROG_F77([ifort g77 gfortran]) +-AC_PROG_FC([gfortran]) ++AC_PROG_FC([ifort gfortran]) + + #AUTOMAKE + #Initialize automake and declare foreign so that we don't need a ChangeLog, INSTALL, etc Index: /issm/oecreview/Archive/21724-22754/ISSM-21816-21817.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21816-21817.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21816-21817.diff (revision 22755) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21816) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21817) +@@ -52,7 +52,7 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,6e-09,5e-08,1e-09,1e-10,1e-13,... +- 4e-10,9e-09,5e-09,1e-09,6e-04,3e-04,1e-09,1e-10,1e-13}; ++ 4e-10,9e-09,5e-09,3e-09,6e-04,5e-04,2e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21816) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21817) +@@ -52,7 +52,7 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,4e-09,5e-08,1e-09,1e-10,1e-13,... +- 1e-10,5e-09,3e-09,2e-7,4e-04,4e-04,1e-09,1e-10,1e-13}; ++ 1e-10,5e-09,3e-09,2e-7,5e-04,4e-04,1e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21817-21818.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21817-21818.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21817-21818.diff (revision 22755) @@ -0,0 +1,129 @@ +Index: ../trunk-jpl/src/m/classes/clusters/aci.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/aci.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/clusters/aci.m (revision 21818) +@@ -0,0 +1,117 @@ ++%ACI class definition ++% ++% Usage: ++% cluster=aci(); ++% cluster=aci('np',3); ++% cluster=aci('np',3,'login','username'); ++ ++classdef aci ++ properties (SetAccess=public) ++ % {{{ ++ name=''; ++ login=''; ++ nodes=0; ++ ppn=0; ++ time=0; ++ port=0; ++ queue=''; ++ codepath=''; ++ executionpath=''; ++ modules={}; ++ end ++ %}}} ++ methods ++ function cluster=aci(varargin) % {{{ ++ ++ %initialize cluster using default settings if provided ++ if (exist('aci_settings')==2), aci_settings; end ++ ++ %use provided options to change fields ++ cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); ++ end ++ %}}} ++ function disp(cluster) % {{{ ++ % display the object ++ disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); ++ disp(sprintf(' name: %s',cluster.name)); ++ disp(sprintf(' login: %s',cluster.login)); ++ disp(sprintf(' port: %i',cluster.port)); ++ disp(sprintf(' time: %i (in minutes)',cluster.time)); ++ disp(sprintf(' nodes: %i (number of nodes)',cluster.nodes)); ++ disp(sprintf(' ppn: %i (process per nodes)',cluster.ppn)); ++ disp(sprintf(' queue: %s',cluster.queue)); ++ disp(sprintf(' codepath: %s',cluster.codepath)); ++ disp(sprintf(' executionpath: %s',cluster.executionpath)); ++ end ++ %}}} ++ function md = checkconsistency(cluster,md,solution,analyses) % {{{ ++ ++ available_queues={'brp106_a_g_sc_default','open'}; ++ queue_requirements_time=[Inf 48*60]; ++ queue_requirements_np=[260 260]; ++ ++ QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.ppn*cluster.nodes,1) ++ ++ %Miscelaneous ++ if cluster.ppn>20, md = checkmessage(md,'cannot request more that 20 cores per node'); end ++ if isempty(cluster.login), md = checkmessage(md,'login empty'); end ++ if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end ++ if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end ++ end ++ %}}} ++ function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ ++ ++ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end ++ if(isgprof), disp('gprof not supported by cluster, ignoring...'); end ++ ++ %write queuing script ++ fid=fopen([modelname '.queue'],'w'); ++ fprintf(fid,'#PBS -A %s\n', cluster.queue); %open or brp106.... ++ fprintf(fid,'#PBS -l nodes=%i:ppn=%i:stmem\n',cluster.nodes,cluster.ppn); ++ fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); % walltime is in seconds ++ fprintf(fid,'#PBS -o %s.outlog\n',(modelname)); ++ fprintf(fid,'#PBS -e %s.errlog\n',(modelname)); ++ fprintf(fid,'source ~/.bashrc\n'); ++ fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); ++ for i=1:numel(cluster.modules) ++ fprintf(fid,'module load %s\n', cluster.modules{i}); ++ end ++ fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.nodes*cluster.ppn,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); ++ if ~io_gather, %concatenate the output files: ++ fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); ++ end ++ fclose(fid); ++ end %}}} ++ function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ ++ ++ %compress the files into one zip. ++ compressstring=['tar -zcf ' dirname '.tar.gz ']; ++ for i=1:numel(filelist), ++ compressstring = [compressstring ' ' filelist{i}]; ++ end ++ system(compressstring); ++ ++ disp('uploading input file and queueing script'); ++ issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']}); ++ ++ end %}}} ++ function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ ++ ++ disp('launching solution sequence on remote cluster'); ++ if ~isempty(restart) ++ launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && hostname && qsub ' modelname '.queue ']; ++ else ++ launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... ++ ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && hostname && qsub ' modelname '.queue ']; ++ end ++ issmssh(cluster.name,cluster.login,cluster.port,launchcommand); ++ end %}}} ++ function Download(cluster,dirname,filelist)% {{{ ++ ++ %copy files from cluster to current directory ++ directory=[cluster.executionpath '/' dirname '/']; ++ issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); ++ ++ end %}}} ++ end ++end + +Property changes on: ../trunk-jpl/src/m/classes/clusters/aci.m +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property Index: /issm/oecreview/Archive/21724-22754/ISSM-21818-21819.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21818-21819.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21818-21819.diff (revision 22755) @@ -0,0 +1,44 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21818) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21819) +@@ -1735,7 +1735,7 @@ + } + else{ + /*last chance for the output definition, if the enum is one of Outputdefinition[1-10]Enum:*/ +- if(output_enum>=Outputdefinition1Enum && output_enum <=Outputdefinition10Enum){ ++ if(output_enum>=Outputdefinition1Enum && output_enum <=Outputdefinition100Enum){ + double_result = OutputDefinitionsResponsex(this,output_enum); + if(save_results){ + results->AddResult(new GenericExternalResult(results->Size()+1,output_string,reCast(double_result),step,time)); +@@ -2031,7 +2031,13 @@ + case MaterialsRheologyBbarEnum: this->ElementResponsex(responses,MaterialsRheologyBbarEnum); break; + case VelEnum: this->ElementResponsex(responses,VelEnum); break; + case FrictionCoefficientEnum: NodalValuex(responses, FrictionCoefficientEnum,elements,nodes, vertices, loads, materials, parameters); break; +- default: _error_("response descriptor \"" << EnumToStringx(response_descriptor_enum) << "\" not supported yet!"); break; ++ default: ++ if(response_descriptor_enum>=Outputdefinition1Enum && response_descriptor_enum <=Outputdefinition100Enum){ ++ IssmDouble double_result = OutputDefinitionsResponsex(this,response_descriptor_enum); ++ *responses=double_result; ++ } ++ else _error_("response descriptor \"" << EnumToStringx(response_descriptor_enum) << "\" not supported yet!"); ++ break; + } + + } +Index: ../trunk-jpl/src/m/classes/model.m +=================================================================== +--- ../trunk-jpl/src/m/classes/model.m (revision 21818) ++++ ../trunk-jpl/src/m/classes/model.m (revision 21819) +@@ -182,6 +182,11 @@ + md.friction.coefficient=project2d(md,md.friction.coefficient,1); + md.friction.p=project2d(md,md.friction.p,1); + md.friction.q=project2d(md,md.friction.q,1); ++ elseif isa(md.friction,'frictioncoulomb'), ++ md.friction.coefficient=project2d(md,md.friction.coefficient,1); ++ md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1); ++ md.friction.p=project2d(md,md.friction.p,1); ++ md.friction.q=project2d(md,md.friction.q,1); + elseif isa(md.friction,'frictionhydro'), + md.friction.q=project2d(md,md.friction.q,1); + md.friction.C=project2d(md,md.friction.C,1); Index: /issm/oecreview/Archive/21724-22754/ISSM-21819-21820.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21819-21820.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21819-21820.diff (revision 22755) @@ -0,0 +1,303 @@ +Index: ../trunk-jpl/test/NightlyRun/test408.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test408.m (revision 21819) ++++ ../trunk-jpl/test/NightlyRun/test408.m (revision 21820) +@@ -10,12 +10,12 @@ + md.friction.p=ones(md.mesh.numberofelements,1); + md.friction.q=ones(md.mesh.numberofelements,1); + md.friction.coefficientcoulomb=0.02*ones(md.mesh.numberofvertices,1); +-md=extrude(md,3,1); + md.transient.isthermal=0; + md.transient.isgroundingline=1; + md=setflowequation(md,'SSA','all'); + md.cluster=generic('name',oshostname(),'np',3); + md.transient.requested_outputs={'default','GroundedArea','FloatingArea','TotalFloatingBmb','TotalGroundedBmb','TotalSmb'}; ++md=extrude(md,3,1); + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test426.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test426.m (revision 21819) ++++ ../trunk-jpl/test/NightlyRun/test426.m (revision 21820) +@@ -9,23 +9,23 @@ + md.geometry.thickness(:)=1000.; + md.geometry.surface=md.geometry.base+md.geometry.thickness; + md.smb.mass_balance(:)=100.; +-md=extrude(md,3,1.); + md=setflowequation(md,'SSA','all'); + md.transient.isstressbalance=0; + md.transient.isgroundingline=1; + md.groundingline.migration='AggressiveMigration'; +-md.transient.requested_outputs={'IceVolume','IceVolumeAboveFloatation'}; ++md.transient.requested_outputs={'IceVolume','IceVolumeAboveFloatation','IceMass'}; ++md=extrude(md,3,1.); + md.cluster=generic('name',oshostname(),'np',3); + + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1','IceVolume1','IceVolumeAboveFloatation1',... +- 'Bed2','Surface2','Thickness2','Floatingice2','IceVolume2','IceVolumeAboveFloatation2',... +- 'Bed3','Surface3','Thickness3','Floatingice3','IceVolume3','IceVolumeAboveFloatation3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-11,1e-10,1e-11,3e-11,2e-12,5e-12,... +- 1e-10,1e-10,1e-10,5e-11,2e-12,5e-12}; ++field_names ={'Bed1','Surface1','Thickness1','Floatingice1','IceVolume1','IceVolumeAboveFloatation1','IceMass1',... ++ 'Bed2','Surface2','Thickness2','Floatingice2','IceVolume2','IceVolumeAboveFloatation2','IceMass2',... ++ 'Bed3','Surface3','Thickness3','Floatingice3','IceVolume3','IceVolumeAboveFloatation3','IceMass3'}; ++field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... ++ 1e-11,1e-10,1e-11,3e-11,2e-12,5e-12,2e-12,... ++ 1e-10,1e-10,1e-10,5e-11,2e-12,5e-12,2e-12}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +@@ -33,6 +33,7 @@ + (md.results.TransientSolution(1).MaskGroundediceLevelset),... + (md.results.TransientSolution(1).IceVolume),... + (md.results.TransientSolution(1).IceVolumeAboveFloatation),... ++ (md.results.TransientSolution(1).IceMass),... + (md.results.TransientSolution(2).Base),... + (md.results.TransientSolution(2).Surface),... + (md.results.TransientSolution(2).Thickness),... +@@ -39,6 +40,7 @@ + (md.results.TransientSolution(2).MaskGroundediceLevelset),... + (md.results.TransientSolution(2).IceVolume),... + (md.results.TransientSolution(2).IceVolumeAboveFloatation),... ++ (md.results.TransientSolution(2).IceMass),... + (md.results.TransientSolution(3).Base),... + (md.results.TransientSolution(3).Surface),... + (md.results.TransientSolution(3).Thickness),... +@@ -45,4 +47,5 @@ + (md.results.TransientSolution(3).MaskGroundediceLevelset),... + (md.results.TransientSolution(3).IceVolume),... + (md.results.TransientSolution(3).IceVolumeAboveFloatation),... ++ (md.results.TransientSolution(3).IceMass),... + }; +Index: ../trunk-jpl/test/NightlyRun/test444.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test444.m (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test444.m (revision 21820) +@@ -0,0 +1,107 @@ ++%Test Name: SquareSheetShelfTranSSA2dAggressiveDakotaSampRegionalOutput ++md=triangle(model(),'../Exp/Square.exp',150000.); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md.geometry.bed=md.geometry.base; ++pos=find(md.mask.groundedice_levelset<0); ++md.geometry.bed(pos)=md.geometry.base(pos)-10; ++md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); ++md.friction.p=ones(md.mesh.numberofelements,1); ++md.friction.q=ones(md.mesh.numberofelements,1); ++md.transient.isthermal=0; ++md.transient.isgroundingline=1; ++md.groundingline.migration='AggressiveMigration'; ++ ++md.settings.output_frequency=3; ++md=setflowequation(md,'SSA','all'); ++md.cluster=generic('name',oshostname(),'np',3); ++ ++regionalmask=zeros(md.mesh.numberofvertices,1); ++in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'../Exp/SquareHalfRight.exp','node',1); ++regionalmask(find(in))=1; ++md.transient.requested_outputs={'default','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1',... ++ 'IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation'}; ++md.outputdefinition.definitions{1}=regionaloutput('name','GroundedArea1','outputnamestring','GroundedArea','mask',regionalmask,... ++ 'definitionstring','Outputdefinition1'); ++md.outputdefinition.definitions{2}=regionaloutput('name','FloatingArea1','outputnamestring','FloatingArea','mask',regionalmask,... ++ 'definitionstring','Outputdefinition2'); ++md.outputdefinition.definitions{3}=regionaloutput('name','TotalFloatingBmb1','outputnamestring','TotalFloatingBmb','mask',regionalmask,... ++ 'definitionstring','Outputdefinition3'); ++md.outputdefinition.definitions{4}=regionaloutput('name','TotalGroundedBmb1','outputnamestring','TotalGroundedBmb','mask',regionalmask,... ++ 'definitionstring','Outputdefinition4'); ++md.outputdefinition.definitions{5}=regionaloutput('name','IceMass1','outputnamestring','IceMass','mask',regionalmask,... ++ 'definitionstring','Outputdefinition5'); ++md.outputdefinition.definitions{6}=regionaloutput('name','IceVolume1','outputnamestring','IceVolume','mask',regionalmask,... ++ 'definitionstring','Outputdefinition6'); ++md.outputdefinition.definitions{7}=regionaloutput('name','IceVolumeAboveFloatation1','outputnamestring','IceVolumeAboveFloatation','mask',regionalmask,... ++ 'definitionstring','Outputdefinition7'); ++md.outputdefinition.definitions{8}=regionaloutput('name','TotalSmb1','outputnamestring','TotalSmb','mask',regionalmask,... ++ 'definitionstring','Outputdefinition8'); ++ ++md=extrude(md,3,1); ++md=collapse(md); ++ ++%Dakota options ++ ++%dakota version ++version=IssmConfig('_DAKOTA_VERSION_'); version=version(1:3); version=str2num(version); ++ ++md.qmu.variables.drag_coefficient=normal_uncertain('scaled_BasalforcingsFloatingiceMeltingRate',1,0.1); ++ ++md.qmu.responses.IceMass1=response_function('Outputdefinition5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.IceVolume1=response_function('Outputdefinition6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.IceVolumeAboveFloatation1=response_function('Outputdefinition7',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.IceVolumeAboveFloatation=response_function('IceVolumeAboveFloatation',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.GroundedArea1=response_function('Outputdefinition1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.FloatingArea1=response_function('Outputdefinition2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.TotalFloatingBmb1=response_function('Outputdefinition3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.TotalGroundedBmb1=response_function('Outputdefinition4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.TotalSmb1=response_function('Outputdefinition8',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++ ++md.qmu.method =dakota_method('nond_samp'); ++md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),... ++ 'seed',1234,... ++ 'samples',20,... ++ 'sample_type','random'); ++ ++%% a variety of parameters ++md.qmu.params.direct=true; ++md.qmu.params.analysis_components=''; ++md.qmu.params.tabular_graphics_data=true; ++ ++if version>=6, ++ md.qmu.params.analysis_driver='matlab'; ++ md.qmu.params.evaluation_scheduling='master'; ++ md.qmu.params.processors_per_evaluation=2; ++else ++ md.qmu.params.analysis_driver='stressbalance'; ++ md.qmu.params.evaluation_concurrency=1; ++end ++ ++%partitioning ++md.qmu.numberofpartitions=20; ++md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); ++md.qmu.partition=md.qmu.partition-1; ++md.qmu.isdakota=1; ++ ++md.stressbalance.reltol=10^-5; %tighten for qmu analyses ++ ++md=solve(md,'Transient','overwrite','y'); ++ ++%Fields and tolerances to track changes ++md.qmu.results=md.results.dakota; ++ ++%we put all the mean and stdev data in the montecarlo field, which we will use to test for success. ++md.results.dakota.montecarlo=[]; ++for i=1:8, ++ md.results.dakota.montecarlo=[md.results.dakota.montecarlo md.results.dakota.dresp_out(i).mean]; ++end ++for i=1:8, ++ md.results.dakota.montecarlo=[md.results.dakota.montecarlo md.results.dakota.dresp_out(i).stddev]; ++end ++field_names ={'montecarlo'}; ++field_tolerances={1e-11}; ++field_values={... ++ md.results.dakota.montecarlo,... ++ }; ++ +Index: ../trunk-jpl/test/Archives/Archive444.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive444.arch +=================================================================== +--- ../trunk-jpl/test/Archives/Archive444.arch (nonexistent) ++++ ../trunk-jpl/test/Archives/Archive444.arch (revision 21820) + +Property changes on: ../trunk-jpl/test/Archives/Archive444.arch +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +\ No newline at end of property +Index: ../trunk-jpl/test/NightlyRun/test443.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test443.m (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test443.m (revision 21820) +@@ -0,0 +1,76 @@ ++%Test Name: SquareSheetShelfTranSSA3dAggressiveRegionalOutput ++md=triangle(model(),'../Exp/Square.exp',150000.); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md.geometry.bed=md.geometry.base; ++pos=find(md.mask.groundedice_levelset<0); ++md.geometry.bed(pos)=md.geometry.base(pos)-10; ++md.friction=frictioncoulomb(); ++md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); ++md.friction.p=ones(md.mesh.numberofelements,1); ++md.friction.q=ones(md.mesh.numberofelements,1); ++md.friction.coefficientcoulomb=0.02*ones(md.mesh.numberofvertices,1); ++md.transient.isthermal=0; ++md.transient.isgroundingline=1; ++md.groundingline.migration='AggressiveMigration'; ++ ++md.settings.output_frequency=2; ++md=setflowequation(md,'SSA','all'); ++md.cluster=generic('name',oshostname(),'np',3); ++ ++regionalmask=zeros(md.mesh.numberofvertices,1); ++in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'../Exp/SquareHalfRight.exp','node',1); ++regionalmask(find(in))=1; ++md.transient.requested_outputs={'default','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1',... ++ 'IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation2','IceVolumeAboveFloatation'}; ++md.outputdefinition.definitions{1}=regionaloutput('name','GroundedArea1','outputnamestring','GroundedArea','mask',regionalmask,... ++ 'definitionstring','Outputdefinition1'); ++md.outputdefinition.definitions{2}=regionaloutput('name','FloatingArea1','outputnamestring','FloatingArea','mask',regionalmask,... ++ 'definitionstring','Outputdefinition2'); ++md.outputdefinition.definitions{3}=regionaloutput('name','TotalFloatingBmb1','outputnamestring','TotalFloatingBmb','mask',regionalmask,... ++ 'definitionstring','Outputdefinition3'); ++md.outputdefinition.definitions{4}=regionaloutput('name','TotalGroundedBmb1','outputnamestring','TotalGroundedBmb','mask',regionalmask,... ++ 'definitionstring','Outputdefinition4'); ++md.outputdefinition.definitions{5}=regionaloutput('name','IceMass1','outputnamestring','IceMass','mask',regionalmask,... ++ 'definitionstring','Outputdefinition5'); ++md.outputdefinition.definitions{6}=regionaloutput('name','IceVolume1','outputnamestring','IceVolume','mask',regionalmask,... ++ 'definitionstring','Outputdefinition6'); ++md.outputdefinition.definitions{7}=regionaloutput('name','IceVolumeAboveFloatation1','outputnamestring','IceVolumeAboveFloatation','mask',regionalmask,... ++ 'definitionstring','Outputdefinition7'); ++md.outputdefinition.definitions{8}=regionaloutput('name','TotalSmb1','outputnamestring','TotalSmb','mask',regionalmask,... ++ 'definitionstring','Outputdefinition8'); ++md.outputdefinition.definitions{9}=regionaloutput('name','IceVolumeAboveFloatation2','outputnamestring','IceVolumeAboveFloatation',... ++ 'maskexpstring','../Exp/SquareHalfRight.exp','definitionstring','Outputdefinition9','model',md); ++ ++md=extrude(md,3,1); ++md=solve(md,'Transient'); ++ ++%Fields and tolerances to track changes ++field_names ={'IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation21',... ++ 'Thickness1','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1',... ++ 'IceMass3','IceVolume3','IceVolumeAboveFloatation3','IceVolumeAboveFloatation23',... ++ 'Thickness3','GroundedArea3','FloatingArea3','TotalFloatingBmb3','TotalGroundedBmb3','TotalSmb3'}; ++field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; ++field_values={... ++ (md.results.TransientSolution(1).IceMass1),... ++ (md.results.TransientSolution(1).IceVolume1),... ++ (md.results.TransientSolution(1).IceVolumeAboveFloatation1),... ++ (md.results.TransientSolution(1).IceVolumeAboveFloatation2),... ++ (md.results.TransientSolution(1).Thickness),... ++ (md.results.TransientSolution(1).GroundedArea1),... ++ (md.results.TransientSolution(1).FloatingArea1),... ++ (md.results.TransientSolution(1).TotalFloatingBmb1),... ++ (md.results.TransientSolution(1).TotalGroundedBmb1),... ++ (md.results.TransientSolution(1).TotalSmb1),... ++ (md.results.TransientSolution(3).IceMass1),... ++ (md.results.TransientSolution(3).IceVolume1),... ++ (md.results.TransientSolution(3).IceVolumeAboveFloatation1),... ++ (md.results.TransientSolution(3).IceVolumeAboveFloatation2),... ++ (md.results.TransientSolution(3).Thickness),... ++ (md.results.TransientSolution(3).GroundedArea1),... ++ (md.results.TransientSolution(3).FloatingArea1),... ++ (md.results.TransientSolution(3).TotalFloatingBmb1),... ++ (md.results.TransientSolution(3).TotalGroundedBmb1),... ++ (md.results.TransientSolution(3).TotalSmb1),... ++ }; +Index: ../trunk-jpl/test/Archives/Archive443.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive443.arch +=================================================================== +--- ../trunk-jpl/test/Archives/Archive443.arch (nonexistent) ++++ ../trunk-jpl/test/Archives/Archive443.arch (revision 21820) + +Property changes on: ../trunk-jpl/test/Archives/Archive443.arch +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +\ No newline at end of property +Index: ../trunk-jpl/test/Archives/Archive426.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21820-21821.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21820-21821.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21820-21821.diff (revision 22755) @@ -0,0 +1,19 @@ +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21820) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21821) +@@ -3075,10 +3075,10 @@ + - ((*tcvj)(0)->r.y -(*tcvj)(2)->r.y)*(bv.r.x -(*tcvj)(2)->r.x)); + IssmDouble area_3 =((bv.r.x -(*tcvj)(1)->r.x)*((*tcvj)(0)->r.y-(*tcvj)(1)->r.y) + - (bv.r.y -(*tcvj)(1)->r.y)*((*tcvj)(0)->r.x-(*tcvj)(1)->r.x)); +- // if(area_1<0 || area_2<0 || area_3<0){ +- // pointsoutside = true; +- // continue; +- // } ++ if(area_1<0 || area_2<0 || area_3<0){ ++ pointsoutside = true; ++ continue; ++ } + if(!bv.GeomEdgeHook){ + vertices[nbv].r = bv.r; + vertices[nbv].PreviousNumber = i+1; Index: /issm/oecreview/Archive/21724-22754/ISSM-21821-21822.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21821-21822.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21821-21822.diff (revision 22755) @@ -0,0 +1,51 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21821) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21822) +@@ -4308,7 +4308,7 @@ + + /*Get vector to create metric*/ + int numberofvertices = this->vertices->NumberOfVertices(); +- Vector *vector = new Vector(numberofvertices); ++ Vector *vector = NULL; + GetVectorFromInputsx(&vector,this,this->amrbamg->fieldenum,VertexSIdEnum); + vector->Assemble(); + IssmDouble* vector_serial = vector->ToMPISerial(); +@@ -4318,17 +4318,18 @@ + this->amrbamg->ExecuteRefinementBamg(vector_serial,&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); + if(newnumberofvertices<=0 || newnumberofelements<=0) _error_("Error in the refinement process."); + } +- else{ ++ ++ xDelete(vector_serial); ++ ++ /*Send new mesh to others CPU*/ ++ ISSM_MPI_Bcast(&newnumberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ ISSM_MPI_Bcast(&newnumberofelements,1,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ if(my_rank){ + newx=xNew(newnumberofvertices); + newy=xNew(newnumberofvertices); + newz=xNew(newnumberofvertices); + newelementslist=xNew(newnumberofelements*this->GetElementsWidth()); + } +- xDelete(vector_serial); +- +- /*Send new mesh to others CPU*/ +- ISSM_MPI_Bcast(&newnumberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +- ISSM_MPI_Bcast(&newnumberofelements,1,ISSM_MPI_INT,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(newx,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(newy,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(newz,newnumberofvertices,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21821) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21822) +@@ -31,7 +31,7 @@ + this->options->errg = 0.1; + this->options->gradation = 1.5; + this->options->Hessiantype = 0; +- this->options->MaxCornerAngle = 10; ++ this->options->MaxCornerAngle = 1.e-12; + this->options->maxnbv = 1e6; + this->options->maxsubdiv = 10; + this->options->Metrictype = 0; Index: /issm/oecreview/Archive/21724-22754/ISSM-21822-21823.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21822-21823.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21822-21823.diff (revision 22755) @@ -0,0 +1,8 @@ +Index: ../trunk-jpl/test/Archives/Archive426.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive443.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21823-21824.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21823-21824.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21823-21824.diff (revision 22755) @@ -0,0 +1,38 @@ +Index: ../trunk-jpl/src/m/exp/contourlevelzero.m +=================================================================== +--- ../trunk-jpl/src/m/exp/contourlevelzero.m (revision 21823) ++++ ../trunk-jpl/src/m/exp/contourlevelzero.m (revision 21824) +@@ -18,7 +18,7 @@ + index=md.mesh.elements; + + if isempty(mask), error('mask provided is empty'); end +- if length(mask)~=md.mesh.numberofvertices, error('mask provided should be specified at the vertices of the mesh'); end ++if length(mask)~=md.mesh.numberofvertices, error('mask provided should be specified at the vertices of the mesh'); end + + %initialization of some variables + numberofelements=size(index,1); +@@ -58,9 +58,9 @@ + Range3=sort(Data3,2); + + %find the segments that contain this value +-pos1=(Range1(:,1)level); +-pos2=(Range2(:,1)level); +-pos3=(Range3(:,1)level); ++pos1=(Range1(:,1)=level); ++pos2=(Range2(:,1)=level); ++pos3=(Range3(:,1)=level); + + %get elements + poselem12=(pos1 & pos2); +Index: ../trunk-jpl/src/m/plot/plot_contour.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_contour.m (revision 21823) ++++ ../trunk-jpl/src/m/plot/plot_contour.m (revision 21824) +@@ -269,6 +269,6 @@ + clabel(c,h); + else + %clabel(c,h,'color',color,'FontSize',10,'labelspacing',20000); +- clabel(c,h,'FontSize',10,'labelspacing',20000); ++ %clabel(c,h,'FontSize',10,'labelspacing',20000); + end + end Index: /issm/oecreview/Archive/21724-22754/ISSM-21824-21825.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21824-21825.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21824-21825.diff (revision 22755) @@ -0,0 +1,73 @@ +Index: ../trunk-jpl/test/NightlyRun/test426.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test426.py (revision 21824) ++++ ../trunk-jpl/test/NightlyRun/test426.py (revision 21825) +@@ -17,40 +17,43 @@ + md.geometry.thickness[:]=1000. + md.geometry.surface=md.geometry.base+md.geometry.thickness + md.smb.mass_balance[:]=100. +-md.extrude(3,1.) + md=setflowequation(md,'SSA','all') + md.transient.isstressbalance=False + md.transient.isgroundingline=True + md.groundingline.migration='AggressiveMigration' +-md.transient.requested_outputs=['IceVolume','IceVolumeAboveFloatation'] ++md.transient.requested_outputs=['IceVolume','IceVolumeAboveFloatation','IceMass'] ++md.extrude(3,1.) + md.cluster=generic('name',gethostname(),'np',3) + + md=solve(md,'Transient') + + #Fields and tolerances to track changes +-field_names =['Bed1','Surface1','Thickness1','Floatingice1','IceVolume1','IceVolumeAboveFloatation1', +- 'Bed2','Surface2','Thickness2','Floatingice2','IceVolume2','IceVolumeAboveFloatation2', +- 'Bed3','Surface3','Thickness3','Floatingice3','IceVolume3','IceVolumeAboveFloatation3',] ++field_names =['Bed1','Surface1','Thickness1','Floatingice1','IceVolume1','IceVolumeAboveFloatation1','IceMass1', ++ 'Bed2','Surface2','Thickness2','Floatingice2','IceVolume2','IceVolumeAboveFloatation2','IceMass2', ++ 'Bed3','Surface3','Thickness3','Floatingice3','IceVolume3','IceVolumeAboveFloatation3','IceMass3'] + +-field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, +- 1e-11,1e-10,1e-11,3e-11,2e-12,5e-12, +- 1e-10,1e-10,1e-10,5e-11,2e-12,5e-12] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, ++ 1e-11,1e-10,1e-11,3e-11,2e-12,5e-12,2e-12, ++ 1e-10,1e-10,1e-10,5e-11,2e-12,5e-12,2e-12] + + field_values=[md.results.TransientSolution[0].Base, +- md.results.TransientSolution[0].Surface, +- md.results.TransientSolution[0].Thickness, +- md.results.TransientSolution[0].MaskGroundediceLevelset, +- md.results.TransientSolution[0].IceVolume, +- md.results.TransientSolution[0].IceVolumeAboveFloatation, +- md.results.TransientSolution[1].Base, +- md.results.TransientSolution[1].Surface, +- md.results.TransientSolution[1].Thickness, +- md.results.TransientSolution[1].MaskGroundediceLevelset, +- md.results.TransientSolution[1].IceVolume, +- md.results.TransientSolution[1].IceVolumeAboveFloatation, +- md.results.TransientSolution[2].Base, +- md.results.TransientSolution[2].Surface, +- md.results.TransientSolution[2].Thickness, +- md.results.TransientSolution[2].MaskGroundediceLevelset, +- md.results.TransientSolution[2].IceVolume, +- md.results.TransientSolution[2].IceVolumeAboveFloatation] ++ md.results.TransientSolution[0].Surface, ++ md.results.TransientSolution[0].Thickness, ++ md.results.TransientSolution[0].MaskGroundediceLevelset, ++ md.results.TransientSolution[0].IceVolume, ++ md.results.TransientSolution[0].IceVolumeAboveFloatation, ++ md.results.TransientSolution[0].IceMass, ++ md.results.TransientSolution[1].Base, ++ md.results.TransientSolution[1].Surface, ++ md.results.TransientSolution[1].Thickness, ++ md.results.TransientSolution[1].MaskGroundediceLevelset, ++ md.results.TransientSolution[1].IceVolume, ++ md.results.TransientSolution[1].IceVolumeAboveFloatation, ++ md.results.TransientSolution[1].IceMass, ++ md.results.TransientSolution[2].Base, ++ md.results.TransientSolution[2].Surface, ++ md.results.TransientSolution[2].Thickness, ++ md.results.TransientSolution[2].MaskGroundediceLevelset, ++ md.results.TransientSolution[2].IceVolume, ++ md.results.TransientSolution[2].IceVolumeAboveFloatation, ++ md.results.TransientSolution[2].IceMass] Index: /issm/oecreview/Archive/21724-22754/ISSM-21825-21826.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21825-21826.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21825-21826.diff (revision 22755) @@ -0,0 +1,420 @@ +Index: ../trunk-jpl/src/c/shared/Elements/elements.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Elements/elements.h (revision 21825) ++++ ../trunk-jpl/src/c/shared/Elements/elements.h (revision 21826) +@@ -16,7 +16,7 @@ + // IssmDouble LliboutryDuval(IssmDouble temperature, IssmDouble waterfraction, IssmDouble depth,IssmDouble n); + IssmDouble EstarLambdaS(IssmDouble epseff, IssmDouble epsprime_norm); + void EstarOmega(IssmDouble* omega,IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz, IssmDouble* dvmag); +-void EstarStrainrateQuantities(IssmDouble *pepseff, IssmDouble *pepsprime_norm, IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble* dvmag); ++void EstarStrainrateQuantities(IssmDouble *pepsprime_norm, IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble* dvmag); + IssmDouble PddSurfaceMassBalance(IssmDouble* monthlytemperatures, IssmDouble* monthlyprec, + IssmDouble* pdds, IssmDouble* pds, IssmDouble* melt, IssmDouble* accu, IssmDouble signorm, + IssmDouble yts, IssmDouble h, IssmDouble s, IssmDouble desfac,IssmDouble s0t, +Index: ../trunk-jpl/src/c/shared/Elements/EstarComponents.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Elements/EstarComponents.cpp (revision 21825) ++++ ../trunk-jpl/src/c/shared/Elements/EstarComponents.cpp (revision 21826) +@@ -2,12 +2,12 @@ + #include "../Numerics/types.h" + #include "../Exceptions/exceptions.h" + #include "./elements.h" +-void EstarStrainrateQuantities(IssmDouble *pepseff, IssmDouble *pepsprime_norm, IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble* dvmag){/*{{{*/ ++void EstarStrainrateQuantities(IssmDouble *pepsprime_norm, IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble* dvmag){/*{{{*/ + + /*Intermediaries*/ + IssmDouble omega[3]; + IssmDouble nrsp[3],nrsp_norm; +- IssmDouble eps[3][3],epseff; ++ IssmDouble eps[3][3]; + IssmDouble epsprime[3],epsprime_norm; + + /*Get omega, correction for rigid body rotation*/ +@@ -36,11 +36,6 @@ + eps[1][0] = .5*(dvx[1]+dvy[0]); eps[1][1] = dvy[1]; eps[1][2] = .5*(dvy[2]+dvz[1]); + eps[2][0] = .5*(dvx[2]+dvz[0]); eps[2][1] = .5*(dvy[2]+dvz[1]); eps[2][2] = dvz[2]; + +- /*effective strain rate*/ +- epseff = 0.; +- /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exz^2 + eyz^2 + exx*eyy */ +- epseff = sqrt(eps[0][0]*eps[0][0] + eps[1][1]*eps[1][1] + eps[0][1]*eps[0][1] + eps[0][2]*eps[0][2] + eps[1][2]*eps[1][2] + eps[0][0]*eps[1][1]); +- + /*Compute the shear strain rate on the non rotating shear plane*/ + epsprime[0]=0.; + epsprime[1]=0.; +@@ -72,7 +67,6 @@ + epsprime_norm = sqrt(epsprime[0]*epsprime[0] + epsprime[1]*epsprime[1] + epsprime[2]*epsprime[2]); + + /*Assign output pointers*/ +- *pepseff=epseff; + *pepsprime_norm=epsprime_norm; + }/*}}}*/ + void EstarOmega(IssmDouble* omega,IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz, IssmDouble* dvmag){/*{{{*/ +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21825) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21826) +@@ -47,7 +47,7 @@ + /*Intermediaries*/ + IssmDouble vx,vy,vz,vmag; + IssmDouble dvx[3],dvy[3],dvz[3],dvmag[3]; +- IssmDouble epseff,epsprime; ++ IssmDouble eps[3][3],epseff,epsprime; + int dim; + IssmDouble *xyz_list = NULL; + +@@ -100,7 +100,18 @@ + dvmag[1]=1./(2*sqrt(vmag))*(2*vx*dvx[1]+2*vy*dvy[1]+2*vz*dvz[1]); + dvmag[2]=1./(2*sqrt(vmag))*(2*vx*dvx[2]+2*vy*dvy[2]+2*vz*dvz[2]); + } +- EstarStrainrateQuantities(&epseff,&epsprime,vx,vy,vz,vmag,&dvx[0],&dvy[0],&dvz[0],&dvmag[0]); ++ ++ /*Build strain rate tensor*/ ++ eps[0][0] = dvx[0]; eps[0][1] = .5*(dvx[1]+dvy[0]); eps[0][2] = .5*(dvx[2]+dvz[0]); ++ eps[1][0] = .5*(dvx[1]+dvy[0]); eps[1][1] = dvy[1]; eps[1][2] = .5*(dvy[2]+dvz[1]); ++ eps[2][0] = .5*(dvx[2]+dvz[0]); eps[2][1] = .5*(dvy[2]+dvz[1]); eps[2][2] = dvz[2]; ++ ++ /*effective strain rate*/ ++ epseff = 0.; ++ /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exz^2 + eyz^2 + exx*eyy */ ++ epseff = sqrt(eps[0][0]*eps[0][0] + eps[1][1]*eps[1][1] + eps[0][1]*eps[0][1] + eps[0][2]*eps[0][2] + eps[1][2]*eps[1][2] + eps[0][0]*eps[1][1]); ++ ++ EstarStrainrateQuantities(&epsprime,vx,vy,vz,vmag,&dvx[0],&dvy[0],&dvz[0],&dvmag[0]); + lambdas[iv]=EstarLambdaS(epseff,epsprime); + } + +@@ -676,7 +687,7 @@ + material->GetViscosity_B(&dmudB,eps_eff); + break; + case MatestarEnum: +- material->ViscosityBFS(&dmudB,dim,xyz_list,gauss,vx_input,vy_input,vz_input); ++ material->ViscosityBFS(&dmudB,dim,xyz_list,gauss,vx_input,vy_input,vz_input,eps_eff); + break; + default: _error_("not supported"); + } +@@ -713,7 +724,7 @@ + material->GetViscosity_B(&dmudB,eps_eff); + break; + case MatestarEnum: +- material->ViscosityBHO(&dmudB,dim,xyz_list,gauss,vx_input,vy_input); ++ material->ViscosityBHO(&dmudB,dim,xyz_list,gauss,vx_input,vy_input,eps_eff); + break; + default: _error_("not supported"); + } +@@ -750,7 +761,7 @@ + material->GetViscosity_B(&dmudB,eps_eff); + break; + case MatestarEnum: +- material->ViscosityBSSA(&dmudB,dim,xyz_list,gauss,vx_input,vy_input); ++ material->ViscosityBSSA(&dmudB,dim,xyz_list,gauss,vx_input,vy_input,eps_eff); + break; + default: _error_("not supported"); + } +Index: ../trunk-jpl/src/c/classes/Materials/Matice.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Materials/Matice.h (revision 21825) ++++ ../trunk-jpl/src/c/classes/Materials/Matice.h (revision 21826) +@@ -87,9 +87,9 @@ + void ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surf); + void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); + void ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon); +- void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){_error_("not supported");}; +- void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; +- void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; ++ void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input,IssmDouble eps_eff){_error_("not supported");}; ++ void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble eps_eff){_error_("not supported");}; ++ void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble eps_eff){_error_("not supported");}; + /*}}}*/ + }; + +Index: ../trunk-jpl/src/c/classes/Materials/Matpar.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Materials/Matpar.h (revision 21825) ++++ ../trunk-jpl/src/c/classes/Materials/Matpar.h (revision 21826) +@@ -124,9 +124,9 @@ + void ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surf){_error_("not supported");}; + void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; + void ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){_error_("not supported");}; +- void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){_error_("not supported");}; +- void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; +- void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; ++ void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input,IssmDouble eps_eff){_error_("not supported");}; ++ void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble eps_eff){_error_("not supported");}; ++ void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble eps_eff){_error_("not supported");}; + /*}}}*/ + /*Numerics: {{{*/ + void EnthalpyToThermal(IssmDouble* ptemperature,IssmDouble* pwaterfraction,IssmDouble enthalpy,IssmDouble pressure); +Index: ../trunk-jpl/src/c/classes/Materials/Matestar.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Materials/Matestar.cpp (revision 21825) ++++ ../trunk-jpl/src/c/classes/Materials/Matestar.cpp (revision 21826) +@@ -248,13 +248,13 @@ + _error_("not implemented yet"); + } + /*}}}*/ +-IssmDouble Matestar::GetViscosityGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,bool isdepthaveraged){/*{{{*/ ++IssmDouble Matestar::GetViscosityGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble eps_eff,bool isdepthaveraged){/*{{{*/ + + /*output: */ + IssmDouble viscosity; + + /*Intermediaries*/ +- IssmDouble epseff,epsprime_norm; ++ IssmDouble epsprime_norm; + IssmDouble lambdas; + IssmDouble vmag,dvmag[3]; + IssmDouble B,Ec,Es,E,n; +@@ -272,8 +272,8 @@ + dvmag[2]=1./(2*sqrt(vmag))*(2*vx*dvx[2]+2*vy*dvy[2]+2*vz*dvz[2]); + } + +- EstarStrainrateQuantities(&epseff,&epsprime_norm,vx,vy,vz,vmag,dvx,dvy,dvz,&dvmag[0]); +- lambdas=EstarLambdaS(epseff,epsprime_norm); ++ EstarStrainrateQuantities(&epsprime_norm,vx,vy,vz,vmag,dvx,dvy,dvz,&dvmag[0]); ++ lambdas=EstarLambdaS(eps_eff,epsprime_norm); + + /*Get B and enhancement*/ + n=GetN(); _assert_(n>0.); +@@ -293,24 +293,27 @@ + + /*Compute viscosity*/ + /*if no strain rate, return maximum viscosity*/ +- if(epseff==0.){ ++ if(eps_eff==0.){ + viscosity = 1.e+14/2.; + //viscosity = B; + //viscosity=2.5*pow(10.,17); + } + else{ +- viscosity = B/(2.*pow(E,1./n)*pow(epseff,2./n)); ++ viscosity = B/(2.*pow(E,1./n)*pow(eps_eff,2./n)); + } + ++ /*Checks in debugging mode*/ ++ if(viscosity<=0) _error_("Negative viscosity"); ++ + /*Assign output pointer*/ + return viscosity; + } + /*}}}*/ +-IssmDouble Matestar::GetViscosity_BGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,bool isdepthaveraged){/*{{{*/ ++IssmDouble Matestar::GetViscosity_BGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble eps_eff,bool isdepthaveraged){/*{{{*/ + + /*Intermediaries*/ + IssmDouble dmudB; +- IssmDouble epseff,epsprime_norm; ++ IssmDouble epsprime_norm; + IssmDouble lambdas; + IssmDouble vmag,dvmag[3]; + IssmDouble Ec,Es,E; +@@ -328,8 +331,8 @@ + dvmag[2]=1./(2*sqrt(vmag))*(2*vx*dvx[2]+2*vy*dvy[2]+2*vz*dvz[2]); + } + +- EstarStrainrateQuantities(&epseff,&epsprime_norm,vx,vy,vz,vmag,dvx,dvy,dvz,&dvmag[0]); +- lambdas=EstarLambdaS(epseff,epsprime_norm); ++ EstarStrainrateQuantities(&epsprime_norm,vx,vy,vz,vmag,dvx,dvy,dvz,&dvmag[0]); ++ lambdas=EstarLambdaS(eps_eff,epsprime_norm); + + /*Get enhancement*/ + if (isdepthaveraged==0.){ +@@ -345,8 +348,8 @@ + E = Ec + (Es-Ec)*lambdas*lambdas; _assert_(E>0.); + + /*Compute dmudB*/ +- if(epseff==0.) dmudB = 0.; +- else dmudB = 1./(2.*pow(E,1./3.)*pow(epseff,2./3.)); ++ if(eps_eff==0.) dmudB = 0.; ++ else dmudB = 1./(2.*pow(E,1./3.)*pow(eps_eff,2./3.)); + + /*Assign output*/ + return dmudB; +@@ -407,7 +410,7 @@ + + } + /*}}}*/ +-void Matestar::ViscosityBFS(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){/*{{{*/ ++void Matestar::ViscosityBFS(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input,IssmDouble eps_eff){/*{{{*/ + + /*Intermediaries*/ + IssmDouble vx,vy,vz; +@@ -433,10 +436,10 @@ + } + + /*Compute dmudB*/ +- *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); ++ *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],eps_eff,isdepthaveraged); + } + /*}}}*/ +-void Matestar::ViscosityBHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ ++void Matestar::ViscosityBHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble eps_eff){/*{{{*/ + + /*Intermediaries*/ + IssmDouble vx,vy,vz; +@@ -462,9 +465,9 @@ + dvz[0] = 0.; dvz[1] = 0.; dvz[2] = -dvx[0]-dvy[1]; + + /*Compute viscosity*/ +- *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); ++ *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],eps_eff,isdepthaveraged); + }/*}}}*/ +-void Matestar::ViscosityBSSA(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ ++void Matestar::ViscosityBSSA(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble eps_eff){/*{{{*/ + /*Intermediaries*/ + IssmDouble vx,vy,vz; + IssmDouble dvx[3],dvy[3],dvz[3]; +@@ -492,7 +495,7 @@ + dvz[0] = 0.; dvz[1] = 0.; dvz[2] = -dvx[0]-dvy[1]; + + /*Compute viscosity*/ +- *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); ++ *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],eps_eff,isdepthaveraged); + }/*}}}*/ + void Matestar::ViscosityFS(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){/*{{{*/ + +@@ -499,6 +502,9 @@ + /*Intermediaries*/ + IssmDouble vx,vy,vz; + IssmDouble dvx[3],dvy[3],dvz[3]; ++ IssmDouble epsilon3d[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/ ++ IssmDouble epsilon2d[3]; /* epsilon=[exx,eyy,exy];*/ ++ IssmDouble eps_eff,eps0=1.e-27; + bool isdepthaveraged=0.; + + /*Get velocity derivatives in all directions*/ +@@ -519,8 +525,19 @@ + dvz[0] = 0.; dvz[1] = 0.; dvz[2] = 0.; + } + ++ if(dim==3){ ++ /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exz^2 + eyz^2 + exx*eyy */ ++ element->StrainRateFS(&epsilon3d[0],xyz_list,gauss,vx_input,vy_input,vz_input); ++ eps_eff = sqrt(epsilon3d[0]*epsilon3d[0] + epsilon3d[1]*epsilon3d[1] + epsilon3d[3]*epsilon3d[3] + epsilon3d[4]*epsilon3d[4] + epsilon3d[5]*epsilon3d[5] + epsilon3d[0]*epsilon3d[1]+eps0*eps0); ++ } ++ else{ ++ /* eps_eff^2 = 1/2 ( exx^2 + eyy^2 + 2*exy^2 )*/ ++ element->StrainRateSSA(&epsilon2d[0],xyz_list,gauss,vx_input,vy_input); ++ eps_eff = 1./sqrt(2.)*sqrt(epsilon2d[0]*epsilon2d[0] + epsilon2d[1]*epsilon2d[1] + 2.*epsilon2d[2]*epsilon2d[2]); ++ } ++ + /*Compute viscosity*/ +- *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); ++ *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],eps_eff,isdepthaveraged); + } + /*}}}*/ + void Matestar::ViscosityFSDerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){/*{{{*/ +@@ -531,8 +548,22 @@ + /*Intermediaries*/ + IssmDouble vx,vy,vz; + IssmDouble dvx[3],dvy[3],dvz[3]; ++ IssmDouble epsilon3d[5]; /* epsilon=[exx,eyy,exy,exz,eyz];*/ ++ IssmDouble epsilon2d[5]; /* epsilon=[exx,exy];*/ ++ IssmDouble eps_eff; + bool isdepthaveraged=0.; + ++ if(dim==3){ ++ /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exz^2 + eyz^2 + exx*eyy */ ++ element->StrainRateHO(&epsilon3d[0],xyz_list,gauss,vx_input,vy_input); ++ eps_eff = sqrt(epsilon3d[0]*epsilon3d[0] + epsilon3d[1]*epsilon3d[1] + epsilon3d[2]*epsilon3d[2] + epsilon3d[3]*epsilon3d[3] + epsilon3d[4]*epsilon3d[4] + epsilon3d[0]*epsilon3d[1]); ++ } ++ else{ ++ /* eps_eff^2 = 1/2 (2*exx^2 + 2*exy^2 ) (since eps_zz = - eps_xx)*/ ++ element->StrainRateHO2dvertical(&epsilon2d[0],xyz_list,gauss,vx_input,vy_input); ++ eps_eff = 1./sqrt(2.)*sqrt(2*epsilon2d[0]*epsilon2d[0] + 2*epsilon2d[1]*epsilon2d[1]); ++ } ++ + /*Get velocity derivatives in all directions*/ + _assert_(dim==2 || dim==3); + _assert_(vx_input); +@@ -552,7 +583,7 @@ + dvz[0] = 0.; dvz[1] = 0.; dvz[2] = -dvx[0]-dvy[1]; + + /*Compute viscosity*/ +- *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); ++ *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],eps_eff,isdepthaveraged); + }/*}}}*/ + void Matestar::ViscosityHODerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){/*{{{*/ + _error_("not implemented yet"); +@@ -565,6 +596,9 @@ + /*Intermediaries*/ + IssmDouble vx,vy,vz; + IssmDouble dvx[3],dvy[3],dvz[3]; ++ IssmDouble epsilon2d[3];/* epsilon=[exx,eyy,exy]; */ ++ IssmDouble epsilon1d; /* epsilon=[exx]; */ ++ IssmDouble eps_eff; + bool isdepthaveraged=1.; + + /*Get velocity derivatives in all directions*/ +@@ -588,8 +622,19 @@ + vz = 0.; + dvz[0] = 0.; dvz[1] = 0.; dvz[2] = -dvx[0]-dvy[1]; + ++ if(dim==2){ ++ /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exx*eyy*/ ++ element->StrainRateSSA(&epsilon2d[0],xyz_list,gauss,vx_input,vy_input); ++ eps_eff = sqrt(epsilon2d[0]*epsilon2d[0] + epsilon2d[1]*epsilon2d[1] + epsilon2d[2]*epsilon2d[2] + epsilon2d[0]*epsilon2d[1]); ++ } ++ else{ ++ /* eps_eff^2 = exx^2*/ ++ element->StrainRateSSA1d(&epsilon1d,xyz_list,gauss,vx_input); ++ eps_eff = fabs(epsilon1d); ++ } ++ + /*Compute viscosity*/ +- *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); ++ *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],eps_eff,isdepthaveraged); + }/*}}}*/ + void Matestar::ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){/*{{{*/ + _error_("not implemented yet"); +Index: ../trunk-jpl/src/c/classes/Materials/Matice.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Materials/Matice.cpp (revision 21825) ++++ ../trunk-jpl/src/c/classes/Materials/Matice.cpp (revision 21826) +@@ -723,7 +723,7 @@ + IssmDouble viscosity; + IssmDouble epsilon3d[5];/* epsilon=[exx,eyy,exy,exz,eyz];*/ + IssmDouble epsilon2d[2];/* epsilon=[exx,exy]; */ +- IssmDouble eps_eff,E=1.0; ++ IssmDouble eps_eff; + + if(dim==3){ + /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exz^2 + eyz^2 + exx*eyy */ +Index: ../trunk-jpl/src/c/classes/Materials/Material.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Materials/Material.h (revision 21825) ++++ ../trunk-jpl/src/c/classes/Materials/Material.h (revision 21826) +@@ -52,9 +52,9 @@ + virtual void ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surf)=0; + virtual void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input)=0; + virtual void ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon)=0; +- virtual void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input)=0; +- virtual void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input)=0; +- virtual void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input)=0; ++ virtual void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input,IssmDouble epseff)=0; ++ virtual void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble epseff)=0; ++ virtual void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble epseff)=0; + + }; + #endif +Index: ../trunk-jpl/src/c/classes/Materials/Matestar.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Materials/Matestar.h (revision 21825) ++++ ../trunk-jpl/src/c/classes/Materials/Matestar.h (revision 21826) +@@ -85,12 +85,12 @@ + void ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surf); + void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); + void ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon); +- void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input); +- void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); +- void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); ++ void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input,IssmDouble eps_eff); ++ void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble eps_eff); ++ void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,IssmDouble eps_eff); + /*}}}*/ +- IssmDouble GetViscosityGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,bool isdepthaveraged); +- IssmDouble GetViscosity_BGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,bool isdepthaveraged); ++ IssmDouble GetViscosityGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble eps_eff,bool isdepthaveraged); ++ IssmDouble GetViscosity_BGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble eps_eff,bool isdepthaveraged); + }; + + #endif /* _MATESTAR_H_ */ Index: /issm/oecreview/Archive/21724-22754/ISSM-21826-21827.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21826-21827.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21826-21827.diff (revision 22755) @@ -0,0 +1,296 @@ +Index: ../trunk-jpl/src/m/classes/model.m +=================================================================== +--- ../trunk-jpl/src/m/classes/model.m (revision 21826) ++++ ../trunk-jpl/src/m/classes/model.m (revision 21827) +@@ -176,7 +176,7 @@ + + %Start with changing all the fields from the 3d mesh + +- %dealing with the friciton law ++ %dealing with the friction law + %drag is limited to nodes that are on the bedrock. + if isa(md.friction,'friction'), + md.friction.coefficient=project2d(md,md.friction.coefficient,1); +@@ -205,7 +205,7 @@ + md.friction.m=project2d(md,md.friction.m,1); + else + disp('friction type not supported'); +- end ++ end + + %observations + if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end; +Index: ../trunk-jpl/src/m/classes/regionaloutput.py +=================================================================== +--- ../trunk-jpl/src/m/classes/regionaloutput.py (revision 21826) ++++ ../trunk-jpl/src/m/classes/regionaloutput.py (revision 21827) +@@ -1,8 +1,11 @@ ++from project3d import project3d + from fielddisplay import fielddisplay + from pairoptions import pairoptions + from checkfield import checkfield + from WriteData import WriteData + from MeshProfileIntersection import MeshProfileIntersection ++from ContourToMesh import ContourToMesh ++import numpy as np + import os + + class regionaloutput(object): +@@ -36,10 +39,14 @@ + self=options.AssignObjectFields(self) + + #get name +- modelname=getfieldvalue(options,'model'); +- self.maskexpstring=getfieldvalue(options,'maskexpstring'); +- self.setmaskfromexp(self,md) +- error('regionaloutput error message: ''mask'' field or ''maskexpstring'' and ''model'' fields should be defined!'); ++ if options.getfieldvalue('model',0): ++ if options.getfieldvalue('maskexpstring',0): ++ modelname=options.getfieldvalue('model') ++ self.maskexpstring=options.getfieldvalue('maskexpstring') ++ self.setmaskfromexp(modelname) ++ ++ if (len(self.mask)<=1 & np.any(np.isnan(self.mask))): ++ error('regionaloutput error message: ''mask'' field or ''maskexpstring'' and ''model'' fields should be defined!'); + + #}}} + def __repr__(self): # {{{ +@@ -60,7 +67,7 @@ + return self + #}}} + def setmaskfromexp(self,md): # {{{ +- if len(self.maskexpstring,0) > 0: ++ if len(self.maskexpstring) > 0: + self.mask=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,self.maskexpstring,'node',1) + + return self +@@ -73,11 +80,11 @@ + if not isinstance(self.outputnamestring, basestring): + raise RuntimeError("regionaloutput error message: 'outputnamestring' field should be a string!") + +- if len(self.maskexpstring,0) > 0: +- if not os.path.isfile(self.profilename): ++ if len(self.maskexpstring) > 0: ++ if not os.path.isfile(self.maskexpstring): + raise RuntimeError("regionaloutput error message: file name for mask exp does not point to a legitimate file on disk!") + else: +- self.setmaskfromexp(self,md) ++ self.setmaskfromexp(md) + + OutputdefinitionStringArray=[] + for i in range(1,100): +@@ -84,15 +91,14 @@ + x='Outputdefinition'+str(i) + OutputdefinitionStringArray.append(x) + +- md = checkfield(md,'field',self.definitionstring,'values',OutputdefinitionStringArray]) +- md = checkfield(md,'field',self.mask,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1) +- ++ md = checkfield(md,'field',self.definitionstring,'values',OutputdefinitionStringArray) ++ md = checkfield(md,'field',self.mask,'size',[md.mesh.numberofvertices],'NaN',1,'Inf',1) + return md + # }}} + def marshall(self,prefix,md,fid): # {{{ + + #before marshalling, make sure mask is set: +- self.setmaskfromexp(self,md) ++ self.setmaskfromexp(md) + + #ok, marshall strings and mask: + WriteData(fid,prefix,'data',self.name,'name','md.regionaloutput.name','format','String') +Index: ../trunk-jpl/src/m/classes/model.py +=================================================================== +--- ../trunk-jpl/src/m/classes/model.py (revision 21826) ++++ ../trunk-jpl/src/m/classes/model.py (revision 21827) +@@ -688,12 +688,20 @@ + if md.mesh.domaintype().lower() != '3d': + raise StandardError("only a 3D model can be collapsed") + ++ #dealing with the friction law + #drag is limited to nodes that are on the bedrock. +- md.friction.coefficient=project2d(md,md.friction.coefficient,1) ++ if hasattr(md.friction,'coefficient'): md.friction.coefficient=project2d(md,md.friction.coefficient,1) + + #p and q (same deal, except for element that are on the bedrock: ) +- md.friction.p=project2d(md,md.friction.p,1) +- md.friction.q=project2d(md,md.friction.q,1) ++ if hasattr(md.friction,'p'): md.friction.p=project2d(md,md.friction.p,1) ++ if hasattr(md.friction,'q'): md.friction.q=project2d(md,md.friction.q,1) ++ ++ if hasattr(md.friction,'coefficientcoulomb'): md.friction.q=project2d(md,md.friction.coefficientcoulomb,1) ++ if hasattr(md.friction,'C'): md.friction.q=project2d(md,md.friction.C,1) ++ if hasattr(md.friction,'As'): md.friction.q=project2d(md,md.friction.As,1) ++ if hasattr(md.friction,'effective_pressure'): md.friction.q=project2d(md,md.friction.effective_pressure,1) ++ if hasattr(md.friction,'water_layer'): md.friction.q=project2d(md,md.friction.water_layer,1) ++ if hasattr(md.friction,'m'): md.friction.q=project2d(md,md.friction.m,1) + + #observations + if not np.isnan(md.inversion.vx_obs).all(): md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers) +@@ -730,8 +738,7 @@ + md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1) + md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1) + +- +- # Hydrologydc variables ++ # Hydrologydc variables + if hasattr(md.hydrology,'hydrologydc'): + md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1) + md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1) +@@ -793,9 +800,8 @@ + setattr(fieldr,solutionsubfield,project2d(md,subfield,1)) + elif np.size(subfield)==md.mesh.numberofelements: + setattr(fieldr,solutionsubfield,project2d(md,subfield,1)) +- else: +- setattr(fieldr,solutionsubfield,subfield) + ++ + #Initialize with the 2d mesh + mesh=mesh2d() + mesh.x=md.mesh.x2d +@@ -811,6 +817,9 @@ + if md.mesh.long.size==md.mesh.numberofvertices: mesh.long=project2d(md,md.mesh.long,1) + mesh.epsg=md.mesh.epsg + md.mesh=mesh ++ md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices)[0] ++ md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity)[0] ++ md.mesh.segments=contourenvelope(md) + + return md + +Index: ../trunk-jpl/test/NightlyRun/test443.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test443.m (revision 21826) ++++ ../trunk-jpl/test/NightlyRun/test443.m (revision 21827) +@@ -43,6 +43,7 @@ + 'maskexpstring','../Exp/SquareHalfRight.exp','definitionstring','Outputdefinition9','model',md); + + md=extrude(md,3,1); ++md2=collapse(md); + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +@@ -49,9 +50,10 @@ + field_names ={'IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation21',... + 'Thickness1','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1',... + 'IceMass3','IceVolume3','IceVolumeAboveFloatation3','IceVolumeAboveFloatation23',... +- 'Thickness3','GroundedArea3','FloatingArea3','TotalFloatingBmb3','TotalGroundedBmb3','TotalSmb3'}; ++ 'Thickness3','GroundedArea3','FloatingArea3','TotalFloatingBmb3','TotalGroundedBmb3','TotalSmb3',... ++ 'ExtrudedMask','CollapsedMask'}; + field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; + field_values={... + (md.results.TransientSolution(1).IceMass1),... + (md.results.TransientSolution(1).IceVolume1),... +@@ -73,4 +75,6 @@ + (md.results.TransientSolution(3).TotalFloatingBmb1),... + (md.results.TransientSolution(3).TotalGroundedBmb1),... + (md.results.TransientSolution(3).TotalSmb1),... ++ length(md.outputdefinition.definitions{1}.mask),... ++ length(md2.outputdefinition.definitions{1}.mask),... + }; +Index: ../trunk-jpl/test/NightlyRun/test408.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test408.py (revision 21826) ++++ ../trunk-jpl/test/NightlyRun/test408.py (revision 21827) +@@ -23,10 +23,10 @@ + md.friction.coefficientcoulomb=0.02*np.ones(md.mesh.numberofvertices) + md.transient.isthermal=False + md.transient.isgroundingline=True +-md.extrude(3,1.) + md=setflowequation(md,'SSA','all') + md.cluster=generic('name',gethostname(),'np',3) + md.transient.requested_outputs=['default','GroundedArea','FloatingArea','TotalFloatingBmb','TotalGroundedBmb','TotalSmb'] ++md.extrude(3,1.) + md=solve(md,'Transient') + + #Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test443.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test443.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test443.py (revision 21827) +@@ -0,0 +1,80 @@ ++#Test Name: SquareSheetShelfTranSSA3dAggressiveRegionalOutput ++import numpy as np ++from model import * ++from socket import gethostname ++ ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from frictioncoulomb import frictioncoulomb ++from ContourToMesh import ContourToMesh ++from regionaloutput import regionaloutput ++ ++md=triangle(model(),'../Exp/Square.exp',150000.) ++md=setmask(md,'../Exp/SquareShelf.exp','') ++md=parameterize(md,'../Par/SquareSheetShelf.py') ++md.geometry.bed=copy.deepcopy(md.geometry.base) ++pos=np.nonzero(md.mask.groundedice_levelset<0.) ++md.geometry.bed[pos]=md.geometry.bed[pos]-10 ++md.friction=frictioncoulomb() ++md.friction.coefficient=20*np.ones(md.mesh.numberofvertices) ++md.friction.p=1*np.ones(md.mesh.numberofelements) ++md.friction.q=1*np.ones(md.mesh.numberofelements) ++md.friction.coefficientcoulomb=0.02*np.ones(md.mesh.numberofvertices) ++md.transient.isthermal=False ++md.transient.isgroundingline=True ++md.groundingline.migration='AggressiveMigration'; ++ ++md.settings.output_frequency=2 ++md=setflowequation(md,'SSA','all') ++md.cluster=generic('name',gethostname(),'np',3) ++ ++regionalmask=np.zeros((md.mesh.numberofvertices)) ++inflag=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'../Exp/SquareHalfRight.exp','node',1) ++regionalmask[np.nonzero(inflag)[0]] = 1. ++md.transient.requested_outputs=['default','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1','IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation2','IceVolumeAboveFloatation'] ++ ++md.outputdefinition.definitions=[regionaloutput('name','GroundedArea1','outputnamestring','GroundedArea','mask',regionalmask,'definitionstring','Outputdefinition1'), ++ regionaloutput('name','FloatingArea1','outputnamestring','FloatingArea','mask',regionalmask,'definitionstring','Outputdefinition2'), ++ regionaloutput('name','TotalFloatingBmb1','outputnamestring','TotalFloatingBmb','mask',regionalmask,'definitionstring','Outputdefinition3'), ++ regionaloutput('name','TotalGroundedBmb1','outputnamestring','TotalGroundedBmb','mask',regionalmask,'definitionstring','Outputdefinition4'), ++ regionaloutput('name','IceMass1','outputnamestring','IceMass','mask',regionalmask,'definitionstring','Outputdefinition5'), ++ regionaloutput('name','IceVolume1','outputnamestring','IceVolume','mask',regionalmask,'definitionstring','Outputdefinition6'), ++ regionaloutput('name','IceVolumeAboveFloatation1','outputnamestring','IceVolumeAboveFloatation','mask',regionalmask,'definitionstring','Outputdefinition7'), ++ regionaloutput('name','TotalSmb1','outputnamestring','TotalSmb','mask',regionalmask,'definitionstring','Outputdefinition8'), ++ regionaloutput('name','IceVolumeAboveFloatation2','outputnamestring','IceVolumeAboveFloatation','maskexpstring','../Exp/SquareHalfRight.exp','definitionstring','Outputdefinition9','model',md)] ++ ++md.extrude(3,1.) ++md2=copy.deepcopy(md) ++md2.collapse() ++md=solve(md,'Transient') ++ ++#Fields and tolerances to track changes ++field_names =['IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation21','Thickness1','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1','IceMass3','IceVolume3','IceVolumeAboveFloatation3','IceVolumeAboveFloatation23','Thickness3','GroundedArea3','FloatingArea3','TotalFloatingBmb3','TotalGroundedBmb3','TotalSmb3','ExtrudedMask','CollapsedMask'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results.TransientSolution[0].IceMass1,\ ++ md.results.TransientSolution[0].IceVolume1,\ ++ md.results.TransientSolution[0].IceVolumeAboveFloatation1,\ ++ md.results.TransientSolution[0].IceVolumeAboveFloatation2,\ ++ md.results.TransientSolution[0].Thickness,\ ++ md.results.TransientSolution[0].GroundedArea1,\ ++ md.results.TransientSolution[0].FloatingArea1,\ ++ md.results.TransientSolution[0].TotalFloatingBmb1,\ ++ md.results.TransientSolution[0].TotalGroundedBmb1,\ ++ md.results.TransientSolution[0].TotalSmb1,\ ++ md.results.TransientSolution[2].IceMass1,\ ++ md.results.TransientSolution[2].IceVolume1,\ ++ md.results.TransientSolution[2].IceVolumeAboveFloatation1,\ ++ md.results.TransientSolution[2].IceVolumeAboveFloatation2,\ ++ md.results.TransientSolution[2].Thickness,\ ++ md.results.TransientSolution[2].GroundedArea1,\ ++ md.results.TransientSolution[2].FloatingArea1,\ ++ md.results.TransientSolution[2].TotalFloatingBmb1,\ ++ md.results.TransientSolution[2].TotalGroundedBmb1,\ ++ md.results.TransientSolution[2].TotalSmb1,\ ++ len(md.outputdefinition.definitions[0].mask),\ ++ len(md2.outputdefinition.definitions[0].mask),\ ++ ] +Index: ../trunk-jpl/test/Archives/Archive443.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21827-21828.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21827-21828.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21827-21828.diff (revision 22755) @@ -0,0 +1,536 @@ +Index: ../trunk-jpl/src/c/modules/InterpFromMeshToGridx/InterpFromMeshToGridx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/InterpFromMeshToGridx/InterpFromMeshToGridx.cpp (revision 21827) ++++ ../trunk-jpl/src/c/modules/InterpFromMeshToGridx/InterpFromMeshToGridx.cpp (revision 21828) +@@ -5,19 +5,12 @@ + #include "./InterpFromMeshToGridx.h" + #include "../../shared/shared.h" + +-void InterpFromMeshToGridx(double** px_m,double** py_m,double** pgriddata,double* index_mesh, double* x_mesh, double* y_mesh, int nods,int nels, double* data_mesh, int data_length, double xmin,double ymax,double xposting,double yposting,int nlines,int ncols,double default_value) { ++void InterpFromMeshToGridx(double** pgriddata,double* index_mesh, double* x_mesh, double* y_mesh, int nods,int nels, double* data_mesh,int data_length,double* x_grid,double* y_grid,int nlines,int ncols,double default_value){ + +- /*Output*/ +- double* griddata=NULL; +- double* x_grid=NULL; +- double* y_grid=NULL; +- + /*Intermediary*/ +- int i,j,n; ++ int i,j; + int i1,i2,j1,j2; + int interpolation_type; +- bool debug; +- int xflip,yflip; + double area; + double area_1,area_2,area_3; + double x_tria_min,y_tria_min; +@@ -27,74 +20,59 @@ + double data_value; + + /*some checks*/ +- if (nels<1 || nods<3 || nlines<1 || ncols<1 || xposting==0 || yposting==0){ +- _error_("nothing to be done according to the mesh given in input"); +- } ++ if(nels<1 || nods<3 || nlines<2 || ncols<2) _error_("nothing to be done according to the mesh given in input"); + + /*figure out what kind of interpolation is needed*/ +- if (data_length==nods){ +- interpolation_type=1; +- } +- else if (data_length==nels){ +- interpolation_type=2; +- } +- else{ +- _error_("length of vector data not supported yet. It should be of length (number of nodes) or (number of elements)!"); +- } ++ if(data_length==nods) interpolation_type=1; ++ else if(data_length==nels) interpolation_type=2; ++ else _error_("length of vector data not supported yet. It should be of length (number of nodes) or (number of elements)!"); + + /*First, allocate pointers: */ +- griddata=xNewZeroInit(nlines*ncols); +- x_grid=xNewZeroInit(ncols); +- y_grid=xNewZeroInit(nlines); ++ double* griddata=xNewZeroInit(nlines*ncols); + + /*Set debug to 1 if there are lots of elements*/ +- debug=(bool)((double)ncols*nlines*nels >= 5*pow(10.,10.)); ++ bool debug=(bool)((double)ncols*nlines*nels >= 5.e10); + + /*Initialize coordintes and griddata*/ +- for(i=0;ix_tria_max) x_tria_max=x_mesh[(int)index_mesh[3*n+i]-1]; + if(y_mesh[(int)index_mesh[3*n+i]-1]x_grid_max) || (x_tria_maxy_grid_max) || (y_tria_maxx_grid_max) || (x_tria_maxy_grid_max) || (y_tria_maxy_tria_max) || (y_grid[i]-10e-12 && area_2>-10e-12 && area_3>-10e-12){ ++ if(area_1>-10e-12 && area_2>-10e-12 && area_3>-10e-12){ + + /*Yes ! compute the value on the point*/ +- if (interpolation_type==1){ ++ if(interpolation_type==1){ + /*nodal interpolation*/ + data_value=area_1*data_mesh[(int)index_mesh[3*n+0]-1]+area_2*data_mesh[(int)index_mesh[3*n+1]-1]+area_3*data_mesh[(int)index_mesh[3*n+2]-1]; + } +@@ -168,11 +146,8 @@ + } + } + } +- if (debug) +- _printf_("\r interpolation progress: "<(y); + xDelete(meshdata); + xDelete(griddata); +- xDelete(x_m); +- xDelete(y_m); ++ xDelete(xgrid); ++ xDelete(ygrid); + + /*end module: */ + MODULEEND(); +Index: ../trunk-jpl/src/wrappers/InterpFromMeshToGrid/InterpFromMeshToGrid.h +=================================================================== +--- ../trunk-jpl/src/wrappers/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 21827) ++++ ../trunk-jpl/src/wrappers/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 21828) +@@ -32,17 +32,11 @@ + #define X prhs[1] + #define Y prhs[2] + #define MESHDATA prhs[3] +-#define XMIN prhs[4] +-#define YMAX prhs[5] +-#define XPOSTING prhs[6] +-#define YPOSTING prhs[7] +-#define NLINES prhs[8] +-#define NCOLS prhs[9] +-#define DEFAULTVALUE prhs[10] ++#define XGRID prhs[4] ++#define YGRID prhs[5] ++#define DEFAULTVALUE prhs[6] + /* serial output macros: */ +-#define XM (mxArray**)&plhs[0] +-#define YM (mxArray**)&plhs[1] +-#define GRIDDATA (mxArray**)&plhs[2] ++#define GRIDDATA (mxArray**)&plhs[0] + #endif + + #ifdef _HAVE_PYTHON_MODULES_ +@@ -51,23 +45,17 @@ + #define X PyTuple_GetItem(args,1) + #define Y PyTuple_GetItem(args,2) + #define MESHDATA PyTuple_GetItem(args,3) +-#define XMIN PyTuple_GetItem(args,4) +-#define YMAX PyTuple_GetItem(args,5) +-#define XPOSTING PyTuple_GetItem(args,6) +-#define YPOSTING PyTuple_GetItem(args,7) +-#define NLINES PyTuple_GetItem(args,8) +-#define NCOLS PyTuple_GetItem(args,9) ++#define XGRID PyTuple_GetItem(args,4) ++#define YGRID PyTuple_GetItem(args,5) + #define DEFAULTVALUE PyTuple_GetItem(args,10) + /* serial output macros: */ +-#define XM output,0 +-#define YM output,1 +-#define GRIDDATA output,2 ++#define GRIDDATA output,0 + #endif + + /* serial arg counts: */ + #undef NLHS +-#define NLHS 3 ++#define NLHS 1 + #undef NRHS +-#define NRHS 11 ++#define NRHS 7 + + #endif /* _INTERPFROMMESHTOGRID_H*/ +Index: ../trunk-jpl/src/m/miscellaneous/diagnostics.m +=================================================================== +--- ../trunk-jpl/src/m/miscellaneous/diagnostics.m (revision 21827) ++++ ../trunk-jpl/src/m/miscellaneous/diagnostics.m (revision 21828) +@@ -45,11 +45,10 @@ + xposting=getfieldvalue(options,'velposting',500); + yposting=getfieldvalue(options,'velposting',500); + +- xmin=min(md.mesh.x); ymax=max(md.mesh.y); +- ncols=(max(md.mesh.x)-min(md.mesh.x))/xposting+1; +- nlines=(max(md.mesh.y)-min(md.mesh.y))/yposting+1; ++ xm=min(md.mesh.x):posting:max(md.mesh.x); ++ ym=min(md.mesh.y):posting:max(md.mesh.y); + +- [xm,ym,vel]=InterpFromMeshToGrid(md.mesh.elements,md.mesh.x,md.mesh.y,vel,xmin,ymax,xposting,yposting,nlines,ncols,0); ++ vel=InterpFromMeshToGrid(md.mesh.elements,md.mesh.x,md.mesh.y,vel,xm,ym,0.); + vel=uint16(flipud(vel)); + + imwrite(vel,[path '/veltemp.tif'],'tiff'); +Index: ../trunk-jpl/src/m/modules/InterpFromMeshToGrid.py +=================================================================== +--- ../trunk-jpl/src/m/modules/InterpFromMeshToGrid.py (revision 21827) ++++ ../trunk-jpl/src/m/modules/InterpFromMeshToGrid.py (revision 21828) +@@ -1,6 +1,6 @@ + from InterpFromMeshToGrid_python import InterpFromMeshToGrid_python + +-def InterpFromMeshToGrid(index,x,y,data,xmin,ymax,xposting,yposting,nlines,ncols,default_value): ++def InterpFromMeshToGrid(index,x,y,data,xgrid,ygrid,default_value): + """ + INTERPFROMMESHTOGRID - Interpolation of a data defined on a mesh onto a grid + +@@ -10,10 +10,10 @@ + index,x,y: delaunay triangulation defining the mesh + meshdata: vertex values of data to be interpolated + +- xmin,ymax,posting,nlines,ncols: parameters that define the grid ++ xgrid,ygrid,: parameters that define the grid + default_value: value of points located out of the mesh + """ + # Call mex module +- x_m,y_m,griddata=InterpFromMeshToGrid_python(index,x,y,data,xmin,ymax,xposting,yposting,nlines,ncols,default_value) ++ grid=InterpFromMeshToGrid_python(index,x,y,data,xgrid,ygrid,default_value) + # Return +- return x_m,y_m,griddate ++ return grid +Index: ../trunk-jpl/src/m/modules/InterpFromMeshToGrid.m +=================================================================== +--- ../trunk-jpl/src/m/modules/InterpFromMeshToGrid.m (revision 21827) ++++ ../trunk-jpl/src/m/modules/InterpFromMeshToGrid.m (revision 21828) +@@ -1,6 +1,9 @@ +-function [x_m,y_m,griddata] = InterpFromMeshToGrid(index,x,y,data,xmin,ymax,xposting,yposting,nlines,ncols,default_value); ++function grid = InterpFromMeshToGrid(index,x,y,data,xgrid,ygrid,default_value); + %INTERPFROMMESHTOGRID - Interpolation of a data defined on a mesh onto a grid + % ++% Usage: ++% grid = InterpFromMeshToGrid(index,x,y,data,xgrid,ygrid,default_value) ++% + % This function is a multi-threaded mex file that interpolates a field defined on a triangular + % mesh onto a regular grid. + % +@@ -7,14 +10,14 @@ + % index,x,y: delaunay triangulation defining the mesh + % meshdata: vertex values of data to be interpolated + % +-% xmin,ymax,posting,nlines,ncols: parameters that define the grid +-% default_value: value of points located out of the mesh ++% xgrid,ygrid: parameters that define the grid ++% default_value: value of points located out of the mesh + + % Check usage +-if nargin~=11 ++if nargin~=7 + help InterpFromMeshToGrid + error('Wrong usage (see above)'); + end + + % Call mex module +-[x_m,y_m,griddata] = InterpFromMeshToGrid_matlab(index,x,y,data,xmin,ymax,xposting,yposting,nlines,ncols,default_value); ++grid = InterpFromMeshToGrid_matlab(index,x,y,data,xgrid,ygrid,default_value); +Index: ../trunk-jpl/src/m/plot/plot_overlay.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_overlay.m (revision 21827) ++++ ../trunk-jpl/src/m/plot/plot_overlay.m (revision 21828) +@@ -57,26 +57,13 @@ + end + + %InterpFromMeshToGrid +-xmin=min(md.radaroverlay.x); +-ymax=max(md.radaroverlay.y); +-xspacing=(max(md.radaroverlay.x)-min(md.radaroverlay.x))/(length(md.radaroverlay.x) -1); +-yspacing=(max(md.radaroverlay.y)-min(md.radaroverlay.y))/(length(md.radaroverlay.y) -1); +-if(md.radaroverlay.x(end)-md.radaroverlay.x(1)<0) +- xspacing= -xspacing; +-end +-if(md.radaroverlay.y(end)-md.radaroverlay.y(1)<0) +- yspacing= -yspacing; +-end +-nlines=length(md.radaroverlay.y); +-ncols =length(md.radaroverlay.x); + disp('Interpolating data on grid...'); ++x_m = md.radaroverlay.x; ++y_m = md.radaroverlay.y; + if radaronly, +- x_m=xmin:xspacing:xmin+ncols*xspacing; +- y_m=ymax-nlines*yspacing:yspacing:ymax; +- data_grid=NaN*ones(nlines,ncols); ++ data_grid=NaN(size(radar)); + else +- [x_m y_m data_grid]=InterpFromMeshToGrid(elements,x/getfieldvalue(options,'unit',1),y/getfieldvalue(options,'unit',1),... +- data,xmin,ymax,xspacing,yspacing,nlines,ncols,NaN); ++ data_grid=InterpFromMeshToGrid(elements,x/getfieldvalue(options,'unit',1),y/getfieldvalue(options,'unit',1),data,x_m,y_m,NaN); + end + + %Process data_grid (For processing, it is better not to have nan) +@@ -151,7 +138,7 @@ + subplotmodel(plotlines,plotcols,i,options); + + %Plot: +-imagesc(md.radaroverlay.x*getfieldvalue(options,'unit',1),md.radaroverlay.y*getfieldvalue(options,'unit',1),image_rgb);set(gca,'YDir','normal'); ++imagesc(x_m*getfieldvalue(options,'unit',1),y_m*getfieldvalue(options,'unit',1),image_rgb);set(gca,'YDir','normal'); + + %last step: mesh overlay? + if exist(options,'edgecolor'), +Index: ../trunk-jpl/src/m/plot/plot_googlemaps.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_googlemaps.m (revision 21827) ++++ ../trunk-jpl/src/m/plot/plot_googlemaps.m (revision 21828) +@@ -61,14 +61,9 @@ + + %Prepare grid + if size(md.radaroverlay.x,1)==1 | size(md.radaroverlay.x,2)==1, +- xmin=min(md.radaroverlay.x); +- ymax=max(md.radaroverlay.y); +- xspacing=md.radaroverlay.x(2)-md.radaroverlay.x(1); +- yspacing=md.radaroverlay.y(2)-md.radaroverlay.y(1); +- nlines=length(md.radaroverlay.y); +- ncols =length(md.radaroverlay.x); +- [x_m y_m data_grid]=InterpFromMeshToGrid(elements,x/getfieldvalue(options,'unit',1),y/getfieldvalue(options,'unit',1),... +- data,xmin,ymax,xspacing,yspacing,nlines,ncols,NaN); ++ x_m = md.radaroverlay.x; ++ y_m = md.radaroverlay.y; ++ data_grid=InterpFromMeshToGrid(elements,x/getfieldvalue(options,'unit',1),y/getfieldvalue(options,'unit',1),data,x_m,y_m,NaN); + else + X = md.radaroverlay.x; + Y = md.radaroverlay.y; +Index: ../trunk-jpl/src/m/plot/plot_gridded.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_gridded.m (revision 21827) ++++ ../trunk-jpl/src/m/plot/plot_gridded.m (revision 21828) +@@ -22,7 +22,9 @@ + posty=getfieldvalue(options,'posting',diff(ylim)/1000); + + %Interpolating data on grid +-[x_m y_m data_grid]=InterpFromMeshToGrid(elements,x,y,data,xlim(1),ylim(2),postx,posty,round(diff(ylim)/posty),round(diff(xlim)/postx),NaN); ++x_m = xlim(1):postx:xlim(2); ++y_m = ylim(1):posty:ylim(2); ++data_grid=InterpFromMeshToGrid(elements,x,y,data,x_m,y_m,NaN); + data_grid_save = data_grid; + if size(data_grid,1)<3 | size(data_grid,2)<3, + error('data_grid size too small in plot_gridded, check posting and units'); +Index: ../trunk-jpl/src/m/plot/kmlgridded.m +=================================================================== +--- ../trunk-jpl/src/m/plot/kmlgridded.m (revision 21827) ++++ ../trunk-jpl/src/m/plot/kmlgridded.m (revision 21828) +@@ -24,7 +24,9 @@ + end + + %Interpolating data on grid +-[x_m y_m data_grid]=InterpFromMeshToGrid(elements,x,y,data,xlim(1),ylim(2),post,post,round(diff(ylim)/post),round(diff(xlim)/post),NaN); ++x_m = xlim(1):post:xlim(2); ++y_m = ylim(1):post:ylim(2); ++data_grid=InterpFromMeshToGrid(elements,x,y,data,x_m,y_m,NaN); + if size(data_grid,1)<3 | size(data_grid,2)<3, + error('data_grid size too small, check posting and units'); + end +Index: ../trunk-jpl/src/m/kml/kmlimagesc.m +=================================================================== +--- ../trunk-jpl/src/m/kml/kmlimagesc.m (revision 21827) ++++ ../trunk-jpl/src/m/kml/kmlimagesc.m (revision 21828) +@@ -45,11 +45,11 @@ + end + + %figure out nlines and ncols in our image +-nlines=(maxlat-minlat)/posting; +-ncols=(maxlong-minlong)/posting; ++x_m = minlong:posting:maxlong; ++y_m = minlat:posting:maxlat; + + %regrid to lat,long grid +-[x_m,y_m,field]=InterpFromMeshToGrid(md.mesh.elements,md.mesh.long,md.mesh.lat,field,minlong,maxlat,posting,posting,nlines,ncols,NaN); ++field=InterpFromMeshToGrid(md.mesh.elements,md.mesh.long,md.mesh.lat,field,x_m,y_m,NaN); + field=flipud(field); + + %massage and log: Index: /issm/oecreview/Archive/21724-22754/ISSM-21828-21829.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21828-21829.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21828-21829.diff (revision 22755) @@ -0,0 +1,31 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21828) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21829) +@@ -2418,13 +2418,14 @@ + + element->GetVerticesCoordinates(&xyz_list); + for(int i=0;i-720.) r[i] = bx+by; + } + + /*insert new bedrock*/ +@@ -2436,8 +2437,6 @@ + + /*Delete*/ + xDelete(r); +- +- return; + } + /*}}}*/ + void FemModel::AdjustBaseThicknessAndMask(void){/*{{{*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21829-21830.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21829-21830.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21829-21830.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21829) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21830) +@@ -157,7 +157,7 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.basalforcings.lowercrustheat",BasalforcingsLowercrustheatEnum)); + break; + default: +- _error_("Basal forcing model "< %s.errlog >%s.outlog ',... +- cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname); ++ fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog >%s.outlog ',... ++ cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname); + else +- fprintf(fid,'%s --leak-check=full --error-limit=no --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',... +- cluster.valgrind,cluster.valgrindsup,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname); ++ fprintf(fid,'%s --leak-check=full --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog >%s.outlog ',... ++ cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname); + end + end + end Index: /issm/oecreview/Archive/21724-22754/ISSM-21831-21832.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21831-21832.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21831-21832.diff (revision 22755) @@ -0,0 +1,46 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21831) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21832) +@@ -81,6 +81,12 @@ + + /*AMR stuff*/ + this->parameters->FindParam(&amr_frequency,TransientAmrFrequencyEnum); ++ #ifdef _HAVE_NEOPZ_ ++ this->amr = NULL; ++ #endif ++ #ifdef _HAVE_BAMG_ ++ this->amrbamg = NULL; ++ #endif + if(amr_frequency){ + this->parameters->FindParam(&amrtype,AmrTypeEnum); + switch(amrtype){ +@@ -120,6 +126,13 @@ + profiler->Tag(STARTINIT); + this->InitFromFiles(rootpath,inputfilename,outputfilename,toolkitsfilename,lockfilename,restartfilename, solution_type,traceon,X); + profiler->Tag(FINISHINIT); ++ ++ #ifdef _HAVE_NEOPZ_ ++ this->amr = NULL; ++ #endif ++ #ifdef _HAVE_BAMG_ ++ this->amrbamg = NULL; ++ #endif + + /*Save communicator in the parameters dataset: */ + this->parameters->AddObject(new GenericParam(incomm,FemModelCommEnum)); +@@ -288,6 +301,14 @@ + ConfigureObjectsx(output->elements,output->loads,output->nodes,output->vertices,output->materials,output->parameters); + } + ++ /*AMR, no copy for now*/ ++ #ifdef _HAVE_NEOPZ_ ++ this->amr = NULL; ++ #endif ++ #ifdef _HAVE_BAMG_ ++ this->amrbamg = NULL; ++ #endif ++ + /*Reset current configuration: */ + analysis_type=output->analysis_type_list[analysis_counter]; + output->SetCurrentConfiguration(analysis_type); Index: /issm/oecreview/Archive/21724-22754/ISSM-21832-21833.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21832-21833.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21832-21833.diff (revision 22755) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21832) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21833) +@@ -52,7 +52,7 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,6e-09,5e-08,1e-09,1e-10,1e-13,... +- 4e-10,9e-09,5e-09,3e-09,6e-04,5e-04,2e-09,1e-10,1e-13}; ++ 4e-10,3e-08,8e-09,5e-09,7e-04,5e-04,2e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21832) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21833) +@@ -52,7 +52,7 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,4e-09,5e-08,1e-09,1e-10,1e-13,... +- 1e-10,5e-09,3e-09,2e-7,5e-04,4e-04,1e-09,1e-10,1e-13}; ++ 1e-10,2e-08,7e-09,2e-7,9e-04,7e-04,2e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21833-21834.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21833-21834.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21833-21834.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/test/NightlyRun/runme.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/runme.py (revision 21833) ++++ ../trunk-jpl/test/NightlyRun/runme.py (revision 21834) +@@ -182,6 +182,7 @@ + if archive == None: + raise NameError("Field name '"+archive_name+'_field'+str(k+1)+"' does not exist in archive file.") + error_diff=np.amax(np.abs(archive-field),axis=0)/(np.amax(np.abs(archive),axis=0)+float_info.epsilon) ++ error_diff=error_diff[0] + + #disp test result + if (np.any(error_diff>tolerance) or np.isnan(error_diff)): Index: /issm/oecreview/Archive/21724-22754/ISSM-21834-21835.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21834-21835.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21834-21835.diff (revision 22755) @@ -0,0 +1,17 @@ +Index: ../trunk-jpl/test/NightlyRun/test505.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test505.py (revision 21834) ++++ ../trunk-jpl/test/NightlyRun/test505.py (revision 21835) +@@ -18,9 +18,9 @@ + + # Fields and tolerances to track changes + field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsGroundediceMeltingRate1', \ +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2'] +-field_tolerances=[1e-12,1e-12,1e-10,1e-12,1e-13,3e-13,7e-13,3e-13,1e-13,6e-10, \ +- 2e-12,5e-12,1e-10,4e-12,3e-13,1e-11,1e-11,2e-12,1e-11,1e-8] ++ 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2'] ++field_tolerances=[1e-12,1e-12,3e-10,1e-12,1e-13,1e-11,5e-12,9e-12,1e-13,5e-9, \ ++ 5e-11,5e-11,1e-10,2e-11,7e-12,1e-11,1e-11,5e-12,1e-11,2e-8] + field_values=[\ + md.results.TransientSolution[0].Vx,\ + md.results.TransientSolution[0].Vy,\ Index: /issm/oecreview/Archive/21724-22754/ISSM-21835-21836.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21835-21836.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21835-21836.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/test/NightlyRun/runme.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/runme.py (revision 21835) ++++ ../trunk-jpl/test/NightlyRun/runme.py (revision 21836) +@@ -182,7 +182,7 @@ + if archive == None: + raise NameError("Field name '"+archive_name+'_field'+str(k+1)+"' does not exist in archive file.") + error_diff=np.amax(np.abs(archive-field),axis=0)/(np.amax(np.abs(archive),axis=0)+float_info.epsilon) +- error_diff=error_diff[0] ++ if not np.isscalar(error_diff): error_diff=error_diff[0] + + #disp test result + if (np.any(error_diff>tolerance) or np.isnan(error_diff)): Index: /issm/oecreview/Archive/21724-22754/ISSM-21836-21837.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21836-21837.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21836-21837.diff (revision 22755) @@ -0,0 +1,761 @@ +Index: ../trunk-jpl/src/c/bamg/Geometry.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Geometry.cpp (revision 21836) ++++ ../trunk-jpl/src/c/bamg/Geometry.cpp (revision 21837) +@@ -186,12 +186,6 @@ + } + } + +- //MaxCornerAngle +- if (bamgopts->MaxCornerAngle){ +- if(verbose>5) _printf_(" processing MaxCornerAngle\n"); +- MaxCornerAngle=bamgopts->MaxCornerAngle*Pi/180; +- } +- + //TangentAtEdges + if (bamggeom->TangentAtEdges){ + if(verbose>5) _printf_(" processing TangentAtEdges"); +@@ -400,7 +394,6 @@ + _printf_(" pmin (x,y): (" << pmin.x << " " << pmin.y << ")\n"); + _printf_(" pmax (x,y): (" << pmax.x << " " << pmax.y << ")\n"); + _printf_(" coefIcoor: " << coefIcoor << "\n"); +- _printf_(" MaxCornerAngle: " << MaxCornerAngle << "\n"); + + return; + } +@@ -418,7 +411,6 @@ + nbsubdomains=0; + nbcurves=0; + subdomains=NULL; +- MaxCornerAngle = 10*Pi/180; //default is 10 degres + } + /*}}}*/ + double Geometry::MinimalHmin() {/*{{{*/ +@@ -613,19 +605,14 @@ + } + } + +- // angular test on current vertex to guess whether it is a corner (ord = number of edges holding i) +- if(ord==2) { ++ //all vertices provided in geometry are corners (ord = number of edges holding i) ++ vertices[i].SetCorner() ; ++ if(ord==2){ + long n1 = head_v[i]; + long n2 = next_p[n1]; + long i1 = n1/2, i2 = n2/2; // edge number +- long j1 = n1%2, j2 = n2%2; // vertex in the edge +- float angle1= j1 ? OppositeAngle(eangle[i1]) : eangle[i1]; +- float angle2= !j2 ? OppositeAngle(eangle[i2]) : eangle[i2]; +- float da12 = Abs(angle2-angle1); +- if (( da12 >= MaxCornerAngle ) && (da12 <= 2*Pi -MaxCornerAngle)) { +- vertices[i].SetCorner() ; +- } +- // if the edge type/referencenumber a changing then is SetRequired(); ++ long j1 = n1%2, j2 = n2%2; // vertex in the edge ++ /* if the edge type/referencenumber a changing then is SetRequired();*/ + if (edges[i1].type != edges[i2].type || edges[i1].Required()){ + vertices[i].SetRequired(); + } +@@ -633,9 +620,6 @@ + vertices[i].SetRequired(); + } + } +- if(ord != 2) { +- vertices[i].SetCorner(); +- } + + /*close the list around the vertex to have a circular loop*/ + long no=-1, ne = head_v[i]; +Index: ../trunk-jpl/src/c/bamg/Mesh.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.h (revision 21836) ++++ ../trunk-jpl/src/c/bamg/Mesh.h (revision 21837) +@@ -39,6 +39,7 @@ + R2 pmin,pmax; // extrema + double coefIcoor; // coef to integer + ListofIntersectionTriangles lIntTria; ++ int randomseed; //used for random number generation + + long NbVerticesOnGeomVertex; + VertexOnGeom *VerticesOnGeomVertex; +@@ -76,7 +77,7 @@ + I2 R2ToI2(const R2 & P) const; + R2 I2ToR2(const I2 & P) const; + void AddVertex(BamgVertex & s,Triangle * t,long long * =0) ; +- void Insert(bool random); ++ void Insert(); + void Echo(void); + void ForceBoundary(); + void FindSubDomain(int OutSide=0); +@@ -90,7 +91,7 @@ + void MakeBamgQuadtree(); + void MaxSubDivision(double maxsubdiv); + void NewPoints(Mesh &,BamgOpts* bamgopts,int KeepVertices=1); +- long InsertNewPoints(long nbvold,long & NbTSwap,bool random); ++ long InsertNewPoints(long nbvold,long & NbTSwap); + void TrianglesRenumberBySubDomain(bool justcompress=false); + void SmoothingVertex(int =3,double=0.3); + Metric MetricAt (const R2 &) const; +@@ -112,8 +113,8 @@ + void AddMetric(BamgOpts* bamgopts); + void BuildMetric0(BamgOpts* bamgopts); + void BuildMetric1(BamgOpts* bamgopts); +- void AddGeometryMetric(BamgOpts* bamgopts); + void BuildGeometryFromMesh(BamgOpts* bamgopts=NULL); ++ int RandomNumber(int max); + void ReconstructExistingMesh(); + + //Inline methods +@@ -142,6 +143,10 @@ + void TriangulateFromGeom0(BamgOpts* bamgopts);// the real constructor mesh generator + void Triangulate(double* x,double* y,int nods); + void Init(long); ++ int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) ; ++ int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb , ++ AdjacentTriangle & tt1,long long & dets1, ++ long long & detsa,long long & detsb, int & nbswap); + }; + + /*Intermediary*/ +@@ -149,10 +154,7 @@ + void swap(Triangle *t1,short a1, + Triangle *t2,short a2, + BamgVertex *s1,BamgVertex *s2,long long det1,long long det2); +- int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb , +- AdjacentTriangle & tt1,long long & dets1, +- long long & detsa,long long & detsb, int & nbswap); +- int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) ; ++ + inline AdjacentTriangle Previous(const AdjacentTriangle & ta){ + return AdjacentTriangle(ta.t,PreviousEdge[ta.a]); + } +Index: ../trunk-jpl/src/c/bamg/BamgOpts.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgOpts.h (revision 21836) ++++ ../trunk-jpl/src/c/bamg/BamgOpts.h (revision 21837) +@@ -16,7 +16,6 @@ + double errg; + double gradation; + int Hessiantype; +- double MaxCornerAngle; + int maxnbv; + double maxsubdiv; + int Metrictype; +@@ -24,12 +23,10 @@ + int nbsmooth; + double omega; + double power; +- bool random; + int verbose; + + /*Flags*/ + int Crack; +- int geometricalmetric; + int KeepVertices; + int splitcorners; + +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21836) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21837) +@@ -979,57 +979,6 @@ + /*}}}*/ + + /*Methods*/ +- void Mesh::AddGeometryMetric(BamgOpts* bamgopts){/*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, Metric.cpp/IntersectGeomMetric)*/ +- +- /*Get options*/ +- double anisomax = bamgopts->anisomax; +- double errg = bamgopts->errg; +- +- double ss[2]={0.00001,0.99999}; +- double errC = 2*sqrt(2*errg); +- double hmax = Gh.MaximalHmax(); +- double hmin = Gh.MinimalHmin(); +- +- //check that hmax is positive +- _assert_(hmax>0); +- +- //errC cannot be higher than 1 +- if(errC>1) errC=1; +- +- //Set all vertices to "on" +- SetVertexFieldOn(); +- +- //loop over all the vertices on edges +- for(int i=0;iR1tg(s,tg); +- double ht=hmax; +- // err relative to the length of the edge +- if (R1>1.0e-20) { +- ht = Min(Max(errC/R1,hmin),hmax); +- } +- double hn=Min(hmax,ht*anisomax); +- +- if (ht<=0 || hn<=0){ +- _error_("ht<=0 || hn<=0"); +- } +- EigenMetric Vp(1/(ht*ht),1/(hn*hn),tg); +- Metric MVp(Vp); +- edges[i][j].m.IntersectWith(MVp); +- } +- } +- // the problem is for the vertex on vertex +- } +- /*}}}*/ + void Mesh::AddMetric(BamgOpts* bamgopts){/*{{{*/ + // Hessiantype = 0 => H is computed using double L2 projection + // Hessiantype = 1 => H is computed with green formula +@@ -1230,12 +1179,10 @@ + /*Intermediary*/ + int i,j,k,kk,it,jt; + int verbose=0; +- double cutoffradian=10*Pi/180; + + /*Recover options*/ +- if (bamgopts){ ++ if(bamgopts){ + verbose=bamgopts->verbose; +- cutoffradian=bamgopts->MaxCornerAngle*Pi/180; + } + + //display info +@@ -1242,13 +1189,8 @@ + if (verbose>1) _printf_(" construction of the geometry from the 2d mesh\n"); + + //check that the mesh is not empty +- if (nbt<=0 || nbv <=0 ) { +- _error_("nbt or nbv is negative (Mesh empty?)"); +- } ++ if(nbt<=0 || nbv <=0 ) _error_("nbt or nbv is negative (Mesh empty?)"); + +- //Gh is the geometry of the mesh (this), initialize MaxCornerAngle +- if (cutoffradian>=0) Gh.MaxCornerAngle = cutoffradian; +- + /*Construction of the edges*/ + + //initialize st and edge4 +@@ -1446,9 +1388,7 @@ + /*Reconstruct subdomains info*/ + + //check that nbsubdomains is empty +- if (nbsubdomains){ +- _error_("nbsubdomains should be 0"); +- } ++ if(nbsubdomains) _error_("nbsubdomains should be 0"); + nbsubdomains=0; + + //color the subdomains +@@ -2648,51 +2588,51 @@ + void Mesh::Init(long maxnbv_in) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/PreInit)*/ + +- /* initialize random seed: */ +- srand(19999999); +- + /*Initialize fields*/ +- NbRef=0; +- quadtree=NULL; +- nbv=0; +- nbt=0; +- nbe=0; +- edges=NULL; +- nbsubdomains=0; +- subdomains=NULL; +- maxnbv=maxnbv_in; +- maxnbt=2 *maxnbv_in-2; +- NbVertexOnBThVertex=0; +- VertexOnBThVertex=NULL; +- NbVertexOnBThEdge=0; +- VertexOnBThEdge=NULL; +- NbCrackedVertices=0; +- CrackedVertices =NULL; +- NbCrackedEdges =0; +- CrackedEdges =NULL; +- NbVerticesOnGeomVertex=0; +- VerticesOnGeomVertex=NULL; +- NbVerticesOnGeomEdge=0; +- VerticesOnGeomEdge=NULL; ++ this->NbRef = 0; ++ this->quadtree = NULL; ++ this->nbv = 0; ++ this->nbt = 0; ++ this->nbe = 0; ++ this->edges = NULL; ++ this->nbsubdomains = 0; ++ this->subdomains = NULL; ++ this->maxnbv = maxnbv_in; ++ this->maxnbt = 2 *maxnbv_in-2; ++ this->NbVertexOnBThVertex = 0; ++ this->VertexOnBThVertex = NULL; ++ this->NbVertexOnBThEdge = 0; ++ this->VertexOnBThEdge = NULL; ++ this->NbCrackedVertices = 0; ++ this->CrackedVertices = NULL; ++ this->NbCrackedEdges = 0; ++ this->CrackedEdges = NULL; ++ this->NbVerticesOnGeomVertex = 0; ++ this->VerticesOnGeomVertex = NULL; ++ this->NbVerticesOnGeomEdge = 0; ++ this->VerticesOnGeomEdge = NULL; + ++ /*Initialize random seed*/ ++ this->randomseed = 1; ++ + /*Allocate if maxnbv_in>0*/ + if(maxnbv_in){ +- vertices=new BamgVertex[maxnbv]; +- _assert_(vertices); +- orderedvertices=new BamgVertex* [maxnbv]; +- _assert_(orderedvertices); +- triangles=new Triangle[maxnbt]; +- _assert_(triangles); ++ this->vertices=new BamgVertex[this->maxnbv]; ++ this->orderedvertices=new BamgVertex* [this->maxnbv]; ++ this->triangles=new Triangle[this->maxnbt]; ++ _assert_(this->vertices); ++ _assert_(this->orderedvertices); ++ _assert_(this->triangles); + } + else{ +- vertices=NULL; +- orderedvertices=NULL; +- triangles=NULL; +- maxnbt=0; ++ this->vertices = NULL; ++ this->orderedvertices = NULL; ++ this->triangles = NULL; ++ this->maxnbt = 0; + } + } + /*}}}*/ +- void Mesh::Insert(bool random) {/*{{{*/ ++ void Mesh::Insert(){/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/Insert)*/ + + /*Insert points in the existing Geometry*/ +@@ -2739,8 +2679,7 @@ + + //Get Prime number + const long PrimeNumber= BigPrimeNumber(nbv); +- int temp = rand(); if(!random) temp = 756804110; +- int k0=temp%nbv; ++ int k0=this->RandomNumber(nbv); + + //Build orderedvertices + for (i=0; i (BAMG v1.01, Mesh2.cpp/InsertNewPoints)*/ + + long int verbose=0; +@@ -2844,9 +2783,7 @@ + + /*construction of a random order*/ + const long PrimeNumber= BigPrimeNumber(nbv) ; +- //remainder of the division of rand() by nbvnew +- int temp = rand(); if(!random) temp = 1098566905; +- long k3 = temp%nbvnew; ++ long k3 = long(this->RandomNumber(nbvnew)); + //loop over the new points + for (int is3=0; is3random); ++ InsertNewPoints(nbvold,NbTSwap); + } + else Bh.CreateSingleVertexToTriangleConnectivity(); + +@@ -3145,7 +3082,7 @@ + } // end loop for each edge + }// for triangle + +- if (!InsertNewPoints(nbvold,NbTSwap,bamgopts->random)) break; ++ if (!InsertNewPoints(nbvold,NbTSwap)) break; + for (i=nbtold;i4) _printf_(" -- current number of vertices = " << nbv << "\n"); + if (verbose>3) _printf_(" Creating initial Constrained Delaunay Triangulation...\n"); + if (verbose>3) _printf_(" Inserting boundary points\n"); +- Insert(bamgopts->random); ++ Insert(); + + //Force the boundary + if (verbose>3) _printf_(" Forcing boundaries\n"); +@@ -4721,7 +4658,7 @@ + if (verbose>4) _printf_(" -- current number of vertices = " << nbv << "\n"); + if (verbose>3) _printf_(" Creating initial Constrained Delaunay Triangulation...\n"); + if (verbose>3) _printf_(" Inserting boundary points\n"); +- Insert(bamgopts->random); ++ Insert(); + + //Force the boundary + if (verbose>3) _printf_(" Forcing boundaries\n"); +@@ -4736,48 +4673,14 @@ + if (verbose>4) _printf_(" -- current number of vertices = " << nbv << "\n"); + } + /*}}}*/ ++ int Mesh::RandomNumber(int max){/*{{{*/ ++ /* Generate a random number from 0 to max-1 using linear congruential ++ * random number generator*/ + +- /*Intermediary*/ +- AdjacentTriangle CloseBoundaryEdge(I2 A,Triangle *t, double &a,double &b) {/*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/CloseBoundaryEdge)*/ +- +- int k=(*t)(0) ? (( (*t)(1) ? ( (*t)(2) ? -1 : 2) : 1 )) : 0; +- int dir=0; +- if (k<0){ +- _error_("k<0"); +- } +- int kkk=0; +- long long IJ_IA,IJ_AJ; +- AdjacentTriangle edge(t,OppositeEdge[k]); +- for (;;edge = dir >0 ? Next(Adj(Next(edge))) : Previous(Adj(Previous(edge)))) { +- kkk++; +- if (kkk>=1000){ +- _error_("kkk>=1000"); +- } +- BamgVertex &vI = *edge.EdgeVertex(0); +- BamgVertex &vJ = *edge.EdgeVertex(1); +- I2 I=vI, J=vJ, IJ= J-I; +- IJ_IA = (IJ ,(A-I)); +- if (IJ_IA<0) { +- if (dir>0) {a=1;b=0;return edge;}// change of signe => I +- else {dir=-1; +- continue;}};// go in direction i +- IJ_AJ = (IJ ,(J-A)); +- if (IJ_AJ<0) { +- if(dir<0) {a=0;b=1;return edge;} +- else {dir = 1; +- continue;}}// go in direction j +- double IJ2 = IJ_IA + IJ_AJ; +- if (IJ2==0){ +- _error_("IJ2==0"); +- } +- a= IJ_AJ/IJ2; +- b= IJ_IA/IJ2; +- return edge; +- } +- } +- /*}}}*/ +- int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) { /*{{{*/ ++ this->randomseed = (this->randomseed * 1366l + 150889l) % 714025l; ++ return this->randomseed / (714025l / max + 1); ++ } /*}}}*/ ++ int Mesh::ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) { /*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/ForceEdge)*/ + + int NbSwap =0; +@@ -4819,7 +4722,7 @@ + _error_("!v1 || !v2"); + } + long long detss = 0,l=0; +- while ((SwapForForcingEdge( va, vb, tc, detss, det1,det2,NbSwap))) ++ while ((this->SwapForForcingEdge( va, vb, tc, detss, det1,det2,NbSwap))) + if(l++ > 10000000) { + _error_("Loop in forcing Egde, nb de swap=" << NbSwap << ", nb of try swap (" << l << ") too big"); + } +@@ -4852,51 +4755,7 @@ + return NbSwap; + } + /*}}}*/ +- void swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,long long det1,long long det2){ /*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/swap)*/ +- // -------------------------------------------------------------- +- // short a2=aa[a];// les 2 numero de l arete dans les 2 triangles +- // +- // sb sb +- // / | \ / \ ! +- // as1/ | \ /a2 \ ! +- // / | \ / t2 \ ! +- // s1 /t1 | t2 \s2 --> s1 /___as2___\s2 ! +- // \ a1|a2 / \ as1 / +- // \ | / \ t1 / +- // \ | / as2 \ a1/ +- // \ | / \ / +- // sa sa +- // ------------------------------------------------------------- +- int as1 = NextEdge[a1]; +- int as2 = NextEdge[a2]; +- int ap1 = PreviousEdge[a1]; +- int ap2 = PreviousEdge[a2]; +- (*t1)(VerticesOfTriangularEdge[a1][1]) = s2 ; // avant sb +- (*t2)(VerticesOfTriangularEdge[a2][1]) = s1 ; // avant sa +- // mise a jour des 2 adjacences externes +- AdjacentTriangle taas1 = t1->Adj(as1), +- taas2 = t2->Adj(as2), +- tas1(t1,as1), tas2(t2,as2), +- ta1(t1,a1),ta2(t2,a2); +- // externe haut gauche +- taas1.SetAdj2(ta2, taas1.GetAllFlag_UnSwap()); +- // externe bas droite +- taas2.SetAdj2(ta1, taas2.GetAllFlag_UnSwap()); +- // remove the Mark UnMarkSwap +- t1->SetUnMarkUnSwap(ap1); +- t2->SetUnMarkUnSwap(ap2); +- // interne +- tas1.SetAdj2(tas2); +- +- t1->det = det1; +- t2->det = det2; +- +- t1->SetSingleVertexToTriangleConnectivity(); +- t2->SetSingleVertexToTriangleConnectivity(); +- } // end swap +- /*}}}*/ +- int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb ,AdjacentTriangle & tt1,long long & dets1, long long & detsa,long long & detsb, int & NbSwap) {/*{{{*/ ++ int Mesh::SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb ,AdjacentTriangle & tt1,long long & dets1, long long & detsa,long long & detsb, int & NbSwap) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/SwapForForcingEdge)*/ + // l'arete ta coupe l'arete pva pvb + // de cas apres le swap sa coupe toujours +@@ -4983,4 +4842,89 @@ + return ret; + } + /*}}}*/ ++ ++ /*Intermediary*/ ++ AdjacentTriangle CloseBoundaryEdge(I2 A,Triangle *t, double &a,double &b) {/*{{{*/ ++ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/CloseBoundaryEdge)*/ ++ ++ int k=(*t)(0) ? (( (*t)(1) ? ( (*t)(2) ? -1 : 2) : 1 )) : 0; ++ int dir=0; ++ if (k<0){ ++ _error_("k<0"); ++ } ++ int kkk=0; ++ long long IJ_IA,IJ_AJ; ++ AdjacentTriangle edge(t,OppositeEdge[k]); ++ for (;;edge = dir >0 ? Next(Adj(Next(edge))) : Previous(Adj(Previous(edge)))) { ++ kkk++; ++ if (kkk>=1000){ ++ _error_("kkk>=1000"); ++ } ++ BamgVertex &vI = *edge.EdgeVertex(0); ++ BamgVertex &vJ = *edge.EdgeVertex(1); ++ I2 I=vI, J=vJ, IJ= J-I; ++ IJ_IA = (IJ ,(A-I)); ++ if (IJ_IA<0) { ++ if (dir>0) {a=1;b=0;return edge;}// change of signe => I ++ else {dir=-1; ++ continue;}};// go in direction i ++ IJ_AJ = (IJ ,(J-A)); ++ if (IJ_AJ<0) { ++ if(dir<0) {a=0;b=1;return edge;} ++ else {dir = 1; ++ continue;}}// go in direction j ++ double IJ2 = IJ_IA + IJ_AJ; ++ if (IJ2==0){ ++ _error_("IJ2==0"); ++ } ++ a= IJ_AJ/IJ2; ++ b= IJ_IA/IJ2; ++ return edge; ++ } ++ } ++ /*}}}*/ ++ void swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,long long det1,long long det2){ /*{{{*/ ++ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/swap)*/ ++ // -------------------------------------------------------------- ++ // short a2=aa[a];// les 2 numero de l arete dans les 2 triangles ++ // ++ // sb sb ++ // / | \ / \ ! ++ // as1/ | \ /a2 \ ! ++ // / | \ / t2 \ ! ++ // s1 /t1 | t2 \s2 --> s1 /___as2___\s2 ! ++ // \ a1|a2 / \ as1 / ++ // \ | / \ t1 / ++ // \ | / as2 \ a1/ ++ // \ | / \ / ++ // sa sa ++ // ------------------------------------------------------------- ++ int as1 = NextEdge[a1]; ++ int as2 = NextEdge[a2]; ++ int ap1 = PreviousEdge[a1]; ++ int ap2 = PreviousEdge[a2]; ++ (*t1)(VerticesOfTriangularEdge[a1][1]) = s2 ; // avant sb ++ (*t2)(VerticesOfTriangularEdge[a2][1]) = s1 ; // avant sa ++ // mise a jour des 2 adjacences externes ++ AdjacentTriangle taas1 = t1->Adj(as1), ++ taas2 = t2->Adj(as2), ++ tas1(t1,as1), tas2(t2,as2), ++ ta1(t1,a1),ta2(t2,a2); ++ // externe haut gauche ++ taas1.SetAdj2(ta2, taas1.GetAllFlag_UnSwap()); ++ // externe bas droite ++ taas2.SetAdj2(ta1, taas2.GetAllFlag_UnSwap()); ++ // remove the Mark UnMarkSwap ++ t1->SetUnMarkUnSwap(ap1); ++ t2->SetUnMarkUnSwap(ap2); ++ // interne ++ tas1.SetAdj2(tas2); ++ ++ t1->det = det1; ++ t2->det = det2; ++ ++ t1->SetSingleVertexToTriangleConnectivity(); ++ t2->SetSingleVertexToTriangleConnectivity(); ++ } // end swap ++ /*}}}*/ + } +Index: ../trunk-jpl/src/c/bamg/Geometry.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Geometry.h (revision 21836) ++++ ../trunk-jpl/src/c/bamg/Geometry.h (revision 21837) +@@ -31,7 +31,6 @@ + Curve *curves; + R2 pmin,pmax; // domain extrema coordinates + double coefIcoor; // coef to integer coordinates; +- double MaxCornerAngle; + + //Constructor/Destructors + ~Geometry(); +Index: ../trunk-jpl/src/c/bamg/Triangle.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Triangle.cpp (revision 21836) ++++ ../trunk-jpl/src/c/bamg/Triangle.cpp (revision 21837) +@@ -256,7 +256,6 @@ + OnSwap = (Abs(det1) + Abs(det2)) < detA; + + long long detMinNew=Min(det1,det2); +- // if (detMin<0 && (Abs(det1) + Abs(det2) == detA)) OnSwap=BinaryRand();// just for test + if (! OnSwap &&(detMinNew>0)) { + OnSwap = detMin ==0; + if (! OnSwap) { +Index: ../trunk-jpl/src/c/bamg/BamgOpts.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgOpts.cpp (revision 21836) ++++ ../trunk-jpl/src/c/bamg/BamgOpts.cpp (revision 21837) +@@ -10,7 +10,6 @@ + this->errg = 0; + this->gradation = 0; + this->Hessiantype = 0; +- this->MaxCornerAngle = 0; + this->maxnbv = 0; + this->maxsubdiv = 0; + this->Metrictype = 0; +@@ -18,11 +17,9 @@ + this->nbsmooth = 0; + this->omega = 0; + this->power = 0; +- this->random = 0; + this->verbose = 0; + + this->Crack = 0; +- this->geometricalmetric = 0; + this->KeepVertices = 0; + this->splitcorners = 0; + +@@ -67,7 +64,6 @@ + + if (this->Crack!=0 && this->Crack!=1) _error_("'Crack' supported options are 0 and 1"); + if (this->KeepVertices!=0 && this->KeepVertices!=1) _error_("'KeepVertices' supported options are 0 and 1"); +- if (this->geometricalmetric!=0 && this->geometricalmetric!=1) _error_("'geometricalmetric' supported options are 0 and 1"); + + if (this->hmin<=0) _error_("'hmin' option should be >0"); + if (this->hmax<=0 || this->hmaxhmin) _error_("'hmax' option should be between 0 and hmin=" << this->hmin); +Index: ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 21836) ++++ ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 21837) +@@ -148,9 +148,6 @@ + } + } + +- //Add geometry metric if provided +- if(bamgopts->geometricalmetric) BTh.AddGeometryMetric(bamgopts); +- + //Smoothe metric + BTh.SmoothMetric(bamgopts->gradation); + +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 21836) ++++ ../trunk-jpl/src/c/Makefile.am (revision 21837) +@@ -453,8 +453,9 @@ + issm_sources += ./analyses/ExtrapolationAnalysis.cpp + endif + #}}} +-#Gia sources {{{ ++#Gia sources (only if have fortran){{{ + if GIAIVINS ++if FORTRAN + issm_sources += ./cores/gia_core.cpp\ + ./analyses/GiaIvinsAnalysis.cpp\ + ./modules/GiaDeflectionCorex/GiaDeflectionCorex.cpp\ +@@ -466,6 +467,7 @@ + ./modules/GiaDeflectionCorex/stot.f\ + ./modules/GiaDeflectionCorex/what0.f + endif ++endif + #}}} + #Esa sources {{{ + if ESA +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21836) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21837) +@@ -31,7 +31,6 @@ + this->options->errg = 0.1; + this->options->gradation = 1.5; + this->options->Hessiantype = 0; +- this->options->MaxCornerAngle = 1.e-12; + this->options->maxnbv = 1e6; + this->options->maxsubdiv = 10; + this->options->Metrictype = 0; +@@ -39,10 +38,8 @@ + this->options->nbsmooth = 3; + this->options->omega = 1.8; + this->options->power = 1; +- this->options->random = 0; + this->options->verbose = 0; + this->options->Crack = 0; +- this->options->geometricalmetric = 0; + this->options->KeepVertices = 1; /*!!!!! VERY IMPORTANT !!!!!*/ + this->options->splitcorners = 1; + this->options->hmin = hmin; +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 21836) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 21837) +@@ -2059,6 +2059,11 @@ + AC_MSG_ERROR([need at least python or matlab support to compile modules (or use --with-modules=no)]); + fi + ++ dnl check that fortran is provided if GiaIvins is on ++ if test "$HAVE_GIAIVINS" = "yes" && test "$HAVE_FORTRAN" = "no" ; then ++ AC_MSG_ERROR([need fortran compiler to compile GiaIvins (or use --without-GiaIvins )]); ++ fi ++ + dnl check that if we have MPI, we have metis + if test "$HAVE_METIS" = "yes" && test "$HAVE_MPI" = "no" ; then + AC_MSG_ERROR([need mpi if using the metis partitioner!]); Index: /issm/oecreview/Archive/21724-22754/ISSM-21837-21838.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21837-21838.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21837-21838.diff (revision 22755) @@ -0,0 +1,722 @@ +Index: ../trunk-jpl/src/c/bamg/Mesh.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.h (revision 21837) ++++ ../trunk-jpl/src/c/bamg/Mesh.h (revision 21838) +@@ -39,7 +39,6 @@ + R2 pmin,pmax; // extrema + double coefIcoor; // coef to integer + ListofIntersectionTriangles lIntTria; +- int randomseed; //used for random number generation + + long NbVerticesOnGeomVertex; + VertexOnGeom *VerticesOnGeomVertex; +@@ -77,7 +76,7 @@ + I2 R2ToI2(const R2 & P) const; + R2 I2ToR2(const I2 & P) const; + void AddVertex(BamgVertex & s,Triangle * t,long long * =0) ; +- void Insert(); ++ void Insert(bool random); + void Echo(void); + void ForceBoundary(); + void FindSubDomain(int OutSide=0); +@@ -91,7 +90,7 @@ + void MakeBamgQuadtree(); + void MaxSubDivision(double maxsubdiv); + void NewPoints(Mesh &,BamgOpts* bamgopts,int KeepVertices=1); +- long InsertNewPoints(long nbvold,long & NbTSwap); ++ long InsertNewPoints(long nbvold,long & NbTSwap,bool random); + void TrianglesRenumberBySubDomain(bool justcompress=false); + void SmoothingVertex(int =3,double=0.3); + Metric MetricAt (const R2 &) const; +@@ -113,8 +112,8 @@ + void AddMetric(BamgOpts* bamgopts); + void BuildMetric0(BamgOpts* bamgopts); + void BuildMetric1(BamgOpts* bamgopts); ++ void AddGeometryMetric(BamgOpts* bamgopts); + void BuildGeometryFromMesh(BamgOpts* bamgopts=NULL); +- int RandomNumber(int max); + void ReconstructExistingMesh(); + + //Inline methods +@@ -143,10 +142,6 @@ + void TriangulateFromGeom0(BamgOpts* bamgopts);// the real constructor mesh generator + void Triangulate(double* x,double* y,int nods); + void Init(long); +- int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) ; +- int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb , +- AdjacentTriangle & tt1,long long & dets1, +- long long & detsa,long long & detsb, int & nbswap); + }; + + /*Intermediary*/ +@@ -154,7 +149,10 @@ + void swap(Triangle *t1,short a1, + Triangle *t2,short a2, + BamgVertex *s1,BamgVertex *s2,long long det1,long long det2); +- ++ int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb , ++ AdjacentTriangle & tt1,long long & dets1, ++ long long & detsa,long long & detsb, int & nbswap); ++ int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) ; + inline AdjacentTriangle Previous(const AdjacentTriangle & ta){ + return AdjacentTriangle(ta.t,PreviousEdge[ta.a]); + } +Index: ../trunk-jpl/src/c/bamg/BamgOpts.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgOpts.h (revision 21837) ++++ ../trunk-jpl/src/c/bamg/BamgOpts.h (revision 21838) +@@ -16,6 +16,7 @@ + double errg; + double gradation; + int Hessiantype; ++ double MaxCornerAngle; + int maxnbv; + double maxsubdiv; + int Metrictype; +@@ -23,10 +24,12 @@ + int nbsmooth; + double omega; + double power; ++ bool random; + int verbose; + + /*Flags*/ + int Crack; ++ int geometricalmetric; + int KeepVertices; + int splitcorners; + +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21837) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21838) +@@ -979,6 +979,57 @@ + /*}}}*/ + + /*Methods*/ ++ void Mesh::AddGeometryMetric(BamgOpts* bamgopts){/*{{{*/ ++ /*Original code from Frederic Hecht (BAMG v1.01, Metric.cpp/IntersectGeomMetric)*/ ++ ++ /*Get options*/ ++ double anisomax = bamgopts->anisomax; ++ double errg = bamgopts->errg; ++ ++ double ss[2]={0.00001,0.99999}; ++ double errC = 2*sqrt(2*errg); ++ double hmax = Gh.MaximalHmax(); ++ double hmin = Gh.MinimalHmin(); ++ ++ //check that hmax is positive ++ _assert_(hmax>0); ++ ++ //errC cannot be higher than 1 ++ if(errC>1) errC=1; ++ ++ //Set all vertices to "on" ++ SetVertexFieldOn(); ++ ++ //loop over all the vertices on edges ++ for(int i=0;iR1tg(s,tg); ++ double ht=hmax; ++ // err relative to the length of the edge ++ if (R1>1.0e-20) { ++ ht = Min(Max(errC/R1,hmin),hmax); ++ } ++ double hn=Min(hmax,ht*anisomax); ++ ++ if (ht<=0 || hn<=0){ ++ _error_("ht<=0 || hn<=0"); ++ } ++ EigenMetric Vp(1/(ht*ht),1/(hn*hn),tg); ++ Metric MVp(Vp); ++ edges[i][j].m.IntersectWith(MVp); ++ } ++ } ++ // the problem is for the vertex on vertex ++ } ++ /*}}}*/ + void Mesh::AddMetric(BamgOpts* bamgopts){/*{{{*/ + // Hessiantype = 0 => H is computed using double L2 projection + // Hessiantype = 1 => H is computed with green formula +@@ -1179,10 +1230,12 @@ + /*Intermediary*/ + int i,j,k,kk,it,jt; + int verbose=0; ++ double cutoffradian=10*Pi/180; + + /*Recover options*/ +- if(bamgopts){ ++ if (bamgopts){ + verbose=bamgopts->verbose; ++ cutoffradian=bamgopts->MaxCornerAngle*Pi/180; + } + + //display info +@@ -1189,8 +1242,13 @@ + if (verbose>1) _printf_(" construction of the geometry from the 2d mesh\n"); + + //check that the mesh is not empty +- if(nbt<=0 || nbv <=0 ) _error_("nbt or nbv is negative (Mesh empty?)"); ++ if (nbt<=0 || nbv <=0 ) { ++ _error_("nbt or nbv is negative (Mesh empty?)"); ++ } + ++ //Gh is the geometry of the mesh (this), initialize MaxCornerAngle ++ if (cutoffradian>=0) Gh.MaxCornerAngle = cutoffradian; ++ + /*Construction of the edges*/ + + //initialize st and edge4 +@@ -1388,7 +1446,9 @@ + /*Reconstruct subdomains info*/ + + //check that nbsubdomains is empty +- if(nbsubdomains) _error_("nbsubdomains should be 0"); ++ if (nbsubdomains){ ++ _error_("nbsubdomains should be 0"); ++ } + nbsubdomains=0; + + //color the subdomains +@@ -2588,51 +2648,51 @@ + void Mesh::Init(long maxnbv_in) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/PreInit)*/ + ++ /* initialize random seed: */ ++ srand(19999999); ++ + /*Initialize fields*/ +- this->NbRef = 0; +- this->quadtree = NULL; +- this->nbv = 0; +- this->nbt = 0; +- this->nbe = 0; +- this->edges = NULL; +- this->nbsubdomains = 0; +- this->subdomains = NULL; +- this->maxnbv = maxnbv_in; +- this->maxnbt = 2 *maxnbv_in-2; +- this->NbVertexOnBThVertex = 0; +- this->VertexOnBThVertex = NULL; +- this->NbVertexOnBThEdge = 0; +- this->VertexOnBThEdge = NULL; +- this->NbCrackedVertices = 0; +- this->CrackedVertices = NULL; +- this->NbCrackedEdges = 0; +- this->CrackedEdges = NULL; +- this->NbVerticesOnGeomVertex = 0; +- this->VerticesOnGeomVertex = NULL; +- this->NbVerticesOnGeomEdge = 0; +- this->VerticesOnGeomEdge = NULL; ++ NbRef=0; ++ quadtree=NULL; ++ nbv=0; ++ nbt=0; ++ nbe=0; ++ edges=NULL; ++ nbsubdomains=0; ++ subdomains=NULL; ++ maxnbv=maxnbv_in; ++ maxnbt=2 *maxnbv_in-2; ++ NbVertexOnBThVertex=0; ++ VertexOnBThVertex=NULL; ++ NbVertexOnBThEdge=0; ++ VertexOnBThEdge=NULL; ++ NbCrackedVertices=0; ++ CrackedVertices =NULL; ++ NbCrackedEdges =0; ++ CrackedEdges =NULL; ++ NbVerticesOnGeomVertex=0; ++ VerticesOnGeomVertex=NULL; ++ NbVerticesOnGeomEdge=0; ++ VerticesOnGeomEdge=NULL; + +- /*Initialize random seed*/ +- this->randomseed = 1; +- + /*Allocate if maxnbv_in>0*/ + if(maxnbv_in){ +- this->vertices=new BamgVertex[this->maxnbv]; +- this->orderedvertices=new BamgVertex* [this->maxnbv]; +- this->triangles=new Triangle[this->maxnbt]; +- _assert_(this->vertices); +- _assert_(this->orderedvertices); +- _assert_(this->triangles); ++ vertices=new BamgVertex[maxnbv]; ++ _assert_(vertices); ++ orderedvertices=new BamgVertex* [maxnbv]; ++ _assert_(orderedvertices); ++ triangles=new Triangle[maxnbt]; ++ _assert_(triangles); + } + else{ +- this->vertices = NULL; +- this->orderedvertices = NULL; +- this->triangles = NULL; +- this->maxnbt = 0; ++ vertices=NULL; ++ orderedvertices=NULL; ++ triangles=NULL; ++ maxnbt=0; + } + } + /*}}}*/ +- void Mesh::Insert(){/*{{{*/ ++ void Mesh::Insert(bool random) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/Insert)*/ + + /*Insert points in the existing Geometry*/ +@@ -2679,7 +2739,8 @@ + + //Get Prime number + const long PrimeNumber= BigPrimeNumber(nbv); +- int k0=this->RandomNumber(nbv); ++ int temp = rand(); if(!random) temp = 756804110; ++ int k0=temp%nbv; + + //Build orderedvertices + for (i=0; i (BAMG v1.01, Mesh2.cpp/InsertNewPoints)*/ + + long int verbose=0; +@@ -2783,7 +2844,9 @@ + + /*construction of a random order*/ + const long PrimeNumber= BigPrimeNumber(nbv) ; +- long k3 = long(this->RandomNumber(nbvnew)); ++ //remainder of the division of rand() by nbvnew ++ int temp = rand(); if(!random) temp = 1098566905; ++ long k3 = temp%nbvnew; + //loop over the new points + for (int is3=0; is3random); + } + else Bh.CreateSingleVertexToTriangleConnectivity(); + +@@ -3082,7 +3145,7 @@ + } // end loop for each edge + }// for triangle + +- if (!InsertNewPoints(nbvold,NbTSwap)) break; ++ if (!InsertNewPoints(nbvold,NbTSwap,bamgopts->random)) break; + for (i=nbtold;i4) _printf_(" -- current number of vertices = " << nbv << "\n"); + if (verbose>3) _printf_(" Creating initial Constrained Delaunay Triangulation...\n"); + if (verbose>3) _printf_(" Inserting boundary points\n"); +- Insert(); ++ Insert(bamgopts->random); + + //Force the boundary + if (verbose>3) _printf_(" Forcing boundaries\n"); +@@ -4658,7 +4721,7 @@ + if (verbose>4) _printf_(" -- current number of vertices = " << nbv << "\n"); + if (verbose>3) _printf_(" Creating initial Constrained Delaunay Triangulation...\n"); + if (verbose>3) _printf_(" Inserting boundary points\n"); +- Insert(); ++ Insert(bamgopts->random); + + //Force the boundary + if (verbose>3) _printf_(" Forcing boundaries\n"); +@@ -4673,14 +4736,48 @@ + if (verbose>4) _printf_(" -- current number of vertices = " << nbv << "\n"); + } + /*}}}*/ +- int Mesh::RandomNumber(int max){/*{{{*/ +- /* Generate a random number from 0 to max-1 using linear congruential +- * random number generator*/ + +- this->randomseed = (this->randomseed * 1366l + 150889l) % 714025l; +- return this->randomseed / (714025l / max + 1); +- } /*}}}*/ +- int Mesh::ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) { /*{{{*/ ++ /*Intermediary*/ ++ AdjacentTriangle CloseBoundaryEdge(I2 A,Triangle *t, double &a,double &b) {/*{{{*/ ++ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/CloseBoundaryEdge)*/ ++ ++ int k=(*t)(0) ? (( (*t)(1) ? ( (*t)(2) ? -1 : 2) : 1 )) : 0; ++ int dir=0; ++ if (k<0){ ++ _error_("k<0"); ++ } ++ int kkk=0; ++ long long IJ_IA,IJ_AJ; ++ AdjacentTriangle edge(t,OppositeEdge[k]); ++ for (;;edge = dir >0 ? Next(Adj(Next(edge))) : Previous(Adj(Previous(edge)))) { ++ kkk++; ++ if (kkk>=1000){ ++ _error_("kkk>=1000"); ++ } ++ BamgVertex &vI = *edge.EdgeVertex(0); ++ BamgVertex &vJ = *edge.EdgeVertex(1); ++ I2 I=vI, J=vJ, IJ= J-I; ++ IJ_IA = (IJ ,(A-I)); ++ if (IJ_IA<0) { ++ if (dir>0) {a=1;b=0;return edge;}// change of signe => I ++ else {dir=-1; ++ continue;}};// go in direction i ++ IJ_AJ = (IJ ,(J-A)); ++ if (IJ_AJ<0) { ++ if(dir<0) {a=0;b=1;return edge;} ++ else {dir = 1; ++ continue;}}// go in direction j ++ double IJ2 = IJ_IA + IJ_AJ; ++ if (IJ2==0){ ++ _error_("IJ2==0"); ++ } ++ a= IJ_AJ/IJ2; ++ b= IJ_IA/IJ2; ++ return edge; ++ } ++ } ++ /*}}}*/ ++ int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) { /*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/ForceEdge)*/ + + int NbSwap =0; +@@ -4722,7 +4819,7 @@ + _error_("!v1 || !v2"); + } + long long detss = 0,l=0; +- while ((this->SwapForForcingEdge( va, vb, tc, detss, det1,det2,NbSwap))) ++ while ((SwapForForcingEdge( va, vb, tc, detss, det1,det2,NbSwap))) + if(l++ > 10000000) { + _error_("Loop in forcing Egde, nb de swap=" << NbSwap << ", nb of try swap (" << l << ") too big"); + } +@@ -4755,7 +4852,51 @@ + return NbSwap; + } + /*}}}*/ +- int Mesh::SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb ,AdjacentTriangle & tt1,long long & dets1, long long & detsa,long long & detsb, int & NbSwap) {/*{{{*/ ++ void swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,long long det1,long long det2){ /*{{{*/ ++ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/swap)*/ ++ // -------------------------------------------------------------- ++ // short a2=aa[a];// les 2 numero de l arete dans les 2 triangles ++ // ++ // sb sb ++ // / | \ / \ ! ++ // as1/ | \ /a2 \ ! ++ // / | \ / t2 \ ! ++ // s1 /t1 | t2 \s2 --> s1 /___as2___\s2 ! ++ // \ a1|a2 / \ as1 / ++ // \ | / \ t1 / ++ // \ | / as2 \ a1/ ++ // \ | / \ / ++ // sa sa ++ // ------------------------------------------------------------- ++ int as1 = NextEdge[a1]; ++ int as2 = NextEdge[a2]; ++ int ap1 = PreviousEdge[a1]; ++ int ap2 = PreviousEdge[a2]; ++ (*t1)(VerticesOfTriangularEdge[a1][1]) = s2 ; // avant sb ++ (*t2)(VerticesOfTriangularEdge[a2][1]) = s1 ; // avant sa ++ // mise a jour des 2 adjacences externes ++ AdjacentTriangle taas1 = t1->Adj(as1), ++ taas2 = t2->Adj(as2), ++ tas1(t1,as1), tas2(t2,as2), ++ ta1(t1,a1),ta2(t2,a2); ++ // externe haut gauche ++ taas1.SetAdj2(ta2, taas1.GetAllFlag_UnSwap()); ++ // externe bas droite ++ taas2.SetAdj2(ta1, taas2.GetAllFlag_UnSwap()); ++ // remove the Mark UnMarkSwap ++ t1->SetUnMarkUnSwap(ap1); ++ t2->SetUnMarkUnSwap(ap2); ++ // interne ++ tas1.SetAdj2(tas2); ++ ++ t1->det = det1; ++ t2->det = det2; ++ ++ t1->SetSingleVertexToTriangleConnectivity(); ++ t2->SetSingleVertexToTriangleConnectivity(); ++ } // end swap ++ /*}}}*/ ++ int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb ,AdjacentTriangle & tt1,long long & dets1, long long & detsa,long long & detsb, int & NbSwap) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/SwapForForcingEdge)*/ + // l'arete ta coupe l'arete pva pvb + // de cas apres le swap sa coupe toujours +@@ -4842,89 +4983,4 @@ + return ret; + } + /*}}}*/ +- +- /*Intermediary*/ +- AdjacentTriangle CloseBoundaryEdge(I2 A,Triangle *t, double &a,double &b) {/*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/CloseBoundaryEdge)*/ +- +- int k=(*t)(0) ? (( (*t)(1) ? ( (*t)(2) ? -1 : 2) : 1 )) : 0; +- int dir=0; +- if (k<0){ +- _error_("k<0"); +- } +- int kkk=0; +- long long IJ_IA,IJ_AJ; +- AdjacentTriangle edge(t,OppositeEdge[k]); +- for (;;edge = dir >0 ? Next(Adj(Next(edge))) : Previous(Adj(Previous(edge)))) { +- kkk++; +- if (kkk>=1000){ +- _error_("kkk>=1000"); +- } +- BamgVertex &vI = *edge.EdgeVertex(0); +- BamgVertex &vJ = *edge.EdgeVertex(1); +- I2 I=vI, J=vJ, IJ= J-I; +- IJ_IA = (IJ ,(A-I)); +- if (IJ_IA<0) { +- if (dir>0) {a=1;b=0;return edge;}// change of signe => I +- else {dir=-1; +- continue;}};// go in direction i +- IJ_AJ = (IJ ,(J-A)); +- if (IJ_AJ<0) { +- if(dir<0) {a=0;b=1;return edge;} +- else {dir = 1; +- continue;}}// go in direction j +- double IJ2 = IJ_IA + IJ_AJ; +- if (IJ2==0){ +- _error_("IJ2==0"); +- } +- a= IJ_AJ/IJ2; +- b= IJ_IA/IJ2; +- return edge; +- } +- } +- /*}}}*/ +- void swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,long long det1,long long det2){ /*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/swap)*/ +- // -------------------------------------------------------------- +- // short a2=aa[a];// les 2 numero de l arete dans les 2 triangles +- // +- // sb sb +- // / | \ / \ ! +- // as1/ | \ /a2 \ ! +- // / | \ / t2 \ ! +- // s1 /t1 | t2 \s2 --> s1 /___as2___\s2 ! +- // \ a1|a2 / \ as1 / +- // \ | / \ t1 / +- // \ | / as2 \ a1/ +- // \ | / \ / +- // sa sa +- // ------------------------------------------------------------- +- int as1 = NextEdge[a1]; +- int as2 = NextEdge[a2]; +- int ap1 = PreviousEdge[a1]; +- int ap2 = PreviousEdge[a2]; +- (*t1)(VerticesOfTriangularEdge[a1][1]) = s2 ; // avant sb +- (*t2)(VerticesOfTriangularEdge[a2][1]) = s1 ; // avant sa +- // mise a jour des 2 adjacences externes +- AdjacentTriangle taas1 = t1->Adj(as1), +- taas2 = t2->Adj(as2), +- tas1(t1,as1), tas2(t2,as2), +- ta1(t1,a1),ta2(t2,a2); +- // externe haut gauche +- taas1.SetAdj2(ta2, taas1.GetAllFlag_UnSwap()); +- // externe bas droite +- taas2.SetAdj2(ta1, taas2.GetAllFlag_UnSwap()); +- // remove the Mark UnMarkSwap +- t1->SetUnMarkUnSwap(ap1); +- t2->SetUnMarkUnSwap(ap2); +- // interne +- tas1.SetAdj2(tas2); +- +- t1->det = det1; +- t2->det = det2; +- +- t1->SetSingleVertexToTriangleConnectivity(); +- t2->SetSingleVertexToTriangleConnectivity(); +- } // end swap +- /*}}}*/ + } +Index: ../trunk-jpl/src/c/bamg/Geometry.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Geometry.h (revision 21837) ++++ ../trunk-jpl/src/c/bamg/Geometry.h (revision 21838) +@@ -31,6 +31,7 @@ + Curve *curves; + R2 pmin,pmax; // domain extrema coordinates + double coefIcoor; // coef to integer coordinates; ++ double MaxCornerAngle; + + //Constructor/Destructors + ~Geometry(); +Index: ../trunk-jpl/src/c/bamg/Triangle.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Triangle.cpp (revision 21837) ++++ ../trunk-jpl/src/c/bamg/Triangle.cpp (revision 21838) +@@ -256,6 +256,7 @@ + OnSwap = (Abs(det1) + Abs(det2)) < detA; + + long long detMinNew=Min(det1,det2); ++ // if (detMin<0 && (Abs(det1) + Abs(det2) == detA)) OnSwap=BinaryRand();// just for test + if (! OnSwap &&(detMinNew>0)) { + OnSwap = detMin ==0; + if (! OnSwap) { +Index: ../trunk-jpl/src/c/bamg/BamgOpts.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgOpts.cpp (revision 21837) ++++ ../trunk-jpl/src/c/bamg/BamgOpts.cpp (revision 21838) +@@ -10,6 +10,7 @@ + this->errg = 0; + this->gradation = 0; + this->Hessiantype = 0; ++ this->MaxCornerAngle = 0; + this->maxnbv = 0; + this->maxsubdiv = 0; + this->Metrictype = 0; +@@ -17,9 +18,11 @@ + this->nbsmooth = 0; + this->omega = 0; + this->power = 0; ++ this->random = 0; + this->verbose = 0; + + this->Crack = 0; ++ this->geometricalmetric = 0; + this->KeepVertices = 0; + this->splitcorners = 0; + +@@ -64,6 +67,7 @@ + + if (this->Crack!=0 && this->Crack!=1) _error_("'Crack' supported options are 0 and 1"); + if (this->KeepVertices!=0 && this->KeepVertices!=1) _error_("'KeepVertices' supported options are 0 and 1"); ++ if (this->geometricalmetric!=0 && this->geometricalmetric!=1) _error_("'geometricalmetric' supported options are 0 and 1"); + + if (this->hmin<=0) _error_("'hmin' option should be >0"); + if (this->hmax<=0 || this->hmaxhmin) _error_("'hmax' option should be between 0 and hmin=" << this->hmin); +Index: ../trunk-jpl/src/c/bamg/Geometry.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Geometry.cpp (revision 21837) ++++ ../trunk-jpl/src/c/bamg/Geometry.cpp (revision 21838) +@@ -186,6 +186,12 @@ + } + } + ++ //MaxCornerAngle ++ if (bamgopts->MaxCornerAngle){ ++ if(verbose>5) _printf_(" processing MaxCornerAngle\n"); ++ MaxCornerAngle=bamgopts->MaxCornerAngle*Pi/180; ++ } ++ + //TangentAtEdges + if (bamggeom->TangentAtEdges){ + if(verbose>5) _printf_(" processing TangentAtEdges"); +@@ -394,6 +400,7 @@ + _printf_(" pmin (x,y): (" << pmin.x << " " << pmin.y << ")\n"); + _printf_(" pmax (x,y): (" << pmax.x << " " << pmax.y << ")\n"); + _printf_(" coefIcoor: " << coefIcoor << "\n"); ++ _printf_(" MaxCornerAngle: " << MaxCornerAngle << "\n"); + + return; + } +@@ -411,6 +418,7 @@ + nbsubdomains=0; + nbcurves=0; + subdomains=NULL; ++ MaxCornerAngle = 10*Pi/180; //default is 10 degres + } + /*}}}*/ + double Geometry::MinimalHmin() {/*{{{*/ +@@ -605,14 +613,19 @@ + } + } + +- //all vertices provided in geometry are corners (ord = number of edges holding i) +- vertices[i].SetCorner() ; +- if(ord==2){ ++ // angular test on current vertex to guess whether it is a corner (ord = number of edges holding i) ++ if(ord==2) { + long n1 = head_v[i]; + long n2 = next_p[n1]; + long i1 = n1/2, i2 = n2/2; // edge number +- long j1 = n1%2, j2 = n2%2; // vertex in the edge +- /* if the edge type/referencenumber a changing then is SetRequired();*/ ++ long j1 = n1%2, j2 = n2%2; // vertex in the edge ++ float angle1= j1 ? OppositeAngle(eangle[i1]) : eangle[i1]; ++ float angle2= !j2 ? OppositeAngle(eangle[i2]) : eangle[i2]; ++ float da12 = Abs(angle2-angle1); ++ if (( da12 >= MaxCornerAngle ) && (da12 <= 2*Pi -MaxCornerAngle)) { ++ vertices[i].SetCorner() ; ++ } ++ // if the edge type/referencenumber a changing then is SetRequired(); + if (edges[i1].type != edges[i2].type || edges[i1].Required()){ + vertices[i].SetRequired(); + } +@@ -620,6 +633,9 @@ + vertices[i].SetRequired(); + } + } ++ if(ord != 2) { ++ vertices[i].SetCorner(); ++ } + + /*close the list around the vertex to have a circular loop*/ + long no=-1, ne = head_v[i]; +Index: ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 21837) ++++ ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 21838) +@@ -148,6 +148,9 @@ + } + } + ++ //Add geometry metric if provided ++ if(bamgopts->geometricalmetric) BTh.AddGeometryMetric(bamgopts); ++ + //Smoothe metric + BTh.SmoothMetric(bamgopts->gradation); + +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21837) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21838) +@@ -31,6 +31,7 @@ + this->options->errg = 0.1; + this->options->gradation = 1.5; + this->options->Hessiantype = 0; ++ this->options->MaxCornerAngle = 1.e-12; + this->options->maxnbv = 1e6; + this->options->maxsubdiv = 10; + this->options->Metrictype = 0; +@@ -38,8 +39,10 @@ + this->options->nbsmooth = 3; + this->options->omega = 1.8; + this->options->power = 1; ++ this->options->random = 0; + this->options->verbose = 0; + this->options->Crack = 0; ++ this->options->geometricalmetric = 0; + this->options->KeepVertices = 1; /*!!!!! VERY IMPORTANT !!!!!*/ + this->options->splitcorners = 1; + this->options->hmin = hmin; Index: /issm/oecreview/Archive/21724-22754/ISSM-21838-21839.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21838-21839.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21838-21839.diff (revision 22755) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test324.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test324.py (revision 21838) ++++ ../trunk-jpl/test/NightlyRun/test324.py (revision 21839) +@@ -25,7 +25,7 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2',\ + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] + field_tolerances=[1e-13, 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ +- 5*1e-11,1e-13,5e-13,1e-13,1e-13,1e-13,5e-13,1e-13,1e-13,1e-13,\ ++ 5e-11,1e-13,5e-13,5e-11,1e-13,1e-13,5e-13,1e-13,1e-13,1e-13,\ + 1e-10, 1e-12,1e-12,1e-12,1e-13,1e-13,1e-12,1e-12,1e-13,1e-13] + field_values=[\ + md.results.TransientSolution[0].Vx,\ +Index: ../trunk-jpl/test/NightlyRun/test324.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test324.m (revision 21838) ++++ ../trunk-jpl/test/NightlyRun/test324.m (revision 21839) +@@ -15,7 +15,7 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2',... + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'}; + field_tolerances={1e-13, 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... +- 5*1e-11,1e-13,5e-13,1e-13,1e-13,1e-13,5e-13,1e-13,1e-13,1e-13,... ++ 5e-11,1e-13,5e-13,5e-11,1e-13,1e-13,5e-13,1e-13,1e-13,1e-13,... + 1e-10, 1e-12,1e-12,1e-12,1e-13,1e-13,1e-12,1e-12,1e-13,1e-13}; + field_values={... + (md.results.TransientSolution(1).Vx),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21839-21840.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21839-21840.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21839-21840.diff (revision 22755) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 21839) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 21840) +@@ -199,7 +199,17 @@ + make uninstall + make distclean + ./scripts/automakererun.sh ++ if [ $? -ne 0 ]; then ++ echo "autoreconf failed!" ++ exit 1 ++ fi + eval "./configure $ISSM_CONFIG" ++ if [ $? -ne 0 ]; then ++ echo "ISSM configuration failed (see options below)" ++ echo $ISSM_CONFIG ++ echo "ISSM configuration failed!" ++ exit 1 ++ fi + fi + + #4: compile and install ISSM Index: /issm/oecreview/Archive/21724-22754/ISSM-21840-21841.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21840-21841.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21840-21841.diff (revision 22755) @@ -0,0 +1,77 @@ +Index: ../trunk-jpl/test/NightlyRun/test315.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test315.py (revision 21840) ++++ ../trunk-jpl/test/NightlyRun/test315.py (revision 21841) +@@ -21,7 +21,7 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2',\ + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] + field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ +- 1e-10,1e-13,5e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-10,1e-13,5e-13,5e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ + 1e-10,2e-13,5e-13,2e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] + field_values=[\ + md.results.TransientSolution[0].Vx,\ +Index: ../trunk-jpl/test/NightlyRun/test316.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test316.py (revision 21840) ++++ ../trunk-jpl/test/NightlyRun/test316.py (revision 21841) +@@ -17,7 +17,9 @@ + + #Fields and tolerances to track changes + field_names =['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'] +-field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 2e-13,1e-13,1e-13,2e-13,1e-13,1e-13,1e-13] + field_values=[\ + md.results.TransientSolution[0].Vx,\ + md.results.TransientSolution[0].Vy,\ +Index: ../trunk-jpl/test/NightlyRun/test315.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test315.m (revision 21840) ++++ ../trunk-jpl/test/NightlyRun/test315.m (revision 21841) +@@ -12,7 +12,7 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2',... + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'}; + field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,..., +- 1e-10,1e-13,5e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... ++ 1e-10,1e-13,5e-13,5e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... + 1e-10,2e-13,5e-13,2e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; + field_values={... + (md.results.TransientSolution(1).Vx),... +Index: ../trunk-jpl/test/NightlyRun/test316.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test316.m (revision 21840) ++++ ../trunk-jpl/test/NightlyRun/test316.m (revision 21841) +@@ -7,8 +7,13 @@ + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; ++field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1',... ++ 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2',... ++ 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; ++field_tolerances={... ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... ++ 2e-13,1e-13,1e-13,2e-13,1e-13,1e-13,1e-13}; + field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... +Index: ../trunk-jpl/test/NightlyRun/test293.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test293.m (revision 21840) ++++ ../trunk-jpl/test/NightlyRun/test293.m (revision 21841) +@@ -15,7 +15,10 @@ + field_names ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','BasalforcingsFloatingiceMeltingRate1',... + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','BasalforcingsFloatingiceMeltingRate2',... + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','BasalforcingsFloatingiceMeltingRate3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; ++field_tolerances={... ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,2e-13,... ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,2e-13,... ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,2e-13}; + field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21841-21842.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21841-21842.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21841-21842.diff (revision 22755) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/jenkins/windows +=================================================================== +--- ../trunk-jpl/jenkins/windows (revision 21841) ++++ ../trunk-jpl/jenkins/windows (revision 21842) +@@ -10,7 +10,7 @@ + ISSM_CONFIG='--prefix=$ISSM_DIR \ + --with-vendor=MSVC-Win64 \ + --with-cxxoptflags='-fp:strict' \ +- --disable-static \ ++ --disable-static \ + --enable-standalone-libraries \ + --with-fortran=no \ + --without-GiaIvins \ +@@ -59,5 +59,5 @@ + #ex: "'id',[101 102 103]" + + #In Windows, we don't yet have MUMPS, can't do full stokes, so exclude all FS runs. Also exclude all runs with Dakota. And exclude higher order runs that have penalties. And 800+ tests because we don't want to have --with-development since we do the binaries with this version +-MATLAB_NROPTIONS="'exclude',[104, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460,243]" ++MATLAB_NROPTIONS="'exclude',[104, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440,444, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460,243]" + PYTHON_NROPTIONS="" Index: /issm/oecreview/Archive/21724-22754/ISSM-21842-21843.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21842-21843.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21842-21843.diff (revision 22755) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21842) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21843) +@@ -47,12 +47,14 @@ + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Vz1','Pressure1','FloatingiceMeltingrate1',... ++field_names ={... ++ 'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Vz1','Pressure1','FloatingiceMeltingrate1',... + 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; +-field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... ++field_tolerances={... ++ 2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,6e-09,5e-08,1e-09,1e-10,1e-13,... +- 4e-10,3e-08,8e-09,5e-09,7e-04,5e-04,2e-09,1e-10,1e-13}; ++ 4e-10,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21843-21844.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21843-21844.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21843-21844.diff (revision 22755) @@ -0,0 +1,53 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21843) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21844) +@@ -9,6 +9,7 @@ + #endif + + #include ++#include + #include "../cores/cores.h" + #include "../shared/io/io.h" + #include "./classes.h" +@@ -2442,8 +2443,8 @@ + x = xyz_list[3*i+0]; + y = xyz_list[3*i+1]; + +- bx=-150.-728.8*std::pow(x/300000.,2)+343.91*std::pow(x/300000.,4)-50.57*std::pow(x/300000.,6); +- by=500./(1.+std::exp((-2./4000.)*(y-80000./2.-24000.)))+500./(1.+std::exp((2./4000.)*(y-80000./2.+24000.))); ++ bx=-150.-728.8*pow(x/300000.,2)+343.91*pow(x/300000.,4)-50.57*pow(x/300000.,6); ++ by=500./(1.+exp((-2./4000.)*(y-80000./2.-24000.)))+500./(1.+exp((2./4000.)*(y-80000./2.+24000.))); + + r[i] = -720.; + if(bx+by>-720.) r[i] = bx+by; +@@ -3407,11 +3408,12 @@ + ftyy+=(tauyy[n]-smoothedtauyy[elem_vertices[n]])*basis[n]; + ftxy+=(tauxy[n]-smoothedtauxy[elem_vertices[n]])*basis[n]; + } +- error+=Jdet*gauss->weight*( std::pow(ftxx,2)+std::pow(ftyy,2)+std::pow(ftxy,2) ); //e^2 ++ error+=Jdet*gauss->weight*( pow(ftxx,2)+pow(ftyy,2)+pow(ftxy,2) ); //e^2 + } + /*Set the error in the global vector*/ + sid=element->Sid(); +- velementerror->SetValue(sid,std::sqrt(error),INS_VAL);//sqrt( e^2 ) ++ error = sqrt(error);//sqrt(e^2) ++ velementerror->SetValue(sid,error,INS_VAL); + /*Cleanup intermediaries*/ + xDelete(xyz_list); + delete gauss; +@@ -3557,11 +3559,12 @@ + fdHdx+=(GradH[0]-smoothed_dHdx[elem_vertices[n]])*basis[n]; + fdHdy+=(GradH[1]-smoothed_dHdy[elem_vertices[n]])*basis[n]; + } +- error+=Jdet*gauss->weight*( std::pow(fdHdx,2)+std::pow(fdHdy,2) ); //e^2 ++ error+=Jdet*gauss->weight*(pow(fdHdx,2)+pow(fdHdy,2) ); //e^2 + } + /*Set the error in the global vector*/ + sid=element->Sid(); +- velementerror->SetValue(sid,std::sqrt(error),INS_VAL);//sqrt( e^2 ) ++ error = sqrt(error); //sqrt( e^2 ) ++ velementerror->SetValue(sid,error,INS_VAL); + /*Cleanup intermediaries*/ + xDelete(xyz_list); + delete gaussH; Index: /issm/oecreview/Archive/21724-22754/ISSM-21844-21845.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21844-21845.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21844-21845.diff (revision 22755) @@ -0,0 +1,58 @@ +Index: ../trunk-jpl/src/c/classes/ExternalResults/GenericExternalResult.h +=================================================================== +--- ../trunk-jpl/src/c/classes/ExternalResults/GenericExternalResult.h (revision 21844) ++++ ../trunk-jpl/src/c/classes/ExternalResults/GenericExternalResult.h (revision 21845) +@@ -461,53 +461,7 @@ + MARSHALLING(time); + + } /*}}}*/ +-/*Specific instantiations for int*: */ +-#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. +-template <> inline void GenericExternalResult::WriteData(FILE* fid,bool io_gather){ /*{{{*/ + +- int i; +- int my_rank; +- int type; +- int rows,cols; +- char *name = NULL; +- IssmPDouble passiveDouble; +- int* passiveInts; +- +- /*recover my_rank:*/ +- my_rank=IssmComm::GetRank(); +- +- if(io_gather){ +- /*we are gathering the data on cpu 0, don't write on other cpus: */ +- if(my_rank) return; +- } +- +- /*First write enum: */ +- int length=(strlen(this->result_name)+1)*sizeof(char); +- fwrite(&length,sizeof(int),1,fid); +- fwrite(this->result_name,length,1,fid); +- +- /*Now write time and step: */ +- passiveDouble=reCast(time); +- fwrite(&passiveDouble,sizeof(IssmPDouble),1,fid); +- fwrite(&step,sizeof(int),1,fid); +- +- /*writing a int array, type is 4 (see parseresultsfromdisk.m):*/ +- type=4; +- fwrite(&type,sizeof(int),1,fid); +- rows=this->M; +- fwrite(&rows,sizeof(int),1,fid); +- cols=this->N; +- fwrite(&cols,sizeof(int),1,fid); +- +- passiveInts=xNew(this->M*this->N); +- for (i=0;iM*this->N;i++)passiveInts[i]=reCast(value[i]); +- fwrite(passiveInts,cols*rows*sizeof(int),1,fid); +- xDelete(int); +- +-} +-/*}}}*/ +-#endif +- + /*Specific instantiations for IssmPDouble*: */ + template <> inline GenericExternalResult::GenericExternalResult(int in_id, int in_enum_type,IssmPDouble* in_values, int in_M,int in_N,int in_step,IssmDouble in_time){/*{{{*/ + Index: /issm/oecreview/Archive/21724-22754/ISSM-21845-21846.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21845-21846.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21845-21846.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21845) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21846) +@@ -2492,7 +2492,7 @@ + b[i] = base_float; + } + +- if(abs(sl[i])>0) _error_("Sea level value "<0) _error_("Sea level value "<(N_interp*N_data); ++ data_interp=xNew(N_interp*N_data); + + /*read background mesh*/ + Mesh* Th=new Mesh(index_data,x_data,y_data,nods_data,nels_data); +@@ -77,7 +77,7 @@ + + /*Loop over output nodes*/ + for(i=0;ixmax || y_interp[i]ymax){ +@@ -97,9 +97,9 @@ + if (tb.det>0){ + + /*Area coordinates*/ +- areacoord[0]= (double) dete[0]/tb.det; +- areacoord[1]= (double) dete[1]/tb.det; +- areacoord[2]= (double) dete[2]/tb.det; ++ areacoord[0]= reCast(dete[0])/reCast(tb.det); ++ areacoord[1]= reCast(dete[1])/reCast(tb.det); ++ areacoord[2]= reCast(dete[2])/reCast(tb.det); + /*3 vertices of the triangle*/ + i0=Th->GetId(tb[0]); + i1=Th->GetId(tb[1]); Index: /issm/oecreview/Archive/21724-22754/ISSM-21847-21848.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21847-21848.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21847-21848.diff (revision 22755) @@ -0,0 +1,17 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21847) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21848) +@@ -2664,10 +2664,10 @@ + element->AddInput(new DoubleInput(P0input_enums[i],vector[element->sid]));//sid because newfemmodel has just a partitioning + break; + case IntInputEnum: +- element->AddInput(new IntInput(P0input_enums[i],vector[element->sid]));//sid because newfemmodel has just a partitioning ++ element->AddInput(new IntInput(P0input_enums[i],reCast(vector[element->sid])));//sid because newfemmodel has just a partitioning + break; + case BoolInputEnum: +- element->AddInput(new BoolInput(P0input_enums[i],vector[element->sid]));//sid because newfemmodel has just a partitioning ++ element->AddInput(new BoolInput(P0input_enums[i],reCast(vector[element->sid])));//sid because newfemmodel has just a partitioning + break; + default: + _error_(EnumToStringx(P0input_enums[i])<<" Not supported yet"); Index: /issm/oecreview/Archive/21724-22754/ISSM-21848-21849.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21848-21849.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21848-21849.diff (revision 22755) @@ -0,0 +1,17 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21848) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21849) +@@ -3039,9 +3039,9 @@ + elementslist=xNew(numberofelements*elementswidth); + if(numberofelements*elementswidth<0) _error_("numberofelements negative."); + for(int i=0;i(id1[i])+1; //InterpMesh wants Matlab indexing ++ elementslist[elementswidth*i+1] = reCast(id2[i])+1; //InterpMesh wants Matlab indexing ++ elementslist[elementswidth*i+2] = reCast(id3[i])+1; //InterpMesh wants Matlab indexinf + } + + /*Assign pointers*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21849-21850.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21849-21850.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21849-21850.diff (revision 22755) @@ -0,0 +1,68 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21849) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21850) +@@ -4315,7 +4315,7 @@ + }/*}}}*/ + #endif + +-#ifdef _HAVE_BAMG_ ++#if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + void FemModel::ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist){/*{{{*/ + + /*Output*/ +@@ -4413,7 +4413,7 @@ + /*}}}*/ + #endif + +-#ifdef _HAVE_NEOPZ_ ++#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + void FemModel::ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist){/*{{{*/ + + /*pnewelementslist keep vertices in Matlab indexing*/ +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 21849) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 21850) +@@ -19,10 +19,10 @@ + class Materials; + class Profiler; + class Elements; +-#ifdef _HAVE_NEOPZ_ ++#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + #include "./AdaptiveMeshRefinement.h" + #endif +-#ifdef _HAVE_BAMG_ ++#if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + #include "./AmrBamg.h" + #endif + /*}}}*/ +@@ -50,11 +50,11 @@ + Vertices *vertices; //one set of vertices + + //FIXME: do we want only one class and have virtual functions? or keep 2 classes, at least rename AdaptiveMeshRefinement -> AmrNeopz +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + AdaptiveMeshRefinement *amr; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process + #endif + +- #ifdef _HAVE_BAMG_ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + AmrBamg *amrbamg; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process + #endif + +@@ -176,12 +176,12 @@ + void ThicknessZZErrorEstimator(IssmDouble** pelementerror); + void MeanGroundedIceLevelSet(IssmDouble** pmasklevelset); + +- #ifdef _HAVE_BAMG_ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + void ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); + void InitializeAdaptiveRefinementBamg(void); + #endif + +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + /*Adaptive mesh refinement methods*/ + void ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); + void InitializeAdaptiveRefinementNeopz(void); Index: /issm/oecreview/Archive/21724-22754/ISSM-21850-21851.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21850-21851.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21850-21851.diff (revision 22755) @@ -0,0 +1,103 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21850) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21851) +@@ -82,10 +82,10 @@ + + /*AMR stuff*/ + this->parameters->FindParam(&amr_frequency,TransientAmrFrequencyEnum); +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + this->amr = NULL; + #endif +- #ifdef _HAVE_BAMG_ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + this->amrbamg = NULL; + #endif + if(amr_frequency){ +@@ -92,11 +92,11 @@ + this->parameters->FindParam(&amrtype,AmrTypeEnum); + switch(amrtype){ + +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + case AmrNeopzEnum: this->InitializeAdaptiveRefinementNeopz(); break; + #endif + +- #ifdef _HAVE_BAMG_ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + case AmrBamgEnum: this->InitializeAdaptiveRefinementBamg(); break; + #endif + +@@ -128,10 +128,10 @@ + this->InitFromFiles(rootpath,inputfilename,outputfilename,toolkitsfilename,lockfilename,restartfilename, solution_type,traceon,X); + profiler->Tag(FINISHINIT); + +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + this->amr = NULL; + #endif +- #ifdef _HAVE_BAMG_ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + this->amrbamg = NULL; + #endif + +@@ -165,11 +165,11 @@ + if(parameters)delete parameters; + if(results)delete results; + +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + if(amr)delete amr; + #endif + +- #ifdef _HAVE_BAMG_ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + if(amrbamg)delete amrbamg; + #endif + +@@ -303,10 +303,10 @@ + } + + /*AMR, no copy for now*/ +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + this->amr = NULL; + #endif +- #ifdef _HAVE_BAMG_ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + this->amrbamg = NULL; + #endif + +@@ -1558,11 +1558,11 @@ + /*Branch to specific amr depending on requested method*/ + parameters->FindParam(&amrtype,AmrTypeEnum); + switch(amrtype){ +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + case AmrNeopzEnum: this->ReMeshNeopz(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; + #endif + +- #ifdef _HAVE_BAMG_ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + case AmrBamgEnum: this->ReMeshBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; + #endif + +@@ -2720,7 +2720,7 @@ + void FemModel::WriteMeshInResults(void){/*{{{*/ + + //itapopo +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + this->WriteErrorEstimatorsInResults(); + #endif + //itapopo +@@ -2755,7 +2755,7 @@ + y,numberofvertices,1,step,time)); + + //itapopo +- #ifdef _HAVE_NEOPZ_ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + if(IssmComm::GetRank()==0){ + TPZFileStream fstr; + std::stringstream ss; Index: /issm/oecreview/Archive/21724-22754/ISSM-21851-21852.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21851-21852.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21851-21852.diff (revision 22755) @@ -0,0 +1,503 @@ +Index: ../trunk-jpl/src/m/solve/solveiceocean.m +=================================================================== +--- ../trunk-jpl/src/m/solve/solveiceocean.m (nonexistent) ++++ ../trunk-jpl/src/m/solve/solveiceocean.m (revision 21852) +@@ -0,0 +1,143 @@ ++function md=solveiceocean(md,solutionstring,varargin) ++%SOLVE - apply ice/ocean solution sequence for this model ++% ++% Usage: ++% md=solveiceocean(md,solutionstring,varargin) ++% where varargin is a lit of paired arguments of string OR enums ++% ++% solution types available comprise: ++% - 'Stressbalance' or 'sb' ++% - 'Masstransport' or 'mt' ++% - 'Transient' or 'tr' ++% ++% extra options: ++% - loadonly : does not solve. only load results ++% - runtimename : true or false (default is true), makes name unique ++% - checkconsistency : 'yes' or 'no' (default is 'yes'), ensures checks on consistency of model ++% - restart: 'directory name (relative to the execution directory) where the restart file is located. ++% - outbinread : if 0, download the outbin but do not process is (md.results is not updated) ++% ++% Examples: ++% md=solve(md,'Transient'); ++% md=solve(md,'tr'); ++ ++if ~ischar(solutionstring) ++ error('ISSM''s solve function only accepts strings for solution sequences. Type help solve to get a list of supported solutions'); ++end ++ ++%recover and process solve options ++if strcmpi(solutionstring,'sb') || strcmpi(solutionstring,'Stressbalance') ++ solutionstring = 'StressbalanceSolution'; ++elseif strcmpi(solutionstring,'mt') || strcmpi(solutionstring,'Masstransport') ++ solutionstring = 'MasstransportSolution'; ++elseif strcmpi(solutionstring,'tr') || strcmpi(solutionstring,'Transient') ++ solutionstring = 'TransientSolution'; ++else ++ error(['solutionstring ' solutionstring ' not supported!']); ++end ++options=pairoptions(varargin{:},'solutionstring',solutionstring); ++ ++%recover some fields ++md.private.solution=solutionstring; ++cluster=md.cluster; ++if strcmpi(getfieldvalue(options,'batch','no'),'yes') batch=1; else batch=0; end ++if ~isclass(cluster,'localpfe'), ++ error('cannot run ice/ocean simulation on any other cluster than localpfe'); ++end ++ ++%check model consistency ++if strcmpi(getfieldvalue(options,'checkconsistency','yes'),'yes'), ++ if md.verbose.solution, ++ disp('checking model consistency'); ++ end ++ ismodelselfconsistent(md), ++end ++ ++%If we are restarting, actually use the provided runtime name: ++restart=getfieldvalue(options,'restart',''); ++%First, build a runtime name that is unique ++if restart==1 ++ %Leave the runtimename as is ++else ++ if ~isempty(restart), ++ md.private.runtimename=restart; ++ elseif getfieldvalue(options,'runtimename',true), ++ c=clock; ++ md.private.runtimename=sprintf('%s-%02i-%02i-%04i-%02i-%02i-%02i-%i',md.miscellaneous.name,c(2),c(3),c(1),c(4),c(5),floor(c(6)),feature('GetPid')); ++ else ++ md.private.runtimename=md.miscellaneous.name; ++ end ++end ++ ++%if running qmu analysis, some preprocessing of dakota files using models ++%fields needs to be carried out. ++if md.qmu.isdakota, ++ md=preqmu(md,options); ++end ++ ++%Do we load results only? ++if getfieldvalue(options,'loadonly',false), ++ md=loadresultsfromcluster(md); ++ return; ++end ++ ++%Write all input files ++marshall(md); % bin file ++ToolkitsFile(md.toolkits,[md.miscellaneous.name '.toolkits']); % toolkits file ++BuildQueueScriptIceOcean(cluster,md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof,md.qmu.isdakota); % queue file ++ ++%Upload all required files ++modelname = md.miscellaneous.name; ++filelist = {[modelname '.bin '] [modelname '.toolkits ']}; ++if ispc, ++ filelist{end+1}=[modelname '.bat ']; ++else ++ filelist{end+1}=[modelname '.queue ']; ++end ++ ++if md.qmu.isdakota, ++ filelist{end+1} = [modelname '.qmu.in']; ++end ++ ++if isempty(restart), ++ UploadQueueJob(cluster,md.miscellaneous.name,md.private.runtimename,filelist); ++end ++ ++%launch queue job: ++LaunchQueueJobIceOcean(cluster,md.miscellaneous.name,md.private.runtimename,filelist,restart,batch); ++ ++%return if batch: ++if batch, ++ if md.verbose.solution, ++ disp('batch mode requested: not launching job interactively'); ++ disp('launch solution sequence on remote cluster by hand'); ++ end ++ return; ++end ++%wait on lock ++if isnan(md.settings.waitonlock), ++ %load when user enters 'y' ++ disp('solution launched on remote cluster. log in to detect job completion.'); ++ choice=input('Is the job successfully completed? (y/n)','s'); ++ if ~strcmp(choice,'y'), ++ disp('Results not loaded... exiting'); ++ else ++ md=loadresultsfromcluster(md); ++ end ++elseif md.settings.waitonlock>0, ++ %we wait for the done file ++ done=waitonlock(md); ++ if md.verbose.solution, ++ disp('loading results from cluster'); ++ end ++ md=loadresultsfromcluster(md); ++elseif md.settings.waitonlock==0, ++ disp('Model results must be loaded manually with md=loadresultsfromcluster(md);'); ++end ++ ++%post processes qmu results if necessary ++if md.qmu.isdakota, ++ if ~strncmpi(getfieldvalue(options,'keep','y'),'y',1) ++ system(['rm -rf qmu' num2str(feature('GetPid'))]); ++ end ++end +Index: ../trunk-jpl/src/c/main/issm_ocean.cpp +=================================================================== +--- ../trunk-jpl/src/c/main/issm_ocean.cpp (revision 21851) ++++ ../trunk-jpl/src/c/main/issm_ocean.cpp (revision 21852) +@@ -6,98 +6,46 @@ + + int main(int argc,char **argv){ + +-// /*diverse:*/ +-// int nummodels = 2; +-// int* commsizes=xNew(nummodels); +-// int* rankzeros=xNew(nummodels); +-// char** modelnames=xNew(nummodels); +-// char** dirnames=xNew(nummodels); +-// int iceid=0; +-// int oceanid=1; ++ /*diverse:*/ ++ int icecommsize; ++ int rankzeros[2]; ++ int my_rank; ++ ISSM_MPI_Comm worldcomm; ++ + // int modelid; +-// int my_rank; + // int count=0; +-// ISSM_MPI_Comm worldcomm; +-// ISSM_MPI_Comm modelcomm; +-// ISSM_MPI_Comm toonceancomm; +-// ISSM_MPI_Comm fromicecomms; ++ ISSM_MPI_Comm modelcomm; ++ ISSM_MPI_Comm frommitgcm; ++ ISSM_MPI_Comm tomitgcmcomm; + + /*Initialize exception trapping: */ + ExceptionTrapBegin(); + +-// /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ +-// worldcomm=EnvironmentInit(argc,argv); +-// +-// /*What is my rank?:*/ +-// ISSM_MPI_Comm_rank(worldcomm,&my_rank); +-// +-// /*First model is ice, second is ocean*/ +-// for(int i=0;i(strlen(argv[5+3*i])+1); +-// xMemCpy(string,argv[5+3*i],strlen(argv[5+3*i])+1); +-// dirnames[i]=string; +-// +-// string=xNew(strlen(argv[5+3*i+1])+1); +-// xMemCpy(string,argv[5+3*i+1],strlen(argv[5+3*i+1])+1); +-// modelnames[i]=string; +-// +-// commsizes[i]=(int) strtol(argv[5+3*i+2], (char **)NULL, 10); +-// } +-// +-// /*Figure out which model each cpu will belong to: */ +-// count=0; +-// for(int i=0;i=count && my_rank<(count+commsizes[i])){ +-// modelid=i; +-// break; +-// } +-// count+=commsizes[i]; +-// } +-// /*Buil array of who is rank 0 of their own group:*/ +-// count=0; +-// for(int i=0;i(4); +-// arguments[0]=xNew(strlen(argv[0])+1); xMemCpy(arguments[0],argv[0],strlen(argv[0])+1); //executable name +-// arguments[1]=xNew(strlen(argv[1])+1); xMemCpy(arguments[1],argv[1],strlen(argv[1])+1); //solution name +-// arguments[2]=xNew(strlen(argv[5+3*modelid])+1); xMemCpy(arguments[2],argv[5+3*modelid],strlen(argv[5+3*modelid])+1); //directory name +-// arguments[3]=xNew(strlen(argv[5+3*modelid+1])+1); xMemCpy(arguments[3],argv[5+3*modelid+1],strlen(argv[5+3*modelid+1])+1); //model name +-// /*}}}*/ +-// ++ /*First model is ice, second is ocean*/ ++ /*ice comm size: */ ++ icecommsize=(int) strtol(argv[2], (char **)NULL, 10); + +- //REMOVE +- /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ +- ISSM_MPI_Comm comm_init=EnvironmentInit(argc,argv); ++ /*Buil array of who is rank 0 of their own group:*/ ++ rankzeros[0]=0; ++ rankzeros[1]=icecommsize; ++ ++ /*Split world into sub-communicators for each and every model:*/ ++ ISSM_MPI_Comm_split(worldcomm,0, my_rank, &modelcomm); ++ ++ ISSM_MPI_Intercomm_create( modelcomm, 0, worldcomm, rankzeros[1], 0, &tomitgcmcomm); ++ + /*Initialize femmodel from arguments provided command line: */ +- FemModel *femmodel = new FemModel(argc,argv,comm_init); +- ///*Initialize femmodel from arguments provided command line: */ +- //FemModel *femmodel = new FemModel(1,arguments,modelcomm); ++ FemModel *femmodel = new FemModel(argc,argv,modelcomm); + +-// /*Now that the models are initialized, keep communicator information in the parameters datasets of each model: */ +-// femmodel->parameters->AddObject(new GenericParam(worldcomm,WorldCommEnum)); +-// femmodel->parameters->AddObject(new IntParam(NumModelsEnum,nummodels)); +-// femmodel->parameters->AddObject(new IntParam(ModelIdEnum,oceanid)); +-// femmodel->parameters->AddObject(new IntParam(EarthIdEnum,iceid)); +-// if(modelid==earthid) femmodel->parameters->AddObject(new GenericParam(fromicecomms,IcecapToEarthCommEnum)); +-// else femmodel->parameters->AddObject(new GenericParam(toearthcomm,IcecapToEarthCommEnum)); ++ /*Now that the models are initialized, keep communicator information in the parameters datasets of each model: */ ++ femmodel->parameters->AddObject(new GenericParam(worldcomm,WorldCommEnum)); ++ femmodel->parameters->AddObject(new GenericParam(tomitgcmcomm,ToMITgcmCommEnum)); + + /*Solve: */ + femmodel->Solve(); +@@ -117,15 +65,8 @@ + /*Finalize exception trapping: */ + ExceptionTrapEnd(); + +-// /*Free ressources:*/ ++ /*Free ressources:*/ + // xDelete(commsizes); +-// for(int i=0;i(string); +-// string=modelnames[i]; xDelete(string); +-// } +-// xDelete(dirnames); +-// xDelete(modelnames); + + /*Return unix success: */ + return 0; +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21851) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21852) +@@ -15,6 +15,7 @@ + FemModelCommEnum, + WorldCommEnum, + IcecapToEarthCommEnum, ++ ToMITgcmCommEnum, + NumModelsEnum, + ModelIdEnum, + EarthIdEnum, +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21851) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21852) +@@ -23,6 +23,7 @@ + case FemModelCommEnum : return "FemModelComm"; + case WorldCommEnum : return "WorldComm"; + case IcecapToEarthCommEnum : return "IcecapToEarthComm"; ++ case ToMITgcmCommEnum : return "ToMITgcmComm"; + case NumModelsEnum : return "NumModels"; + case ModelIdEnum : return "ModelId"; + case EarthIdEnum : return "EarthId"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21851) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21852) +@@ -23,6 +23,7 @@ + else if (strcmp(name,"FemModelComm")==0) return FemModelCommEnum; + else if (strcmp(name,"WorldComm")==0) return WorldCommEnum; + else if (strcmp(name,"IcecapToEarthComm")==0) return IcecapToEarthCommEnum; ++ else if (strcmp(name,"ToMITgcmComm")==0) return ToMITgcmCommEnum; + else if (strcmp(name,"NumModels")==0) return NumModelsEnum; + else if (strcmp(name,"ModelId")==0) return ModelIdEnum; + else if (strcmp(name,"EarthId")==0) return EarthIdEnum; +@@ -135,11 +136,11 @@ + else if (strcmp(name,"Hydrologyshreve")==0) return HydrologyshreveEnum; + else if (strcmp(name,"HydrologyshreveStabilization")==0) return HydrologyshreveStabilizationEnum; + else if (strcmp(name,"Hydrologydc")==0) return HydrologydcEnum; +- else if (strcmp(name,"SedimentHead")==0) return SedimentHeadEnum; + else stage=2; + } + if(stage==2){ +- if (strcmp(name,"SedimentHeadOld")==0) return SedimentHeadOldEnum; ++ if (strcmp(name,"SedimentHead")==0) return SedimentHeadEnum; ++ else if (strcmp(name,"SedimentHeadOld")==0) return SedimentHeadOldEnum; + else if (strcmp(name,"SedimentHeadResidual")==0) return SedimentHeadResidualEnum; + else if (strcmp(name,"EffectivePressure")==0) return EffectivePressureEnum; + else if (strcmp(name,"EplHead")==0) return EplHeadEnum; +@@ -258,11 +259,11 @@ + else if (strcmp(name,"Damage")==0) return DamageEnum; + else if (strcmp(name,"NewDamage")==0) return NewDamageEnum; + else if (strcmp(name,"StressIntensityFactor")==0) return StressIntensityFactorEnum; +- else if (strcmp(name,"CalvingLaw")==0) return CalvingLawEnum; + else stage=3; + } + if(stage==3){ +- if (strcmp(name,"CalvingCalvingrate")==0) return CalvingCalvingrateEnum; ++ if (strcmp(name,"CalvingLaw")==0) return CalvingLawEnum; ++ else if (strcmp(name,"CalvingCalvingrate")==0) return CalvingCalvingrateEnum; + else if (strcmp(name,"CalvingMeltingrate")==0) return CalvingMeltingrateEnum; + else if (strcmp(name,"CalvingLevermann")==0) return CalvingLevermannEnum; + else if (strcmp(name,"CalvingDev")==0) return CalvingDevEnum; +@@ -381,11 +382,11 @@ + else if (strcmp(name,"BalancethicknessDiffusionCoefficient")==0) return BalancethicknessDiffusionCoefficientEnum; + else if (strcmp(name,"BalancethicknessOmega")==0) return BalancethicknessOmegaEnum; + else if (strcmp(name,"BalancethicknessD0")==0) return BalancethicknessD0Enum; +- else if (strcmp(name,"Smb")==0) return SmbEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"SmbAnalysis")==0) return SmbAnalysisEnum; ++ if (strcmp(name,"Smb")==0) return SmbEnum; ++ else if (strcmp(name,"SmbAnalysis")==0) return SmbAnalysisEnum; + else if (strcmp(name,"SmbSolution")==0) return SmbSolutionEnum; + else if (strcmp(name,"SmbNumRequestedOutputs")==0) return SmbNumRequestedOutputsEnum; + else if (strcmp(name,"SmbRequestedOutputs")==0) return SmbRequestedOutputsEnum; +@@ -504,11 +505,11 @@ + else if (strcmp(name,"Internal")==0) return InternalEnum; + else if (strcmp(name,"MassFlux")==0) return MassFluxEnum; + else if (strcmp(name,"MeltingOffset")==0) return MeltingOffsetEnum; +- else if (strcmp(name,"Misfit")==0) return MisfitEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"Pressure")==0) return PressureEnum; ++ if (strcmp(name,"Misfit")==0) return MisfitEnum; ++ else if (strcmp(name,"Pressure")==0) return PressureEnum; + else if (strcmp(name,"PressurePicard")==0) return PressurePicardEnum; + else if (strcmp(name,"AndroidFrictionCoefficient")==0) return AndroidFrictionCoefficientEnum; + else if (strcmp(name,"ResetPenalties")==0) return ResetPenaltiesEnum; +@@ -627,11 +628,11 @@ + else if (strcmp(name,"Outputdefinition20")==0) return Outputdefinition20Enum; + else if (strcmp(name,"Outputdefinition21")==0) return Outputdefinition21Enum; + else if (strcmp(name,"Outputdefinition22")==0) return Outputdefinition22Enum; +- else if (strcmp(name,"Outputdefinition23")==0) return Outputdefinition23Enum; + else stage=6; + } + if(stage==6){ +- if (strcmp(name,"Outputdefinition24")==0) return Outputdefinition24Enum; ++ if (strcmp(name,"Outputdefinition23")==0) return Outputdefinition23Enum; ++ else if (strcmp(name,"Outputdefinition24")==0) return Outputdefinition24Enum; + else if (strcmp(name,"Outputdefinition25")==0) return Outputdefinition25Enum; + else if (strcmp(name,"Outputdefinition26")==0) return Outputdefinition26Enum; + else if (strcmp(name,"Outputdefinition27")==0) return Outputdefinition27Enum; +@@ -750,12 +751,12 @@ + else if (strcmp(name,"OutputFilePointer")==0) return OutputFilePointerEnum; + else if (strcmp(name,"ToolkitsFileName")==0) return ToolkitsFileNameEnum; + else if (strcmp(name,"RootPath")==0) return RootPathEnum; +- else if (strcmp(name,"OutputFileName")==0) return OutputFileNameEnum; +- else if (strcmp(name,"InputFileName")==0) return InputFileNameEnum; + else stage=7; + } + if(stage==7){ +- if (strcmp(name,"LockFileName")==0) return LockFileNameEnum; ++ if (strcmp(name,"OutputFileName")==0) return OutputFileNameEnum; ++ else if (strcmp(name,"InputFileName")==0) return InputFileNameEnum; ++ else if (strcmp(name,"LockFileName")==0) return LockFileNameEnum; + else if (strcmp(name,"RestartFileName")==0) return RestartFileNameEnum; + else if (strcmp(name,"ToolkitsOptionsAnalyses")==0) return ToolkitsOptionsAnalysesEnum; + else if (strcmp(name,"ToolkitsOptionsStrings")==0) return ToolkitsOptionsStringsEnum; +@@ -873,12 +874,12 @@ + else if (strcmp(name,"Matpar")==0) return MatparEnum; + else if (strcmp(name,"Node")==0) return NodeEnum; + else if (strcmp(name,"Numericalflux")==0) return NumericalfluxEnum; +- else if (strcmp(name,"Neumannflux")==0) return NeumannfluxEnum; +- else if (strcmp(name,"Param")==0) return ParamEnum; + else stage=8; + } + if(stage==8){ +- if (strcmp(name,"Moulin")==0) return MoulinEnum; ++ if (strcmp(name,"Neumannflux")==0) return NeumannfluxEnum; ++ else if (strcmp(name,"Param")==0) return ParamEnum; ++ else if (strcmp(name,"Moulin")==0) return MoulinEnum; + else if (strcmp(name,"Pengrid")==0) return PengridEnum; + else if (strcmp(name,"Penpair")==0) return PenpairEnum; + else if (strcmp(name,"Profiler")==0) return ProfilerEnum; +@@ -996,12 +997,12 @@ + else if (strcmp(name,"GroundedArea")==0) return GroundedAreaEnum; + else if (strcmp(name,"IceMass")==0) return IceMassEnum; + else if (strcmp(name,"IceVolume")==0) return IceVolumeEnum; +- else if (strcmp(name,"IceVolumeAboveFloatation")==0) return IceVolumeAboveFloatationEnum; +- else if (strcmp(name,"TotalFloatingBmb")==0) return TotalFloatingBmbEnum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"TotalGroundedBmb")==0) return TotalGroundedBmbEnum; ++ if (strcmp(name,"IceVolumeAboveFloatation")==0) return IceVolumeAboveFloatationEnum; ++ else if (strcmp(name,"TotalFloatingBmb")==0) return TotalFloatingBmbEnum; ++ else if (strcmp(name,"TotalGroundedBmb")==0) return TotalGroundedBmbEnum; + else if (strcmp(name,"TotalSmb")==0) return TotalSmbEnum; + else if (strcmp(name,"P0")==0) return P0Enum; + else if (strcmp(name,"P0Array")==0) return P0ArrayEnum; +Index: ../trunk-jpl/src/m/classes/clusters/localpfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/localpfe.m (revision 21851) ++++ ../trunk-jpl/src/m/classes/clusters/localpfe.m (revision 21852) +@@ -147,6 +147,24 @@ + end + end + %}}} ++ function BuildQueueScriptIceOcean(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ ++ ++ %write queuing script ++ %what is the executable being called? ++ executable='issm_ocean.exe'; ++ ++ fid=fopen([modelname '.queue'],'w'); ++ fprintf(fid,'#!%s\n',cluster.shell); ++ fprintf(fid,'mpiexec -np %i %s/%s %s %s %s: -np %i ./mitgcmuv\n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,modelname,cluster.npocean); ++ fclose(fid); ++ ++ %in interactive mode, create a run file, and errlog and outlog file ++ if cluster.interactive, ++ fid=fopen([modelname '.errlog'],'w'); fclose(fid); ++ fid=fopen([modelname '.outlog'],'w'); fclose(fid); ++ end ++ end ++ %}}} + function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{ + + %write queuing script +@@ -225,6 +243,21 @@ + issmssh(cluster.name,cluster.login,cluster.port,launchcommand); + + end %}}} ++ function LaunchQueueJobIceOcean(cluster,modelname,dirname,filelist,restart,batch)% {{{ ++ ++ %figure out what shell extension we will use: ++ if isempty(strfind(cluster.shell,'csh')), ++ shellext='sh'; ++ else ++ shellext='csh'; ++ end ++ ++ if cluster.verbose, disp('launching solution sequence on remote cluster'); end ++ ++ launchcommand=['cd ' cluster.executionpath ' && rm -rf *.lock && tar -zxf ' dirname '.tar.gz && rm -rf *.tar.gz']; ++ issmssh(cluster.name,cluster.login,cluster.port,launchcommand); ++ ++ end %}}} + function Download(cluster,dirname,filelist)% {{{ + + if ispc(), Index: /issm/oecreview/Archive/21724-22754/ISSM-21852-21853.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21852-21853.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21852-21853.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/m/classes/clusters/localpfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/localpfe.m (revision 21852) ++++ ../trunk-jpl/src/m/classes/clusters/localpfe.m (revision 21853) +@@ -10,6 +10,7 @@ + name = ''; + login = ''; + np = 1; ++ npocean = 0; + port = 0; + interactive = 1; + codepath = [IssmConfig('ISSM_PREFIX') '/bin']; Index: /issm/oecreview/Archive/21724-22754/ISSM-21853-21854.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21853-21854.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21853-21854.diff (revision 22755) @@ -0,0 +1,31 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21853) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21854) +@@ -88,15 +88,16 @@ + #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + this->amrbamg = NULL; + #endif ++ #if !defined(_HAVE_ADOLC_) + if(amr_frequency){ + this->parameters->FindParam(&amrtype,AmrTypeEnum); + switch(amrtype){ + +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_NEOPZ_) + case AmrNeopzEnum: this->InitializeAdaptiveRefinementNeopz(); break; + #endif + +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) + case AmrBamgEnum: this->InitializeAdaptiveRefinementBamg(); break; + #endif + +@@ -103,6 +104,7 @@ + default: _error_("not implemented yet"); + } + } ++ #endif + + /*Free resources */ + xDelete(lockfilename); Index: /issm/oecreview/Archive/21724-22754/ISSM-21854-21855.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21854-21855.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21854-21855.diff (revision 22755) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 21854) ++++ ../trunk-jpl/src/c/Makefile.am (revision 21855) +@@ -46,11 +46,15 @@ + ./bamg/VertexOnVertex.cpp\ + ./bamg/Mesh.cpp\ + ./shared/Bamg/BigPrimeNumber.cpp\ +- ./classes/AmrBamg.cpp\ + ./modules/Bamgx/Bamgx.cpp\ + ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\ + ./modules/BamgTriangulatex/BamgTriangulatex.cpp ++ ++#do not include AmrBamg with ADOLC ++if !ADOLC ++ issm_sources += ./classes/AmrBamg.cpp + endif ++endif + #}}} + #Core sources{{{ + issm_sources += ./datastructures/DataSet.cpp\ Index: /issm/oecreview/Archive/21724-22754/ISSM-21855-21856.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21855-21856.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21855-21856.diff (revision 22755) @@ -0,0 +1,80 @@ +Index: ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 21855) ++++ ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 21856) +@@ -11,23 +11,23 @@ + using namespace bamg; + using namespace std; + +-int InterpFromMeshToMesh2dx(IssmDouble** pdata_interp,int* index_data,IssmDouble* x_data,IssmDouble* y_data,int nods_data,int nels_data, +- IssmDouble* data,int M_data,int N_data,IssmDouble* x_interp,IssmDouble* y_interp,int N_interp,Options* options){ ++int InterpFromMeshToMesh2dx(double** pdata_interp,int* index_data,double* x_data,double* y_data,int nods_data,int nels_data, ++ double* data,int M_data,int N_data,double* x_interp,double* y_interp,int N_interp,Options* options){ + + /*Output*/ +- IssmDouble* data_interp=NULL; ++ double* data_interp=NULL; + + /*Intermediary*/ +- IssmDouble xmin,xmax,ymin,ymax; ++ double xmin,xmax,ymin,ymax; + bool isdefault; +- IssmDouble defaultvalue; ++ double defaultvalue; + R2 r; + I2 I; + int i,j,k; + int it; + int i0,i1,i2; +- IssmDouble areacoord[3]; +- IssmDouble aa,bb; ++ double areacoord[3]; ++ double aa,bb; + long long dete[3]; + + /*Checks*/ +@@ -45,7 +45,7 @@ + } + + /*Initialize output*/ +- data_interp=xNew(N_interp*N_data); ++ data_interp=xNew(N_interp*N_data); + + /*read background mesh*/ + Mesh* Th=new Mesh(index_data,x_data,y_data,nods_data,nels_data); +@@ -77,7 +77,7 @@ + + /*Loop over output nodes*/ + for(i=0;ixmax || y_interp[i]ymax){ +@@ -97,9 +97,9 @@ + if (tb.det>0){ + + /*Area coordinates*/ +- areacoord[0]= reCast(dete[0])/reCast(tb.det); +- areacoord[1]= reCast(dete[1])/reCast(tb.det); +- areacoord[2]= reCast(dete[2])/reCast(tb.det); ++ areacoord[0]= reCast(dete[0])/reCast(tb.det); ++ areacoord[1]= reCast(dete[1])/reCast(tb.det); ++ areacoord[2]= reCast(dete[2])/reCast(tb.det); + /*3 vertices of the triangle*/ + i0=Th->GetId(tb[0]); + i1=Th->GetId(tb[1]); +Index: ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h (revision 21855) ++++ ../trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h (revision 21856) +@@ -7,7 +7,7 @@ + + #include "../../classes/classes.h" + +-int InterpFromMeshToMesh2dx(IssmDouble** pdata_interp,int* index_data,IssmDouble* x_data,IssmDouble* y_data,int nods_data,int nels_data, +- IssmDouble* data,int M_data,int N_data,IssmDouble* x_interp,IssmDouble* y_interp,int N_interp,Options* options); ++int InterpFromMeshToMesh2dx(double** pdata_interp,int* index_data,double* x_data,double* y_data,int nods_data,int nels_data, ++ double* data,int M_data,int N_data,double* x_interp,double* y_interp,int N_interp,Options* options); + + #endif Index: /issm/oecreview/Archive/21724-22754/ISSM-21856-21857.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21856-21857.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21856-21857.diff (revision 22755) @@ -0,0 +1,40 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 21856) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 21857) +@@ -156,6 +156,7 @@ + #endif + + /*AMR*/ ++ #if !defined(_HAVE_ADOLC_) + void BedrockFromMismipPlus(void); + void AdjustBaseThicknessAndMask(void); + void GetMesh(Vertices* femmodel_vertices,Elements* femmodel_elements,IssmDouble** px, IssmDouble** py, IssmDouble** pz, int** pelementslist); +@@ -175,6 +176,7 @@ + void SmoothedGradThickness(IssmDouble** pdHdx,IssmDouble** pdHdy); + void ThicknessZZErrorEstimator(IssmDouble** pelementerror); + void MeanGroundedIceLevelSet(IssmDouble** pmasklevelset); ++ #endif + + #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + void ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21856) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21857) +@@ -2427,6 +2427,7 @@ + /*}}}*/ + + /*AMR*/ ++#if !defined(_HAVE_ADOLC_) + void FemModel::BedrockFromMismipPlus(void){/*{{{*/ + + /*Insert bedrock from mismip+ setup*/ +@@ -3615,6 +3616,7 @@ + + } + /*}}}*/ ++#endif + + #ifdef _HAVE_DAKOTA_ + void FemModel::DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses){/*{{{*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21857-21858.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21857-21858.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21857-21858.diff (revision 22755) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21857) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 21858) +@@ -181,11 +181,17 @@ + + /*Adaptive mesh refinement*/ + if(amr_frequency){ ++ ++ #if !defined(_HAVE_ADOLC_) + if(save_results) femmodel->WriteMeshInResults(); + if(step%amr_frequency==0 && timeReMesh();//Do not refine the last step + } ++ ++ #else ++ _error_("AMR not suppored with ADOLC"); ++ #endif + } + } + Index: /issm/oecreview/Archive/21724-22754/ISSM-21858-21859.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21858-21859.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21858-21859.diff (revision 22755) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 21858) ++++ ../trunk-jpl/src/c/Makefile.am (revision 21859) +@@ -51,7 +51,8 @@ + ./modules/BamgTriangulatex/BamgTriangulatex.cpp + + #do not include AmrBamg with ADOLC +-if !ADOLC ++if ADOLC ++else + issm_sources += ./classes/AmrBamg.cpp + endif + endif Index: /issm/oecreview/Archive/21724-22754/ISSM-21859-21860.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21859-21860.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21859-21860.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 21859) ++++ ../trunk-jpl/src/c/Makefile.am (revision 21860) +@@ -53,7 +53,7 @@ + #do not include AmrBamg with ADOLC + if ADOLC + else +- issm_sources += ./classes/AmrBamg.cpp ++issm_sources += ./classes/AmrBamg.cpp + endif + endif + #}}} Index: /issm/oecreview/Archive/21724-22754/ISSM-21860-21861.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21860-21861.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21860-21861.diff (revision 22755) @@ -0,0 +1,326 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 21860) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 21861) +@@ -72,7 +72,6 @@ + void InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, char* restartfilename, const int solution_type,bool trace,IssmPDouble* X=NULL); + void InitFromFids(char* rootpath, FILE* IOMODEL, FILE* toolkitsoptionsfid, int in_solution_type, bool trace, IssmPDouble* X=NULL); + void Marshall(char** pmarshalled_data, int* pmarshalled_data_size, int marshall_direction); +- void ReMesh(void); + void Restart(void); + void SetCurrentConfiguration(int configuration_type); + void SetCurrentConfiguration(int configuration_type,int analysis_type); +@@ -157,6 +156,7 @@ + + /*AMR*/ + #if !defined(_HAVE_ADOLC_) ++ void ReMesh(void); + void BedrockFromMismipPlus(void); + void AdjustBaseThicknessAndMask(void); + void GetMesh(Vertices* femmodel_vertices,Elements* femmodel_elements,IssmDouble** px, IssmDouble** py, IssmDouble** pz, int** pelementslist); +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21860) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21861) +@@ -1543,150 +1543,6 @@ + xDelete(control_type); + } + /*}}}*/ +-void FemModel::ReMesh(void){/*{{{*/ +- +- /*Intermediaries*/ +- IssmDouble *newx = NULL; +- IssmDouble *newy = NULL; +- IssmDouble *newz = NULL; +- int *newelementslist = NULL; +- int newnumberofvertices = -1; +- int newnumberofelements = -1; +- bool* my_elements = NULL; +- int* my_vertices = NULL; +- int elementswidth = this->GetElementsWidth();//just tria elements in this version +- int amrtype; +- +- /*Branch to specific amr depending on requested method*/ +- parameters->FindParam(&amrtype,AmrTypeEnum); +- switch(amrtype){ +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) +- case AmrNeopzEnum: this->ReMeshNeopz(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; +- #endif +- +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) +- case AmrBamgEnum: this->ReMeshBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; +- #endif +- +- default: _error_("not implemented yet"); +- } +- +- /*Partitioning the new mesh. Maybe ElementsAndVerticesPartitioning.cpp could be modified to set this without iomodel.*/ +- this->ElementsAndVerticesPartitioning(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,&my_elements,&my_vertices); +- +- if(this->loads->Size()!=0) _error_("not supported yet"); +- +- /*Create vertices*/ +- Vertices* new_vertices=new Vertices(); +- this->CreateVertices(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,my_vertices,newx,newy,newz,new_vertices); +- +- /*Creating elements*/ +- /*Just Tria in this version*/ +- Elements* new_elements=new Elements(); +- this->CreateElements(newnumberofelements,elementswidth,newelementslist,my_elements,new_elements); +- +- /*Creating materials*/ +- Materials* new_materials=new Materials(); +- this->CreateMaterials(newnumberofelements,my_elements,new_materials); +- +- /*Creating nodes and constraints*/ +- /*Just SSA (2D) and P1 in this version*/ +- Nodes* new_nodes=new Nodes(); +- Constraints* new_constraints=new Constraints(); +- +- int nodecounter=0; +- int constraintcounter=0; +- for(int i=0;inummodels;i++){//create nodes for each analysis in analysis_type_list +- +- int analysis_enum = this->analysis_type_list[i]; +- +- /*As the domain is 2D, it is not necessary to create nodes for this analysis*/ +- /*itapopo must verify if domain is not 3D. Only 2D in this version!*/ +- if(analysis_enum==StressbalanceVerticalAnalysisEnum) continue; +- +- this->CreateNodes(newnumberofvertices,my_vertices,nodecounter,analysis_enum,new_nodes); +- if(analysis_enum==StressbalanceAnalysisEnum) this->CreateConstraints(newnumberofvertices,newnumberofelements,nodecounter,constraintcounter,newx,newy,my_vertices,new_constraints); +- this->UpdateElements(newnumberofelements,newelementslist,my_elements,nodecounter,i,new_elements); +- +- if(new_nodes->Size()) nodecounter=new_nodes->MaximumId(); +- constraintcounter = new_constraints->NumberOfConstraints(); +- /*Make sure nodecounter is at least 0 (if no node exists, maxid will be -1*/ +- _assert_(nodecounter>=0); +- } +- +- new_elements->Presort(); +- new_nodes->Presort(); +- new_vertices->Presort(); +- this->loads->Presort(); +- new_materials->Presort(); +- new_constraints->Presort(); +- +- /*reset hooks for elements, loads and nodes: */ +- new_elements->ResetHooks(); +- this->loads->ResetHooks(); +- new_materials->ResetHooks(); +- +- /*do the post-processing of the datasets to get an FemModel that can actually run analyses: */ +- int analysis_type; +- for(int i=0;inummodels;i++){ +- analysis_type=this->analysis_type_list[i]; +- //SetCurrentConfiguration(analysis_type); +- +- this->analysis_counter=i; +- /*Now, plug analysis_counter and analysis_type inside the parameters: */ +- this->parameters->SetParam(this->analysis_counter,AnalysisCounterEnum); +- this->parameters->SetParam(analysis_type,AnalysisTypeEnum); +- this->parameters->SetParam(analysis_type,ConfigurationTypeEnum); +- +- /*configure elements, loads and nodes, for this new analysis: */ +- new_elements->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); +- this->loads->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); +- +- /*take care of toolkits options, that depend on this analysis type (present only after model processor)*/ +- if(this->parameters->Exist(ToolkitsOptionsStringsEnum)){ +- ToolkitsOptionsFromAnalysis(this->parameters,analysis_type); +- if(VerboseSolver()) _printf0_(" toolkits Options set for analysis type: " << EnumToStringx(analysis_type) << "\n"); +- } +- +- ConfigureObjectsx(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); +- if(i==0){ +- VerticesDofx(new_vertices,this->parameters); //only call once, we only have one set of vertices +- } +- SpcNodesx(new_nodes,new_constraints,this->parameters,analysis_type); +- NodesDofx(new_nodes,this->parameters,analysis_type); +- } +- +- /*Finally: interpolate all inputs and insert them into the new elements.*/ +- this->InterpolateInputs(new_vertices,new_elements); +- +- /*Delete old structure and set new pointers*/ +- delete this->vertices; this->vertices = new_vertices; +- delete this->elements; this->elements = new_elements; +- delete this->nodes; this->nodes = new_nodes; +- delete this->constraints; this->constraints = new_constraints; +- delete this->materials; this->materials = new_materials; +- +- GetMaskOfIceVerticesLSMx(this); +- +- /*Insert MISMIP+ bed topography*/ +- if(false) this->BedrockFromMismipPlus(); +- +- /*Adjust base, thickness and mask grounded ice leve set*/ +- if(true) this->AdjustBaseThicknessAndMask(); +- +- /*Reset current configuration: */ +- analysis_type=this->analysis_type_list[this->analysis_counter]; +- SetCurrentConfiguration(analysis_type); +- +- /*Cleanup*/ +- xDelete(newx); +- xDelete(newy); +- xDelete(newz); +- xDelete(newelementslist); +- xDelete(my_vertices); +- xDelete(my_elements); +-} +-/*}}}*/ + void FemModel::RequestedDependentsx(void){/*{{{*/ + + bool isautodiff = false; +@@ -2428,6 +2284,150 @@ + + /*AMR*/ + #if !defined(_HAVE_ADOLC_) ++void FemModel::ReMesh(void){/*{{{*/ ++ ++ /*Intermediaries*/ ++ IssmDouble *newx = NULL; ++ IssmDouble *newy = NULL; ++ IssmDouble *newz = NULL; ++ int *newelementslist = NULL; ++ int newnumberofvertices = -1; ++ int newnumberofelements = -1; ++ bool* my_elements = NULL; ++ int* my_vertices = NULL; ++ int elementswidth = this->GetElementsWidth();//just tria elements in this version ++ int amrtype; ++ ++ /*Branch to specific amr depending on requested method*/ ++ parameters->FindParam(&amrtype,AmrTypeEnum); ++ switch(amrtype){ ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ case AmrNeopzEnum: this->ReMeshNeopz(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; ++ #endif ++ ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ case AmrBamgEnum: this->ReMeshBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; ++ #endif ++ ++ default: _error_("not implemented yet"); ++ } ++ ++ /*Partitioning the new mesh. Maybe ElementsAndVerticesPartitioning.cpp could be modified to set this without iomodel.*/ ++ this->ElementsAndVerticesPartitioning(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,&my_elements,&my_vertices); ++ ++ if(this->loads->Size()!=0) _error_("not supported yet"); ++ ++ /*Create vertices*/ ++ Vertices* new_vertices=new Vertices(); ++ this->CreateVertices(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,my_vertices,newx,newy,newz,new_vertices); ++ ++ /*Creating elements*/ ++ /*Just Tria in this version*/ ++ Elements* new_elements=new Elements(); ++ this->CreateElements(newnumberofelements,elementswidth,newelementslist,my_elements,new_elements); ++ ++ /*Creating materials*/ ++ Materials* new_materials=new Materials(); ++ this->CreateMaterials(newnumberofelements,my_elements,new_materials); ++ ++ /*Creating nodes and constraints*/ ++ /*Just SSA (2D) and P1 in this version*/ ++ Nodes* new_nodes=new Nodes(); ++ Constraints* new_constraints=new Constraints(); ++ ++ int nodecounter=0; ++ int constraintcounter=0; ++ for(int i=0;inummodels;i++){//create nodes for each analysis in analysis_type_list ++ ++ int analysis_enum = this->analysis_type_list[i]; ++ ++ /*As the domain is 2D, it is not necessary to create nodes for this analysis*/ ++ /*itapopo must verify if domain is not 3D. Only 2D in this version!*/ ++ if(analysis_enum==StressbalanceVerticalAnalysisEnum) continue; ++ ++ this->CreateNodes(newnumberofvertices,my_vertices,nodecounter,analysis_enum,new_nodes); ++ if(analysis_enum==StressbalanceAnalysisEnum) this->CreateConstraints(newnumberofvertices,newnumberofelements,nodecounter,constraintcounter,newx,newy,my_vertices,new_constraints); ++ this->UpdateElements(newnumberofelements,newelementslist,my_elements,nodecounter,i,new_elements); ++ ++ if(new_nodes->Size()) nodecounter=new_nodes->MaximumId(); ++ constraintcounter = new_constraints->NumberOfConstraints(); ++ /*Make sure nodecounter is at least 0 (if no node exists, maxid will be -1*/ ++ _assert_(nodecounter>=0); ++ } ++ ++ new_elements->Presort(); ++ new_nodes->Presort(); ++ new_vertices->Presort(); ++ this->loads->Presort(); ++ new_materials->Presort(); ++ new_constraints->Presort(); ++ ++ /*reset hooks for elements, loads and nodes: */ ++ new_elements->ResetHooks(); ++ this->loads->ResetHooks(); ++ new_materials->ResetHooks(); ++ ++ /*do the post-processing of the datasets to get an FemModel that can actually run analyses: */ ++ int analysis_type; ++ for(int i=0;inummodels;i++){ ++ analysis_type=this->analysis_type_list[i]; ++ //SetCurrentConfiguration(analysis_type); ++ ++ this->analysis_counter=i; ++ /*Now, plug analysis_counter and analysis_type inside the parameters: */ ++ this->parameters->SetParam(this->analysis_counter,AnalysisCounterEnum); ++ this->parameters->SetParam(analysis_type,AnalysisTypeEnum); ++ this->parameters->SetParam(analysis_type,ConfigurationTypeEnum); ++ ++ /*configure elements, loads and nodes, for this new analysis: */ ++ new_elements->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); ++ this->loads->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); ++ ++ /*take care of toolkits options, that depend on this analysis type (present only after model processor)*/ ++ if(this->parameters->Exist(ToolkitsOptionsStringsEnum)){ ++ ToolkitsOptionsFromAnalysis(this->parameters,analysis_type); ++ if(VerboseSolver()) _printf0_(" toolkits Options set for analysis type: " << EnumToStringx(analysis_type) << "\n"); ++ } ++ ++ ConfigureObjectsx(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); ++ if(i==0){ ++ VerticesDofx(new_vertices,this->parameters); //only call once, we only have one set of vertices ++ } ++ SpcNodesx(new_nodes,new_constraints,this->parameters,analysis_type); ++ NodesDofx(new_nodes,this->parameters,analysis_type); ++ } ++ ++ /*Finally: interpolate all inputs and insert them into the new elements.*/ ++ this->InterpolateInputs(new_vertices,new_elements); ++ ++ /*Delete old structure and set new pointers*/ ++ delete this->vertices; this->vertices = new_vertices; ++ delete this->elements; this->elements = new_elements; ++ delete this->nodes; this->nodes = new_nodes; ++ delete this->constraints; this->constraints = new_constraints; ++ delete this->materials; this->materials = new_materials; ++ ++ GetMaskOfIceVerticesLSMx(this); ++ ++ /*Insert MISMIP+ bed topography*/ ++ if(false) this->BedrockFromMismipPlus(); ++ ++ /*Adjust base, thickness and mask grounded ice leve set*/ ++ if(true) this->AdjustBaseThicknessAndMask(); ++ ++ /*Reset current configuration: */ ++ analysis_type=this->analysis_type_list[this->analysis_counter]; ++ SetCurrentConfiguration(analysis_type); ++ ++ /*Cleanup*/ ++ xDelete(newx); ++ xDelete(newy); ++ xDelete(newz); ++ xDelete(newelementslist); ++ xDelete(my_vertices); ++ xDelete(my_elements); ++} ++/*}}}*/ + void FemModel::BedrockFromMismipPlus(void){/*{{{*/ + + /*Insert bedrock from mismip+ setup*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21861-21862.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21861-21862.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21861-21862.diff (revision 22755) @@ -0,0 +1,25 @@ +Index: ../trunk-jpl/src/m/classes/clusters/pfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 21861) ++++ ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 21862) +@@ -354,9 +354,8 @@ + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); + fprintf(fid,'module load comp-intel/2016.2.181\n'); + fprintf(fid,'module load mpi-sgi/mpt\n'); +- fprintf(fid,'module load netcdf/4.0\n'); +- fprintf(fid,'module load mpi-mvapich2/1.4.1/gcc\n'); +- fprintf(fid,'module load gcc/4.4.4\n'); ++ fprintf(fid,'module load netcdf/4.4.1.1_mpt\n'); ++ fprintf(fid,'module load mpi-sgi/mpt.2.15r20\n'); + fprintf(fid,'export PATH="$PATH:."\n'); + fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); + fprintf(fid,['cd ' pwd() ' \n\n']); +@@ -369,7 +368,7 @@ + %in interactive mode, create a run file, and errlog and outlog file + if cluster.interactive, + fid=fopen([modelname '.run'],'w'); +- fprintf(fid,'module load mpi-mvapich2/1.4.1/gcc\n'); ++ fprintf(fid,'module load mpi-sgi/mpt.2.15r20\n'); + fprintf(fid,['mpiexec -np %i ./mitgcmuv \n'],np); + fprintf(fid,['touch ' modelname '.lock %s\n']); + fclose(fid); Index: /issm/oecreview/Archive/21724-22754/ISSM-21862-21863.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21862-21863.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21862-21863.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_ampi +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_ampi (revision 21862) ++++ ../trunk-jpl/jenkins/linux64_ross_ampi (revision 21863) +@@ -20,7 +20,7 @@ + --with-python-numpy-dir=/usr/lib/python2.7/dist-packages/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ +- --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ ++ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpifort -lmpi" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ Index: /issm/oecreview/Archive/21724-22754/ISSM-21863-21864.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21863-21864.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21863-21864.diff (revision 22755) @@ -0,0 +1,844 @@ +Index: ../trunk-jpl/src/m/mesh/bamg.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.m (revision 21863) ++++ ../trunk-jpl/src/m/mesh/bamg.m (revision 21864) +@@ -21,7 +21,6 @@ + % - Hessiantype : 0 -> use double L2 projection (default) + % 1 -> use Green formula + % - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1) +-% - MaxCornerAngle : maximum angle of corners in degree (default is 10) + % - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) + % - maxsubdiv : maximum subdivision of exisiting elements (default is 10) + % - metric : matrix (numberofnodes x 3) used as a metric +@@ -33,7 +32,6 @@ + % - omega : relaxation parameter of the smoothing procedure (default is 1.8) + % - power : power applied to the metric (default is 1) + % - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) +-% - geometricalmetric : take the geometry into account to generate the metric (default is 0) + % - verbose : level of verbosity (default is 1) + % + % - vertical : is this a 2d vertical mesh (flowband, default is 0) +@@ -329,7 +327,6 @@ + bamg_options.hmaxVertices=getfieldvalue(options,'hmaxVertices',[]); + bamg_options.hVertices=getfieldvalue(options,'hVertices',[]); + bamg_options.KeepVertices=getfieldvalue(options,'KeepVertices',1); +-bamg_options.MaxCornerAngle=getfieldvalue(options,'MaxCornerAngle',10.); + bamg_options.maxnbv=getfieldvalue(options,'maxnbv',10^6); + bamg_options.maxsubdiv=getfieldvalue(options,'maxsubdiv',10.); + bamg_options.metric=getfieldvalue(options,'metric',[]); +@@ -339,8 +336,6 @@ + bamg_options.omega=getfieldvalue(options,'omega',1.8); + bamg_options.power=getfieldvalue(options,'power',1.); + bamg_options.splitcorners=getfieldvalue(options,'splitcorners',1); +-bamg_options.geometricalmetric=getfieldvalue(options,'geometricalmetric',0); +-bamg_options.random=getfieldvalue(options,'rand',true); + bamg_options.verbose=getfieldvalue(options,'verbose',1); + %}}} + +Index: ../trunk-jpl/src/m/mesh/bamg.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.py (revision 21863) ++++ ../trunk-jpl/src/m/mesh/bamg.py (revision 21864) +@@ -36,7 +36,6 @@ + - Hessiantype : 0 -> use double P2 projection (default) + 1 -> use Green formula + - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1) +- - MaxCornerAngle : maximum angle of corners in degree (default is 10) + - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) + - maxsubdiv : maximum subdivision of exisiting elements (default is 10) + - metric : matrix (numberofnodes x 3) used as a metric +@@ -48,7 +47,6 @@ + - omega : relaxation parameter of the smoothing procedure (default is 1.8) + - power : power applied to the metric (default is 1) + - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) +- - geometricalmetric : take the geometry into account to generate the metric (default is 0) + - verbose : level of verbosity (default is 1) + + - rifts : followed by an ARGUS file that prescribes the rifts +@@ -302,7 +300,6 @@ + bamg_options['hmaxVertices']=options.getfieldvalue('hmaxVertices',np.empty((0,1))) + bamg_options['hVertices']=options.getfieldvalue('hVertices',np.empty((0,1))) + bamg_options['KeepVertices']=options.getfieldvalue('KeepVertices',1) +- bamg_options['MaxCornerAngle']=options.getfieldvalue('MaxCornerAngle',10.) + bamg_options['maxnbv']=options.getfieldvalue('maxnbv',10**6) + bamg_options['maxsubdiv']=options.getfieldvalue('maxsubdiv',10.) + bamg_options['metric']=options.getfieldvalue('metric',np.empty((0,1))) +@@ -312,8 +309,6 @@ + bamg_options['omega']=options.getfieldvalue('omega',1.8) + bamg_options['power']=options.getfieldvalue('power',1.) + bamg_options['splitcorners']=options.getfieldvalue('splitcorners',1) +- bamg_options['geometricalmetric']=options.getfieldvalue('geometricalmetric',0) +- bamg_options['random']=options.getfieldvalue('rand',True) + bamg_options['verbose']=options.getfieldvalue('verbose',1) + #}}} + +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21863) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21864) +@@ -31,7 +31,6 @@ + this->options->errg = 0.1; + this->options->gradation = 1.5; + this->options->Hessiantype = 0; +- this->options->MaxCornerAngle = 1.e-12; + this->options->maxnbv = 1e6; + this->options->maxsubdiv = 10; + this->options->Metrictype = 0; +@@ -39,10 +38,8 @@ + this->options->nbsmooth = 3; + this->options->omega = 1.8; + this->options->power = 1; +- this->options->random = 0; + this->options->verbose = 0; + this->options->Crack = 0; +- this->options->geometricalmetric = 0; + this->options->KeepVertices = 1; /*!!!!! VERY IMPORTANT !!!!!*/ + this->options->splitcorners = 1; + this->options->hmin = hmin; +Index: ../trunk-jpl/src/c/bamg/BamgOpts.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgOpts.h (revision 21863) ++++ ../trunk-jpl/src/c/bamg/BamgOpts.h (revision 21864) +@@ -16,7 +16,6 @@ + double errg; + double gradation; + int Hessiantype; +- double MaxCornerAngle; + int maxnbv; + double maxsubdiv; + int Metrictype; +@@ -24,12 +23,10 @@ + int nbsmooth; + double omega; + double power; +- bool random; + int verbose; + + /*Flags*/ + int Crack; +- int geometricalmetric; + int KeepVertices; + int splitcorners; + +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21863) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21864) +@@ -979,57 +979,6 @@ + /*}}}*/ + + /*Methods*/ +- void Mesh::AddGeometryMetric(BamgOpts* bamgopts){/*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, Metric.cpp/IntersectGeomMetric)*/ +- +- /*Get options*/ +- double anisomax = bamgopts->anisomax; +- double errg = bamgopts->errg; +- +- double ss[2]={0.00001,0.99999}; +- double errC = 2*sqrt(2*errg); +- double hmax = Gh.MaximalHmax(); +- double hmin = Gh.MinimalHmin(); +- +- //check that hmax is positive +- _assert_(hmax>0); +- +- //errC cannot be higher than 1 +- if(errC>1) errC=1; +- +- //Set all vertices to "on" +- SetVertexFieldOn(); +- +- //loop over all the vertices on edges +- for(int i=0;iR1tg(s,tg); +- double ht=hmax; +- // err relative to the length of the edge +- if (R1>1.0e-20) { +- ht = Min(Max(errC/R1,hmin),hmax); +- } +- double hn=Min(hmax,ht*anisomax); +- +- if (ht<=0 || hn<=0){ +- _error_("ht<=0 || hn<=0"); +- } +- EigenMetric Vp(1/(ht*ht),1/(hn*hn),tg); +- Metric MVp(Vp); +- edges[i][j].m.IntersectWith(MVp); +- } +- } +- // the problem is for the vertex on vertex +- } +- /*}}}*/ + void Mesh::AddMetric(BamgOpts* bamgopts){/*{{{*/ + // Hessiantype = 0 => H is computed using double L2 projection + // Hessiantype = 1 => H is computed with green formula +@@ -1230,12 +1179,10 @@ + /*Intermediary*/ + int i,j,k,kk,it,jt; + int verbose=0; +- double cutoffradian=10*Pi/180; + + /*Recover options*/ +- if (bamgopts){ ++ if(bamgopts){ + verbose=bamgopts->verbose; +- cutoffradian=bamgopts->MaxCornerAngle*Pi/180; + } + + //display info +@@ -1242,13 +1189,8 @@ + if (verbose>1) _printf_(" construction of the geometry from the 2d mesh\n"); + + //check that the mesh is not empty +- if (nbt<=0 || nbv <=0 ) { +- _error_("nbt or nbv is negative (Mesh empty?)"); +- } ++ if(nbt<=0 || nbv <=0 ) _error_("nbt or nbv is negative (Mesh empty?)"); + +- //Gh is the geometry of the mesh (this), initialize MaxCornerAngle +- if (cutoffradian>=0) Gh.MaxCornerAngle = cutoffradian; +- + /*Construction of the edges*/ + + //initialize st and edge4 +@@ -1446,9 +1388,7 @@ + /*Reconstruct subdomains info*/ + + //check that nbsubdomains is empty +- if (nbsubdomains){ +- _error_("nbsubdomains should be 0"); +- } ++ if(nbsubdomains) _error_("nbsubdomains should be 0"); + nbsubdomains=0; + + //color the subdomains +@@ -2648,51 +2588,51 @@ + void Mesh::Init(long maxnbv_in) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/PreInit)*/ + +- /* initialize random seed: */ +- srand(19999999); +- + /*Initialize fields*/ +- NbRef=0; +- quadtree=NULL; +- nbv=0; +- nbt=0; +- nbe=0; +- edges=NULL; +- nbsubdomains=0; +- subdomains=NULL; +- maxnbv=maxnbv_in; +- maxnbt=2 *maxnbv_in-2; +- NbVertexOnBThVertex=0; +- VertexOnBThVertex=NULL; +- NbVertexOnBThEdge=0; +- VertexOnBThEdge=NULL; +- NbCrackedVertices=0; +- CrackedVertices =NULL; +- NbCrackedEdges =0; +- CrackedEdges =NULL; +- NbVerticesOnGeomVertex=0; +- VerticesOnGeomVertex=NULL; +- NbVerticesOnGeomEdge=0; +- VerticesOnGeomEdge=NULL; ++ this->NbRef = 0; ++ this->quadtree = NULL; ++ this->nbv = 0; ++ this->nbt = 0; ++ this->nbe = 0; ++ this->edges = NULL; ++ this->nbsubdomains = 0; ++ this->subdomains = NULL; ++ this->maxnbv = maxnbv_in; ++ this->maxnbt = 2 *maxnbv_in-2; ++ this->NbVertexOnBThVertex = 0; ++ this->VertexOnBThVertex = NULL; ++ this->NbVertexOnBThEdge = 0; ++ this->VertexOnBThEdge = NULL; ++ this->NbCrackedVertices = 0; ++ this->CrackedVertices = NULL; ++ this->NbCrackedEdges = 0; ++ this->CrackedEdges = NULL; ++ this->NbVerticesOnGeomVertex = 0; ++ this->VerticesOnGeomVertex = NULL; ++ this->NbVerticesOnGeomEdge = 0; ++ this->VerticesOnGeomEdge = NULL; + ++ /*Initialize random seed*/ ++ this->randomseed = 1; ++ + /*Allocate if maxnbv_in>0*/ + if(maxnbv_in){ +- vertices=new BamgVertex[maxnbv]; +- _assert_(vertices); +- orderedvertices=new BamgVertex* [maxnbv]; +- _assert_(orderedvertices); +- triangles=new Triangle[maxnbt]; +- _assert_(triangles); ++ this->vertices=new BamgVertex[this->maxnbv]; ++ this->orderedvertices=new BamgVertex* [this->maxnbv]; ++ this->triangles=new Triangle[this->maxnbt]; ++ _assert_(this->vertices); ++ _assert_(this->orderedvertices); ++ _assert_(this->triangles); + } + else{ +- vertices=NULL; +- orderedvertices=NULL; +- triangles=NULL; +- maxnbt=0; ++ this->vertices = NULL; ++ this->orderedvertices = NULL; ++ this->triangles = NULL; ++ this->maxnbt = 0; + } + } + /*}}}*/ +- void Mesh::Insert(bool random) {/*{{{*/ ++ void Mesh::Insert(){/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/Insert)*/ + + /*Insert points in the existing Geometry*/ +@@ -2739,8 +2679,7 @@ + + //Get Prime number + const long PrimeNumber= BigPrimeNumber(nbv); +- int temp = rand(); if(!random) temp = 756804110; +- int k0=temp%nbv; ++ int k0=this->RandomNumber(nbv); + + //Build orderedvertices + for (i=0; i (BAMG v1.01, Mesh2.cpp/InsertNewPoints)*/ + + long int verbose=0; +@@ -2844,9 +2783,7 @@ + + /*construction of a random order*/ + const long PrimeNumber= BigPrimeNumber(nbv) ; +- //remainder of the division of rand() by nbvnew +- int temp = rand(); if(!random) temp = 1098566905; +- long k3 = temp%nbvnew; ++ long k3 = long(this->RandomNumber(nbvnew)); + //loop over the new points + for (int is3=0; is3random); ++ InsertNewPoints(nbvold,NbTSwap); + } + else Bh.CreateSingleVertexToTriangleConnectivity(); + +@@ -3145,7 +3082,7 @@ + } // end loop for each edge + }// for triangle + +- if (!InsertNewPoints(nbvold,NbTSwap,bamgopts->random)) break; ++ if (!InsertNewPoints(nbvold,NbTSwap)) break; + for (i=nbtold;i4) _printf_(" -- current number of vertices = " << nbv << "\n"); + if (verbose>3) _printf_(" Creating initial Constrained Delaunay Triangulation...\n"); + if (verbose>3) _printf_(" Inserting boundary points\n"); +- Insert(bamgopts->random); ++ Insert(); + + //Force the boundary + if (verbose>3) _printf_(" Forcing boundaries\n"); +@@ -4721,7 +4658,7 @@ + if (verbose>4) _printf_(" -- current number of vertices = " << nbv << "\n"); + if (verbose>3) _printf_(" Creating initial Constrained Delaunay Triangulation...\n"); + if (verbose>3) _printf_(" Inserting boundary points\n"); +- Insert(bamgopts->random); ++ Insert(); + + //Force the boundary + if (verbose>3) _printf_(" Forcing boundaries\n"); +@@ -4736,48 +4673,14 @@ + if (verbose>4) _printf_(" -- current number of vertices = " << nbv << "\n"); + } + /*}}}*/ ++ int Mesh::RandomNumber(int max){/*{{{*/ ++ /* Generate a random number from 0 to max-1 using linear congruential ++ * random number generator*/ + +- /*Intermediary*/ +- AdjacentTriangle CloseBoundaryEdge(I2 A,Triangle *t, double &a,double &b) {/*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/CloseBoundaryEdge)*/ +- +- int k=(*t)(0) ? (( (*t)(1) ? ( (*t)(2) ? -1 : 2) : 1 )) : 0; +- int dir=0; +- if (k<0){ +- _error_("k<0"); +- } +- int kkk=0; +- long long IJ_IA,IJ_AJ; +- AdjacentTriangle edge(t,OppositeEdge[k]); +- for (;;edge = dir >0 ? Next(Adj(Next(edge))) : Previous(Adj(Previous(edge)))) { +- kkk++; +- if (kkk>=1000){ +- _error_("kkk>=1000"); +- } +- BamgVertex &vI = *edge.EdgeVertex(0); +- BamgVertex &vJ = *edge.EdgeVertex(1); +- I2 I=vI, J=vJ, IJ= J-I; +- IJ_IA = (IJ ,(A-I)); +- if (IJ_IA<0) { +- if (dir>0) {a=1;b=0;return edge;}// change of signe => I +- else {dir=-1; +- continue;}};// go in direction i +- IJ_AJ = (IJ ,(J-A)); +- if (IJ_AJ<0) { +- if(dir<0) {a=0;b=1;return edge;} +- else {dir = 1; +- continue;}}// go in direction j +- double IJ2 = IJ_IA + IJ_AJ; +- if (IJ2==0){ +- _error_("IJ2==0"); +- } +- a= IJ_AJ/IJ2; +- b= IJ_IA/IJ2; +- return edge; +- } +- } +- /*}}}*/ +- int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) { /*{{{*/ ++ this->randomseed = (this->randomseed * 1366l + 150889l) % 714025l; ++ return this->randomseed / (714025l / max + 1); ++ } /*}}}*/ ++ int Mesh::ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) { /*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/ForceEdge)*/ + + int NbSwap =0; +@@ -4819,7 +4722,7 @@ + _error_("!v1 || !v2"); + } + long long detss = 0,l=0; +- while ((SwapForForcingEdge( va, vb, tc, detss, det1,det2,NbSwap))) ++ while ((this->SwapForForcingEdge( va, vb, tc, detss, det1,det2,NbSwap))) + if(l++ > 10000000) { + _error_("Loop in forcing Egde, nb de swap=" << NbSwap << ", nb of try swap (" << l << ") too big"); + } +@@ -4852,51 +4755,7 @@ + return NbSwap; + } + /*}}}*/ +- void swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,long long det1,long long det2){ /*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/swap)*/ +- // -------------------------------------------------------------- +- // short a2=aa[a];// les 2 numero de l arete dans les 2 triangles +- // +- // sb sb +- // / | \ / \ ! +- // as1/ | \ /a2 \ ! +- // / | \ / t2 \ ! +- // s1 /t1 | t2 \s2 --> s1 /___as2___\s2 ! +- // \ a1|a2 / \ as1 / +- // \ | / \ t1 / +- // \ | / as2 \ a1/ +- // \ | / \ / +- // sa sa +- // ------------------------------------------------------------- +- int as1 = NextEdge[a1]; +- int as2 = NextEdge[a2]; +- int ap1 = PreviousEdge[a1]; +- int ap2 = PreviousEdge[a2]; +- (*t1)(VerticesOfTriangularEdge[a1][1]) = s2 ; // avant sb +- (*t2)(VerticesOfTriangularEdge[a2][1]) = s1 ; // avant sa +- // mise a jour des 2 adjacences externes +- AdjacentTriangle taas1 = t1->Adj(as1), +- taas2 = t2->Adj(as2), +- tas1(t1,as1), tas2(t2,as2), +- ta1(t1,a1),ta2(t2,a2); +- // externe haut gauche +- taas1.SetAdj2(ta2, taas1.GetAllFlag_UnSwap()); +- // externe bas droite +- taas2.SetAdj2(ta1, taas2.GetAllFlag_UnSwap()); +- // remove the Mark UnMarkSwap +- t1->SetUnMarkUnSwap(ap1); +- t2->SetUnMarkUnSwap(ap2); +- // interne +- tas1.SetAdj2(tas2); +- +- t1->det = det1; +- t2->det = det2; +- +- t1->SetSingleVertexToTriangleConnectivity(); +- t2->SetSingleVertexToTriangleConnectivity(); +- } // end swap +- /*}}}*/ +- int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb ,AdjacentTriangle & tt1,long long & dets1, long long & detsa,long long & detsb, int & NbSwap) {/*{{{*/ ++ int Mesh::SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb ,AdjacentTriangle & tt1,long long & dets1, long long & detsa,long long & detsb, int & NbSwap) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/SwapForForcingEdge)*/ + // l'arete ta coupe l'arete pva pvb + // de cas apres le swap sa coupe toujours +@@ -4983,4 +4842,89 @@ + return ret; + } + /*}}}*/ ++ ++ /*Intermediary*/ ++ AdjacentTriangle CloseBoundaryEdge(I2 A,Triangle *t, double &a,double &b) {/*{{{*/ ++ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/CloseBoundaryEdge)*/ ++ ++ int k=(*t)(0) ? (( (*t)(1) ? ( (*t)(2) ? -1 : 2) : 1 )) : 0; ++ int dir=0; ++ if (k<0){ ++ _error_("k<0"); ++ } ++ int kkk=0; ++ long long IJ_IA,IJ_AJ; ++ AdjacentTriangle edge(t,OppositeEdge[k]); ++ for (;;edge = dir >0 ? Next(Adj(Next(edge))) : Previous(Adj(Previous(edge)))) { ++ kkk++; ++ if (kkk>=1000){ ++ _error_("kkk>=1000"); ++ } ++ BamgVertex &vI = *edge.EdgeVertex(0); ++ BamgVertex &vJ = *edge.EdgeVertex(1); ++ I2 I=vI, J=vJ, IJ= J-I; ++ IJ_IA = (IJ ,(A-I)); ++ if (IJ_IA<0) { ++ if (dir>0) {a=1;b=0;return edge;}// change of signe => I ++ else {dir=-1; ++ continue;}};// go in direction i ++ IJ_AJ = (IJ ,(J-A)); ++ if (IJ_AJ<0) { ++ if(dir<0) {a=0;b=1;return edge;} ++ else {dir = 1; ++ continue;}}// go in direction j ++ double IJ2 = IJ_IA + IJ_AJ; ++ if (IJ2==0){ ++ _error_("IJ2==0"); ++ } ++ a= IJ_AJ/IJ2; ++ b= IJ_IA/IJ2; ++ return edge; ++ } ++ } ++ /*}}}*/ ++ void swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,long long det1,long long det2){ /*{{{*/ ++ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/swap)*/ ++ // -------------------------------------------------------------- ++ // short a2=aa[a];// les 2 numero de l arete dans les 2 triangles ++ // ++ // sb sb ++ // / | \ / \ ! ++ // as1/ | \ /a2 \ ! ++ // / | \ / t2 \ ! ++ // s1 /t1 | t2 \s2 --> s1 /___as2___\s2 ! ++ // \ a1|a2 / \ as1 / ++ // \ | / \ t1 / ++ // \ | / as2 \ a1/ ++ // \ | / \ / ++ // sa sa ++ // ------------------------------------------------------------- ++ int as1 = NextEdge[a1]; ++ int as2 = NextEdge[a2]; ++ int ap1 = PreviousEdge[a1]; ++ int ap2 = PreviousEdge[a2]; ++ (*t1)(VerticesOfTriangularEdge[a1][1]) = s2 ; // avant sb ++ (*t2)(VerticesOfTriangularEdge[a2][1]) = s1 ; // avant sa ++ // mise a jour des 2 adjacences externes ++ AdjacentTriangle taas1 = t1->Adj(as1), ++ taas2 = t2->Adj(as2), ++ tas1(t1,as1), tas2(t2,as2), ++ ta1(t1,a1),ta2(t2,a2); ++ // externe haut gauche ++ taas1.SetAdj2(ta2, taas1.GetAllFlag_UnSwap()); ++ // externe bas droite ++ taas2.SetAdj2(ta1, taas2.GetAllFlag_UnSwap()); ++ // remove the Mark UnMarkSwap ++ t1->SetUnMarkUnSwap(ap1); ++ t2->SetUnMarkUnSwap(ap2); ++ // interne ++ tas1.SetAdj2(tas2); ++ ++ t1->det = det1; ++ t2->det = det2; ++ ++ t1->SetSingleVertexToTriangleConnectivity(); ++ t2->SetSingleVertexToTriangleConnectivity(); ++ } // end swap ++ /*}}}*/ + } +Index: ../trunk-jpl/src/c/bamg/Geometry.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Geometry.h (revision 21863) ++++ ../trunk-jpl/src/c/bamg/Geometry.h (revision 21864) +@@ -31,7 +31,6 @@ + Curve *curves; + R2 pmin,pmax; // domain extrema coordinates + double coefIcoor; // coef to integer coordinates; +- double MaxCornerAngle; + + //Constructor/Destructors + ~Geometry(); +Index: ../trunk-jpl/src/c/bamg/Triangle.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Triangle.cpp (revision 21863) ++++ ../trunk-jpl/src/c/bamg/Triangle.cpp (revision 21864) +@@ -256,7 +256,6 @@ + OnSwap = (Abs(det1) + Abs(det2)) < detA; + + long long detMinNew=Min(det1,det2); +- // if (detMin<0 && (Abs(det1) + Abs(det2) == detA)) OnSwap=BinaryRand();// just for test + if (! OnSwap &&(detMinNew>0)) { + OnSwap = detMin ==0; + if (! OnSwap) { +Index: ../trunk-jpl/src/c/bamg/BamgOpts.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgOpts.cpp (revision 21863) ++++ ../trunk-jpl/src/c/bamg/BamgOpts.cpp (revision 21864) +@@ -10,7 +10,6 @@ + this->errg = 0; + this->gradation = 0; + this->Hessiantype = 0; +- this->MaxCornerAngle = 0; + this->maxnbv = 0; + this->maxsubdiv = 0; + this->Metrictype = 0; +@@ -18,11 +17,9 @@ + this->nbsmooth = 0; + this->omega = 0; + this->power = 0; +- this->random = 0; + this->verbose = 0; + + this->Crack = 0; +- this->geometricalmetric = 0; + this->KeepVertices = 0; + this->splitcorners = 0; + +@@ -67,7 +64,6 @@ + + if (this->Crack!=0 && this->Crack!=1) _error_("'Crack' supported options are 0 and 1"); + if (this->KeepVertices!=0 && this->KeepVertices!=1) _error_("'KeepVertices' supported options are 0 and 1"); +- if (this->geometricalmetric!=0 && this->geometricalmetric!=1) _error_("'geometricalmetric' supported options are 0 and 1"); + + if (this->hmin<=0) _error_("'hmin' option should be >0"); + if (this->hmax<=0 || this->hmaxhmin) _error_("'hmax' option should be between 0 and hmin=" << this->hmin); +Index: ../trunk-jpl/src/c/bamg/Geometry.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Geometry.cpp (revision 21863) ++++ ../trunk-jpl/src/c/bamg/Geometry.cpp (revision 21864) +@@ -186,12 +186,6 @@ + } + } + +- //MaxCornerAngle +- if (bamgopts->MaxCornerAngle){ +- if(verbose>5) _printf_(" processing MaxCornerAngle\n"); +- MaxCornerAngle=bamgopts->MaxCornerAngle*Pi/180; +- } +- + //TangentAtEdges + if (bamggeom->TangentAtEdges){ + if(verbose>5) _printf_(" processing TangentAtEdges"); +@@ -400,7 +394,6 @@ + _printf_(" pmin (x,y): (" << pmin.x << " " << pmin.y << ")\n"); + _printf_(" pmax (x,y): (" << pmax.x << " " << pmax.y << ")\n"); + _printf_(" coefIcoor: " << coefIcoor << "\n"); +- _printf_(" MaxCornerAngle: " << MaxCornerAngle << "\n"); + + return; + } +@@ -418,7 +411,6 @@ + nbsubdomains=0; + nbcurves=0; + subdomains=NULL; +- MaxCornerAngle = 10*Pi/180; //default is 10 degres + } + /*}}}*/ + double Geometry::MinimalHmin() {/*{{{*/ +@@ -613,19 +605,14 @@ + } + } + +- // angular test on current vertex to guess whether it is a corner (ord = number of edges holding i) +- if(ord==2) { ++ //all vertices provided in geometry are corners (ord = number of edges holding i) ++ vertices[i].SetCorner() ; ++ if(ord==2){ + long n1 = head_v[i]; + long n2 = next_p[n1]; + long i1 = n1/2, i2 = n2/2; // edge number +- long j1 = n1%2, j2 = n2%2; // vertex in the edge +- float angle1= j1 ? OppositeAngle(eangle[i1]) : eangle[i1]; +- float angle2= !j2 ? OppositeAngle(eangle[i2]) : eangle[i2]; +- float da12 = Abs(angle2-angle1); +- if (( da12 >= MaxCornerAngle ) && (da12 <= 2*Pi -MaxCornerAngle)) { +- vertices[i].SetCorner() ; +- } +- // if the edge type/referencenumber a changing then is SetRequired(); ++ long j1 = n1%2, j2 = n2%2; // vertex in the edge ++ /* if the edge type/referencenumber a changing then is SetRequired();*/ + if (edges[i1].type != edges[i2].type || edges[i1].Required()){ + vertices[i].SetRequired(); + } +@@ -633,9 +620,6 @@ + vertices[i].SetRequired(); + } + } +- if(ord != 2) { +- vertices[i].SetCorner(); +- } + + /*close the list around the vertex to have a circular loop*/ + long no=-1, ne = head_v[i]; +Index: ../trunk-jpl/src/c/bamg/Mesh.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.h (revision 21863) ++++ ../trunk-jpl/src/c/bamg/Mesh.h (revision 21864) +@@ -39,6 +39,7 @@ + R2 pmin,pmax; // extrema + double coefIcoor; // coef to integer + ListofIntersectionTriangles lIntTria; ++ int randomseed; //used for random number generation + + long NbVerticesOnGeomVertex; + VertexOnGeom *VerticesOnGeomVertex; +@@ -76,7 +77,7 @@ + I2 R2ToI2(const R2 & P) const; + R2 I2ToR2(const I2 & P) const; + void AddVertex(BamgVertex & s,Triangle * t,long long * =0) ; +- void Insert(bool random); ++ void Insert(); + void Echo(void); + void ForceBoundary(); + void FindSubDomain(int OutSide=0); +@@ -90,7 +91,7 @@ + void MakeBamgQuadtree(); + void MaxSubDivision(double maxsubdiv); + void NewPoints(Mesh &,BamgOpts* bamgopts,int KeepVertices=1); +- long InsertNewPoints(long nbvold,long & NbTSwap,bool random); ++ long InsertNewPoints(long nbvold,long & NbTSwap); + void TrianglesRenumberBySubDomain(bool justcompress=false); + void SmoothingVertex(int =3,double=0.3); + Metric MetricAt (const R2 &) const; +@@ -112,8 +113,8 @@ + void AddMetric(BamgOpts* bamgopts); + void BuildMetric0(BamgOpts* bamgopts); + void BuildMetric1(BamgOpts* bamgopts); +- void AddGeometryMetric(BamgOpts* bamgopts); + void BuildGeometryFromMesh(BamgOpts* bamgopts=NULL); ++ int RandomNumber(int max); + void ReconstructExistingMesh(); + + //Inline methods +@@ -142,6 +143,10 @@ + void TriangulateFromGeom0(BamgOpts* bamgopts);// the real constructor mesh generator + void Triangulate(double* x,double* y,int nods); + void Init(long); ++ int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) ; ++ int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb , ++ AdjacentTriangle & tt1,long long & dets1, ++ long long & detsa,long long & detsb, int & nbswap); + }; + + /*Intermediary*/ +@@ -149,10 +154,7 @@ + void swap(Triangle *t1,short a1, + Triangle *t2,short a2, + BamgVertex *s1,BamgVertex *s2,long long det1,long long det2); +- int SwapForForcingEdge(BamgVertex * & pva ,BamgVertex * & pvb , +- AdjacentTriangle & tt1,long long & dets1, +- long long & detsa,long long & detsb, int & nbswap); +- int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret) ; ++ + inline AdjacentTriangle Previous(const AdjacentTriangle & ta){ + return AdjacentTriangle(ta.t,PreviousEdge[ta.a]); + } +Index: ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 21863) ++++ ../trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 21864) +@@ -148,9 +148,6 @@ + } + } + +- //Add geometry metric if provided +- if(bamgopts->geometricalmetric) BTh.AddGeometryMetric(bamgopts); +- + //Smoothe metric + BTh.SmoothMetric(bamgopts->gradation); + +Index: ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp (revision 21863) ++++ ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp (revision 21864) +@@ -536,7 +536,6 @@ + FetchData(&bamgopts->errg,mxGetField(dataref,0,"errg")); + FetchData(&bamgopts->gradation,mxGetField(dataref,0,"gradation")); + FetchData(&bamgopts->Hessiantype,mxGetField(dataref,0,"Hessiantype")); +- FetchData(&bamgopts->MaxCornerAngle,mxGetField(dataref,0,"MaxCornerAngle")); + FetchData(&bamgopts->maxnbv,mxGetField(dataref,0,"maxnbv")); + FetchData(&bamgopts->maxsubdiv,mxGetField(dataref,0,"maxsubdiv")); + FetchData(&bamgopts->Metrictype,mxGetField(dataref,0,"Metrictype")); +@@ -544,11 +543,9 @@ + FetchData(&bamgopts->nbsmooth,mxGetField(dataref,0,"nbsmooth")); + FetchData(&bamgopts->omega,mxGetField(dataref,0,"omega")); + FetchData(&bamgopts->power,mxGetField(dataref,0,"power")); +- FetchData(&bamgopts->random,mxGetField(dataref,0,"random")); + FetchData(&bamgopts->verbose,mxGetField(dataref,0,"verbose")); + + FetchData(&bamgopts->Crack,mxGetField(dataref,0,"Crack")); +- FetchData(&bamgopts->geometricalmetric,mxGetField(dataref,0,"geometricalmetric")); + FetchData(&bamgopts->KeepVertices,mxGetField(dataref,0,"KeepVertices")); + FetchData(&bamgopts->splitcorners,mxGetField(dataref,0,"splitcorners")); + +Index: ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp (revision 21863) ++++ ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp (revision 21864) +@@ -691,7 +691,6 @@ + FetchData(&bamgopts->errg,PyDict_GetItemString(py_dict,"errg")); + FetchData(&bamgopts->gradation,PyDict_GetItemString(py_dict,"gradation")); + FetchData(&bamgopts->Hessiantype,PyDict_GetItemString(py_dict,"Hessiantype")); +- FetchData(&bamgopts->MaxCornerAngle,PyDict_GetItemString(py_dict,"MaxCornerAngle")); + FetchData(&bamgopts->maxnbv,PyDict_GetItemString(py_dict,"maxnbv")); + FetchData(&bamgopts->maxsubdiv,PyDict_GetItemString(py_dict,"maxsubdiv")); + FetchData(&bamgopts->Metrictype,PyDict_GetItemString(py_dict,"Metrictype")); +@@ -699,11 +698,9 @@ + FetchData(&bamgopts->nbsmooth,PyDict_GetItemString(py_dict,"nbsmooth")); + FetchData(&bamgopts->omega,PyDict_GetItemString(py_dict,"omega")); + FetchData(&bamgopts->power,PyDict_GetItemString(py_dict,"power")); +- FetchData(&bamgopts->random,PyDict_GetItemString(py_dict,"random")); + FetchData(&bamgopts->verbose,PyDict_GetItemString(py_dict,"verbose")); + + FetchData(&bamgopts->Crack,PyDict_GetItemString(py_dict,"Crack")); +- FetchData(&bamgopts->geometricalmetric,PyDict_GetItemString(py_dict,"geometricalmetric")); + FetchData(&bamgopts->KeepVertices,PyDict_GetItemString(py_dict,"KeepVertices")); + FetchData(&bamgopts->splitcorners,PyDict_GetItemString(py_dict,"splitcorners")); + Index: /issm/oecreview/Archive/21724-22754/ISSM-21864-21865.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21864-21865.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21864-21865.diff (revision 22755) @@ -0,0 +1,149 @@ +Index: ../trunk-jpl/src/c/bamg/Mesh.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.h (revision 21864) ++++ ../trunk-jpl/src/c/bamg/Mesh.h (revision 21865) +@@ -94,7 +94,7 @@ + long InsertNewPoints(long nbvold,long & NbTSwap); + void TrianglesRenumberBySubDomain(bool justcompress=false); + void SmoothingVertex(int =3,double=0.3); +- Metric MetricAt (const R2 &) const; ++ Metric MetricAt (const R2 &); + GeomEdge* ProjectOnCurve( Edge & AB, BamgVertex & A, BamgVertex & B,double theta, BamgVertex & R,VertexOnEdge & BR,VertexOnGeom & GR); + long GetId(const Triangle & t) const; + long GetId(const Triangle * t) const; +@@ -103,7 +103,7 @@ + long GetId(const Edge & t) const; + long GetId(const Edge * t) const; + BamgVertex* NearestVertex(int i,int j) ; +- Triangle* TriangleFindFromCoord(const I2 & ,long long [3],Triangle *tstart=0) const; ++ Triangle* TriangleFindFromCoord(const I2 & ,long long [3],Triangle *tstart=0); + void ReadMesh(int* index,double* x,double* y,int nods,int nels); + void ReadMesh(BamgMesh* bamgmesh, BamgOpts* bamgopts); + void WriteMesh(BamgMesh* bamgmesh,BamgOpts* bamgopts); +Index: ../trunk-jpl/src/c/bamg/BamgVertex.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgVertex.cpp (revision 21864) ++++ ../trunk-jpl/src/c/bamg/BamgVertex.cpp (revision 21865) +@@ -121,7 +121,7 @@ + return ret; + } + /*}}}*/ +- double BamgVertex::Smoothing(Mesh &Th,const Mesh &BTh,Triangle* &tstart ,double omega){/*{{{*/ ++ double BamgVertex::Smoothing(Mesh &Th,Mesh &BTh,Triangle* &tstart ,double omega){/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/Smoothing)*/ + + BamgVertex* s=this; +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21864) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21865) +@@ -2949,7 +2949,7 @@ + } + } + /*}}}*/ +- Metric Mesh::MetricAt(const R2 & A) const { /*{{{*/ ++ Metric Mesh::MetricAt(const R2 & A){ /*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MetricAt)*/ + + I2 a = R2ToI2(A); +@@ -3870,7 +3870,7 @@ + return R2( (double) P.x/coefIcoor+pmin.x, (double) P.y/coefIcoor+pmin.y); + } + /*}}}*/ +- Triangle * Mesh::TriangleFindFromCoord(const I2 & B,long long det3[3], Triangle *tstart) const {/*{{{*/ ++ Triangle * Mesh::TriangleFindFromCoord(const I2 & B,long long det3[3], Triangle *tstart){/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/FindTriangleContening)*/ + + Triangle * t=0; +@@ -3945,7 +3945,7 @@ + // 2 => two way go in way 1 or 2 randomly + + if (k==0) break; +- if (k==2 && BinaryRand()) Exchange(ii[0],ii[1]); ++ if (k==2 && this->RandomNumber(1)) Exchange(ii[0],ii[1]); + _assert_(k<3); + AdjacentTriangle t1 = t->Adj(jj=ii[0]); + if ((t1.det() < 0 ) && (k == 2)) +@@ -4794,7 +4794,7 @@ + if ((dets1 <=0 && dets2 <=0) || (dets2 >=0 && detsb >=0)) + ToSwap =1; + else // swap alleatoire +- if (BinaryRand()) ++ if (this->RandomNumber(1)) + ToSwap =2; + } + if (ToSwap) NbSwap++, +Index: ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.h (revision 21864) ++++ ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.h (revision 21865) +@@ -62,7 +62,7 @@ + void Init(); + int NewItem(Triangle *tt,double d0,double d1,double d2); + int NewItem(R2 ,const Metric &); +- void SplitEdge(const Mesh &,const R2 &,const R2 &,int nbegin=0); ++ void SplitEdge(Mesh &,const R2 &,const R2 &,int nbegin=0); + double Length(); + long NewPoints(BamgVertex *,long &nbv,long maxnbv); + void ReShape(); +Index: ../trunk-jpl/src/c/bamg/BamgVertex.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgVertex.h (revision 21864) ++++ ../trunk-jpl/src/c/bamg/BamgVertex.h (revision 21865) +@@ -41,7 +41,7 @@ + + /*methods (No constructor and no destructors...)*/ + BamgVertex(); +- double Smoothing(Mesh & ,const Mesh & ,Triangle * & ,double =1); ++ double Smoothing(Mesh & ,Mesh & ,Triangle * & ,double =1); + void MetricFromHessian(const double Hxx,const double Hyx, const double Hyy, const double smin,const double smax,const double s,const double err,BamgOpts* bamgopts); + void Echo(); + int GetReferenceNumber() const; +Index: ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.cpp (revision 21864) ++++ ../trunk-jpl/src/c/bamg/ListofIntersectionTriangles.cpp (revision 21865) +@@ -187,7 +187,7 @@ + lIntTria = nw; // copy pointer + } + /*}}}*/ +- void ListofIntersectionTriangles::SplitEdge(const Mesh & Bh, const R2 &A,const R2 &B,int nbegin) {/*{{{*/ ++ void ListofIntersectionTriangles::SplitEdge(Mesh & Bh, const R2 &A,const R2 &B,int nbegin) {/*{{{*/ + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/ListofIntersectionTriangles)*/ + + Triangle *tbegin, *t; +Index: ../trunk-jpl/src/c/shared/Bamg/BinaryRand.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Bamg/BinaryRand.h (revision 21864) ++++ ../trunk-jpl/src/c/shared/Bamg/BinaryRand.h (nonexistent) +@@ -1,18 +0,0 @@ +-#ifndef _BINARYRAND_H_ +-#define _BINARYRAND_H_ +- +-#include +- +-/*Return 1 or 0 randomly*/ +-inline int BinaryRand(){ +- #ifdef RAND_MAX +- /*RAND_MAX is defined by stdlib.h and is usually 32767*/ +- const long HalfRandMax = RAND_MAX/2; +- return rand() < HalfRandMax; +- #else +- /*For sun machines, RAND_MAX is not defined, use 2^24*/ +- return rand() & 16384; +- #endif +-} +- +-#endif +Index: ../trunk-jpl/src/c/shared/Bamg/shared.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Bamg/shared.h (revision 21864) ++++ ../trunk-jpl/src/c/shared/Bamg/shared.h (revision 21865) +@@ -7,7 +7,6 @@ + + #include "Abs.h" + #include "BigPrimeNumber.h" +-#include "BinaryRand.h" + #include "Exchange.h" + #include "extrema.h" + #include "HeapSort.h" Index: /issm/oecreview/Archive/21724-22754/ISSM-21865-21866.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21865-21866.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21865-21866.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 21865) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 21866) +@@ -9,6 +9,7 @@ + + #Server URI + SERVER='https://ross.ics.uci.edu:8080' ++SERVER='http://ross.ics.uci.edu:8080' + + #Get configuration + #Source config file{{{ Index: /issm/oecreview/Archive/21724-22754/ISSM-21866-21867.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21866-21867.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21866-21867.diff (revision 22755) @@ -0,0 +1,39 @@ +Index: ../trunk-jpl/src/c/bamg/Mesh.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.h (revision 21866) ++++ ../trunk-jpl/src/c/bamg/Mesh.h (revision 21867) +@@ -167,22 +167,5 @@ + inline void Adj(GeomEdge * & on,int &i){ + int j=i;i=on->AdjVertexIndex[i];on=on->Adj[j]; + } +- inline double qualite(const BamgVertex &va,const BamgVertex &vb,const BamgVertex &vc){ +- double ret; +- I2 ia=va,ib=vb,ic=vc; +- I2 ab=ib-ia,bc=ic-ib,ac=ic-ia; +- long long deta=Det(ab,ac); +- if (deta <=0) ret = -1; +- else { +- double a = sqrt((double) (ac,ac)), +- b = sqrt((double) (bc,bc)), +- c = sqrt((double) (ab,ab)), +- p = a+b+c; +- double h= Max(Max(a,b),c),ro=deta/p; +- ret = ro/h; +- } +- return ret; +- } +- + } + #endif +Index: ../trunk-jpl/src/c/bamg/Triangle.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/Triangle.h (revision 21866) ++++ ../trunk-jpl/src/c/bamg/Triangle.h (revision 21867) +@@ -59,7 +59,6 @@ + void SetUnMarkUnSwap(int a); + + //Inline methods +- double qualite() ; + void Set(const Triangle &,const Mesh &,Mesh &); + int In(BamgVertex *v) const { return vertices[0]==v || vertices[1]==v || vertices[2]==v ;} + BamgVertex* GetVertex(int i){return vertices[i];}; // FIXME: this is used to avoid BamgVertex * operator() Index: /issm/oecreview/Archive/21724-22754/ISSM-21868-21869.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21868-21869.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21868-21869.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 21868) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 21869) +@@ -9,7 +9,7 @@ + + #Server URI + SERVER='https://ross.ics.uci.edu:8080' +-SERVER='http://ross.ics.uci.edu:8080' ++#SERVER='http://ross.ics.uci.edu:8080' + + #Get configuration + #Source config file{{{ Index: /issm/oecreview/Archive/21724-22754/ISSM-21869-21870.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21869-21870.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21869-21870.diff (revision 22755) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/test/Archives/Archive703.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive701.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive119.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive702.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive514.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21870-21871.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21870-21871.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21870-21871.diff (revision 22755) @@ -0,0 +1,93 @@ +Index: ../trunk-jpl/jenkins/linux64_caladan +=================================================================== +--- ../trunk-jpl/jenkins/linux64_caladan (revision 21870) ++++ ../trunk-jpl/jenkins/linux64_caladan (revision 21871) +@@ -63,5 +63,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-PYTHON_NROPTIONS="--exclude 119 514 701 702 435" +-MATLAB_NROPTIONS="'exclude',[119,514,701,702,435]" ++PYTHON_NROPTIONS="--exclude 701 702 435" ++MATLAB_NROPTIONS="'exclude',[701,702,435]" +Index: ../trunk-jpl/jenkins/macosx_pine-island +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island (revision 21870) ++++ ../trunk-jpl/jenkins/macosx_pine-island (revision 21871) +@@ -53,6 +53,6 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-## bamg mesh FS ++## FS + PYTHON_NROPTIONS="" +-MATLAB_NROPTIONS="'exclude',[119,514,701,702,703,435,IdFromString('Dakota')]" ++MATLAB_NROPTIONS="'exclude',[701,702,703,435,IdFromString('Dakota')]" +Index: ../trunk-jpl/jenkins/linux64_ross_test +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_test (revision 21870) ++++ ../trunk-jpl/jenkins/linux64_ross_test (revision 21871) +@@ -63,5 +63,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-PYTHON_NROPTIONS="--exclude 119 243 514 701 702 435" +-MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,435]" ++PYTHON_NROPTIONS="--exclude 243 701 702 435" ++MATLAB_NROPTIONS="'exclude',[243,701,702,435]" +Index: ../trunk-jpl/jenkins/linux64_ross +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross (revision 21870) ++++ ../trunk-jpl/jenkins/linux64_ross (revision 21871) +@@ -66,6 +66,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-PYTHON_NROPTIONS="--exclude 119 243 514 701 702 435" ++PYTHON_NROPTIONS="--exclude 243 701 702 435" + MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" +-#MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,435,IdFromString('Dakota')]" +Index: ../trunk-jpl/jenkins/linux64_ross_python +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_python (revision 21870) ++++ ../trunk-jpl/jenkins/linux64_ross_python (revision 21871) +@@ -57,5 +57,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-PYTHON_NROPTIONS="--exclude 119 243 514 701 702 435" ++PYTHON_NROPTIONS="--exclude 243 701 702 435" + MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" +Index: ../trunk-jpl/jenkins/linux64_ross_static +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_static (revision 21870) ++++ ../trunk-jpl/jenkins/linux64_ross_static (revision 21871) +@@ -57,6 +57,6 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-## bamg mesh FS ++## FS + #PYTHON_NROPTIONS="" +-#MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,435,IdFromString('Dakota')]" ++#MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]" +Index: ../trunk-jpl/jenkins/linux64_ross_dakota +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_dakota (revision 21870) ++++ ../trunk-jpl/jenkins/linux64_ross_dakota (revision 21871) +@@ -62,4 +62,4 @@ + #by Matlab and runme.m + #ex: "'id',[101 102 103]" + PYTHON_NROPTIONS="" +-MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,435]" ++MATLAB_NROPTIONS="'exclude',[243,701,702,435]" +Index: ../trunk-jpl/jenkins/macosx_pine-island_dakota_static +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_dakota_static (revision 21870) ++++ ../trunk-jpl/jenkins/macosx_pine-island_dakota_static (revision 21871) +@@ -63,4 +63,4 @@ + #ex: "'id',[101 102 103]" + ## bamg mesh FS + #PYTHON_NROPTIONS="" +-#MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,435,IdFromString('Dakota')]" ++#MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]" Index: /issm/oecreview/Archive/21724-22754/ISSM-21871-21872.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21871-21872.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21871-21872.diff (revision 22755) @@ -0,0 +1,598 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21872) +@@ -83,7 +83,6 @@ + int GetNumberOfNodes(int enum_type); + int GetNumberOfVertices(void); + void GetSolutionFromInputsOneDof(Vector* solution,int enum_type); +- Element* GetUpperElement(void){_error_("not implemented yet");}; + void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid); + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list); + void GetVerticesCoordinatesTop(IssmDouble** pxyz_list); +Index: ../trunk-jpl/src/c/classes/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21872) +@@ -1126,33 +1126,6 @@ + xDelete(doflist); + } + /*}}}*/ +-Penta* Penta::GetSurfacePenta(void){/*{{{*/ +- +- /*Output*/ +- Penta* penta=NULL; +- +- /*Go through all pentas till the surface is reached*/ +- penta=this; +- for(;;){ +- /*Stop if we have reached the surface, else, take upper penta*/ +- if (penta->IsOnSurface()) break; +- +- /* get upper Penta*/ +- penta=penta->GetUpperPenta(); +- _assert_(penta->Id()!=this->id); +- } +- +- /*return output*/ +- return penta; +-} +-/*}}}*/ +-Element* Penta::GetUpperElement(void){/*{{{*/ +- +- /*Output*/ +- Element* upper_element=this->GetUpperPenta(); +- return upper_element; +-} +-/*}}}*/ + Penta* Penta::GetUpperPenta(void){/*{{{*/ + + Penta* upper_penta=NULL; +@@ -1319,103 +1292,70 @@ + xDelete(control_type); + } + /*}}}*/ +-void Penta::InputDepthAverageAtBase(int enum_type,int average_enum_type){/*{{{*/ ++void Penta::InputDepthAverageAtBase(int original_enum,int average_enum){/*{{{*/ + +- int step,i; ++ IssmDouble Jdet,value; + IssmDouble xyz_list[NUMVERTICES][3]; +- IssmDouble Helem_list[NUMVERTICES]; +- IssmDouble zeros_list[NUMVERTICES]={0.0}; +- IssmDouble p0top1_list[NUMVERTICES]; +- Penta* penta=NULL; +- Input* original_input=NULL; +- Input* element_integrated_input=NULL; +- Input* total_integrated_input=NULL; +- Input* element_thickness_input=NULL; +- Input* total_thickness_input=NULL; +- Input* depth_averaged_input=NULL; ++ IssmDouble xyz_list_line[2][3]; ++ IssmDouble total[NUMVERTICES] = {0.}; ++ IssmDouble intz[NUMVERTICES] = {0.}; ++ Input *original_input = NULL; ++ Input *depth_averaged_input = NULL; + +- /*recover parameters: */ +- + /*Are we on the base? If not, return*/ + if(!IsOnBase()) return; + +- /*OK, we are on bed. Initialize global inputs as 0*/ +- total_thickness_input =new PentaInput(ThicknessEnum,zeros_list,P1Enum); +- + /*Now follow all the upper element from the base to the surface to integrate the input*/ +- penta=this; +- step =0; ++ Penta* penta = this; ++ int step = 0; + for(;;){ + +- /*Step1: Get original input (to be depth avegaged): */ +- original_input=(Input*)penta->inputs->GetInput(enum_type); +- if(!original_input) _error_("could not find input with enum " << EnumToStringx(enum_type)); ++ /*Step1: Get original input (to be depth-avegaged): */ ++ original_input=(Input*)penta->inputs->GetInput(original_enum); ++ if(!original_input) _error_("could not find input with enum " << EnumToStringx(original_enum)); + +- /*If first time, initialize total_integrated_input*/ +- if (step==0){ +- if (original_input->ObjectEnum()==PentaInputEnum) +- total_integrated_input=new PentaInput(average_enum_type,zeros_list,P1Enum); +- else if (original_input->ObjectEnum()==ControlInputEnum) +- total_integrated_input=new PentaInput(average_enum_type,zeros_list,P1Enum); +- else if (original_input->ObjectEnum()==DoubleInputEnum) +- total_integrated_input=new DoubleInput(average_enum_type,0.0); +- else{ +- _error_("object " << EnumToStringx(original_input->ObjectEnum()) << " not supported yet"); +- } +- } +- + /*Step2: Create element thickness input*/ + ::GetVerticesCoordinates(&xyz_list[0][0],penta->vertices,NUMVERTICES); +- for(i=0;i<3;i++){ +- Helem_list[i]=xyz_list[i+3][2]-xyz_list[i][2]; +- Helem_list[i+3]=Helem_list[i]; +- } +- element_thickness_input=new PentaInput(ThicknessEnum,Helem_list,P1Enum); +- +- /*Step3: Vertically integrate A COPY of the original*/ +- if(original_input->ObjectEnum()==PentaInputEnum){ +- if(((PentaInput*)original_input)->interpolation_type==P0Enum){ +- original_input->GetInputValue(&p0top1_list[i]); +- element_integrated_input= new PentaInput(original_input->InstanceEnum(),p0top1_list,P1Enum); +- element_integrated_input->VerticallyIntegrate(element_thickness_input); ++ for(int iv=0;iv<3;iv++){ ++ /*Get segment length*/ ++ for(int i=0;i<3;i++){ ++ xyz_list_line[0][i]=xyz_list[iv][i]; ++ xyz_list_line[1][i]=xyz_list[iv+3][i]; + } +- else{ +- element_integrated_input= (Input*)original_input->copy(); +- element_integrated_input->VerticallyIntegrate(element_thickness_input); ++ /*Integrate over edge*/ ++ Gauss* gauss=penta->NewGaussLine(iv,iv+3,3); ++ for(int ig=gauss->begin();igend();ig++){ ++ gauss->GaussPoint(ig); ++ penta->JacobianDeterminantLine(&Jdet,&xyz_list_line[0][0],gauss); ++ original_input->GetInputValue(&value,gauss); ++ total[iv] += value*Jdet*gauss->weight; ++ intz[iv] += Jdet*gauss->weight; + } ++ delete gauss; + } +- else{ +- element_integrated_input= (Input*)original_input->copy(); +- element_integrated_input->VerticallyIntegrate(element_thickness_input); +- } + +- /*Add contributions to global inputs*/ +- total_integrated_input->AXPY(element_integrated_input,1.0); +- total_thickness_input ->AXPY(element_thickness_input,1.0); +- +- /*Clean up*/ +- delete element_thickness_input; +- delete element_integrated_input; +- + /*Stop if we have reached the surface, else, take upper penta*/ +- if (penta->IsOnSurface()) break; ++ if(penta->IsOnSurface()) break; + + /* get upper Penta*/ +- penta=penta->GetUpperPenta(); +- _assert_(penta->Id()!=this->id); +- +- /*increase couter*/ ++ penta=penta->GetUpperPenta(); _assert_(penta->Id()!=this->id); + step++; + } + +- /*OK, now we only need to divide the depth integrated input by the total thickness!*/ +- depth_averaged_input=total_integrated_input->PointwiseDivide(total_thickness_input); +- depth_averaged_input->ChangeEnum(average_enum_type); ++ /*Now we only need to divide the depth integrated input by the total thickness!*/ ++ for(int iv=0;iv<3;iv++){ ++ total[iv ] = total[iv]/intz[iv]; ++ total[iv+3] = total[iv]; ++ } ++ switch(original_input->ObjectEnum()){ ++ case PentaInputEnum: ++ case ControlInputEnum: ++ depth_averaged_input=new PentaInput(average_enum,&total[0],P1Enum); ++ break; ++ default: ++ _error_("Interpolation " << EnumToStringx(original_input->ObjectEnum()) << " not supported yet"); ++ } + +- /*Clean up*/ +- delete total_thickness_input; +- delete total_integrated_input; +- + /*Finally, add to inputs*/ + this->inputs->AddInput((Input*)depth_averaged_input); + } +Index: ../trunk-jpl/src/c/classes/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21872) +@@ -84,8 +84,6 @@ + int GetNumberOfVertices(void); + Penta* GetLowerPenta(void); + void GetSolutionFromInputsOneDof(Vector* solution,int enum_type); +- Penta* GetSurfacePenta(void); +- Element* GetUpperElement(void); + Penta* GetUpperPenta(void); + void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid); + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list); +Index: ../trunk-jpl/src/c/classes/Elements/Seg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21872) +@@ -72,7 +72,6 @@ + int GetNumberOfNodes(int enum_type){_error_("not implemented yet");}; + int GetNumberOfVertices(void); + void GetSolutionFromInputsOneDof(Vector* solution,int enum_type){_error_("not implemented yet");}; +- Element* GetUpperElement(void){_error_("not implemented yet");}; + void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid){_error_("not implemented yet");}; + void GetVerticesCoordinates(IssmDouble** pxyz_list); + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Elements/Tetra.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21872) +@@ -78,7 +78,6 @@ + int GetNumberOfNodes(int enum_type){_error_("not implemented yet");}; + int GetNumberOfVertices(void); + void GetSolutionFromInputsOneDof(Vector* solution,int enum_type){_error_("not implemented yet");}; +- Element* GetUpperElement(void){_error_("not implemented yet");}; + void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid){_error_("not implemented yet");}; + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list); + void GetVerticesCoordinatesTop(IssmDouble** pxyz_list); +Index: ../trunk-jpl/src/c/classes/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21872) +@@ -215,7 +215,6 @@ + virtual int GetNumberOfNodes(int enum_type)=0; + virtual int GetNumberOfVertices(void)=0; + virtual void GetSolutionFromInputsOneDof(Vector* solution,int solutionenum)=0; +- virtual Element* GetUpperElement(void)=0; + virtual void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid)=0; + virtual void GetVerticesCoordinatesBase(IssmDouble** xyz_list)=0; + virtual void GetVerticesCoordinatesTop(IssmDouble** xyz_list)=0; +Index: ../trunk-jpl/src/c/classes/Inputs/DoubleArrayInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/DoubleArrayInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/DoubleArrayInput.h (revision 21872) +@@ -70,8 +70,6 @@ + IssmDouble MinAbs(void){_error_("not implemented yet");}; + void Scale(IssmDouble scale_factor){_error_("not implemented yet");}; + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters){_error_("not implemented yet");}; +- void VerticallyIntegrate(Input* thickness_input){_error_("not implemented yet");}; + /*}}}*/ + + }; +Index: ../trunk-jpl/src/c/classes/Inputs/DoubleInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/DoubleInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/DoubleInput.h (revision 21872) +@@ -71,8 +71,6 @@ + IssmDouble MinAbs(void); + void Scale(IssmDouble scale_factor); + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters); +- void VerticallyIntegrate(Input* thickness_input); + /*}}}*/ + + }; +Index: ../trunk-jpl/src/c/classes/Inputs/TetraInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TetraInput.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/TetraInput.cpp (revision 21872) +@@ -417,17 +417,3 @@ + for(int i=0;iNumberofNodes(this->interpolation_type); +- IssmDouble squaremin; +- +- /*Now, figure out minimum of valuescopy: */ +- squaremin=pow(this->values[0],2); +- for(int i=1;ivalues[i],2)values[i],2); +- } +- /*Assign output pointers:*/ +- *psquaremin=squaremin; +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Inputs/ControlInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/ControlInput.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/ControlInput.cpp (revision 21872) +@@ -281,6 +281,3 @@ + this->values=xDynamicCast(this->savedvalues->copy()); + this->values->AXPY(gradient,scalar); + }/*}}}*/ +-void ControlInput::VerticallyIntegrate(Input* thickness_input){/*{{{*/ +- values->VerticallyIntegrate(thickness_input); +-}/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Inputs/SegInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/SegInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/SegInput.h (revision 21872) +@@ -73,8 +73,6 @@ + IssmDouble MinAbs(void){_error_("not implemented yet");}; + void Scale(IssmDouble scale_factor){_error_("not implemented yet");}; + void Set(IssmDouble setvalue){_error_("not implemented yet");}; +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters){_error_("not implemented yet");}; +- void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; + + }; + #endif /* _SEGINPUT_H */ +Index: ../trunk-jpl/src/c/classes/Inputs/Input.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/Input.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/Input.h (revision 21872) +@@ -52,8 +52,6 @@ + virtual IssmDouble MinAbs(void)=0; + virtual void Scale(IssmDouble scale_factor)=0; + virtual void Set(IssmDouble setvalue)=0; +- virtual void SquareMin(IssmDouble* psquaremin,Parameters* parameters)=0; +- virtual void VerticallyIntegrate(Input* thickness_input)=0; + + virtual int GetResultArraySize(void)=0; + virtual int GetResultInterpolation(void)=0; +Index: ../trunk-jpl/src/c/classes/Inputs/TetraInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TetraInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/TetraInput.h (revision 21872) +@@ -73,8 +73,6 @@ + IssmDouble MinAbs(void); + void Scale(IssmDouble scale_factor); + void Set(IssmDouble setvalue); +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters); +- void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; + + }; + #endif /* _TETRAINPUT_H */ +Index: ../trunk-jpl/src/c/classes/Inputs/ControlInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/ControlInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/ControlInput.h (revision 21872) +@@ -84,9 +84,7 @@ + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; + void SetGradient(Input* gradient_in); + void SetInput(Input* in_input); +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters){_error_("not implemented yet");}; + void UpdateValue(IssmDouble scalar); +- void VerticallyIntegrate(Input* thickness_input); + /*}}}*/ + + }; +Index: ../trunk-jpl/src/c/classes/Inputs/IntInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/IntInput.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/IntInput.cpp (revision 21872) +@@ -160,9 +160,3 @@ + value=reCast(dvalue); + } + /*}}}*/ +-void IntInput::SquareMin(IssmDouble* psquaremin,Parameters* parameters){/*{{{*/ +- +- /*square min of an integer is the square of the integer itself: */ +- *psquaremin=pow((IssmDouble)value,2); +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h (revision 21872) +@@ -79,9 +79,7 @@ + void ScaleGradient(IssmDouble scale){_error_("not implemented yet");}; + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; + void SetGradient(Input* gradient_in){_error_("not implemented yet");}; +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters){_error_("not implemented yet");}; + void UpdateValue(IssmDouble scalar){_error_("not implemented yet");}; +- void VerticallyIntegrate(Input* thickness_input){_error_("not implemented yet");}; + /*}}}*/ + + }; +Index: ../trunk-jpl/src/c/classes/Inputs/BoolInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/BoolInput.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/BoolInput.cpp (revision 21872) +@@ -156,8 +156,3 @@ + /*a bool cannot be scaled: */ + } + /*}}}*/ +-void BoolInput::SquareMin(IssmDouble* psquaremin,Parameters* parameters){/*{{{*/ +- /*square of a bool is the bool itself: */ +- *psquaremin=value; +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Inputs/IntInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/IntInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/IntInput.h (revision 21872) +@@ -72,8 +72,6 @@ + IssmDouble MinAbs(void){_error_("Min not implemented for integers");}; + void Scale(IssmDouble scale_factor); + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters); +- void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; + /*}}}*/ + + }; +Index: ../trunk-jpl/src/c/classes/Inputs/TriaInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TriaInput.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/TriaInput.cpp (revision 21872) +@@ -450,17 +450,3 @@ + for(int i=0;iNumberofNodes(this->interpolation_type); +- IssmDouble squaremin; +- +- /*Now, figure out minimum of valuescopy: */ +- squaremin=pow(this->values[0],2); +- for(int i=1;ivalues[i],2)values[i],2); +- } +- /*Assign output pointers:*/ +- *psquaremin=squaremin; +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Inputs/BoolInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/BoolInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/BoolInput.h (revision 21872) +@@ -68,8 +68,6 @@ + IssmDouble MinAbs(void){_error_("Min not implemented for booleans");}; + void Scale(IssmDouble scale_factor); + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; +- void SquareMin(IssmDouble* psquaremin, Parameters* parameters); +- void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; + /*}}}*/ + + }; +Index: ../trunk-jpl/src/c/classes/Inputs/TriaInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TriaInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/TriaInput.h (revision 21872) +@@ -73,8 +73,6 @@ + IssmDouble MinAbs(void); + void Scale(IssmDouble scale_factor); + void Set(IssmDouble setvalue); +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters); +- void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; + + }; + #endif /* _TRIAINPUT_H */ +Index: ../trunk-jpl/src/c/classes/Inputs/PentaInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/PentaInput.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/PentaInput.cpp (revision 21872) +@@ -406,49 +406,3 @@ + for(int i=0;iNumberofNodes(this->interpolation_type); +- IssmDouble squaremin; +- +- /*Now, figure out minimum of valuescopy: */ +- squaremin=pow(this->values[0],2); +- for(int i=1;ivalues[i],2)values[i],2); +- } +- /*Assign output pointers:*/ +- *psquaremin=squaremin; +-} +-/*}}}*/ +-void PentaInput::VerticallyIntegrate(Input* thickness_input){/*{{{*/ +- +- IssmDouble thickness; +- IssmDouble value=0.; +- +- /*Check that input provided is a thickness*/ +- if (thickness_input->InstanceEnum()!=ThicknessEnum) _error_("Input provided is not a Thickness (enum_type is " << EnumToStringx(thickness_input->InstanceEnum()) << ")"); +- +- /*vertically integrate depending on type (and use P1 interpolation from now on)*/ +- switch(this->interpolation_type){ +- case P1Enum: +- case P1bubbleEnum: +- case P1xP2Enum: +- case P1xP3Enum: +- case P2Enum: +- { +- this->interpolation_type=P1Enum; +- GaussPenta *gauss=new GaussPenta(); +- for(int iv=0;iv<3;iv++){ +- gauss->GaussVertex(iv); +- thickness_input->GetInputValue(&thickness,gauss); +- this->values[iv]=0.5*(this->values[iv]+this->values[iv+3]) * thickness; +- this->values[iv+3]=this->values[iv]; +- } +- delete gauss; +- return; +- } +- default: +- _error_("not supported yet for type "<interpolation_type)); +- } +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp (revision 21872) +@@ -534,20 +534,3 @@ + return minabs; + } + /*}}}*/ +-void TransientInput::SquareMin(IssmDouble* psquaremin,Parameters* parameters){/*{{{*/ +- +- IssmDouble time; +- +- /*First, recover current time from parameters: */ +- parameters->FindParam(&time,TimeEnum); +- +- /*Retrieve interpolated values for this time step: */ +- Input* input=GetTimeInput(time); +- +- /*Call input function*/ +- input->SquareMin(psquaremin,parameters); +- +- delete input; +- +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Inputs/DoubleInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/DoubleInput.cpp (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/DoubleInput.cpp (revision 21872) +@@ -244,30 +244,3 @@ + value=value*scale_factor; + } + /*}}}*/ +-void DoubleInput::SquareMin(IssmDouble* psquaremin,Parameters* parameters){/*{{{*/ +- +- /*square min of a IssmDouble is the square of the IssmDouble itself: */ +- *psquaremin=pow(value,2); +-} +-/*}}}*/ +-void DoubleInput::VerticallyIntegrate(Input* thickness_input){/*{{{*/ +- +- /*Intermediaries*/ +- IssmDouble thickness_value; +- +- /*Check that input provided is a thickness*/ +- if (thickness_input->InstanceEnum()!=ThicknessEnum) _error_("Input provided is not a Thickness (enum_type is " << EnumToStringx(thickness_input->InstanceEnum()) << ")"); +- +- /*vertically integrate depending on type:*/ +- switch(thickness_input->ObjectEnum()){ +- +- case PentaInputEnum: +- thickness_input->GetInputAverage(&thickness_value); +- this->value=this->value*thickness_value; +- return; +- +- default: +- _error_("not implemented yet"); +- } +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Inputs/PentaInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/PentaInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/PentaInput.h (revision 21872) +@@ -72,8 +72,6 @@ + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; + Input* SpawnTriaInput(int index1,int index2,int index3); + Input* SpawnSegInput(int index1,int index2); +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters); +- void VerticallyIntegrate(Input* thickness_input); + + }; + #endif /* _PENTAINPUT_H */ +Index: ../trunk-jpl/src/c/classes/Inputs/TransientInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TransientInput.h (revision 21871) ++++ ../trunk-jpl/src/c/classes/Inputs/TransientInput.h (revision 21872) +@@ -79,8 +79,6 @@ + IssmDouble MinAbs(void); + void Scale(IssmDouble scale_factor){_error_("not implemented yet");}; + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; +- void SquareMin(IssmDouble* psquaremin,Parameters* parameters); +- void VerticallyIntegrate(Input* thickness_forcing){_error_("not supported yet");}; + /*}}}*/ + + }; Index: /issm/oecreview/Archive/21724-22754/ISSM-21872-21873.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21872-21873.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21872-21873.diff (revision 22755) @@ -0,0 +1,33 @@ +Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21872) ++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21873) +@@ -220,7 +220,7 @@ + InputUpdateFromConstantx(elements,1.,FrictionQEnum); + break; + default: +- _error_("not supported"); ++ _error_("friction law not supported"); + } + + /*Free data: */ +Index: ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 21872) ++++ ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 21873) +@@ -196,8 +196,14 @@ + iomodel->FetchDataToInput(elements,"md.initialization.pressure",PressureEnum); + iomodel->FetchDataToInput(elements,"md.initialization.temperature",TemperatureEnum); + break; ++ case 9: ++ iomodel->FetchDataToInput(elements,"md.friction.coefficient",FrictionCoefficientEnum); ++ iomodel->FetchDataToInput(elements,"md.friction.pressure_adjusted_temperature",FrictionPressureAdjustedTemperatureEnum); ++ InputUpdateFromConstantx(elements,1.,FrictionPEnum); ++ InputUpdateFromConstantx(elements,1.,FrictionQEnum); ++ break; + default: +- _error_("not supported"); ++ _error_("friction law not supported"); + } + }/*}}}*/ + void ThermalAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21873-21874.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21873-21874.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21873-21874.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 21873) ++++ ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 21874) +@@ -229,7 +229,7 @@ + int frictionlaw; + iomodel->FindConstant(&frictionlaw,"md.friction.law"); + if(frictionlaw==4 || frictionlaw==6) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); +- if(frictionlaw==3 || frictionlaw==1) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); ++ if(frictionlaw==3 || frictionlaw==1 || frictionlaw==9) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + + }/*}}}*/ + Index: /issm/oecreview/Archive/21724-22754/ISSM-21874-21875.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21874-21875.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21874-21875.diff (revision 22755) @@ -0,0 +1,23 @@ +Index: ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 21874) ++++ ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 21875) +@@ -228,8 +228,16 @@ + /*Deal with friction parameters*/ + int frictionlaw; + iomodel->FindConstant(&frictionlaw,"md.friction.law"); +- if(frictionlaw==4 || frictionlaw==6) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); +- if(frictionlaw==3 || frictionlaw==1 || frictionlaw==9) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); ++ if(frictionlaw==4 || frictionlaw==6){ ++ parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); ++ } ++ if(frictionlaw==3 || frictionlaw==1){ ++ parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); ++ } ++ if(frictionlaw==9){ ++ parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); ++ parameters->AddObject(new IntParam(FrictionCouplingEnum,0)); ++ } + + }/*}}}*/ + Index: /issm/oecreview/Archive/21724-22754/ISSM-21875-21876.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21875-21876.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21875-21876.diff (revision 22755) @@ -0,0 +1,92 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21875) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21876) +@@ -2679,6 +2679,7 @@ + /*}}}*/ + void Tria::ResetHooks(){/*{{{*/ + ++ if(this->nodes) xDelete(this->nodes); + this->nodes=NULL; + this->vertices=NULL; + this->material=NULL; +Index: ../trunk-jpl/src/c/classes/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21875) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21876) +@@ -171,7 +171,7 @@ + this->inputs->AddInput(new PentaInput(input_enum,values,interpolation_enum)); + } + /*}}}*/ +-void Penta::BasalNodeIndices(int* pnumindices,int** pindices,int finiteelement){/*{{{*/ ++void Penta::BasalNodeIndices(int* pnumindices,int** pindices,int finiteelement){/*{{{*/ + + PentaRef::BasalNodeIndices(pnumindices,pindices,finiteelement); + +@@ -2212,6 +2212,7 @@ + /*}}}*/ + void Penta::ResetHooks(){/*{{{*/ + ++ if(this->nodes) xDelete(this->nodes); + this->nodes=NULL; + this->vertices=NULL; + this->material=NULL; +Index: ../trunk-jpl/src/c/classes/Elements/Tetra.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tetra.cpp (revision 21875) ++++ ../trunk-jpl/src/c/classes/Elements/Tetra.cpp (revision 21876) +@@ -807,6 +807,7 @@ + /*}}}*/ + void Tetra::ResetHooks(){/*{{{*/ + ++ if(this->nodes) xDelete(this->nodes); + this->nodes=NULL; + this->vertices=NULL; + this->material=NULL; +Index: ../trunk-jpl/src/c/classes/Dakota/IssmParallelDirectApplicInterface.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Dakota/IssmParallelDirectApplicInterface.cpp (revision 21875) ++++ ../trunk-jpl/src/c/classes/Dakota/IssmParallelDirectApplicInterface.cpp (revision 21876) +@@ -48,7 +48,8 @@ + + FemModel* femmodel; + +- char **responses_descriptors = NULL; //these are our! there are only numresponsedescriptors of them, not d_numresponses!!! ++ char **responses_descriptors = NULL; //these are ours! there are only numresponsedescriptors of them, not d_numresponses!!! ++ char *response_descriptor = NULL; + int numresponsedescriptors; + int solution_type; + bool control_analysis = false; +@@ -127,6 +128,11 @@ + xDelete(variable_descriptor); + } + xDelete(variable_descriptors); ++ for(i=0;i(response_descriptor); ++ } ++ if(responses_descriptors) xDelete(responses_descriptors); + xDelete(responses); + delete femmodel; + +Index: ../trunk-jpl/src/c/main/issm_dakota.cpp +=================================================================== +--- ../trunk-jpl/src/c/main/issm_dakota.cpp (revision 21875) ++++ ../trunk-jpl/src/c/main/issm_dakota.cpp (revision 21876) +@@ -83,6 +83,10 @@ + /* Execute the environment:*/ + env.execute(); + ++ xDelete(dakota_input_file); ++ xDelete(dakota_output_file); ++ xDelete(dakota_error_file); ++ + /*Return unix success: */ + return 0; + #else +@@ -89,4 +93,5 @@ + Cout << "ISSM Dakota executable was compiled without support of Dakota! Will just return now!" << "\n"; + return 1; + #endif ++ + } Index: /issm/oecreview/Archive/21724-22754/ISSM-21876-21877.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21876-21877.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21876-21877.diff (revision 22755) @@ -0,0 +1,150 @@ +Index: ../trunk-jpl/test/NightlyRun/test119.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test119.m (revision 21876) ++++ ../trunk-jpl/test/NightlyRun/test119.m (revision 21877) +@@ -1,18 +1,18 @@ + %Test Name: SquareBamgMesh + + %Simple mesh +-md=bamg(model(),'domain','../Exp/Square.exp','hmax',100000.,'rand',false); ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',100000.); + x1=md.mesh.x; + y1=md.mesh.y; + + %hVertices +-md=bamg(model(),'domain','../Exp/Square.exp','hmax',300000.,'hVertices',[10000. 100000. 400000. 100000.]','rand',false); ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',300000.,'hVertices',[10000. 100000. 400000. 100000.]'); + x2=md.mesh.x; + y2=md.mesh.y; + + %big mesh + t0=clock; +-md=bamg(model(),'domain','../Exp/Square.exp','hmax',3000.,'rand',false); ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',3000.); + nbelements=md.mesh.numberofelements; + if nbelements>267895-50 & nbelements<267895+50 + nbewithinrange = 1.; +Index: ../trunk-jpl/test/NightlyRun/test119.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test119.py (revision 21876) ++++ ../trunk-jpl/test/NightlyRun/test119.py (revision 21877) +@@ -7,18 +7,18 @@ + + + #Simple mesh +-md=bamg(model(),'domain','../Exp/Square.exp','hmax',100000.,'rand',False) ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',100000.) + x1=md.mesh.x + y1=md.mesh.y + + #hVertices +-md=bamg(model(),'domain','../Exp/Square.exp','hmax',300000.,'hVertices',np.array([10000.,100000.,400000.,100000.]).reshape(-1,1),'rand',False) ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',300000.,'hVertices',np.array([10000.,100000.,400000.,100000.]).reshape(-1,1)) + x2=md.mesh.x + y2=md.mesh.y + + #big mesh + t0=time.time() +-md=bamg(model(),'domain','../Exp/Square.exp','hmax',3000.,'rand',False) ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',3000.) + nbelements=md.mesh.numberofelements + elapsedtime=time.time()-t0 + if nbelements>267895-50 and nbelements<267895+50: +Index: ../trunk-jpl/test/NightlyRun/test514.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test514.m (revision 21876) ++++ ../trunk-jpl/test/NightlyRun/test514.m (revision 21877) +@@ -2,7 +2,7 @@ + %Simple mesh 1 + hVertices=10000.*ones(27,1); + hVertices(1:5)=1000.; +-md=bamg(model(),'domain','../Exp/Pig.exp','hmax',20000.,'hVertices',hVertices,'gradation',3.,'geometricalmetric',1); ++md=bamg(model(),'domain','../Exp/Pig.exp','hmax',20000.,'hVertices',hVertices,'gradation',3.); + x1=md.mesh.x; + y1=md.mesh.y; + +@@ -17,12 +17,12 @@ + hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vy_obs,'node'); + metric=ComputeMetric(hessian,2./9.,1.,1000.,25.*10.^3,[]); + md.miscellaneous.dummy=metric; +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1); ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.); + x3=md2.mesh.x; + y3=md2.mesh.y; + + %refine existing mesh 2 +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.); ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'anisomax',1.); + x4=md2.mesh.x; + y4=md2.mesh.y; + +@@ -29,17 +29,17 @@ + %refine existing mesh 3 + hVertices=NaN*ones(md.mesh.numberofvertices,1); + hVertices(find(md.mesh.vertexonboundary))=500; +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.,'hVertices',hVertices); ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'anisomax',1.,'hVertices',hVertices); + x5=md2.mesh.x; + y5=md2.mesh.y; + + %refine existing mesh 4 +-md2=bamg(md,'field',md.inversion.vy_obs,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',0,'err',1.); ++md2=bamg(md,'field',md.inversion.vy_obs,'hmin',1000.,'hmax',20000.,'gradation',3.,'Hessiantype',0,'err',1.); + x6=md2.mesh.x; + y6=md2.mesh.y; + + %refine existing mesh 5 +-md2=bamg(md,'field',[md.inversion.vy_obs md.geometry.thickness],'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',1,'err',[10. 100.]); ++md2=bamg(md,'field',[md.inversion.vy_obs md.geometry.thickness],'hmin',1000.,'hmax',20000.,'gradation',3.,'Hessiantype',1,'err',[10. 100.]); + x7=md2.mesh.x; + y7=md2.mesh.y; + +Index: ../trunk-jpl/test/NightlyRun/test514.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test514.py (revision 21876) ++++ ../trunk-jpl/test/NightlyRun/test514.py (revision 21877) +@@ -13,7 +13,7 @@ + #Simple mesh 1 + hVertices=10000.*np.ones((27)) + hVertices[0:5]=1000. +-md=bamg(model(),'domain','../Exp/Pig.exp','hmax',20000.,'hVertices',hVertices,'gradation',3.,'geometricalmetric',1) ++md=bamg(model(),'domain','../Exp/Pig.exp','hmax',20000.,'hVertices',hVertices,'gradation',3.) + x1=md.mesh.x + y1=md.mesh.y + +@@ -28,12 +28,12 @@ + hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vy_obs,'node') + metric=ComputeMetric(hessian,2./9.,1.,1000.,25.*10.**3,[]) + md.miscellaneous.dummy=metric +-md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1) ++md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.) + x3=md2.mesh.x + y3=md2.mesh.y + + #refine existing mesh 2 +-md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.) ++md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'anisomax',1.) + x4=md2.mesh.x + y4=md2.mesh.y + +@@ -40,17 +40,17 @@ + #refine existing mesh 3 + hVertices=np.nan*np.ones((md.mesh.numberofvertices)) + hVertices[np.nonzero(md.mesh.vertexonboundary)]=500. +-md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.,'hVertices',hVertices) ++md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'anisomax',1.,'hVertices',hVertices) + x5=md2.mesh.x + y5=md2.mesh.y + + #refine existing mesh 4 +-md2=bamg(copy.deepcopy(md),'field',md.inversion.vy_obs,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',0,'err',np.array([[1.]])) ++md2=bamg(copy.deepcopy(md),'field',md.inversion.vy_obs,'hmin',1000.,'hmax',20000.,'gradation',3.,'Hessiantype',0,'err',np.array([[1.]])) + x6=md2.mesh.x + y6=md2.mesh.y + + #refine existing mesh 5 +-md2=bamg(copy.deepcopy(md),'field',np.hstack((md.inversion.vy_obs,md.geometry.thickness)),'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',1,'err',np.array([[10.,100.]])) ++md2=bamg(copy.deepcopy(md),'field',np.hstack((md.inversion.vy_obs,md.geometry.thickness)),'hmin',1000.,'hmax',20000.,'gradation',3.,'Hessiantype',1,'err',np.array([[10.,100.]])) + x7=md2.mesh.x + y7=md2.mesh.y + Index: /issm/oecreview/Archive/21724-22754/ISSM-21877-21878.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21877-21878.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21877-21878.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/classes/Dakota/IssmParallelDirectApplicInterface.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Dakota/IssmParallelDirectApplicInterface.cpp (revision 21877) ++++ ../trunk-jpl/src/c/classes/Dakota/IssmParallelDirectApplicInterface.cpp (revision 21878) +@@ -128,7 +128,7 @@ + xDelete(variable_descriptor); + } + xDelete(variable_descriptors); +- for(i=0;i(response_descriptor); + } Index: /issm/oecreview/Archive/21724-22754/ISSM-21878-21879.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21878-21879.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21878-21879.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21878) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21879) +@@ -52,7 +52,7 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,4e-09,5e-08,1e-09,1e-10,1e-13,... +- 1e-10,2e-08,7e-09,2e-7,9e-04,7e-04,2e-09,1e-10,1e-13}; ++ 1e-10,2e-08,7e-09,2e-7,1e-03,8e-04,2e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21879-21880.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21879-21880.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21879-21880.diff (revision 22755) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/test/NightlyRun/test343.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test343.m (revision 21879) ++++ ../trunk-jpl/test/NightlyRun/test343.m (revision 21880) +@@ -20,8 +20,14 @@ + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +-field_names ={'Vx1','Vy1','Vel1','Bed1','Surface1','Thickness1','SMB1','TotalSmb1','Vx2','Vy2','Vel2','Bed2','Surface2','Thickness2','SMB2','TotalSmb2','Vx3','Vy3','Vel3','Bed3','Surface3','Thickness3','SMB3','TotalSmb3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1.5e-13,1e-13}; ++field_names ={... ++ 'Vx1','Vy1','Vel1','Bed1','Surface1','Thickness1','SMB1','TotalSmb1',... ++ 'Vx2','Vy2','Vel2','Bed2','Surface2','Thickness2','SMB2','TotalSmb2',... ++ 'Vx3','Vy3','Vel3','Bed3','Surface3','Thickness3','SMB3','TotalSmb3'}; ++field_tolerances={... ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,... ++ 1e-12,1e-12,1e-12,1e-13,1e-13,1e-13,1.5e-13,1e-13}; + field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21880-21881.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21880-21881.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21880-21881.diff (revision 22755) @@ -0,0 +1,58 @@ +Index: ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp (revision 21880) ++++ ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp (revision 21881) +@@ -995,30 +995,34 @@ + /*FUNCTION mxGetAssignedField{{{*/ + mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number,const char* field){ + +- //output +- mxArray* mxfield=NULL; ++ /*Output*/ ++ mxArray *mxfield = NULL; + +- //input +- mxArray *inputs[2]; +- mxArray *pindex = NULL; +- const char *fnames[2]; +- mwSize ndim = 2; +- mwSize onebyone[2] = {1,1}; ++ if(mxIsStruct(pmxa_array)){ ++ mxfield = mxGetField(pmxa_array,number,field); ++ } ++ else{ ++ /*This is an object, mxGetField returns NULL in old version of matlab (we do not have access to them)*/ + +- //We want to call the subsasgn method, and get the returned array.This ensures that if we are running +- //large sized problems, the data is truly loaded from disk by the model subsasgn class method. +- inputs[0]=(mxArray*)pmxa_array; //this is the model ++ /*Intermediaries*/ ++ mxArray *inputs[2]; ++ mwSize ndim = 2; ++ mwSize onebyone[2] = {1,1}; + +- //create index structure used in the assignment (index.type='.' and index.subs='x' for field x for ex) +- fnames[0] = "type"; +- fnames[1] = "subs"; +- pindex=mxCreateStructArray( ndim,onebyone,2,fnames); +- mxSetField( pindex, 0, "type",mxCreateString(".")); +- mxSetField( pindex, 0, "subs",mxCreateString(field)); +- inputs[1]=pindex; ++ /*create index structure used in the assignment (index.type='.' and index.subs='x' for field x*/ ++ const char *fnames[2]; ++ fnames[0] = "type"; fnames[1] = "subs"; ++ mxArray* pindex=mxCreateStructArray( ndim,onebyone,2,fnames); ++ mxSetField( pindex, 0, "type",mxCreateString(".")); ++ mxSetField( pindex, 0, "subs",mxCreateString(field)); ++ inputs[0]=(mxArray*)pmxa_array; //this is the model ++ inputs[1]=pindex; + +- mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref"); ++ mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref"); ++ } + ++ if(mxfield == NULL) _error_("Could not find field "<< field <<" in structure"); ++ + return mxfield; + }/*}}}*/ + Index: /issm/oecreview/Archive/21724-22754/ISSM-21881-21882.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21881-21882.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21881-21882.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21881) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21882) +@@ -486,6 +486,7 @@ + + /*Retrieve all inputs and parameters*/ + element->GetVerticesCoordinates(&xyz_list); ++ element->FindParam(&migration_style,GroundinglineMigrationEnum); + element->FindParam(&dt,TimesteppingTimeStepEnum); + Input* gmb_input = element->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(gmb_input); + Input* fmb_input = element->GetInput(BasalforcingsFloatingiceMeltingRateEnum); _assert_(fmb_input); Index: /issm/oecreview/Archive/21724-22754/ISSM-21882-21883.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21882-21883.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21882-21883.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/analyses/AdjointHorizAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/AdjointHorizAnalysis.cpp (revision 21882) ++++ ../trunk-jpl/src/c/analyses/AdjointHorizAnalysis.cpp (revision 21883) +@@ -2171,6 +2171,8 @@ + else{ + alpha=(pow(q_exp-1,q_exp-1))/pow(q_exp,q_exp); + } ++ ++ vmag = sqrt(vx*vx + vy*vy); + Chi = vmag/(pow(C_param,n)*pow(Neff,n)*As); + Gamma = (Chi/(1.+alpha*pow(Chi,q_exp))); + Index: /issm/oecreview/Archive/21724-22754/ISSM-21883-21884.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21883-21884.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21883-21884.diff (revision 22755) @@ -0,0 +1,11 @@ +Index: ../trunk-jpl/jenkins/windows +=================================================================== +--- ../trunk-jpl/jenkins/windows (revision 21883) ++++ ../trunk-jpl/jenkins/windows (revision 21884) +@@ -59,5 +59,5 @@ + #ex: "'id',[101 102 103]" + + #In Windows, we don't yet have MUMPS, can't do full stokes, so exclude all FS runs. Also exclude all runs with Dakota. And exclude higher order runs that have penalties. And 800+ tests because we don't want to have --with-development since we do the binaries with this version +-MATLAB_NROPTIONS="'exclude',[104, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440,444, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460,243]" ++MATLAB_NROPTIONS="'exclude',[104,119, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440,444, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460,243]" + PYTHON_NROPTIONS="" Index: /issm/oecreview/Archive/21724-22754/ISSM-21884-21885.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21884-21885.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21884-21885.diff (revision 22755) @@ -0,0 +1,28 @@ +Index: ../trunk-jpl/test/Archives/Archive442.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive802.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive803.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive430.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive805.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive431.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive441.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21885-21886.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21885-21886.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21885-21886.diff (revision 22755) @@ -0,0 +1,195 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21885) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21886) +@@ -1192,6 +1192,38 @@ + *phi=4.*epsilon_eff*epsilon_eff*viscosity; + } + /*}}}*/ ++void Element::GetSolutionFromInputsOneDof(Vector* solution, int enum_type){/*{{{*/ ++ ++ int *doflist = NULL; ++ IssmDouble value; ++ ++ /*Fetch number of nodes for this finite element*/ ++ int numnodes = this->GetNumberOfNodes(); ++ ++ /*Fetch dof list and allocate solution vector*/ ++ GetDofList(&doflist,NoneApproximationEnum,GsetEnum); ++ IssmDouble* values = xNew(numnodes); ++ ++ /*Get inputs*/ ++ Input* enum_input=inputs->GetInput(enum_type); _assert_(enum_input); ++ ++ /*Ok, we have the values, fill in the array: */ ++ Gauss* gauss=this->NewGauss(); ++ for(int i=0;iGaussNode(this->element_type,i); ++ ++ enum_input->GetInputValue(&value,gauss); ++ values[i]=value; ++ } ++ ++ solution->SetValues(numnodes,doflist,values,INS_VAL); ++ ++ /*Free ressources:*/ ++ xDelete(doflist); ++ xDelete(values); ++ delete gauss; ++} ++/*}}}*/ + /* void Element::GetVectorFromInputs(Vector* vector,int input_enum){/\*{{{*\/ */ + + /* /\*Fetch number vertices for this element and allocate arrays*\/ */ +Index: ../trunk-jpl/src/c/classes/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21885) ++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21886) +@@ -100,6 +100,7 @@ + void GetNodesLidList(int* lidlist); + void GetNodesSidList(int* sidlist); + void GetPhi(IssmDouble* phi, IssmDouble* epsilon, IssmDouble viscosity); ++ void GetSolutionFromInputsOneDof(Vector* solution,int solutionenum); + void GetVectorFromInputs(Vector* vector, int name_enum, int type); + void GetVertexPidList(int* pidlist); + void GetVerticesConnectivityList(int* connectivitylist); +@@ -214,7 +215,6 @@ + virtual int GetNumberOfNodes(void)=0; + virtual int GetNumberOfNodes(int enum_type)=0; + virtual int GetNumberOfVertices(void)=0; +- virtual void GetSolutionFromInputsOneDof(Vector* solution,int solutionenum)=0; + virtual void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid)=0; + virtual void GetVerticesCoordinatesBase(IssmDouble** xyz_list)=0; + virtual void GetVerticesCoordinatesTop(IssmDouble** xyz_list)=0; +Index: ../trunk-jpl/src/c/classes/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21885) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21886) +@@ -1438,38 +1438,6 @@ + return NUMVERTICES; + } + /*}}}*/ +-void Tria::GetSolutionFromInputsOneDof(Vector* solution, int enum_type){/*{{{*/ +- +- int *doflist = NULL; +- IssmDouble value; +- +- /*Fetch number of nodes for this finite element*/ +- int numnodes = this->NumberofNodes(this->element_type); +- +- /*Fetch dof list and allocate solution vector*/ +- GetDofList(&doflist,NoneApproximationEnum,GsetEnum); +- IssmDouble* values = xNew(numnodes); +- +- /*Get inputs*/ +- Input* enum_input=inputs->GetInput(enum_type); _assert_(enum_input); +- +- /*Ok, we have the values, fill in the array: */ +- GaussTria* gauss=new GaussTria(); +- for(int i=0;iGaussNode(this->element_type,i); +- +- enum_input->GetInputValue(&value,gauss); +- values[i]=value; +- } +- +- solution->SetValues(numnodes,doflist,values,INS_VAL); +- +- /*Free ressources:*/ +- xDelete(doflist); +- xDelete(values); +- delete gauss; +-} +-/*}}}*/ + void Tria::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data,bool onsid){/*{{{*/ + + int vertexidlist[NUMVERTICES]; +Index: ../trunk-jpl/src/c/classes/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21885) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21886) +@@ -82,7 +82,6 @@ + int GetNumberOfNodes(void); + int GetNumberOfNodes(int enum_type); + int GetNumberOfVertices(void); +- void GetSolutionFromInputsOneDof(Vector* solution,int enum_type); + void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid); + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list); + void GetVerticesCoordinatesTop(IssmDouble** pxyz_list); +Index: ../trunk-jpl/src/c/classes/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21885) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21886) +@@ -1096,36 +1096,6 @@ + return NUMVERTICES; + } + /*}}}*/ +-void Penta::GetSolutionFromInputsOneDof(Vector* solution, int enum_type){/*{{{*/ +- +- const int numdof=NDOF1*NUMVERTICES; +- +- int i; +- int* doflist=NULL; +- IssmDouble values[numdof]; +- IssmDouble enum_value; +- GaussPenta *gauss=NULL; +- +- /*Get dof list: */ +- GetDofList(&doflist,NoneApproximationEnum,GsetEnum); +- Input* enum_input=inputs->GetInput(enum_type); _assert_(enum_input); +- +- gauss=new GaussPenta(); +- for(i=0;iGaussVertex(i); +- enum_input->GetInputValue(&enum_value,gauss); +- values[i]=enum_value; +- } +- +- /*Add value to global vector*/ +- solution->SetValues(numdof,doflist,values,INS_VAL); +- +- /*Free ressources:*/ +- delete gauss; +- xDelete(doflist); +-} +-/*}}}*/ + Penta* Penta::GetUpperPenta(void){/*{{{*/ + + Penta* upper_penta=NULL; +Index: ../trunk-jpl/src/c/classes/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21885) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21886) +@@ -83,7 +83,6 @@ + int GetNumberOfNodes(int enum_type); + int GetNumberOfVertices(void); + Penta* GetLowerPenta(void); +- void GetSolutionFromInputsOneDof(Vector* solution,int enum_type); + Penta* GetUpperPenta(void); + void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid); + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list); +Index: ../trunk-jpl/src/c/classes/Elements/Seg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21885) ++++ ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21886) +@@ -71,7 +71,6 @@ + int GetNumberOfNodes(void); + int GetNumberOfNodes(int enum_type){_error_("not implemented yet");}; + int GetNumberOfVertices(void); +- void GetSolutionFromInputsOneDof(Vector* solution,int enum_type){_error_("not implemented yet");}; + void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid){_error_("not implemented yet");}; + void GetVerticesCoordinates(IssmDouble** pxyz_list); + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Elements/Tetra.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21885) ++++ ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21886) +@@ -77,7 +77,6 @@ + int GetNumberOfNodes(void); + int GetNumberOfNodes(int enum_type){_error_("not implemented yet");}; + int GetNumberOfVertices(void); +- void GetSolutionFromInputsOneDof(Vector* solution,int enum_type){_error_("not implemented yet");}; + void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data,bool onsid){_error_("not implemented yet");}; + void GetVerticesCoordinatesBase(IssmDouble** pxyz_list); + void GetVerticesCoordinatesTop(IssmDouble** pxyz_list); Index: /issm/oecreview/Archive/21724-22754/ISSM-21886-21887.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21886-21887.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21886-21887.diff (revision 22755) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21886) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21887) +@@ -53,8 +53,8 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={... + 2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,6e-09,5e-08,1e-09,1e-10,1e-13,... +- 4e-10,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-10,1e-13}; ++ 5e-09,5e-09,5e-09,5e-09,6e-09,9e-05,9e-05,5e-09,1e-13,... ++ 4e-10,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-10,4e-10}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21887-21888.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21887-21888.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21887-21888.diff (revision 22755) @@ -0,0 +1,35 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21887) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21888) +@@ -53,8 +53,8 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={... + 2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... +- 5e-09,5e-09,5e-09,5e-09,6e-09,9e-05,9e-05,5e-09,1e-13,... +- 4e-10,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-10,4e-10}; ++ 5e-09,5e-09,5e-09,5e-09,9e-05,9e-05,9e-05,5e-09,1e-13,... ++ 4e-10,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-8,4e-10}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +Index: ../trunk-jpl/test/NightlyRun/test119.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test119.m (revision 21887) ++++ ../trunk-jpl/test/NightlyRun/test119.m (revision 21888) +@@ -1,7 +1,10 @@ + %Test Name: SquareBamgMesh + + %Simple mesh +-md=bamg(model(),'domain','../Exp/Square.exp','hmax',100000.); ++disp(' -======== STARTING==========='); ++md=model(); ++disp('ok'); ++md=bamg(md,'domain','../Exp/Square.exp','hmax',100000.); + x1=md.mesh.x; + y1=md.mesh.y; + +Index: ../trunk-jpl/test/Archives/Archive435.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21888-21889.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21888-21889.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21888-21889.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/modules/AllocateSystemMatricesx/AllocateSystemMatricesx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AllocateSystemMatricesx/AllocateSystemMatricesx.cpp (revision 21888) ++++ ../trunk-jpl/src/c/modules/AllocateSystemMatricesx/AllocateSystemMatricesx.cpp (revision 21889) +@@ -194,7 +194,7 @@ + + /*Reinitialize flags to false*/ + j=0; +- while(true){ ++ while(j=0){ + flags[flagsindices[j]] = false; + flagsindices[j] = -1; Index: /issm/oecreview/Archive/21724-22754/ISSM-21889-21890.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21889-21890.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21889-21890.diff (revision 22755) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21889) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21890) +@@ -519,8 +519,15 @@ + thickness_input->GetInputValue(&thickness,gauss); + + if(migration_style==SubelementMigrationEnum){ +- if (phi<0.00000001) mb=gmb; +- else mb=(1-phi)*fmb+phi*gmb; // phi is the fraction of grounded ice so (1-phi) is floating ++ if (phi>0.999999999) mb=gmb; ++ else{ ++ mb=(1-phi)*fmb+phi*gmb; // phi is the fraction of grounded ice so (1-phi) is floating ++ printf("mg %g \n",mb); ++ printf("phi %g \n",phi); ++ printf("fmb%g \n",fmb); ++ printf("gmb%g \n",gmb); ++ printf("\n"); ++ } + } + else if(migration_style==SubelementMigration2Enum){ + if(gllevelset>0.) mb=gmb; Index: /issm/oecreview/Archive/21724-22754/ISSM-21890-21891.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21890-21891.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21890-21891.diff (revision 22755) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21890) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21891) +@@ -520,14 +520,7 @@ + + if(migration_style==SubelementMigrationEnum){ + if (phi>0.999999999) mb=gmb; +- else{ +- mb=(1-phi)*fmb+phi*gmb; // phi is the fraction of grounded ice so (1-phi) is floating +- printf("mg %g \n",mb); +- printf("phi %g \n",phi); +- printf("fmb%g \n",fmb); +- printf("gmb%g \n",gmb); +- printf("\n"); +- } ++ else mb=(1-phi)*fmb+phi*gmb; // phi is the fraction of grounded ice so (1-phi) is floating + } + else if(migration_style==SubelementMigration2Enum){ + if(gllevelset>0.) mb=gmb; Index: /issm/oecreview/Archive/21724-22754/ISSM-21891-21892.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21891-21892.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21891-21892.diff (revision 22755) @@ -0,0 +1,169 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21891) ++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21892) +@@ -250,6 +250,7 @@ + virtual Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order)=0; + virtual Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order_horiz,int order_vert)=0; + virtual Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,bool mainlyfloating,int order)=0; ++ virtual Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,int order)=0; + virtual Gauss* NewGaussBase(int order)=0; + virtual Gauss* NewGaussLine(int vertex1,int vertex2,int order)=0; + virtual Gauss* NewGaussTop(int order)=0; +Index: ../trunk-jpl/src/c/classes/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21891) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21892) +@@ -2347,6 +2347,11 @@ + return new GaussTria(point1,fraction1,fraction2,mainlyfloating,order); + } + /*}}}*/ ++Gauss* Tria::NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,int order){/*{{{*/ ++ ++ return new GaussTria(point1,fraction1,fraction2,order); ++} ++/*}}}*/ + Gauss* Tria::NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order_horiz,int order_vert){/*{{{*/ + + IssmDouble area_coordinates[2][3]; +Index: ../trunk-jpl/src/c/classes/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21891) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21892) +@@ -180,6 +180,7 @@ + Gauss* NewGauss(int order); + Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order); + Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,bool mainlyfloating,int order); ++ Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,int order); + Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order_horiz,int order_vert); + Gauss* NewGaussBase(int order); + Gauss* NewGaussLine(int vertex1,int vertex2,int order){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Elements/Seg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21891) ++++ ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21892) +@@ -109,6 +109,7 @@ + Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order); + Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order_horiz,int order_vert){_error_("not implemented yet");}; + Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,bool mainlyfloating,int order){_error_("not implemented yet");}; ++ Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,int order){_error_("not implemented yet");}; + Gauss* NewGaussBase(int order){_error_("not implemented yet");}; + Gauss* NewGaussLine(int vertex1,int vertex2,int order){_error_("not implemented yet");}; + Gauss* NewGaussTop(int order){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Elements/Tetra.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21891) ++++ ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21892) +@@ -117,6 +117,7 @@ + Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order){_error_("not implemented yet");}; + Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order_horiz,int order_vert); + Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,bool mainlyfloating,int order){_error_("not implemented yet");}; ++ Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,int order){_error_("not implemented yet");}; + Gauss* NewGaussBase(int order); + Gauss* NewGaussLine(int vertex1,int vertex2,int order){_error_("not implemented yet");}; + Gauss* NewGaussTop(int order); +Index: ../trunk-jpl/src/c/classes/gauss/GaussTria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/gauss/GaussTria.cpp (revision 21891) ++++ ../trunk-jpl/src/c/classes/gauss/GaussTria.cpp (revision 21892) +@@ -286,6 +286,63 @@ + coord3=UNDEF; + } + /*}}}*/ ++GaussTria::GaussTria(int index,IssmDouble r1,IssmDouble r2,int order){/*{{{*/ ++ ++ /* ++ * ^ ++ * ------------------ ++ * 1|\ | ++ * | \ | ++ * | \ | ++ * | \ | ++ * | \ | ++ * | \ | ++ * | +(x,y) \ | ++ * | \| ++ * +---------------+--> ++ * 0 1 ++ * ++ */ ++ int ig; ++ IssmDouble x,y; ++ IssmDouble xy_list[3][2]; ++ ++ /*Double number of gauss points*/ ++ GaussTria *gauss1 = NULL; ++ GaussTria *gauss2 = NULL; ++ gauss1=new GaussTria(index,r1,r2,1,order); //for the mainly floating part ++ gauss2=new GaussTria(index,r1,r2,0,order); //for the mainly grounded part ++ ++ this->numgauss = gauss1->numgauss + gauss2->numgauss; ++ this->coords1=xNew(this->numgauss); ++ this->coords2=xNew(this->numgauss); ++ this->coords3=xNew(this->numgauss); ++ this->weights=xNew(this->numgauss); ++ ++ for(ig=0;ignumgauss;ig++){ // Add the first triangle gauss points ++ this->coords1[ig]=gauss1->coords1[ig]; ++ this->coords2[ig]=gauss1->coords2[ig]; ++ this->coords3[ig]=gauss1->coords3[ig]; ++ this->weights[ig]=gauss1->weights[ig]; ++ } ++ for(ig=0;ignumgauss;ig++){ // Add the second triangle gauss points ++ this->coords1[gauss1->numgauss+ig]=gauss2->coords1[ig]; ++ this->coords2[gauss1->numgauss+ig]=gauss2->coords2[ig]; ++ this->coords3[gauss1->numgauss+ig]=gauss2->coords3[ig]; ++ this->weights[gauss1->numgauss+ig]=gauss2->weights[ig]; ++ } ++ ++ /*Delete gauss points*/ ++ delete gauss1; ++ delete gauss2; ++ ++ /*Initialize static fields as undefined*/ ++ weight=UNDEF; ++ coord1=UNDEF; ++ coord2=UNDEF; ++ coord3=UNDEF; ++} ++/*}}}*/ + GaussTria::~GaussTria(){/*{{{*/ + xDelete(weights); + xDelete(coords3); +Index: ../trunk-jpl/src/c/classes/gauss/GaussTria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/gauss/GaussTria.h (revision 21891) ++++ ../trunk-jpl/src/c/classes/gauss/GaussTria.h (revision 21892) +@@ -30,6 +30,7 @@ + GaussTria(int order); + GaussTria(int index1,int index2,int order); + GaussTria(int index,IssmDouble r1, IssmDouble r2,bool maintlyfloating,int order); ++ GaussTria(int index,IssmDouble r1, IssmDouble r2,int order); + GaussTria(IssmDouble area_coordinates[2][3],int order); + ~GaussTria(); + +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21891) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21892) +@@ -499,7 +499,7 @@ + if(migration_style==SubelementMigration2Enum){ + gllevelset_input=element->GetInput(MaskGroundediceLevelsetEnum); _assert_(gllevelset_input); + element->GetGroundedPart(&point1,&fraction1,&fraction2,&mainlyfloating); +- gauss = element->NewGauss(point1,fraction1,fraction2,mainlyfloating,3); ++ gauss = element->NewGauss(point1,fraction1,fraction2,3); + } + else{ + gauss = element->NewGauss(3); +Index: ../trunk-jpl/src/c/classes/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21891) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21892) +@@ -120,6 +120,7 @@ + Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order){_error_("not implemented yet");}; + Gauss* NewGauss(IssmDouble* xyz_list, IssmDouble* xyz_list_front,int order_horiz,int order_vert); + Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,bool mainlyfloating,int order); ++ Gauss* NewGauss(int point1,IssmDouble fraction1,IssmDouble fraction2,int order){_error_("not implemented yet");}; + Gauss* NewGaussBase(int order); + Gauss* NewGaussLine(int vertex1,int vertex2,int order); + Gauss* NewGaussTop(int order); Index: /issm/oecreview/Archive/21724-22754/ISSM-21892-21893.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21892-21893.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21892-21893.diff (revision 22755) @@ -0,0 +1,16 @@ +Index: ../trunk-jpl/test/Archives/Archive441.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive442.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive435.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive430.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21893-21894.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21893-21894.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21893-21894.diff (revision 22755) @@ -0,0 +1,36 @@ +Index: ../trunk-jpl/src/c/classes/Inputs/PentaInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/PentaInput.cpp (revision 21893) ++++ ../trunk-jpl/src/c/classes/Inputs/PentaInput.cpp (revision 21894) +@@ -245,6 +245,18 @@ + for(int i=0;i<3;i++) this->values[i] =this->values[3+i]; + } + break; ++ case P1xP3Enum: ++ if(start==-1){ ++ for(int i=0+3;i<12;i+=3) this->values[i]=this->values[0]; ++ for(int i=1+3;i<12;i+=3) this->values[i]=this->values[1]; ++ for(int i=2+3;i<12;i+=3) this->values[i]=this->values[2]; ++ } ++ else{ ++ for(int i=0;i<9;i+=3) this->values[i]=this->values[9]; ++ for(int i=1;i<9;i+=3) this->values[i]=this->values[10]; ++ for(int i=2;i<9;i+=3) this->values[i]=this->values[11]; ++ } ++ break; + default: + _error_("not supported yet for type "<interpolation_type)); + } +Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21893) ++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21894) +@@ -312,6 +312,8 @@ + Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + ComputeBasalMeltingrate(element); + } ++ femmodel->parameters->SetParam(BasalforcingsGroundediceMeltingRateEnum,InputToExtrudeEnum); ++ extrudefrombase_core(femmodel); + }/*}}}*/ + void EnthalpyAnalysis::ComputeBasalMeltingrate(Element* element){/*{{{*/ + /*Calculate the basal melt rates of the enthalpy model after Aschwanden 2012*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21894-21895.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21894-21895.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21894-21895.diff (revision 22755) @@ -0,0 +1,40 @@ +Index: ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21894) ++++ ../trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp (revision 21895) +@@ -312,6 +312,8 @@ + Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + ComputeBasalMeltingrate(element); + } ++ ++ /*extrude inputs*/ + femmodel->parameters->SetParam(BasalforcingsGroundediceMeltingRateEnum,InputToExtrudeEnum); + extrudefrombase_core(femmodel); + }/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21894) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21895) +@@ -1517,7 +1517,21 @@ + this->inputs->AddInput(transientinput); + xDelete(times); + } +- else _error_("nodal vector is either numberofvertices or numberofvertices+1 long. Field provided (" << EnumToStringx(vector_enum) << ") is " << M << " long"); ++ else if(M==iomodel->numberofelements){ ++ ++ /*This is a Patch!*/ ++ xDelete(values); ++ values = xNew(N); ++ for(int j=0;jSid()*N+j]; ++ ++ if (N==this->GetNumberOfNodes(P1Enum) ) this->AddInput(vector_enum,values,P1Enum); ++ else if(N==this->GetNumberOfNodes(P1xP3Enum)) this->AddInput(vector_enum,values,P1xP3Enum); ++ else _error_("Patch interpolation not supported yet"); ++ ++ } ++ else{ ++ _error_("nodal vector is either numberofvertices or numberofvertices+1 long. Field provided (" << EnumToStringx(vector_enum) << ") is " << M << " long"); ++ } + + xDelete(values); + xDelete(vertexids); Index: /issm/oecreview/Archive/21724-22754/ISSM-21895-21896.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21895-21896.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21895-21896.diff (revision 22755) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21895) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21896) +@@ -54,7 +54,7 @@ + field_tolerances={... + 2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 5e-09,5e-09,5e-09,5e-09,9e-05,9e-05,9e-05,5e-09,1e-13,... +- 4e-10,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-8,4e-10}; ++ 4e-09,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-8,4e-10}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21895) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21896) +@@ -52,7 +52,7 @@ + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 3e-11,3e-11,9e-10,7e-11,4e-09,5e-08,1e-09,1e-10,1e-13,... +- 1e-10,2e-08,7e-09,2e-7,1e-03,8e-04,2e-09,1e-10,1e-13}; ++ 9e-10,2e-08,7e-09,2e-7,1e-03,8e-04,2e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21896-21897.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21896-21897.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21896-21897.diff (revision 22755) @@ -0,0 +1,49 @@ +Index: ../trunk-jpl/src/c/classes/Inputs/SegInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/SegInput.h (revision 21896) ++++ ../trunk-jpl/src/c/classes/Inputs/SegInput.h (revision 21897) +@@ -67,7 +67,7 @@ + void GetVectorFromInputs(Vector* vector,int* doflist){_error_("not implemented yet");}; + int GetInputInterpolationType(){_error_("not implemented yet!");}; + IssmDouble InfinityNorm(void){_error_("not implemented yet");}; +- IssmDouble Max(void){_error_("not implemented yet");}; ++ IssmDouble Max(void); + IssmDouble MaxAbs(void){_error_("not implemented yet");}; + IssmDouble Min(void); + IssmDouble MinAbs(void){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Inputs/SegInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/SegInput.cpp (revision 21896) ++++ ../trunk-jpl/src/c/classes/Inputs/SegInput.cpp (revision 21897) +@@ -113,6 +113,17 @@ + + } + /*}}}*/ ++IssmDouble SegInput::Max(void){/*{{{*/ ++ ++ const int numnodes=this->NumberofNodes(this->interpolation_type); ++ IssmDouble max=values[0]; ++ ++ for(int i=1;imax) max=values[i]; ++ } ++ return max; ++} ++/*}}}*/ + IssmDouble SegInput::Min(void){/*{{{*/ + + const int numnodes=this->NumberofNodes(this->interpolation_type); +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 21896) ++++ ../trunk-jpl/src/c/Makefile.am (revision 21897) +@@ -500,9 +500,6 @@ + #}}} + + #Wrapper sources +-#Bamg sources {{{ +- +-#}}} + #Kml sources {{{ + kml_sources = ./modules/Exp2Kmlx/Exp2Kmlx.cpp\ + ./modules/Kml2Expx/Kml2Expx.cpp\ Index: /issm/oecreview/Archive/21724-22754/ISSM-21897-21898.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21897-21898.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21897-21898.diff (revision 22755) @@ -0,0 +1,54 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Seg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Seg.cpp (revision 21897) ++++ ../trunk-jpl/src/c/classes/Elements/Seg.cpp (revision 21898) +@@ -167,6 +167,36 @@ + + *pxyz_front=xyz_front; + }/*}}}*/ ++IssmDouble Seg::GetGroundedPortion(IssmDouble* xyz_list){/*{{{*/ ++ /*Computeportion of the element that is grounded*/ ++ ++ bool mainlyfloating = true; ++ const IssmPDouble epsilon = 1.e-15; ++ IssmDouble phi; ++ IssmDouble gl[NUMVERTICES]; ++ ++ /*Recover parameters and values*/ ++ parameters->FindParam(&domaintype,DomainTypeEnum); ++ GetInputListOnVertices(&gl[0],MaskGroundediceLevelsetEnum); ++ ++ /*Be sure that values are not zero*/ ++ if(gl[0]==0.) gl[0]=gl[0]+epsilon; ++ if(gl[1]==0.) gl[1]=gl[1]+epsilon; ++ ++ if(gl[0]>0 && gl[1]>0) phi=1; // All grounded ++ else if(gl[0]<0 && gl[1]<0) phi=0; // All floating ++ else if(gl[0]<0 && gl[1]>0){ //1 grounded ++ phi=1./(1.-gl[0]/gl[1]); ++ } ++ else if(gl[1]<0 && gl[0]>0){ //0 grounded ++ phi=1./(1.-gl[1]/gl[0]); ++ } ++ ++ if(phi>1 || phi<0) _error_("Error. Problem with portion of grounded element: value should be between 0 and 1"); ++ ++ return phi; ++} ++/*}}}*/ + int Seg::GetNumberOfNodes(void){/*{{{*/ + return this->NumberofNodes(this->element_type); + } +Index: ../trunk-jpl/src/c/classes/Elements/Seg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21897) ++++ ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21898) +@@ -61,7 +61,7 @@ + Element* GetBasalElement(void){_error_("not implemented yet");}; + int GetElementType(void){_error_("not implemented yet");}; + void GetGroundedPart(int* point1,IssmDouble* fraction1, IssmDouble* fraction2,bool* mainlyfloating){_error_("not implemented yet");}; +- IssmDouble GetGroundedPortion(IssmDouble* xyz_list){_error_("not implemented yet");}; ++ IssmDouble GetGroundedPortion(IssmDouble* xyz_list); + void GetIcefrontCoordinates(IssmDouble** pxyz_front,IssmDouble* xyz_list,int levelsetenum); + void GetInputValue(IssmDouble* pvalue,Node* node,int enumtype){_error_("not implemented yet");}; + void GetLevelCoordinates(IssmDouble** pxyz_front,IssmDouble* xyz_list,int levelsetenum,IssmDouble level){_error_("not implemented");}; Index: /issm/oecreview/Archive/21724-22754/ISSM-21898-21899.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21898-21899.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21898-21899.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Seg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Seg.cpp (revision 21898) ++++ ../trunk-jpl/src/c/classes/Elements/Seg.cpp (revision 21899) +@@ -176,7 +176,6 @@ + IssmDouble gl[NUMVERTICES]; + + /*Recover parameters and values*/ +- parameters->FindParam(&domaintype,DomainTypeEnum); + GetInputListOnVertices(&gl[0],MaskGroundediceLevelsetEnum); + + /*Be sure that values are not zero*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21899-21900.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21899-21900.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21899-21900.diff (revision 22755) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21899) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 21900) +@@ -268,7 +268,9 @@ + element->FindParam(&stabilization,MasstransportStabilizationEnum); + Input* vxaverage_input=element->GetInput(VxAverageEnum); _assert_(vxaverage_input); + Input* vyaverage_input=NULL; +- if(dim==2) vyaverage_input=element->GetInput(VyAverageEnum); _assert_(vyaverage_input); ++ if(dim==2){ ++ vyaverage_input=element->GetInput(VyAverageEnum); _assert_(vyaverage_input); ++ } + + h = element->CharacteristicLength(); + Index: /issm/oecreview/Archive/21724-22754/ISSM-21900-21901.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21900-21901.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21900-21901.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21900) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21901) +@@ -51,7 +51,7 @@ + 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; + field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,4e-09,5e-08,1e-09,1e-10,1e-13,... ++ 3e-11,3e-11,9e-10,7e-11,6e-09,7e-08,1e-09,1e-10,1e-13,... + 9e-10,2e-08,7e-09,2e-7,1e-03,8e-04,2e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21901-21902.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21901-21902.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21901-21902.diff (revision 22755) @@ -0,0 +1,4 @@ +Index: ../trunk-jpl/test/Archives/Archive437.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21902-21903.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21902-21903.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21902-21903.diff (revision 22755) @@ -0,0 +1,23 @@ +Index: ../trunk-jpl/test/NightlyRun/test435.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test435.m (revision 21902) ++++ ../trunk-jpl/test/NightlyRun/test435.m (revision 21903) +@@ -47,12 +47,14 @@ + md=solve(md,'Transient'); + + %Fields and tolerances to track changes +-field_names ={'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Vz1','Pressure1','FloatingiceMeltingrate1',... ++field_names ={... ++ 'Bed1','Surface1','Thickness1','Floatingice1','Vx1','Vy1','Vz1','Pressure1','FloatingiceMeltingrate1',... + 'Bed2','Surface2','Thickness2','Floatingice2','Vx2','Vy2','Vz2','Pressure2','FloatingiceMeltingrate2',... + 'Bed3','Surface3','Thickness3','Floatingice3','Vx3','Vy3','Vz3','Pressure3','FloatingiceMeltingrate3',}; +-field_tolerances={2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... +- 3e-11,3e-11,9e-10,7e-11,6e-09,7e-08,1e-09,1e-10,1e-13,... +- 9e-10,2e-08,7e-09,2e-7,1e-03,8e-04,2e-09,1e-10,1e-13}; ++field_tolerances={... ++ 2e-11,5e-12,2e-11,1e-11,5e-10,3e-08,6e-10,1e-13,1e-13,... ++ 3e-11,3e-11,9e-10,7e-11,6e-09,9e-08,1e-09,1e-10,1e-13,... ++ 9e-10,2e-08,7e-09,2e-7 ,1e-03,8e-04,2e-09,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21903-21904.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21903-21904.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21903-21904.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/test/NightlyRun/test442.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test442.m (revision 21903) ++++ ../trunk-jpl/test/NightlyRun/test442.m (revision 21904) +@@ -54,7 +54,7 @@ + field_tolerances={... + 2e-11,5e-12,2e-11,1e-11,5e-10,1e-08,6e-10,1e-13,1e-13,... + 5e-09,5e-09,5e-09,5e-09,9e-05,9e-05,9e-05,5e-09,1e-13,... +- 4e-09,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-8,4e-10}; ++ 8e-09,3e-08,8e-09,5e-09,8e-04,6e-04,2e-09,1e-8,4e-10}; + field_values={... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21904-21905.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21904-21905.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21904-21905.diff (revision 22755) @@ -0,0 +1,71 @@ +Index: ../trunk-jpl/etc/environment.sh +=================================================================== +--- ../trunk-jpl/etc/environment.sh (revision 21904) ++++ ../trunk-jpl/etc/environment.sh (revision 21905) +@@ -96,6 +96,9 @@ + libpathappend "$PETSC_DIR/lib" + fi + ++SCOTCH_DIR="$ISSM_DIR/externalpackages/scotch/install" ++libpathappend "$SCOTCH_DIR/lib" ++ + SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" + libpathappend "$SLEPC_DIR/lib" + +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 21904) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 21905) +@@ -713,7 +713,7 @@ + dnl scotch libraries + if test "x$HAVE_SCOTCH" = "xyes"; then + SCOTCHINCL="-DNOFILEIO -I$SCOTCH_ROOT/include -DSCOTCH_VERSION=\\\"UNKNOWN\\\"" +- SCOTCHLIB="-L$SCOTCH_ROOT/lib -lnfioscotch -lnfioscotcherr -lnfioscotcherrexit -lscotchmetis" ++ SCOTCHLIB="-L$SCOTCH_ROOT/lib -lnfioscotch -lnfioscotcherr -lnfioscotcherrexit " + AC_DEFINE([_HAVE_SCOTCH_],[1],[with Scotch in ISSM src]) + AC_SUBST([SCOTCHINCL]) + AC_SUBST([SCOTCHLIB]) +Index: ../trunk-jpl/externalpackages/scotch/scotch.patch +=================================================================== +--- ../trunk-jpl/externalpackages/scotch/scotch.patch (revision 21904) ++++ ../trunk-jpl/externalpackages/scotch/scotch.patch (revision 21905) +@@ -2226,12 +2226,11 @@ + --- src/src/libscotch/parser_ll.l 2013-05-06 14:14:21.000000000 -0700 + *************** + *** 192,197 **** +---- 192,214 ---- ++--- 192,213 ---- + stratParserInit ( + const char * const string) /*+ Strategy string to parse +*/ + { + + /* reset static variables from previous runs (jes, 4/29/10) */ +-+ yy_current_buffer = 0; + + yy_hold_char = (char) 0; + + yy_n_chars=0; /* number of characters read into yy_ch_buf */ + + yy_c_buf_p = (char *) 0; +Index: ../trunk-jpl/src/m/partition/partitioner.m +=================================================================== +--- ../trunk-jpl/src/m/partition/partitioner.m (revision 21904) ++++ ../trunk-jpl/src/m/partition/partitioner.m (revision 21905) +@@ -40,6 +40,7 @@ + md.mesh.numberofelements=md.mesh.numberofelements2d; + md.qmu.vertex_weight=[]; + md.mesh.vertexconnectivity=[]; ++ recomputeadjacency='on'; + end + + %adjacency matrix if needed: +@@ -79,10 +80,12 @@ + %are we using weights? + if strcmpi(getfieldvalue(options,'weighting'),'on'), + weights=floor(md.qmu.vertex_weight/min(md.qmu.vertex_weight)); ++ else ++ weights=[]; + end + maptab=Scotch(md.qmu.adjacency,[],weights,[],'cmplt',[npart]); + +- part=maptab(:,2);%index partitions from 1 up. like metis. ++ part=maptab(:,2)+1;%index partitions from 1 up. like metis. + + elseif strcmpi(package,'linear'), + Index: /issm/oecreview/Archive/21724-22754/ISSM-21905-21906.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21905-21906.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21905-21906.diff (revision 22755) @@ -0,0 +1,16 @@ +Index: ../trunk-jpl/etc/environment.csh +=================================================================== +--- ../trunk-jpl/etc/environment.csh (revision 21905) ++++ ../trunk-jpl/etc/environment.csh (revision 21906) +@@ -19,6 +19,11 @@ + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib + endif + ++set SCOTCH_DIR="$ISSM_DIR/externalpackages/scotch/install" ++if (-d $SCOTCH_DIR) then ++ setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SCOTCH_DIR/lib ++endif ++ + #SLEPC + set SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" + if (-d $SLEPC_DIR) then Index: /issm/oecreview/Archive/21724-22754/ISSM-21906-21907.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21906-21907.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21906-21907.diff (revision 22755) @@ -0,0 +1,100 @@ +Index: ../trunk-jpl/externalpackages/scotch/install_macosx64.sh +=================================================================== +--- ../trunk-jpl/externalpackages/scotch/install_macosx64.sh (nonexistent) ++++ ../trunk-jpl/externalpackages/scotch/install_macosx64.sh (revision 21907) +@@ -0,0 +1,57 @@ ++#!/bin/bash ++set -eu ++ ++# Some cleanup ++rm -rf scotch_5.1 ++rm -rf src ++rm -rf install ++ ++# Create src and install directories ++mkdir src install ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/scotch_5.1.6.tar.gz' 'scotch_5.1.6.tar.gz' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ptscotch_user5.1.pdf' 'ptscotch_user5.1.pdf' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/scotch_user5.1.pdf' 'scotch_user5.1.pdf' ++ ++# Untar ++tar -xvzf scotch_5.1.6.tar.gz ++ ++# Apply patches (all at once, since many) ++# (written by diff -rc old_src new_src > scotch.patch) ++patch -p0 < scotch.patch ++ ++# Move scotch to src directory ++mv scotch_5.1/* src ++rm -rf scotch_5.1 ++ ++# Build scotch ++cp -p Makefile.inc.mac src/src/Makefile.inc ++cp -p gmap_mex.c src/src/scotch ++cp -p gmapx.c src/src/scotch ++cd src/src ++# For stand-alone scotch modules: ++make scotch ++make clean ++# For no-file-io scotch modules: ++make nfioscotch ++# Clean up ++make clean ++cd ../.. ++ ++# Populate install directory ++cp -pr src/grf install ++cp -pr src/tgt install ++cp -pr src/doc install ++cp -pr src/man install ++mkdir install/include ++cp -p src/src/libscotch/module.h install/include/scotch_module.h ++cp -p src/src/libscotch/common.h install/include/scotch_common.h ++cp -p src/include/scotch.h install/include/ ++cp -p src/src/scotch/gmap.h install/include/scotch_gmap.h ++mkdir install/lib ++mv src/lib/* install/lib ++mkdir install/bin ++mv src/bin/* install/bin ++#cp -p gmap.m install/bin ++#cp -p gpart.m install/bin + +Property changes on: ../trunk-jpl/externalpackages/scotch/install_macosx64.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property +Index: ../trunk-jpl/externalpackages/scotch/Makefile.inc.mac +=================================================================== +--- ../trunk-jpl/externalpackages/scotch/Makefile.inc.mac (nonexistent) ++++ ../trunk-jpl/externalpackages/scotch/Makefile.inc.mac (revision 21907) +@@ -0,0 +1,26 @@ ++EXE = ++LIB = .a ++OBJ = .o ++MEX = .mexa64 ++ ++MAKE = make ++AR = ar ++ARFLAGS = -ruv ++CAT = cat ++CCS = gcc ++CCP = mpicc ++CCD = mpicc ++CCM = ${MATLAB_DIR}/bin/mex ++#CFLAGS = -m64 -O3 -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DMATLAB -fPIC -I${MATLAB_DIR}/extern/include ++CFLAGS = -m64 -O3 -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -fPIC ++#LDFLAGS = -lz -lm -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat ++#LDFLAGS = -lz -lm -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat ++LDFLAGS = -lz -lm ++MFLAGS = -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include -largeArrayDims ++CP = cp ++LEX = flex ++LN = ln ++MKDIR = mkdir ++MV = mv ++RANLIB = ranlib ++YACC = yacc Index: /issm/oecreview/Archive/21724-22754/ISSM-21907-21908.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21907-21908.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21907-21908.diff (revision 22755) @@ -0,0 +1,220 @@ +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21907) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21908) +@@ -794,6 +794,9 @@ + SealevelEmotionEnum, + SealevelAbsoluteEnum, + SealevelEustaticEnum, ++ SealevelInertiaTensorXZEnum, ++ SealevelInertiaTensorYZEnum, ++ SealevelInertiaTensorZZEnum, + SealevelObsEnum, + SealevelWeightsEnum, + SealevelriseDeltathicknessEnum, +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21907) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21908) +@@ -774,6 +774,9 @@ + case SealevelEmotionEnum : return "SealevelEmotion"; + case SealevelAbsoluteEnum : return "SealevelAbsolute"; + case SealevelEustaticEnum : return "SealevelEustatic"; ++ case SealevelInertiaTensorXZEnum : return "SealevelInertiaTensorXZ"; ++ case SealevelInertiaTensorYZEnum : return "SealevelInertiaTensorYZ"; ++ case SealevelInertiaTensorZZEnum : return "SealevelInertiaTensorZZ"; + case SealevelObsEnum : return "SealevelObs"; + case SealevelWeightsEnum : return "SealevelWeights"; + case SealevelriseDeltathicknessEnum : return "SealevelriseDeltathickness"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21907) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21908) +@@ -792,6 +792,9 @@ + else if (strcmp(name,"SealevelEmotion")==0) return SealevelEmotionEnum; + else if (strcmp(name,"SealevelAbsolute")==0) return SealevelAbsoluteEnum; + else if (strcmp(name,"SealevelEustatic")==0) return SealevelEustaticEnum; ++ else if (strcmp(name,"SealevelInertiaTensorXZ")==0) return SealevelInertiaTensorXZEnum; ++ else if (strcmp(name,"SealevelInertiaTensorYZ")==0) return SealevelInertiaTensorYZEnum; ++ else if (strcmp(name,"SealevelInertiaTensorZZ")==0) return SealevelInertiaTensorZZEnum; + else if (strcmp(name,"SealevelObs")==0) return SealevelObsEnum; + else if (strcmp(name,"SealevelWeights")==0) return SealevelWeightsEnum; + else if (strcmp(name,"SealevelriseDeltathickness")==0) return SealevelriseDeltathicknessEnum; +@@ -871,13 +874,13 @@ + else if (strcmp(name,"Matdamageice")==0) return MatdamageiceEnum; + else if (strcmp(name,"Matenhancedice")==0) return MatenhancediceEnum; + else if (strcmp(name,"Matestar")==0) return MatestarEnum; +- else if (strcmp(name,"Matpar")==0) return MatparEnum; +- else if (strcmp(name,"Node")==0) return NodeEnum; +- else if (strcmp(name,"Numericalflux")==0) return NumericalfluxEnum; + else stage=8; + } + if(stage==8){ +- if (strcmp(name,"Neumannflux")==0) return NeumannfluxEnum; ++ if (strcmp(name,"Matpar")==0) return MatparEnum; ++ else if (strcmp(name,"Node")==0) return NodeEnum; ++ else if (strcmp(name,"Numericalflux")==0) return NumericalfluxEnum; ++ else if (strcmp(name,"Neumannflux")==0) return NeumannfluxEnum; + else if (strcmp(name,"Param")==0) return ParamEnum; + else if (strcmp(name,"Moulin")==0) return MoulinEnum; + else if (strcmp(name,"Pengrid")==0) return PengridEnum; +@@ -994,13 +997,13 @@ + else if (strcmp(name,"MaxVz")==0) return MaxVzEnum; + else if (strcmp(name,"MaxAbsVz")==0) return MaxAbsVzEnum; + else if (strcmp(name,"FloatingArea")==0) return FloatingAreaEnum; +- else if (strcmp(name,"GroundedArea")==0) return GroundedAreaEnum; +- else if (strcmp(name,"IceMass")==0) return IceMassEnum; +- else if (strcmp(name,"IceVolume")==0) return IceVolumeEnum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"IceVolumeAboveFloatation")==0) return IceVolumeAboveFloatationEnum; ++ if (strcmp(name,"GroundedArea")==0) return GroundedAreaEnum; ++ else if (strcmp(name,"IceMass")==0) return IceMassEnum; ++ else if (strcmp(name,"IceVolume")==0) return IceVolumeEnum; ++ else if (strcmp(name,"IceVolumeAboveFloatation")==0) return IceVolumeAboveFloatationEnum; + else if (strcmp(name,"TotalFloatingBmb")==0) return TotalFloatingBmbEnum; + else if (strcmp(name,"TotalGroundedBmb")==0) return TotalGroundedBmbEnum; + else if (strcmp(name,"TotalSmb")==0) return TotalSmbEnum; +Index: ../trunk-jpl/src/c/cores/sealevelrise_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/sealevelrise_core.cpp (revision 21907) ++++ ../trunk-jpl/src/c/cores/sealevelrise_core.cpp (revision 21908) +@@ -82,8 +82,6 @@ + + Sg=sealevelrise_core_noneustatic(femmodel,Sg_eustatic); //ocean loading tems (2nd and 5th terms on the RHS of Farrel and Clark) + +- +- + /*compute other geodetic signatures, such as absolute sea level chagne, components of 3-D crustal motion: */ + /*Initialize:*/ + U_radial = new Vector(gsize); +Index: ../trunk-jpl/src/c/cores/sealevelrise_core_noneustatic.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/sealevelrise_core_noneustatic.cpp (revision 21907) ++++ ../trunk-jpl/src/c/cores/sealevelrise_core_noneustatic.cpp (revision 21908) +@@ -36,6 +36,9 @@ + IssmDouble *longitude = NULL; + IssmDouble *radius = NULL; + IssmDouble eustatic; ++ IssmDouble Ixz; ++ IssmDouble Iyz; ++ IssmDouble Izz; + + /*Recover some parameters: */ + femmodel->parameters->FindParam(&max_nonlinear_iterations,SealevelriseMaxiterEnum); +@@ -82,10 +85,16 @@ + if(rotation){ + /*call rotational feedback module: */ + Sgo_rot = new Vector(gsize); Sgo_rot->Assemble(); +- femmodel->SealevelriseRotationalFeedback(Sgo_rot,Sg_old,latitude,longitude,radius); ++ femmodel->SealevelriseRotationalFeedback(Sgo_rot,Sg_old,&Ixz,&Iyz,&Izz,latitude,longitude,radius); + Sgo_rot->Assemble(); + ++ /*save changes in inertia tensor as results: */ ++ femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelInertiaTensorXZEnum,Ixz)); ++ femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelInertiaTensorYZEnum,Iyz)); ++ femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelInertiaTensorZZEnum,Izz)); ++ + Sgo->AXPY(Sgo_rot,1); ++ delete Sgo_rot; + } + + /*we need to average Sgo over the ocean: RHS term 5 in Eq.4 of Farrel and clarke. Only the elements can do that: */ +@@ -92,7 +101,7 @@ + Sgo_oceanaverage=femmodel->SealevelriseOceanAverage(Sgo); + + /*Sg is the sum of the eustatic term, and the ocean terms: */ +- Sg_eustatic->Copy(Sg); Sg->AXPY(Sgo,1); ++ Sg_eustatic->Copy(Sg); Sg->AXPY(Sgo,1); delete Sgo; + Sg->Shift(-Sgo_oceanaverage); + + /*convergence criterion:*/ +@@ -111,7 +120,6 @@ + + /*some minor verbosing adjustment:*/ + if(count>1)verboseconvolution=false; +- + } + if(VerboseConvergence()) _printf0_("\n total number of iterations: " << count-1 << "\n"); + +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 21907) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 21908) +@@ -136,7 +136,7 @@ + #ifdef _HAVE_SEALEVELRISE_ + void SealevelriseEustatic(Vector* pSgi, IssmDouble* peustatic, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius); + void SealevelriseNonEustatic(Vector* pSgo, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius,bool verboseconvolution); +- void SealevelriseRotationalFeedback(Vector* pSgo_rot, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius); ++ void SealevelriseRotationalFeedback(Vector* pSgo_rot, Vector* pSg_old, IssmDouble* pIxz, IssmDouble* pIyz, IssmDouble* pIzz, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius); + void SealevelriseGeodetic(Vector* pUp, Vector* pNorth, Vector* pEast, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius, IssmDouble* xx, IssmDouble* yy, IssmDouble* zz); + IssmDouble SealevelriseOceanAverage(Vector* Sg); + #endif +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21907) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21908) +@@ -3919,7 +3919,7 @@ + xDelete(Sg_old); + } + /*}}}*/ +-void FemModel::SealevelriseRotationalFeedback(Vector* pSgo_rot, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius){/*{{{*/ ++void FemModel::SealevelriseRotationalFeedback(Vector* pSgo_rot, Vector* pSg_old, IssmDouble* pIxz, IssmDouble* pIyz, IssmDouble* pIzz, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius){/*{{{*/ + + /*serialized vectors:*/ + IssmDouble* Sg_old=NULL; +@@ -3995,6 +3995,11 @@ + /*Assemble mesh velocity*/ + pSgo_rot->Assemble(); + ++ /*Assign output pointers:*/ ++ *pIxz=moi_list[0]; ++ *pIyz=moi_list[1]; ++ *pIzz=moi_list[2]; ++ + /*Free ressources:*/ + xDelete(Sg_old); + +Index: ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp (revision 21907) ++++ ../trunk-jpl/src/c/analyses/SealevelriseAnalysis.cpp (revision 21908) +@@ -126,8 +126,13 @@ + G_elastic_local[i-lower_row]= (love_k[nl-1]-love_h[nl-1])/2.0/sin(alpha/2.0); + U_elastic_local[i-lower_row]= (love_h[nl-1])/2.0/sin(alpha/2.0); + H_elastic_local[i-lower_row]= 0; +- IssmDouble Pn,Pn1,Pn2; +- IssmDouble Pn_p,Pn_p1,Pn_p2; ++ IssmDouble Pn = 0.; ++ IssmDouble Pn1 = 0.; ++ IssmDouble Pn2 = 0.; ++ IssmDouble Pn_p = 0.; ++ IssmDouble Pn_p1 = 0.; ++ IssmDouble Pn_p2 = 0.; ++ + for (int n=0;n(X_out); + xDelete(G); + xDelete(X); +- MODULEEND(); + #else + _error_("m1qn3 is not installed"); + #endif ++ MODULEEND(); ++ + } + + Index: /issm/oecreview/Archive/21724-22754/ISSM-21910-21911.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21910-21911.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21910-21911.diff (revision 22755) @@ -0,0 +1,2045 @@ +Index: ../trunk-jpl/src/m/classes/clusters/generic.js +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/generic.js (revision 21910) ++++ ../trunk-jpl/src/m/classes/clusters/generic.js (revision 21911) +@@ -52,6 +52,7 @@ + return; + } //}}} + var request = new XMLHttpRequest(); ++ request.open("POST", this.url, true); + $(callbackid).html(sprintf("%-16s", "CONNECTING...")).prop("disabled", true); + request.position = 0; //Keep track of current parsing position in repsonseText + request.timeout = 180000; +@@ -156,7 +157,6 @@ + + var data = new Blob([nplength,npbuffer,codeversionlength,codeversionbuffer,runtimenamelength,runtimenamebuffer,namelength,namebuffer,toolkitslength,toolkitsbuffer,solutionlength,solutionbuffer,binlength,binbuffer]); + +- request.open("POST", this.url, true); + request.responseType = 'application/octet-stream'; + request.send(data); + +Index: ../trunk-jpl/src/m/plot/plot_mesh.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_mesh.js (revision 21910) ++++ ../trunk-jpl/src/m/plot/plot_mesh.js (revision 21911) +@@ -30,7 +30,7 @@ + scale = [1, 1, options.getfieldvalue('heightscale', 1)]; + } + else { +- vertices = Node.prototype.scaleVertices(md, x, y, z, options.getfieldvalue('heightscale', 1)); ++ vertices = Node.prototype.scaleVertices(md, x, y, z, elements, options.getfieldvalue('heightscale', 1), options.getfieldvalue('maskscale',{})); + scale = [1, 1, 1]; + } + +Index: ../trunk-jpl/src/m/plot/webgl.js +=================================================================== +--- ../trunk-jpl/src/m/plot/webgl.js (revision 21910) ++++ ../trunk-jpl/src/m/plot/webgl.js (revision 21911) +@@ -8,9 +8,11 @@ + if (!isEmptyOrUndefined(canvas.draw) && canvas.draw.handler !== 0) { window.cancelAnimationFrame(canvas.draw.handler); } + if (!isEmptyOrUndefined(canvas.animation) && canvas.animation.handler !== 0) { clearInterval(canvas.animation.handler); } + initWebGL(canvas, options); +- initializeMarker(canvas); + draw(canvas); + canvas.initialized = true; ++ ++ //The onStart event triggers once per plotmodel call load after WebGL and canvas initialization are complete ++ canvas.selector.trigger('onStart', [canvas]); + } + return canvas; + } +@@ -33,9 +35,9 @@ + var mc = new Hammer(canvas); + mc.add(new Hammer.Pan({threshold: 0, pointers: 0})); + mc.add(new Hammer.Pinch({threshold: 0})).recognizeWith(mc.get('pan')); +- mc.on('tap press', function (ev) {onTap(ev, canvas);}); ++ mc.on('tap', function (ev) {onTap(ev, canvas);}); + mc.on('panstart panmove', function (ev) {onPan(ev, canvas, displayview);}); +- mc.on('pinchstart pinchmove', function (ev) {onPinch(ev, canvas, displayview);}); ++ mc.on('pinchstart pinchmove', function (ev) {onPinch(ev, canvas, displayview);}); + canvas.addEventListener('mousewheel', function (ev) {onZoom(ev, canvas, displayzoom)}, false); + canvas.addEventListener('DOMMouseScroll', function (ev) {onZoom(ev, canvas, displayzoom)}, false); + +@@ -45,6 +47,7 @@ + canvas.unitNode = {}; + canvas.unitData = {}; + canvas.unitMovieData = {}; ++ + canvas.gl = gl; + canvas.rootPath = options.getfieldvalue('rootpath', '../../../js/'); + canvas.id = options.getfieldvalue('canvasid', '.sim-canvas'); +@@ -56,80 +59,98 @@ + } + + //Add context state variables ++ canvas.render = options.getfieldvalue('render', {}); + canvas.controlSensitivity = options.getfieldvalue('controlsensitivity', 1); ++ canvas.overlayHandlers = {}; + var backgroundcolor = new RGBColor(options.getfieldvalue('backgroundcolor', 'lightcyan')); + if (backgroundcolor.ok) { canvas.backgroundcolor = [backgroundcolor.r/255.0, backgroundcolor.g/255.0, backgroundcolor.b/255.0, 1.0]; } + else { throw Error(sprintf('s%s%s\n','initWebGL error message: cound not find out background color for curent canvas ', canvas)); } + + //Property intiialization, using values from options first, then from default values. ++ var atmosphere = options.getfieldvalue('atmosphere', {}); ++ canvas.atmosphere = { //Default Values ++ wavelength_r: defaultFor(atmosphere.wavelength_r, 0.65), //0.65 Red wavelength (micrometers) ++ wavelength_g: defaultFor(atmosphere.wavelength_g, 0.57), //0.57 Green wavelength (micrometers) ++ wavelength_b: defaultFor(atmosphere.wavelength_b, 0.475), //0.475 Green wavelength (micrometers) ++ eSun: defaultFor(atmosphere.eSun, 100.0), //20.0 Sun intensity ++ kRayleigh: defaultFor(atmosphere.kRayleigh, 0.0025), //0.0025 Rayleigh scattering amount ++ kMie: defaultFor(atmosphere.kMie, 0.000), //0.01 Mie scattering amount ++ g: defaultFor(atmosphere.g, -0.99), //-0.99 Mie phase asymmetry/direction factor ++ hdr_exposure: defaultFor(atmosphere.hdr_exposure, 0.8), //0.8 High Dynamic Range Exposure ++ scaleHeight: defaultFor(atmosphere.scaleHeight, 1.25), //1.025 Scale of height of atmosphere to earth radius. ++ scaleDepth: defaultFor(atmosphere.scaleDepth, 0.25), //0.25 Percentage altitude at which the atmosphere's average density is found ++ a: defaultFor(atmosphere.a, -0.00287), //-0.00287 Scaling constant a ++ b: defaultFor(atmosphere.b, 0.459), //0.459 Scaling constant b ++ c: defaultFor(atmosphere.c, 3.83), //3.83 Scaling constant c ++ d: defaultFor(atmosphere.d, -6.80), //-6.80 Scaling constant d ++ e: defaultFor(atmosphere.e, 3.6), //5.25 Scaling constant e. Lower when increasing atmosphere scale. ++ attenuation: defaultFor(atmosphere.attenuation, 0.5) //0.5 Strength of atmospheric scattering on ground shading. ++ }; ++ updateAtmosphereParameters(canvas); + var animation = options.getfieldvalue('movies', {}); + canvas.animation = { +- frame: defaultFor(animation.frame, 0), +- play: defaultFor(animation.play, true), +- increment: defaultFor(animation.increment, true), +- fps: defaultFor(animation.fps, 4), +- interval: defaultFor(animation.interval, 1000 / animation.fps), +- loop: defaultFor(animation.loop, true), +- handler: defaultFor(animation.handler, 0) ++ frame: defaultFor(animation.frame, 0), ++ play: defaultFor(animation.play, true), ++ increment: defaultFor(animation.increment, true), ++ fps: defaultFor(animation.fps, 4), ++ interval: defaultFor(animation.interval, 1000 / defaultFor(animation.fps, 4)), ++ loop: defaultFor(animation.loop, true), ++ handler: defaultFor(animation.handler, 0) + } + var brush = options.getfieldvalue('brush', {}); + canvas.brush = { +- enabled: defaultFor(brush.enabled, false), +- strength: defaultFor(brush.strength, 0.075), +- falloff: defaultFor(brush.falloff, 0.5), +- hit: defaultFor(brush.hit, {}) ++ enabled: defaultFor(brush.enabled, false), ++ strength: defaultFor(brush.strength, 0.075), ++ falloff: defaultFor(brush.falloff, 0.5), ++ hit: defaultFor(brush.hit, {}) + }; + var camera = options.getfieldvalue('camera', {}); + canvas.camera = { +- position: defaultFor(camera.position, vec3.create()), +- rotation: defaultFor(camera.rotation, vec3.create()), +- near: defaultFor(camera.near, 1e3), +- far: defaultFor(camera.far, 1e10), +- fov: defaultFor(camera.fov, 45), +- vMatrix: defaultFor(camera.vMatrix, mat4.create()), +- pMatrix: defaultFor(camera.pMatrix, mat4.create()), +- vpMatrix: defaultFor(camera.vpMatrix, mat4.create()), +- vInverseMatrix: defaultFor(camera.vInverseMatrix, mat4.create()), +- pInverseMatrix: defaultFor(camera.pInverseMatrix, mat4.create()), +- vpInverseMatrix: defaultFor(camera.vpInverseMatrix, mat4.create()), +- ready: defaultFor(camera.ready, false) ++ position: defaultFor(camera.position, vec3.create()), ++ rotation: defaultFor(camera.rotation, quat.create()), ++ relativePosition: defaultFor(camera.relativePosition, vec3.create()), ++ direction: defaultFor(camera.direction, vec3.create()), ++ near: defaultFor(camera.near, 1e3), ++ far: defaultFor(camera.far, 1e10), ++ fov: defaultFor(camera.fov, 45), ++ vMatrix: defaultFor(camera.vMatrix, mat4.create()), ++ pMatrix: defaultFor(camera.pMatrix, mat4.create()), ++ vpMatrix: defaultFor(camera.vpMatrix, mat4.create()), ++ vInverseMatrix: defaultFor(camera.vInverseMatrix, mat4.create()), ++ pInverseMatrix: defaultFor(camera.pInverseMatrix, mat4.create()), ++ vpInverseMatrix: defaultFor(camera.vpInverseMatrix, mat4.create()), ++ ready: defaultFor(camera.ready, false) + }; +- var clouds = options.getfieldvalue('clouds', {}); +- canvas.clouds = { +- enabled: defaultFor(clouds.enabled, false), +- height: defaultFor(clouds.height, 7500), +- quantity: defaultFor(clouds.quantity, 10), +- hit: defaultFor(clouds.hit, {}) +- }; + var dataMarkers = options.getfieldvalue('datamarkers', {}); + canvas.dataMarkers = { +- enabled: defaultFor(dataMarkers.enabled, true), +- values: defaultFor(dataMarkers.values, []), +- image: defaultFor(dataMarkers.image, canvas.rootPath+'textures/data_marker.svg'), +- size: defaultFor(dataMarkers.size, [32, 32]), +- format: defaultFor(dataMarkers.format, ['X: %.2e
Y: %.2e
Z: %.2e
Value: %0.1f', 'x', 'y', 'z', 'value']), +- animated: defaultFor(dataMarkers.animated, false), +- labels: defaultFor(dataMarkers.labels, []), +- font: defaultFor(dataMarkers.font, ''), +- marker: defaultFor(dataMarkers.marker, document.getElementById('sim-data-marker-' + canvas.id)), +- reposition: defaultFor(dataMarkers.reposition, true) ++ enabled: defaultFor(dataMarkers.enabled, true), ++ values: defaultFor(dataMarkers.values, []), ++ image: defaultFor(dataMarkers.image, canvas.rootPath + 'textures/data_marker.svg'), ++ size: defaultFor(dataMarkers.size, [32, 32]), ++ format: defaultFor(dataMarkers.format, ['X: %.2e
Y: %.2e
Z: %.2e
Value: %0.1f', 'x', 'y', 'z', 'value']), ++ animated: defaultFor(dataMarkers.animated, false), ++ labels: defaultFor(dataMarkers.labels, []), ++ font: defaultFor(dataMarkers.font, ''), ++ marker: defaultFor(dataMarkers.marker, document.getElementById('sim-data-marker-' + canvas.id)), ++ reposition: defaultFor(dataMarkers.reposition, true) + }; + var draw = options.getfieldvalue('draw', {}); + canvas.draw = { +- ready: defaultFor(draw.ready, false), +- handler: defaultFor(draw.handler, null) ++ ready: defaultFor(draw.ready, false), ++ handler: defaultFor(draw.handler, null) + }; + var view = options.getfieldvalue('view', {}); + canvas.view = { +- position: defaultFor(view.position, [0.0, 0.0, 0.0]), +- rotation: defaultFor(view.rotation, [0, 90]), +- zoom: defaultFor(view.zoom, 1.0), +- zoomLimits: defaultFor(view.zoomLimits, [0.001, 100.0]), +- lastZoom: defaultFor(view.lastZoom, 1.0), +- azimuthLimits: defaultFor(view.azimuthLimits, [0, 360]), +- elevationLimits: defaultFor(view.elevationLimits, [-180, 180]), +- panningEnabled: defaultFor(view.panningEnabled, false), +- twod: defaultFor(view.twod, false) ++ position: defaultFor(view.position, [0.0, 0.0, 0.0]), ++ rotation: defaultFor(view.rotation, [0, 90]), ++ zoom: defaultFor(view.zoom, 1.0), ++ zoomLimits: defaultFor(view.zoomLimits, [0.001, 100.0]), ++ lastZoom: defaultFor(view.lastZoom, 1.0), ++ azimuthLimits: defaultFor(view.azimuthLimits, [0, 360]), ++ elevationLimits: defaultFor(view.elevationLimits, [-180, 180]), ++ panningEnabled: defaultFor(view.panningEnabled, false), ++ preventDefaultOnPan: defaultFor(view.preventDefaultOnPan, false), ++ twod: defaultFor(view.twod, false) + }; + + //Override with parameters from URL, if any +@@ -170,10 +191,11 @@ + function loadShaders(gl, rootPath) { //{{{ + var shaders = {}; + shaders.Colored = new GL.Shader.fromURL(rootPath+'shaders/Colored.vsh', rootPath+'shaders/Colored.fsh', null, gl); ++ shaders.ColoredDiffuse = new GL.Shader.fromURL(rootPath+'shaders/ColoredDiffuse.vsh', rootPath+'shaders/ColoredDiffuse.fsh', null, gl); + shaders.Textured = new GL.Shader.fromURL(rootPath+'shaders/Textured.vsh', rootPath+'shaders/Textured.fsh', null, gl); ++ shaders.TexturedDiffuse = new GL.Shader.fromURL(rootPath+'shaders/TexturedDiffuse.vsh', rootPath+'shaders/TexturedDiffuse.fsh', null, gl); + shaders.SkyFromSpace = new GL.Shader.fromURL(rootPath+'shaders/SkyFromSpace.vert', rootPath+'shaders/SkyFromSpace.frag', null, gl); + shaders.GroundFromSpace = new GL.Shader.fromURL(rootPath+'shaders/GroundFromSpace.vert', rootPath+'shaders/GroundFromSpace.frag', null, gl); +- shaders.Clouds = new GL.Shader.fromURL(rootPath+'shaders/Clouds.vert', rootPath+'shaders/Clouds.frag', null, gl); + return shaders; + } //}}} + function initTexture(gl, imageSource) { //{{{ +@@ -183,6 +205,24 @@ + } + return gl.textures[imageSource]; + } //}}} ++function updateAtmosphereParameters(canvas) { ++ //Precalculate derived atmosphere shader parameters ++ //TODO: Find a better way to structure this ++ var atm = canvas.atmosphere; ++ atm.inv_wavelength4 = [1.0 / Math.pow(atm.wavelength_r, 4), 1.0 / Math.pow(atm.wavelength_g, 4), 1.0 / Math.pow(atm.wavelength_b, 4)]; ++ atm.innerRadius = 6.371e6; ++ atm.innerRadius2 = atm.innerRadius * atm.innerRadius; ++ atm.outerRadius = atm.innerRadius * atm.scaleHeight; ++ atm.outerRadius2 = atm.outerRadius * atm.outerRadius; ++ atm.krESun = atm.kRayleigh * atm.eSun; ++ atm.kmESun = atm.kMie * atm.eSun; ++ atm.kr4PI = atm.kRayleigh * 4 * Math.PI; ++ atm.km4PI = atm.kMie * 4 * Math.PI; ++ atm.scale = 1.0 / (atm.outerRadius - atm.innerRadius); ++ atm.scaleOverScaleDepth = atm.scale / atm.scaleDepth; ++ atm.g2 = atm.g * atm.g; ++ canvas.atmosphere = atm; ++} + function clamp(value, min, max) { //{{{ + return Math.max(min, Math.min(value, max)); + } //}}} +@@ -252,106 +292,93 @@ + } + } //}}} + //}}} +-//{{{ Interface Functions ++//{{{ Interaction Functions + function onTap(ev, canvas) { //{{{ +- //Sets up a marker on a canvas that will track a point on the mesh. Can be dismissed by closing the display or clicking the marker. + ev.preventDefault(); + +- if (canvas.clouds.enabled) { +- for (var i = 0; i < canvas.clouds.quantity; i++) { +- raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.nodes["clouds" + i]); +- } +- } +- var hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.unitNode); +- if ('cities' in canvas.nodes) { +- var hitCities = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.nodes.cities); +- canvas.nodes.cities.hit = hitCities; +- updateCities(canvas); +- } ++ var hit = raycastXY(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.unitNode); + +- canvas.brush.hit = hit; +- +- if (canvas.dataMarkers.enabled) { +- canvas.dataMarkers.marker.selector.closed = false; +- canvas.dataMarkers.marker.hit = hit; +- updateMarker(canvas, true); +- } +- +- brushModify(canvas); ++ //Trigger any handlers attatched to this canvas event. ++ canvas.selector.trigger('onTap', [ev, canvas, hit]); + } //}}} + function onPan(ev, canvas, displaylog) { //{{{ + ev.preventDefault(); + +- if (canvas.dataMarkers.enabled) { +- if (!isEmptyOrUndefined(canvas.unitNode)) { +- canvas.brush.hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.unitNode); +- brushModify(canvas); +- } +- } +- +- if (canvas.clouds.enabled) { +- if (!isEmptyOrUndefined(canvas.nodes['overlay'])) { +- canvas.clouds.hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, canvas.nodes['overlay']); +- updateClouds(canvas); +- } +- } +- + if (ev.type === 'panstart') { + canvas.lastDeltaX = 0; + canvas.lastDeltaY = 0; + } +- if (ev.srcEvent.shiftKey || ev.pointers.length === 2) { +- if (!canvas.view.panningEnabled) return; +- var deltaX = (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth / canvas.view.zoom * 2 * canvas.controlSensitivity * 6.371e6; +- var deltaY = (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight / canvas.view.zoom * 2 * canvas.controlSensitivity * 6.371e6; +- +- if (canvas.view.twod) { +- canvas.view.position[0] += Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaX - Math.sin(DEG2RAD * 0) * deltaY; +- canvas.view.position[2] += Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaX + Math.cos(DEG2RAD * 0) * deltaY; ++ ++ //Trigger any handlers attatched to this canvas event. ++ canvas.selector.trigger('onPan', [ev, canvas]); ++ ++ //If any onPan handler sets preventDefaultOnPan to true, skips default onPan camera behavior ++ if (!canvas.view.preventDefaultOnPan) { ++ //If panning with two fingers or shift key, translate camera center ++ if (ev.srcEvent.shiftKey || ev.pointers.length === 2) { ++ if (canvas.view.panningEnabled) { ++ var deltaX = (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth / canvas.view.zoom * 2 * canvas.controlSensitivity * 6.371e6; ++ var deltaY = (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight / canvas.view.zoom * 2 * canvas.controlSensitivity * 6.371e6; ++ ++ //TODO: convert canvas.view.rotation from az/el euler to quaternion ++ if (canvas.view.twod) { ++ canvas.view.position[0] += Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaX - Math.sin(DEG2RAD * 0) * deltaY; ++ canvas.view.position[2] += Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaX + Math.cos(DEG2RAD * 0) * deltaY; ++ } ++ else { ++ canvas.view.position[0] += Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaX - Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaY; ++ canvas.view.position[2] += Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaX + Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaY; ++ } ++ } + } ++ //Else, rotate around camera center + else { +- canvas.view.position[0] += Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaX - Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaY; +- canvas.view.position[2] += Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaX + Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaY; ++ canvas.view.rotation[0] += (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth * 2 * canvas.controlSensitivity * RAD2DEG; ++ canvas.view.rotation[1] += (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight * -2 * canvas.controlSensitivity * RAD2DEG; ++ ++ if (canvas.view.rotation[0] > 360) { canvas.view.rotation[0] -= 360; }; ++ if (canvas.view.rotation[0] < -360) { canvas.view.rotation[0] += 360; }; ++ if (canvas.view.rotation[1] > 180) { canvas.view.rotation[1] -= 360; }; ++ if (canvas.view.rotation[1] < -180) { canvas.view.rotation[1] += 360; }; ++ ++ canvas.view.rotation[0] = clamp(canvas.view.rotation[0], canvas.view.azimuthLimits[0], canvas.view.azimuthLimits[1]); ++ canvas.view.rotation[1] = clamp(canvas.view.rotation[1], canvas.view.elevationLimits[0], canvas.view.elevationLimits[1]); ++ ++ if (displaylog) { console.log(canvas.view.rotation); } + } +- } ++ } + +- else { +- canvas.view.rotation[0] += (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth * 2 * canvas.controlSensitivity * RAD2DEG; +- canvas.view.rotation[1] += (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight * -2 * canvas.controlSensitivity * RAD2DEG; +- +- if (canvas.view.rotation[0] > 360) { canvas.view.rotation[0] -= 360; }; +- if (canvas.view.rotation[0] < -360) { canvas.view.rotation[0] += 360; }; +- if (canvas.view.rotation[1] > 180) { canvas.view.rotation[1] -= 360; }; +- if (canvas.view.rotation[1] < -180) { canvas.view.rotation[1] += 360; }; +- +- canvas.view.rotation[0] = clamp(canvas.view.rotation[0], canvas.view.azimuthLimits[0], canvas.view.azimuthLimits[1]); +- canvas.view.rotation[1] = clamp(canvas.view.rotation[1], canvas.view.elevationLimits[0], canvas.view.elevationLimits[1]) +- } ++ canvas.view.preventDefaultOnPan = false; + canvas.lastDeltaX = ev.deltaX; + canvas.lastDeltaY = ev.deltaY; +- +- canvas.dataMarkers.reposition = true; +- +- if (displaylog) { console.log(canvas.view.rotation); } + } //}}} + function onPinch(ev, canvas, displaylog) { //{{{ + ev.preventDefault(); + if (ev.type === 'pinchstart') { canvas.view.lastZoom = canvas.view.zoom; } +- else { modifyZoom(ev.scale * canvas.view.lastZoom, canvas, displaylog); } ++ else { modifyZoom(ev.scale * canvas.view.lastZoom, canvas, displaylog, ev, 0); } + } //}}} + function onZoom(ev, canvas, displaylog) { //{{{ + ev.preventDefault(); +- var delta = clamp(ev.scale || ev.wheelDelta || -ev.detail, -1, 1) * canvas.controlSensitivity * canvas.view.zoom / 20; +- modifyZoom(canvas.view.zoom + delta, canvas, displaylog); ++ var delta = clamp(ev.scale || ev.wheelDelta || -ev.detail, -1, 1) * canvas.controlSensitivity * canvas.view.zoom / 2; ++ modifyZoom(canvas.view.zoom + delta, canvas, displaylog, ev, 0); + } //}}} +-function modifyZoom(value, canvas, displaylog) { //{{{ +- canvas.view.zoom = clamp(value, canvas.view.zoomLimits[0], canvas.view.zoomLimits[1]); +- canvas.dataMarkers.reposition = true; +- if (displaylog) { console.log(canvas.view.zoom); } ++function modifyZoom(value, canvas, displaylog, ev, duration) { //{{{ ++ if (isEmptyOrUndefined(duration)) duration = 200; ++ var targetZoom = clamp(value, canvas.view.zoomLimits[0], canvas.view.zoomLimits[1]); ++ var currentZoom = canvas.view.zoom; ++ animateValue( ++ 0, ++ 1.0, ++ duration, ++ function(value, info) { ++ canvas.view.zoom = currentZoom * (1 - value) + targetZoom * value; ++ if (displaylog) { console.log(canvas.view.zoom); } ++ ++ //Trigger any handlers attatched to this canvas event. ++ canvas.selector.trigger('onZoom', [ev, canvas]); ++ } ++ ); + } //}}} +-function modifyDataMarkersEnabled(value, canvas) { //{{{ +- canvas.dataMarkers.enabled = value; +-} //}}} + function toggleMoviePlay(canvas) { //{{{ + canvas.animation.play = !canvas.animation.play; + if (canvas.animation.play){ +@@ -363,291 +390,42 @@ + canvas.playButton.find('span').addClass('fa-play'); + } + } //}}} +-//}}} +-//{{{ Interaction Functions +-function raycast(canvas, x, y, node) { //{{{ +- //Performs raycast on canvas.unitNode.mesh using x/y screen coordinates. Returns hit objects with hit position, coords, and indicies of ray-triangle intersection. ++function screenToWorldPoint(canvas, x, y) { //{{{ ++ var viewportX = (x - canvas.width / 2) / (canvas.width / 2); ++ var viewportY = (canvas.height / 2 - y) / (canvas.height / 2); ++ var origin = vec3.transformMat4(vec3.create(), [viewportX, viewportY, 0], canvas.camera.vpInverseMatrix); ++ return origin; ++} //}}} ++function screenToModelRay(canvas, x, y, node) { //{{{ ++ var inverseMVPMatrix = mat4.invert(mat4.create(), mat4.multiply(mat4.create(), canvas.camera.vpMatrix, node.modelMatrix)); ++ var viewportX = (x - canvas.width / 2) / (canvas.width / 2); ++ var viewportY = (canvas.height / 2 - y) / (canvas.height / 2); ++ var origin = vec3.transformMat4(vec3.create(), [viewportX, viewportY, 0], inverseMVPMatrix); ++ var far = vec3.transformMat4(vec3.create(), [viewportX, viewportY, 1.0], inverseMVPMatrix); ++ var direction = vec3.subtract(vec3.create(), far, origin); ++ return {'origin':origin, 'direction':direction}; ++} //}}} ++function raycast(canvas, origin, direction, node) { //{{{ ++ //Performs raycast on given node using ray origin and direction vectors. ++ //Returns hit objects with hit position, normals, barycentric coordinates, element number, and indices of ray-triangle intersection. + //TODO: Diagnose marker issues with orthographic views and slr-eustatic updates when switching between basins. +- var inverseMVPMatrix = mat4.invert(mat4.create(), mat4.multiply(mat4.create(), canvas.camera.vpMatrix, node.modelMatrix)); +- var origin = vec3.transformMat4(vec3.create(), [(x - canvas.width / 2) / (canvas.width / 2), (canvas.height / 2 - y) / (canvas.height / 2), 0], inverseMVPMatrix); +- var far = far || vec3.transformMat4(vec3.create(), [(x - canvas.width / 2) / (canvas.width / 2), (canvas.height / 2 - y) / (canvas.height / 2), 1.0], inverseMVPMatrix); +- var ray = vec3.subtract(vec3.create(), far, origin); +- +- var mesh = node.mesh; +- +- if (!mesh) { return; } +- if (!node.octree) { node.octree = new GL.Octree(mesh); } ++ if (!node.octree) { node.octree = new GL.Octree(node.mesh); } + +- var hit = node.octree.testRay(origin, ray, 1e3, 1e10); +- +- if(!hit) { return; } ++ var hit = node.octree.testRay(origin, direction, 1e3, 1e10); ++ if (!hit) { return; } + +- if (node.name.startsWith("clouds")) { canvas.clouds.selected = node.name; alert("New selected cloud: " + canvas.clouds.selected); } +- + hit.modelPos = vec3.copy(vec3.create(), hit.pos); + vec3.transformMat4(hit.pos, hit.pos, node.modelMatrix); +- vec3.transformMat4(hit.normal, hit.normal, node.modelMatrix); +- ++ + return hit; + } //}}} +-function updateCities(canvas) { +- //Update selected city +- var hit = canvas.nodes.cities.hit; +- if (hit) { +- citiesIndex = Math.floor(hit.indices[0] / ((ArrayMax(canvas.nodes.cities.mesh.getIndexBuffer('triangles').data) + 1) / cities.length)); +- cityName = cities[citiesIndex]; +- if (cityName !== $('#gfm-sim-controls-select-city').val()) { +- $('#gfm-sim-controls-select-city').val(cityName).selectmenu("refresh"); +- changeCity(canvas); +- } +- } +-} +-function brushModify(canvas) { //{{{ +- //This function takes in the canvas and x/y coordinates, performing a raycast against the mesh, and modifies the mesh using a the canvas.brush.strength and canvas.brush.falloff properties. +- //Currently the brush extends to the raycasted element and its immediate neighbors. +- //TODO: Allow variable brush size/additional neighbors. Allow the function to work on multiple models (currently hardcoded to md model). +- if (!canvas.unitNode || canvas.brush.enabled != 'on') { return; } +- +- var hit = canvas.brush.hit; +- +- if (hit) { +- var bufferVertices = canvas.unitNode.mesh.getBuffer('vertices'); +- var vertices = bufferVertices.data; +- var bufferCoords = canvas.unitNode.mesh.getBuffer('coords'); +- var coords = bufferCoords.data; +- +- //Query nearby elements and store indicies of affected vertices using pregenerated vertexconnectivity list (from NodeConnectivity) +- var baseIndices = new Set(hit.indices); +- var connectedIndices = new Set(hit.indices); +- var connectedElement; +- var indices; +- var lengthIndex = md.mesh.vertexconnectivity[0].length - 1; +- var length; +- for (var i = 0; i < 3; i++) { +- length = md.mesh.vertexconnectivity[hit.indices[i]][lengthIndex]; +- for (var j = 0; j < length; j++) { +- //Shift elements down by one (matlab 1-based index to 0-based index) +- connectedElement = md.mesh.vertexconnectivity[hit.indices[i]][j] - 1; +- indices = md.mesh.elements[connectedElement]; +- connectedIndices.add(indices[0] - 1); +- connectedIndices.add(indices[1] - 1); +- connectedIndices.add(indices[2] - 1); +- } +- } +- +- //Apply modifications to included vertices in mesh using brush strength and falloff. +- var strength; +- for (var index of connectedIndices) { +- if (!baseIndices.has(index)) { +- strength = canvas.brush.strength * canvas.brush.falloff; +- } +- else { +- strength = canvas.brush.strength; +- } +- vertices[index*3+2] += strength * 100; +- md.geometry.surface[index] += strength; +- md.geometry.thickness[index] += strength; +- coords[index*2+1] += strength; +- canvas.unitData[index] += strength; +- } +- +- //Update mesh on GPU +- bufferVertices.upload(canvas.gl.DYNAMIC_DRAW); +- bufferCoords.upload(canvas.gl.DYNAMIC_DRAW); +- canvas.unitNode.octree = new GL.Octree(canvas.unitNode.mesh); +- } ++function raycastXY(canvas, x, y, node) { //{{{ ++ //Performs raycast on given node using x and y screenspace coordinates. ++ //Returns hit objects with hit position, normals, barycentric coordinates, element number, and indices of ray-triangle intersection. ++ //TODO: Diagnose marker issues with orthographic views and slr-eustatic updates when switching between basins. ++ var ray = screenToModelRay(canvas, x, y, node); ++ return raycast(canvas, ray.origin, ray.direction, node); + } //}}} +-function updateClouds(canvas) { +- //Update clouds if rendered +- //TODO: Steven, the hit now queries the radaroverlay. +- if (canvas.nodes[canvas.clouds.selected]) { +- var v1 = vec3.fromValues(vertices[hit.indices[0] * 3], vertices[hit.indices[0] * 3 + 1], vertices[hit.indices[0] * 3 + 2]); +- var v2 = vec3.fromValues(vertices[hit.indices[1] * 3], vertices[hit.indices[1] * 3 + 1], vertices[hit.indices[1] * 3 + 2]); +- var v3 = vec3.fromValues(vertices[hit.indices[2] * 3], vertices[hit.indices[2] * 3 + 1], vertices[hit.indices[2] * 3 + 2]); +- vec3.transformMat4(v1, v1, canvas.unitNode.modelMatrix);//move out of brushModify, perhaps onto onPan +- vec3.transformMat4(v2, v2, canvas.unitNode.modelMatrix); +- vec3.transformMat4(v3, v3, canvas.unitNode.modelMatrix); +- var x = (v1[0] + v2[0] + v3[0]) / 3;// + Math.floor((Math.random() * (1 + 10000 - (-10000)) + (-10000))); +- var y = (v1[1] + v2[1] + v3[1]) / 3;// + Math.floor((Math.random() * (1 + 10000 - (-10000)) + (-10000))); +- var z = (v1[2] + v2[2] + v3[2]) / 3; +- canvas.nodes[canvas.clouds.selected].translation = [x, y + canvas.clouds.height, z]; +- updateModelMatrix(canvas.nodes[canvas.clouds.selected]); +- } +-} +-function initializeMarker(canvas) { //{{{ +- //Initialize data marker and tooltip display once per page load +- var marker = $('#' + canvas.dataMarkers.marker.id); +- var size = canvas.dataMarkers.size; +- if (!marker.hasClass('tooltipstered')) { +- marker.css({ +- 'position': 'absolute', +- 'left': -size[0] + 'px', +- 'top': -size[1] + '0px', +- 'width': size[0] + 'px', +- 'height': size[1] + 'px', +- 'pointer-events': 'all', +- 'cursor': 'pointer', +- 'display': 'none' +- }); +- marker.tooltipster({ +- contentAsHTML: true, +- maxWidth: 320, +- maxHeight: 320, +- zIndex: 1000, +- trigger: 'custom', +- triggerOpen: { +- mouseenter: false, +- originClick: true, +- touchstart: false +- }, +- triggerClose: { +- mouseleave: false, +- originClick: true, +- touchleave: false +- }, +- }); +- marker.on('click touch', function () { +- marker.fadeOut(175); +- marker.tooltipster('close'); +- marker.closed = true; +- }); +- marker.closed = false; +- canvas.dataMarkers.marker.selector = marker; +- } +- updateMarker(canvas, true); +-} //}}} +-function repositionMarker(canvas) { //{{{ +- //Mover marker to point to mouse position, offset in y by 1 to enable immediate clicking. +- //Return if no marker hit exists, the camera is not rendering, or if no reposition has been scheduled. +- if (isEmptyOrUndefined(canvas.dataMarkers.marker.hit) || !canvas.camera.ready || !canvas.dataMarkers.reposition) { return; } +- var size = canvas.dataMarkers.size; +- var screenPoint = vec3.transformMat4(vec3.create(), canvas.dataMarkers.marker.hit.pos, canvas.camera.vpMatrix); +- var x = (screenPoint[0] + 1.0) * (canvas.width / 2) + canvas.selector.offset().left; +- var y = (-screenPoint[1] + 1.0) * (canvas.height / 2) + canvas.selector.offset().top; +- canvas.dataMarkers.marker.selector.css({ +- 'left': (Math.round(x) - size[0] / 2) + 'px', +- 'top': (Math.round(y) - size[1] + 1) + 'px' +- }); +- if (canvas.dataMarkers.marker.selector.tooltipster('status').state != 'closed') { canvas.dataMarkers.marker.selector.tooltipster('reposition'); } +- canvas.dataMarkers.reposition = false; +-} //}}} +-function updateMarker(canvas, reset) { //{{{ +- //Retrieve data value fields and plots them on data marker popup if a hit has been registered. +- //TODO: Automatically pick up any field of size md.mesh.numberofelements +- //If no marker has been placed, no update is needed. If canvas is resimulating and unitNode has not been set yet, wait and try again. +- if (!canvas.dataMarkers.enabled || isEmptyOrUndefined(canvas.dataMarkers.marker.hit)) { return; } +- if (isEmptyOrUndefined(canvas.unitNode) || isEmptyOrUndefined(canvas.unitNode.mesh)) { setTimeout( function(){ updateMarker(canvas, reset); }, 750); return; } +- +- var hit = canvas.dataMarkers.marker.hit; +- +- var coords = canvas.unitNode.mesh.vertexBuffers.coords.data; +- var latitude = md.mesh.lat; +- var longitude = md.mesh.long; +- var thickness; +- var velocity; +- if (md.results[0]) { +- thickness = md.results[canvas.animation.frame].Thickness; +- velocity = md.results[canvas.animation.frame].Vel; +- } +- else { +- thickness = md.geometry.thickness; +- velocity = md.initialization.vel; +- } +- +- //Construct new argument array of the data display format for sprintf using first first argument as the formatSpecifier string and the rest as the additional arguments. +- var labels = canvas.dataMarkers.labels.slice(); +- for (var i = 0; i < labels.length; i++) { +- if (labels[i].toLowerCase() === 'x') { labels[i] = hit.modelPos[0]; } +- else if (labels[i].toLowerCase() === 'y') { labels[i] = hit.modelPos[1]; } +- else if (labels[i].toLowerCase() === 'z') { labels[i] = hit.modelPos[2]; } +- else if (labels[i].toLowerCase() === 'latitude') { +- var hitLatitude = [latitude[hit.indices[0]], latitude[hit.indices[1]], latitude[hit.indices[2]]]; +- var valueLatitude = Math.abs(hitLatitude[0] * hit.uvw[0] + hitLatitude[1] * hit.uvw[1] + hitLatitude[2] * hit.uvw[2]); +- labels[i] = valueLatitude; +- } +- else if (labels[i].toLowerCase() === 'longitude') { +- var hitLongitude = [longitude[hit.indices[0]], longitude[hit.indices[1]], longitude[hit.indices[2]]]; +- var valueLongitude = Math.abs(hitLongitude[0] * hit.uvw[0] + hitLongitude[1] * hit.uvw[1] + hitLongitude[2] * hit.uvw[2]); +- labels[i] = valueLongitude; +- } +- else if (labels[i].toLowerCase() === 'thickness') { +- var hitThickness = [thickness[hit.indices[0]], thickness[hit.indices[1]], thickness[hit.indices[2]]]; +- var valueThickness = hitThickness[0] * hit.uvw[0] + hitThickness[1] * hit.uvw[1] + hitThickness[2] * hit.uvw[2]; +- labels[i] = valueThickness; +- } +- else if (labels[i].toLowerCase() === 'velocity') { +- var hitVelocity = [velocity[hit.indices[0]], velocity[hit.indices[1]], velocity[hit.indices[2]]]; +- var valueVelocity = hitVelocity[0] * hit.uvw[0] + hitVelocity[1] * hit.uvw[1] + hitVelocity[2] * hit.uvw[2]; +- labels[i] = valueVelocity; +- } +- else if (labels[i].toLowerCase() === 'value') { +- var hitCoords = [coords[hit.indices[0]*2], coords[hit.indices[0]*2+1], coords[hit.indices[1]*2], coords[hit.indices[1]*2+1], coords[hit.indices[2]*2], coords[hit.indices[2]*2+1]]; +- var u = hitCoords[0] * hit.uvw[0] + hitCoords[2] * hit.uvw[1] + hitCoords[4] * hit.uvw[2]; +- var v = hitCoords[1] * hit.uvw[0] + hitCoords[3] * hit.uvw[1] + hitCoords[5] * hit.uvw[2]; +- var value = canvas.unitNode.caxis[0] * (1.0 - v) + canvas.unitNode.caxis[1] * v; +- labels[i] = value; +- } +- } +- +- //Apply changes to tooltip +- $('#tooltip-content-data-marker-' + canvas.id).html(sprintf.apply(null, canvas.dataMarkers.format.concat(labels))); +- $('#tooltip-content-data-marker-' + canvas.id).css({'font': canvas.dataMarkers.font}); +- +- //If animated, setup animation loop to update plot as movie plays. +- if (canvas.dataMarkers.animated) { +- var isEmpty = (canvas.dataMarkers.values.length === 0); +- var lastUpdatedIndex = (canvas.dataMarkers.values.length - 1); +- var newMovieFrame = (!isEmpty && canvas.dataMarkers.values[lastUpdatedIndex][0] != canvas.animation.frame); +- //If new data marker has been placed, reinitialize plot. If not, push new value into plot value array. +- if (reset) { +- canvas.dataMarkers.values = []; +- newMovieFrame = true; +- for (var currentFrame = 0; currentFrame < (canvas.unitNode.movieLength); currentFrame++) { +- coords = canvas.unitMovieData[currentFrame]; +- var hitCoords = [coords[hit.indices[0]*2], coords[hit.indices[0]*2+1], coords[hit.indices[1]*2], coords[hit.indices[1]*2+1], coords[hit.indices[2]*2], coords[hit.indices[2]*2+1]]; +- var u = hitCoords[0] * hit.uvw[0] + hitCoords[2] * hit.uvw[1] + hitCoords[4] * hit.uvw[2]; +- var v = hitCoords[1] * hit.uvw[0] + hitCoords[3] * hit.uvw[1] + hitCoords[5] * hit.uvw[2]; +- var value = canvas.unitNode.caxis[0] * (1.0 - v) + canvas.unitNode.caxis[1] * v; +- canvas.dataMarkers.values.push([currentFrame, value]); +- } +- } +- else { +- if (canvas.animation.lastFrame > canvas.animation.frame) { +- canvas.dataMarkers.values = []; +- } +- if (isEmpty || newMovieFrame) { +- coords = canvas.unitMovieData[canvas.animation.frame]; +- var hitValues = [coords[hit.indices[0]], coords[hit.indices[1]], coords[hit.indices[2]]]; +- var value = hitValues[0] * hit.uvw[0] + hitValues[1] * hit.uvw[1] + hitValues[2] * hit.uvw[2]; +- canvas.dataMarkers.values.push([canvas.animation.frame, value]); +- } +- } +- +- //Replot data marker popup using update data value array. +- if (isEmpty || newMovieFrame) { +- var dataLabels = {'latitude': valueLatitude, 'longitude': valueLongitude, 'thickness': valueThickness, 'velocity': valueVelocity, 'value': value}; +- var dataDisplay = canvas.dataMarkers.values.slice(0, canvas.animation.frame + 1); +- plot( +- 'id', '#sim-plot', +- 'type', 'bar', +- 'width', 400, +- 'height', 300, +- 'nticks', 25, +- 'xlabel', 'Time', +- 'ylabel', 'Value', +- 'title', 'Changes Over Time', +- 'datalabels', canvas.dataMarkers.labels, +- 'labelvalues', dataLabels, +- 'data', dataDisplay +- ); +- } +- } +- canvas.dataMarkers.reposition = true; +- if (reset && !canvas.dataMarkers.marker.selector.closed) { +- canvas.dataMarkers.marker.selector.fadeIn(175); +- canvas.dataMarkers.marker.selector.tooltipster('open'); +- } +-} //}}} + function animateValue(current, target, duration, stepCallback, doneCallback) { //{{{ + //Animates scalar value for length duration, calling callback each step. + //TODO: Specify lerp easing as option (cubic, linear, cosine). +@@ -668,24 +446,31 @@ + var azimuthRotationMatrix = mat4.create(); + var elevationRotationMatrix = mat4.create(); + var aspectRatio = canvas.clientWidth / canvas.clientHeight; +- var cameraPosition = vec3.create(); ++ var camera = canvas.camera; ++ var view = canvas.view; + +- if (canvas.view.twod) { mat4.ortho(pMatrix, -aspectRatio*6.371e6/canvas.view.zoom, aspectRatio*6.371e6/canvas.view.zoom, -6.371e6/canvas.view.zoom, 6.371e6/canvas.view.zoom, canvas.camera.near, canvas.camera.far); } +- else { mat4.perspective(pMatrix, canvas.camera.fov * DEG2RAD, aspectRatio, canvas.camera.near, canvas.camera.far); } ++ if (view.twod) { mat4.ortho(pMatrix, -aspectRatio*6.371e6/view.zoom, aspectRatio*6.371e6/view.zoom, -6.371e6/view.zoom, 6.371e6/view.zoom, camera.near, camera.far); } ++ else { mat4.perspective(pMatrix, camera.fov * DEG2RAD, aspectRatio, camera.near, camera.far); } + + //Apply worldspace translation +- mat4.translate(vMatrix, translateMatrix, vec3.negate(vec3.create(), canvas.view.position)); ++ mat4.translate(vMatrix, translateMatrix, vec3.negate(vec3.create(), view.position)); + + //Calculate rotation around camera focal point about worldspace origin +- if (canvas.view.twod) { ++ if (view.twod) { + mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, -DEG2RAD * 0, [0, 1, 0]); + mat4.rotate(elevationRotationMatrix, elevationRotationMatrix, DEG2RAD * 90, [1, 0, 0]); + mat4.multiply(rotationMatrix, elevationRotationMatrix, azimuthRotationMatrix); + } + else { +- mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, -DEG2RAD * (canvas.view.rotation[0] + 90), [0, 1, 0]); +- mat4.rotate(elevationRotationMatrix, elevationRotationMatrix, DEG2RAD * canvas.view.rotation[1], [1, 0, 0]); ++ mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, -DEG2RAD * (view.rotation[0] + 90), [0, 1, 0]); ++ mat4.rotate(elevationRotationMatrix, elevationRotationMatrix, DEG2RAD * view.rotation[1], [1, 0, 0]); + mat4.multiply(rotationMatrix, elevationRotationMatrix, azimuthRotationMatrix); ++ //var quaternionWorldX = Node.prototype.eulerToQuaternion(0, 0, DEG2RAD * (view.rotation[0])); ++ //var quaternionWorldY = Node.prototype.eulerToQuaternion(0, DEG2RAD * (view.rotation[1]), 0); ++ //var quaternionWorldZ = Node.prototype.eulerToQuaternion(DEG2RAD * (view.rotation[2]), 0, 0); ++ //var quaternionTemp = quat.multiply(quat.create(), quaternionWorldY, quaternionWorldX); ++ //quat.multiply(camera.rotation, quaternionWorldZ, quaternionTemp); ++ //mat4.fromQuat(rotationMatrix, camera.rotation); + } + + //Apply rotation transform +@@ -693,20 +478,22 @@ + + //Apply screenspace translation to emulate rotation around point + mat4.identity(translateMatrix); +- mat4.translate(translateMatrix, translateMatrix, [0.0, 0.0, -6.371e6/canvas.view.zoom]); ++ mat4.translate(translateMatrix, translateMatrix, [0.0, 0.0, -6.371e6/view.zoom]); + mat4.multiply(vMatrix, translateMatrix, vMatrix); + + //Apply projection matrix to get camera matrix +- mat4.copy(canvas.camera.vMatrix, vMatrix); +- mat4.multiply(canvas.camera.vpMatrix, pMatrix, vMatrix); ++ mat4.copy(camera.vMatrix, vMatrix); ++ mat4.multiply(camera.vpMatrix, pMatrix, vMatrix); + + //Calculate inverse view matrix fields for lighting and raycasts +- mat4.invert(canvas.camera.vInverseMatrix, canvas.camera.vMatrix); +- mat4.invert(canvas.camera.vpInverseMatrix, canvas.camera.vpMatrix); ++ mat4.invert(camera.vInverseMatrix, camera.vMatrix); ++ mat4.invert(camera.vpInverseMatrix, camera.vpMatrix); + +- vec3.transformMat4(canvas.camera.position, cameraPosition, canvas.camera.vpInverseMatrix); +- canvas.camera.ready = true; +- repositionMarker(canvas); ++ vec3.transformMat4(camera.position, vec3.create(), camera.vInverseMatrix); ++ vec3.sub(camera.relativePosition, camera.position, view.position); ++ vec3.normalize(camera.direction, camera.relativePosition); ++ ++ camera.ready = true; + }//}}} + function drawSceneGraphNode(canvas, node) { //{{{ + if (!node.enabled) { return; } +@@ -717,13 +504,12 @@ + var mvpMatrix = mat4.create(); + mat4.multiply(mvpMatrix, canvas.camera.vpMatrix, node.modelMatrix); + +- var mvMatrix = mat4.create(); +- mat4.multiply(mvMatrix, canvas.camera.vMatrix, node.modelMatrix); ++ var normalMatrix = mat3.create(); ++ var tempMatrix = mat4.create(); ++ mat4.invert(tempMatrix, node.modelMatrix); ++ mat4.transpose(tempMatrix, tempMatrix); ++ mat3.fromMat4(normalMatrix, tempMatrix); + +- var normalMatrix = mat4.create(); +- mat4.invert(normalMatrix, node.modelMatrix); +- mat4.transpose(normalMatrix, normalMatrix); +- + if (node.texture) { node.texture.bind(0); } + if (node.disableDepthTest) { gl.disable(gl.DEPTH_TEST); } + if (node.enableCullFace) { gl.enable(gl.CULL_FACE); } +@@ -731,88 +517,75 @@ + gl.cullFace(node.cullFace); + gl.lineWidth(node.lineWidth); + gl.blendFunc(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA); +- ++ + //Setup for light that originates from camera +- var origin = vec3.fromValues(0, 0, 0); +- var lightOrigin = vec3.fromValues(0, 0, 0); +- var cameraPositionRelative = vec3.create(); +- vec3.transformMat4(origin, origin, canvas.camera.vInverseMatrix); +- vec3.normalize(lightOrigin, lightOrigin); +- vec3.sub(cameraPositionRelative, origin, node.translation); +- cameraHeight = vec3.length(cameraPositionRelative); ++ var atm = canvas.atmosphere; ++ var lightOrigin = vec3.create(); + +- var atm = { //Default Values +- wavelength_r: 0.65, //0.65 Red wavelength (micrometers) +- wavelength_g: 0.57, //0.57 Green wavelength (micrometers) +- wavelength_b: 0.475, //0.475 Green wavelength (micrometers) +- eSun: 100.0, //20.0 Sun intensity +- kRayleigh: 0.0025, //0.0025 Rayleigh scattering amount +- kMie: 0.000, //0.01 Mie scattering amount +- g: -0.99, //-0.99 Mie phase asymmetry/direction factor +- hdr_exposure: 0.8, //0.8 High Dynamic Range Exposure +- scale: 1.25, //1.025 Scale of atmosphere. WARNING: Change atmosphereScale in applyoptions.js, and scaling constants. +- scaleDepth: 0.25, //0.25 Percentage altitude at which the atmosphere's average density is found +- a: -0.00287, //-0.00287 Scaling constant a +- b: 0.459, //0.459 Scaling constant b +- c: 3.83, //3.83 Scaling constant c +- d: -6.80, //-6.80 Scaling constant d +- e: 3.6, //5.25 Scaling constant e. Lower when increasing atmosphere scale. +- attenuation: 0.5 //0.5 Strength of atmospheric scattering on ground shading. +- }; +- +- var inv_wavelength4 = [1.0 / Math.pow(atm.wavelength_r, 4), 1.0 / Math.pow(atm.wavelength_g, 4), 1.0 / Math.pow(atm.wavelength_b, 4)]; +- var innerRadius = 6.371e6; +- var outerRadius = innerRadius*atm.scale; +- var scale = 1.0 / (outerRadius - innerRadius); +- var scaleDepth = atm.scaleDepth; +- + node.shader.uniforms({ +- m4MVP: mvpMatrix, +- m4Normal: normalMatrix, +- m4Model: node.modelMatrix, +- u_lightPosition: lightOrigin, +- //u_lightPosition: [1.0, 1.0, 1.0], +- u_diffuseColor: node.diffuseColor, +- u_texture: 0, +- u_alpha: node.alpha, +- u_maskZerosColor: node.maskZerosColor, +- u_maskZerosEnabled: node.maskZerosEnabled, +- u_maskZerosTolerance: node.maskZerosTolerance, +- u_maskZerosZeroValue: node.maskZerosZeroValue, +- u_maskEnabled: node.maskEnabled, +- u_maskHeight: node.maskHeight, +- u_maskColor: node.maskColor, +- u_pointSize: node.pointSize, +- v3CameraPosition: origin, +- v3Translate: node.translation, +- v3LightPos: lightOrigin, +- v3InvWavelength: inv_wavelength4, +- fOuterRadius: outerRadius, +- fOuterRadius2: outerRadius * outerRadius, +- fInnerRadius: innerRadius, +- fInnerRadius2: innerRadius * innerRadius, +- fKrESun: atm.kRayleigh * atm.eSun, +- fKmESun: atm.kMie * atm.eSun, +- fKr4PI: atm.kRayleigh * 4 * Math.PI, +- fKm4PI: atm.kMie * 4 * Math.PI, +- fScale: scale, +- fScaleDepth: scaleDepth, +- fScaleOverScaleDepth: scale/scaleDepth, +- v3LightPosFrag: lightOrigin, +- fHdrExposure: atm.hdr_exposure, +- g: atm.g, +- g2: atm.g * atm.g, +- a: atm.a, +- b: atm.b, +- c: atm.c, +- d: atm.d, +- e: atm.e, +- attenuation: atm.attenuation ++ m4MVP: mvpMatrix, ++ m3Normal: normalMatrix, ++ m4Model: node.modelMatrix, ++ u_alpha: node.alpha, ++ u_ambientColor: node.ambientColor, ++ u_cameraPosition: canvas.camera.position, ++ u_diffuseColor: node.diffuseColor, ++ u_lightDirection: canvas.camera.direction, ++ u_lightingBias: node.lightingBias, ++ u_maskZerosColor: node.maskZerosColor, ++ u_maskZerosEnabled: node.maskZerosEnabled, ++ u_maskZerosTolerance: node.maskZerosTolerance, ++ u_maskZerosZeroValue: node.maskZerosZeroValue, ++ u_maskEnabled: node.maskEnabled, ++ u_maskHeight: node.maskHeight, ++ u_maskColor: node.maskColor, ++ u_pointSize: node.pointSize, ++ u_specularColor: node.specularColor, ++ u_specularPower: node.specularPower, ++ u_specularStrength: node.specularStrength, ++ u_texture: 0, ++ v3CameraPosition: canvas.camera.position, ++ v3Translate: node.translation, ++ v3LightPos: lightOrigin, ++ v3InvWavelength: atm.inv_wavelength4, ++ fOuterRadius: atm.outerRadius, ++ fOuterRadius2: atm.outerRadius2, ++ fInnerRadius: atm.innerRadius, ++ fInnerRadius2: atm.innerRadius2, ++ fKrESun: atm.krESun, ++ fKmESun: atm.kmESun, ++ fKr4PI: atm.kr4PI, ++ fKm4PI: atm.km4PI, ++ fScale: atm.scale, ++ fScaleDepth: atm.scaleDepth, ++ fScaleOverScaleDepth: atm.scaleOverScaleDepth, ++ v3LightPosFrag: lightOrigin, ++ fHdrExposure: atm.hdr_exposure, ++ g: atm.g, ++ g2: atm.g2, ++ a: atm.a, ++ b: atm.b, ++ c: atm.c, ++ d: atm.d, ++ e: atm.e, ++ attenuation: atm.attenuation + }).draw(node.mesh, node.drawMode, 'triangles'); + + gl.enable(gl.DEPTH_TEST); + gl.disable(gl.CULL_FACE); + } //}}} ++function canvasResize(canvas) { ++ var rect = canvas.getBoundingClientRect(); ++ canvas.width = rect.width; ++ canvas.height = rect.height; ++ canvas.gl.viewport(0, 0, canvas.width, canvas.height); ++ ++ if (!isEmptyOrUndefined(canvas.overlaycanvas)) { ++ rect = canvas.overlaycanvas.getBoundingClientRect(); ++ canvas.overlaycanvas.width = rect.width; ++ canvas.overlaycanvas.height = rect.height; ++ } ++} + function draw(canvas) { //{{{ + //Ensure all nodes are ready to render + //TODO: Come up with better way to check if shaders are ready, or move outside of main draw function +@@ -832,21 +605,21 @@ + + //Begin rendering nodes + if (canvas.draw.ready) { +- var rect = canvas.getBoundingClientRect(); +- canvas.width = rect.width; +- canvas.height = rect.height; ++ //Handle canvas resizing and viewport/screenspace coordinate synchronization ++ canvasResize(canvas); + + var gl = canvas.gl; + gl.makeCurrent(); //litegl function to handle switching between multiple canvases +- gl.viewport(0, 0, canvas.width, canvas.height); + gl.clearColor(canvas.backgroundcolor[0], canvas.backgroundcolor[1], canvas.backgroundcolor[2], canvas.backgroundcolor[3]); + gl.clear(gl.COLOR_BUFFER_BIT | gl.DEPTH_BUFFER_BIT); + + updateCameraMatrix(canvas); + +- if (canvas.textcanvas) { canvas.textcanvas.draw(canvas); } +- if (canvas.overlaycanvas) { canvas.overlaycanvas.draw(canvas); } ++ //Trigger any handlers attatched to this canvas event. ++ canvas.selector.trigger('onPreRender', [canvas]); + ++ for (var handler in canvas.overlayHandlers) { canvas.overlayHandlers[handler](canvas); } ++ + var drawPassNumber = 3; + for (var i = drawPassNumber - 1; i >= 0; --i) { + for (var node in nodes) { +Index: ../trunk-jpl/src/m/plot/plot_overlay.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_overlay.js (revision 21910) ++++ ../trunk-jpl/src/m/plot/plot_overlay.js (revision 21911) +@@ -40,7 +40,7 @@ + scale = [1, 1, options.getfieldvalue('heightscale', 1)]; + } + else { +- vertices = Node.prototype.scaleVertices(md, x, y, z, options.getfieldvalue('heightscale', 1)); ++ vertices = Node.prototype.scaleVertices(md, x, y, z, elements, options.getfieldvalue('heightscale', 1), options.getfieldvalue('maskscale',{})); + scale = [1, 1, 1]; + } + +@@ -51,11 +51,13 @@ + 'canvas', canvas, + 'options', options, + 'name', 'overlay', +- 'shaderName', 'ground' in options.getfieldvalue('render', {}) ? 'GroundFromSpace' : 'Textured', ++ 'shaderName', 'ground' in options.getfieldvalue('render', {}) ? 'GroundFromSpace' : 'TexturedDiffuse', + 'alpha', options.getfieldvalue('outeralpha', 1.0), + //'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, md.mesh.classname() === 'mesh3dsurface' ? (zlim[0] + zlim[1]) / 2 : zlim[0]], + 'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2], +- 'diffuseColor', 'white', ++ 'ambientColor', [0.1, 0.1, 0.1 ,1.0], ++ 'diffuseColor', [1.0, 1.0, 1.0 ,1.0], ++ 'specularStrength', 0.0, + 'maskEnabled', options.getfieldvalue('outermask','off') == 'on', + 'maskHeight', options.getfieldvalue('outermaskheight', 150.0), + 'maskColor', options.getfieldvalue('outermaskcolor',[0.0, 0.0, 1.0, 1.0]), +@@ -64,12 +66,12 @@ + 'scale', scale + ); + //}}} +- ++ + var xRange = xlim[1] - xlim[0]; + var yRange = ylim[1] - ylim[0]; + var coordArray = [new Array(x.length), new Array(x.length)]; ++ + //generate mesh: +- + if (md.mesh.classname() == 'mesh3dsurface') { + var xyz, magnitude; + for(var i = 0; i < x.length; i++){ +@@ -86,5 +88,5 @@ + coordArray[1][i] = (vertices[1][i] - ylim[0]) / yRange; + } + } +- node.patch('Faces', elements, 'Vertices', vertices, 'FaceVertexCData', coordArray, 'FaceColor', 'interp', 'EdgeColor', edgecolor); ++ node.patch('Faces', elements, 'Vertices', vertices, 'FaceVertexCData', coordArray, 'FaceColor', 'interp'); + } //}}} +Index: ../trunk-jpl/src/m/plot/plot_quiver.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_quiver.js (revision 21910) ++++ ../trunk-jpl/src/m/plot/plot_quiver.js (revision 21911) +@@ -36,7 +36,7 @@ + scale = [1, 1, options.getfieldvalue('heightscale', 1)]; + } + else { +- vertices = Node.prototype.scaleVertices(md, x, y, z, options.getfieldvalue('heightscale', 1)); ++ vertices = Node.prototype.scaleVertices(md, x, y, z, elements, options.getfieldvalue('heightscale', 1), options.getfieldvalue('maskscale',{})); + scale = [1, 1, 1]; + } + +Index: ../trunk-jpl/src/m/plot/plot_unit.js +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_unit.js (revision 21910) ++++ ../trunk-jpl/src/m/plot/plot_unit.js (revision 21911) +@@ -12,7 +12,7 @@ + // return; + //} + //else { +- ++ + //{{{ declare variables: + //Process data and model + var meshresults = processmesh(md, data, options); +@@ -36,23 +36,25 @@ + scale = [1, 1, options.getfieldvalue('heightscale', 1)]; + } + else { +- vertices = Node.prototype.scaleVertices(md, x, y, z, options.getfieldvalue('heightscale', 1)); ++ vertices = Node.prototype.scaleVertices(md, x, y, z, elements, options.getfieldvalue('heightscale', 1), options.getfieldvalue('maskscale',{})); + scale = [1, 1, 1]; + } + + //Compute gl variables: +- var edgecolor = options.getfieldvalue('edgecolor', 'black'); ++ var edgecolor = options.getfieldvalue('edgecolor', [1.0, 1.0, 1.0 ,1.0]); + var maskzeros = options.getfieldvalue('maskzeros', {}); + var node = new Node( + 'canvas', canvas, + 'options', options, + 'name', 'unit', +- 'shaderName', 'Textured', ++ 'shaderName', 'TexturedDiffuse', + 'alpha', options.getfieldvalue('alpha', 1.0), + 'caxis', options.getfieldvalue('caxis',[ArrayMin(data), ArrayMax(data)]), + //'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, md.mesh.classname() === 'mesh3dsurface' ? (zlim[0] + zlim[1]) / 2 : zlim[0]], + 'center', [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2], ++ 'lightingBias', 0.8, + 'diffuseColor', edgecolor, ++ 'specularStrength', 0.0, + 'enabled', options.getfieldvalue('nodata','off') == 'off', + 'log', options.getfieldvalue('log',false), + 'maskEnabled', options.getfieldvalue('innermask','off') == 'on', +Index: ../trunk-jpl/src/m/plot/webgl_node.js +=================================================================== +--- ../trunk-jpl/src/m/plot/webgl_node.js (revision 21910) ++++ ../trunk-jpl/src/m/plot/webgl_node.js (revision 21911) +@@ -5,7 +5,7 @@ + // node=new Node('canvas', canvas); + + function Node() { //{{{ +- //properties ++ //properties + // {{{ + var args = Array.prototype.slice.call(arguments); + var options = new pairoptions(args.slice(0,args.length)); +@@ -14,52 +14,96 @@ + this.options = options.getfieldvalue('options', null), + this.gl = canvas.gl; + +- this.alpha = options.getfieldvalue('alpha', 1.0), +- this.animation = options.getfieldvalue('animation', {}), +- this.arrays = options.getfieldvalue('arrays', {}), +- this.caxis = options.getfieldvalue('caxis', [0.0, 1.0]), +- this.center = options.getfieldvalue('center', vec3.create()), +- this.cullFace = options.getfieldvalue('cullFace', this.gl.BACK), +- this.computeIndices = options.getfieldvalue('computeIndices', true), +- this.disableDepthTest = options.getfieldvalue('disableDepthTest', false), +- this.diffuseColor = options.getfieldvalue('diffuseColor', [0.0, 0.0, 0.0, 1.0]), +- this.drawMode = options.getfieldvalue('drawMode', this.gl.TRIANGLES), +- this.drawOrder = options.getfieldvalue('drawOrder', 1), +- this.enabled = options.getfieldvalue('enabled', true), +- this.enableCullFace = options.getfieldvalue('enableCullFace', true), +- this.hideOcean = options.getfieldvalue('hideOcean', false), +- this.lineWidth = options.getfieldvalue('lineWidth', 1.0), +- this.log = options.getfieldvalue('log', false), +- this.maskColor = options.getfieldvalue('maskColor', vec4.fromValues(0.0, 0.0, 1.0, 1.0)), +- this.maskEnabled = options.getfieldvalue('maskEnabled', false), +- this.maskHeight = options.getfieldvalue('maskHeight', 150.0), +- this.maskZerosColor = options.getfieldvalue('maskZerosColor', [1.0, 1.0, 1.0, 1.0]), +- this.maskZerosEnabled = options.getfieldvalue('maskZerosEnabled', false), +- this.maskZerosTolerance = options.getfieldvalue('maskZerosTolerance', 1e-6), +- this.maskZerosZeroValue = options.getfieldvalue('maskZerosZeroValue', 0.5), +- this.mesh = options.getfieldvalue('mesh', undefined), +- this.name = options.getfieldvalue('name', 'node'), +- this.nanIndices = options.getfieldvalue('nanIndices', new Set()), +- this.octree = options.getfieldvalue('octree', undefined), +- this.pointSize = options.getfieldvalue('pointSize', 15.0), +- this.shaderName = options.getfieldvalue('shaderName', 'Colored'), +- this.shader = options.getfieldvalue('shader', this.gl.shaders[this.shaderName]), +- this.texture = options.getfieldvalue('texture', undefined), +- this.scale = options.getfieldvalue('scale', vec3.fromValues(1, 1, 1)), +- this.rotation = options.getfieldvalue('rotation', vec3.create()), +- this.translation = options.getfieldvalue('translation', vec3.create()), +- this.modelMatrix = options.getfieldvalue('modelMatrix', mat4.create()), +- this.rotationMatrix = options.getfieldvalue('rotationMatrix', mat4.create()), +- this.inverseModelMatrix = options.getfieldvalue('inverseModelMatrix', mat4.create()), +- this.inverseRotationMatrix = options.getfieldvalue('inverseRotationMatrix', mat4.create()) ++ this.alpha = options.getfieldvalue('alpha', 1.0); //Shading transparency. ++ this.ambientColor = options.getfieldvalue('ambientColor', [0.0, 0.0, 0.0, 1.0]); //Ambient color used in lighting. ++ this.animation = options.getfieldvalue('animation', {}); //Animtation parameters. ++ this.arrays = options.getfieldvalue('arrays', {}); //Storage for webgl arrays. ++ this.caxis = options.getfieldvalue('caxis', [0.0, 1.0]); //Color axis for texturing. ++ this.center = options.getfieldvalue('center', vec3.create()); //Center of rotation/scaling. ++ this.cullFace = options.getfieldvalue('cullFace', this.gl.BACK); //GL enum for face culling back/front faces. ++ this.computeIndices = options.getfieldvalue('computeIndices', true); //Specifies whether or not indices need to be computed during patching. ++ this.disableDepthTest = options.getfieldvalue('disableDepthTest', false); //GL enum for enabling/disabling depth testing. ++ this.diffuseColor = options.getfieldvalue('diffuseColor', [0.0, 0.0, 0.0, 1.0]); //Diffuse color in vec4 rgba format. ++ this.drawMode = options.getfieldvalue('drawMode', this.gl.TRIANGLES); //GL enum for draw mode. ++ this.drawOrder = options.getfieldvalue('drawOrder', 1); //Drawing order for non-depth tested/transparent objects. Higher numbers are drawn. first. ++ this.enabled = options.getfieldvalue('enabled', true); //Toggles display of this nodde. ++ this.enableCullFace = options.getfieldvalue('enableCullFace', true); //Toggles use of face culling. ++ this.hideOcean = options.getfieldvalue('hideOcean', false); //ISSM shader uniform controlling ocean masking ++ this.lineWidth = options.getfieldvalue('lineWidth', 1.0); //Controls width of gl lines. No reliable support across windows platforms. ++ this.lightingBias = options.getfieldvalue('lightingBias', 0.0); //Controls width of gl lines. No reliable support across windows platforms. ++ this.log = options.getfieldvalue('log', false); //Controls logarithmic color axis scaling for texturing. ++ this.maskColor = options.getfieldvalue('maskColor', vec4.fromValues(0.0, 0.0, 1.0, 1.0)); //ISSM shader uniform controlling ocean masking color. ++ this.maskEnabled = options.getfieldvalue('maskEnabled', false); //ISSM shader uniform toggling ocean masking. ++ this.maskHeight = options.getfieldvalue('maskHeight', 150.0); //ISSM shader uniform controlling height at which ocean masking is cut off. ++ this.maskZerosColor = options.getfieldvalue('maskZerosColor', [1.0, 1.0, 1.0, 1.0]); //ISSM shader uniform controlling value masking color. ++ this.maskZerosEnabled = options.getfieldvalue('maskZerosEnabled', false); //ISSM shader uniform toggling value masking. ++ this.maskZerosTolerance = options.getfieldvalue('maskZerosTolerance', 1e-6); //ISSM shader uniform controlling tolerance of value to zero value when masking. ++ this.maskZerosZeroValue = options.getfieldvalue('maskZerosZeroValue', 0.5); //ISSM shader uniform controlling zero value masking offset. ++ this.mesh = options.getfieldvalue('mesh', undefined); //Litegl GL.Mesh class used for drawing. ++ this.name = options.getfieldvalue('name', 'node'); //Name of node. ++ this.nanIndices = options.getfieldvalue('nanIndices', new Set()); //Set of NaN indices to mask out of mesh. ++ this.octree = options.getfieldvalue('octree', undefined); //Fast raytracing octree object. ++ this.pointSize = options.getfieldvalue('pointSize', 15.0); //Size of points when displaying GL.POINTS. ++ this.shaderName = options.getfieldvalue('shaderName', 'Colored'); //Name of shader to use. ++ this.shader = options.getfieldvalue('shader', this.gl.shaders[this.shaderName]); //Compiled shader object. ++ this.specularColor = options.getfieldvalue('specularColor', [1.0, 1.0, 1.0, 1.0]); //Specular reflection color used in lighting. ++ this.specularStrength = options.getfieldvalue('specularStrength', 1.0); //Specular reflection power - represents specular highlight sharpness. ++ this.specularPower = options.getfieldvalue('specularPower', 5); //Specular reflection power - represents specular highlight sharpness. ++ this.texture = options.getfieldvalue('texture', undefined); //GL texture object. ++ this.scale = options.getfieldvalue('scale', vec3.fromValues(1, 1, 1)); //XYZ scaling of the node. ++ this.renderObject = options.getfieldvalue('renderObject', {}); //Field for additional render object state information not necessarily related to node display. ++ this.rotation = options.getfieldvalue('rotation', vec3.create()); //XYZ rotation of the node. ++ this.rotationQuaternion = options.getfieldvalue('rotationQuaternion', quat.create()); //Quaternion rotation of the node. Not currently in use. ++ this.translation = options.getfieldvalue('translation', vec3.create()); //XYZ translation of the node. ++ this.modelMatrix = options.getfieldvalue('modelMatrix', mat4.create()); //Model matrix computed from updateModelMatrix function. ++ this.translationMatrix = options.getfieldvalue('translationMatrix', mat4.create()); //Intermediate translation matrix computed from updateModelMatrix function. ++ this.rotationMatrix = options.getfieldvalue('rotationMatrix', mat4.create()); //Intermediate rotation matrix computed from updateModelMatrix function. ++ this.scaleMatrix = options.getfieldvalue('scaleMatrix', mat4.create()); //Intermediate scale matrix computed from updateModelMatrix function. ++ this.inverseModelMatrix = options.getfieldvalue('inverseModelMatrix', mat4.create()); //Inverse model matrix. ++ this.inverseRotationMatrix = options.getfieldvalue('inverseRotationMatrix', mat4.create()); //Inverse rotation matrix. + //}}} + //initialize {{{ +- //if (this.name in canvas.nodes) abort? ++ //if (this.name in canvas.nodes) abort? + this.updateModelMatrix(); + this.updateDiffuseColor(); + canvas.nodes[this.name] = this; + //}}} + } //}}} ++Node.prototype.eulerToQuaternion = function(pitch, roll, yaw) { //{{{ ++ var t0 = Math.cos(yaw * 0.5); ++ var t1 = Math.sin(yaw * 0.5); ++ var t2 = Math.cos(roll * 0.5); ++ var t3 = Math.sin(roll * 0.5); ++ var t4 = Math.cos(pitch * 0.5); ++ var t5 = Math.sin(pitch * 0.5); ++ ++ var w = t0 * t2 * t4 + t1 * t3 * t5; ++ var x = t0 * t3 * t4 - t1 * t2 * t5; ++ var y = t0 * t2 * t5 + t1 * t3 * t4; ++ var z = t1 * t2 * t4 - t0 * t3 * t5; ++ return quat.fromValues(x, y, z, w); ++} //}}} ++Node.prototype.quaternionToEuler = function(q) { //{{{ ++ var ysqr = q[1] * q[1]; ++ ++ // roll (x-axis rotation) ++ var t0 = +2.0 * (q[3] * q[0] + q[1] * q[2]); ++ var t1 = +1.0 - 2.0 * (q[0] * q[0] + ysqr); ++ var roll = Math.atan2(t0, t1); ++ ++ // pitch (y-axis rotation) ++ var t2 = +2.0 * (q[3] * q[1] - q[2] * q[0]); ++ t2 = t2 > 1.0 ? 1.0 : t2; ++ t2 = t2 < -1.0 ? -1.0 : t2; ++ var pitch = Math.asin(t2); ++ ++ // yaw (z-axis rotation) ++ var t3 = +2.0 * (q[3] * q[2] + q[0] * q[1]); ++ var t4 = +1.0 - 2.0 * (ysqr + q[2] * q[2]); ++ var yaw = Math.atan2(t3, t4); ++ ++ return [pitch * RAD2DEG, roll * RAD2DEG, yaw * RAD2DEG]; ++} //}}} + Node.prototype.updateModelMatrix = function() { //{{{ + //Update the model matrix if rotation, scale, or translation have been manually modified. + var modelMatrix = mat4.create(); +@@ -82,7 +126,14 @@ + var xRotationMatrix = mat4.create(); + mat4.rotate(xRotationMatrix, xRotationMatrix, DEG2RAD * this.rotation[0], [1.0, 0.0, 0.0]); + mat4.multiply(rotationMatrix, xRotationMatrix, rotationMatrix); +- mat4.multiply(modelMatrix, rotationMatrix, modelMatrix); ++ mat4.multiply(modelMatrix, rotationMatrix, modelMatrix); ++ ++ //var rotationQuaternionX = this.eulerToQuaternion(0, -DEG2RAD * this.rotation[0], 0); ++ //var rotationQuaternionY = this.eulerToQuaternion(DEG2RAD * this.rotation[1], 0, 0); ++ //mat4.fromQuat(this.rotationMatrix, quat.multiply(quat.create(), rotationQuaternionY, rotationQuaternionX)); ++ ++ //mat4.multiply(this.modelMatrix, this.rotationMatrix, this.modelMatrix); ++ + + mat4.identity(translationMatrix); + mat4.translate(translationMatrix, translationMatrix, this.center); //relative translation +@@ -123,7 +174,7 @@ + } //}}} + Node.prototype.patch = function() { //{{{ + //Emulates the behavior of MATLAB patch function by constructing a mesh from arguments. +- //Limitations: ++ //Limitations: + // -Expects pair labeled arguments ('FaceColor','none',...). + // -Only handles Face/Vertices/FaceVertexCData element/node plots. + // -Only supports FaceColor 'interp' and 'none'. +@@ -148,7 +199,7 @@ + this.patchIndices(faces, faceColor); + + this.mesh = GL.Mesh.load(this.arrays, null, null, this.gl); +- //this.mesh.computeNormals(); ++ this.mesh.computeNormals(); + this.computeOctree(); + } //}}} + Node.prototype.patchVertices = function(faceVertexCData, faces, vertices) { //{{{ +@@ -238,7 +289,7 @@ + //Use logarithmic scaling if it is valid + if (this.log !== false && this.log !== 'off') { + caxis = [ +- Math.log10(caxis[0]) / Math.log10(this.log), ++ Math.log10(caxis[0]) / Math.log10(this.log), + Math.log10(caxis[1]) / Math.log10(this.log) + ]; + } +@@ -388,7 +439,8 @@ + var coordinateObject = vertices[i]; + var j = 0; + if (isEmptyOrUndefined(indices)) { +- for (var key in object) { ++ for (var key in coordinateObject) { ++ console.log(key); + array[j++] = coordinateObject[key]; + } + } +@@ -406,7 +458,7 @@ + var z = vertices[2]; + var meshVertices = mesh.getBuffer('vertices').data; + var meshIndicies = mesh.getIndexBuffer('triangles').data; +- var indicies = new Uint16Array(meshIndicies.length * x.length); ++ var indices = new Uint16Array(meshIndicies.length * x.length); + var size = meshVertices.length * x.length / 3; + newX = new Float32Array(size); + newY = new Float32Array(size); +@@ -422,27 +474,48 @@ + } + var offset = i * meshVertices.length / 3; + for (var j = 0; j < meshIndicies.length;) { +- indicies[e++] = meshIndicies[j++] + offset; ++ indices[e++] = meshIndicies[j++] + offset; + } + } + +- this.patch('Faces', indicies, 'Vertices', [newX, newY, newZ], 'FaceColor', 'interp'); ++ this.patch('Faces', indices, 'Vertices', [newX, newY, newZ], 'FaceColor', 'interp'); + } //}}} +-Node.prototype.scaleVertices = function(md, x, y, z, scale) { //{{{ ++Node.prototype.scaleVertices = function(md, x, y, z, elements, scale, maskObject) { //{{{ + //Scales and returns vertices x, y, and z by factor scale. Uses md.geometry.scale for heightscaling in 3d meshes. + if (md.mesh.classname() === 'mesh3dsurface') { +- var xyz, magnitude; +- x = x.slice(); +- y = y.slice(); +- z = z.slice(); +- for(var i = 0; i < x.length; i++) { +- xyz = vec3.fromValues(x[i], y[i], z[i]); +- magnitude = 1 + md.geometry.surface[i] * scale / vec3.length(xyz); +- vec3.scale(xyz, xyz, magnitude); +- x[i] = xyz[0]; +- y[i] = xyz[1]; +- z[i] = xyz[2]; ++ if (!maskObject.enabled) { ++ var xyz, magnitude; ++ x = x.slice(); ++ y = y.slice(); ++ z = z.slice(); ++ for(var i = 0; i < x.length; i++) { ++ xyz = vec3.fromValues(x[i], y[i], z[i]); ++ magnitude = 1 + md.geometry.surface[i] * scale / vec3.length(xyz); ++ vec3.scale(xyz, xyz, magnitude); ++ x[i] = xyz[0]; ++ y[i] = xyz[1]; ++ z[i] = xyz[2]; ++ } + } ++ else { ++ var mask = maskObject.mask; ++ var maskScale = maskObject.scale; ++ var element; ++ for (var i = 0; i < mask.length; i++) { ++ if (mask[i] === 1) { ++ element = elements[i]; ++ for (var j = 0; j < 3; j++) { ++ xyz = vec3.fromValues(x[element[j] - 1], y[element[j] - 1], z[element[j] - 1]); ++ magnitude = 1 + md.geometry.surface[element[j] - 1] * scale * maskScale / vec3.length(xyz); ++ vec3.scale(xyz, xyz, magnitude); ++ x[element[j] - 1] = xyz[0]; ++ y[element[j] - 1] = xyz[1]; ++ z[element[j] - 1] = xyz[2]; ++ } ++ ++ } ++ } ++ } + } + else { + z = z.slice(); +Index: ../trunk-jpl/src/m/plot/applyoptions.js +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.js (revision 21910) ++++ ../trunk-jpl/src/m/plot/applyoptions.js (revision 21911) +@@ -5,7 +5,7 @@ + // applyoptions(md, data, options) + // + // See also: PLOTMODEL, PARSE_OPTIONS +- ++ + //{{{ colorbar + var gl = canvas.gl; + if (options.exist('colorbar')) { +@@ -15,7 +15,7 @@ + var colorbarinnerlabels = options.getfieldvalue('colorbarinnerlabels','off'); + var ccanvasid, ctitleid, clabelsid, ccanvas, ctitle, clabels, ccontext, cmap, colorbar, cwidth, cheight, cgradient, color, y, x; + //}}} +- //{{{ Create colorbar labels ++ //{{{ Create colorbar labels + var labels = []; + var cdivisions = options.getfieldvalue('colorbarnticks', 6); + var caxisdelta = caxis[1] - caxis[0]; +@@ -48,7 +48,7 @@ + } + } //}}} + //{{{ Initialize colorbar canvas +- ccanvasid = options.getfieldvalue('colorbarid', options.getfieldvalue('canvasid').replace('canvas','colorbar-canvas')); ++ ccanvasid = options.getfieldvalue('colorbarid', options.getfieldvalue('canvasid').replace('canvas','colorbar-canvas')); + ccanvas = $('#'+ccanvasid)[0]; + cwidth = ccanvas.width*options.getfieldvalue('colorbarwidth', 1); + cheight = ccanvas.height*options.getfieldvalue('colorbarheight', 1); +@@ -62,7 +62,7 @@ + //{{{ Draw colorbar gradient + 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)]; ++ color = [Math.round(color[0]*255), Math.round(color[1]*255), Math.round(color[2]*255)]; + cgradient.addColorStop(i/colorbar.length*(cdivisions/(cdivisions+1.0))+(1.0/(cdivisions+1.0)),'rgba('+color.toString()+', 1.0)'); + } + ccontext.fillStyle=cgradient; +@@ -106,7 +106,7 @@ + ctitle = $('#'+ctitleid); + if (options.exist('colorbartitle')) { ctitle.html(options.getfieldvalue('colorbartitle')); } + //}}} +- } ++ } + } //}}} + //{{{ texture canvas + var tcontext, tcanvas, tcanvasid, tURL, tgradient; +@@ -118,15 +118,15 @@ + } + tcontext = tcanvas.getContext('2d'); + tgradient = tcontext.createLinearGradient(0, 0, 0, 256); +- ++ + var cmap = options.getfieldvalue('colormap','jet'); + var colorbar = colorbars[cmap]; + 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)]; ++ color = [Math.round(color[0]*255), Math.round(color[1]*255), Math.round(color[2]*255)]; + tgradient.addColorStop(i/colorbar.length,'rgba('+color.toString()+', 1.0)'); + } +- ++ + tcontext.fillStyle = tgradient; + tcontext.fillRect(0, 0, 256, 256); + tURL = tcanvas.toDataURL(); +@@ -133,102 +133,54 @@ + canvas.unitNode.texture = initTexture(canvas.gl, tURL); + //}}} + //{{{ text display +- if (options.exist('textlabels')) { +- var textcanvas, textcanvasid; +- textcanvasid = options.getfieldvalue('textcanvasid', options.getfieldvalue('canvasid')+'-text'); +- textcanvas = $('#'+textcanvasid); +- textcanvas.textlabels = options.getfieldvalue('textlabels',[]); ++ var overlaycanvasid = options.getfieldvalue('overlayid', options.getfieldvalue('canvasid')+'-overlay'); ++ var overlaycanvas = $('#'+overlaycanvasid)[0]; ++ if (!isEmptyOrUndefined(overlaycanvas)) { ++ //Get drawing context and save reference on main WebGL canvas ++ var ctx = overlaycanvas.getContext('2d'); ++ canvas.overlaycanvas = overlaycanvas; + +- //setup drawing function for text canvas draw calls +- textcanvas.draw = function(canvas) { +- var textcontext, textlabels, textlabel, textcanvaswidth, textcanvasheight, textcoordinates; +- var textposition = vec3.create(); +- var mvpMatrix = mat4.create(); +- +- //ensure correct canvas coordinate scaling +- textcanvaswidth = this[0].clientWidth; +- textcanvasheight = this[0].clientHeight; +- this[0].width = textcanvaswidth; +- this[0].height = textcanvasheight; +- +- textcontext = this[0].getContext('2d'); +- textlabels = options.getfieldvalue('textlabels',[]); +- textcontext.clearRect(0, 0, textcanvaswidth, textcanvasheight); +- +- //worldspace to screenspace transformation for text +- for (text in textlabels) { +- textlabel = textlabels[text]; +- mat4.multiply(mvpMatrix, canvas.camera.vpMatrix, canvas.nodes.overlay.modelMatrix); +- textposition = vec3.transformMat4(textposition, textlabel.pos, mvpMatrix); +- if (textposition[2] > 1) { //clip coordinates with z > 1 +- continue; +- } +- textcoordinates = [(textposition[0]+1.0)/2.0*textcanvaswidth, (-textposition[1]+1.0)/2.0*textcanvasheight]; //NDC to screenspace +- textcontext.font = String(options.getfieldvalue('colorbarfontsize', 18))+'px "Lato", Helvetica, Arial, sans-serif'; +- textcontext.fillStyle = options.getfieldvalue('colorbarfontcolor','black'); +- textcontext.strokeStyle = options.getfieldvalue('colorbarfontcolor','black'); +- textcontext.textAlign = 'center'; +- textcontext.textBaseline = 'middle'; +- textcontext.fillText(textlabel.text, textcoordinates[0], textcoordinates[1]); +- textcontext.strokeText(textlabel.text, textcoordinates[0], textcoordinates[1]); +- } ++ //Resize interal viewport coordinates to match screenspace coordinates ++ var rect = overlaycanvas.getBoundingClientRect(); ++ overlaycanvas.width = rect.width; ++ overlaycanvas.height = rect.height; ++ ++ //Clear canvas each frame for any new drawings ++ canvas.overlayHandlers['draw'] = function(overlaycanvas) { ++ ctx.clearRect(0, 0, overlaycanvas.width, overlaycanvas.height); + } +- canvas.textcanvas = textcanvas; +- } //}}} ++ } + //{{{ lat long overlay + if (options.exist('latlongoverlay')) { +- var overlaycanvasid = options.getfieldvalue('latlongoverlayid', options.getfieldvalue('canvasid')+'-overlay'); +- var overlaycanvas = $('#'+overlaycanvasid)[0]; + var latitudes = { + //'-90': 1, + //'-65': .999, + '-60': 0.994046875, +- //'-55': 0.983187500000002, +- //'-50': 0.97173550854167, + '-45': 0.955729166666666, +- //'-40': 0.94218750000000218, +- //'-35': 0.94218750000000218, + '-30': 0.9226562500000024, +- //'-25': 0.87934895833333526, +- //'-20': 0.856572916666669, + //'-15': 0.830729166666665, +- //'-10': 0.803552708333336, +- //'-5': 0.77395833333333541, + '0': 0.74218749999999811, +- //'5': 0.70950364583333347, +- //'10': 0.67479166666666823, + //'15': 0.63932291666666663, +- //'20': 0.60171875, +- //'25': 0.563453125, + '30': 0.523390625000001, +- //'35': 0.48401875, +- //'40': 0.44296875, + '45': 0.4020001, +- //'50': 0.3578125, +- //'55': 0.311875, + '60': 0.26953124999999978, + //'65': 0.225390625, +- //'70': 0.18125, +- //'75': 0.13541666666666671, +- //'80': 0.08953125, +- //'85': 0.046250000000000013, + //'90': 0.0, + } + var longitudes = [-150, -120, -90, -60, -30, 0, 30, 60, 90, 120, 150, 180]; +- overlaycanvas.draw = function(canvas) { +- var rect = overlaycanvas.getBoundingClientRect(); +- overlaycanvas.width = rect.width; +- overlaycanvas.height = rect.height; +- var ctx = overlaycanvas.getContext('2d'); ++ canvas.overlayHandlers['latlong'] = function(canvas) { ++ //Transform from world space to viewport space + var centerx = overlaycanvas.width / 2; + var centery = overlaycanvas.height / 2; + var radius = (overlaycanvas.height) / 2; ++ ++ //Draw latitudes + ctx.setLineDash([5, 10]); + for(latitude in latitudes) { + ctx.beginPath(); + ctx.arc(centerx, centery, radius * latitudes[latitude], 0, 2 * Math.PI); + ctx.stroke(); +- ctx.font = String(options.getfieldvalue('colorbarfontsize', 18))+'px "Lato", Helvetica, Arial, sans-serif'; ++ ctx.font = 'bold ' + String(options.getfieldvalue('colorbarfontsize', 18))+'px "Lato", Helvetica, Arial, sans-serif'; + ctx.fillStyle = options.getfieldvalue('colorbarfontcolor','black'); + ctx.strokeStyle = options.getfieldvalue('colorbarfontcolor','black'); + ctx.textAlign = 'center'; +@@ -236,6 +188,7 @@ + ctx.fillText(latitude, centerx, centery + radius * latitudes[latitude]); + ctx.strokeText(latitude, centerx, centery + radius * latitudes[latitude]); + } ++ //Draw longitudes + ctx.setLineDash([1, 0]); + for (longitude in longitudes) { + ctx.beginPath(); +@@ -244,39 +197,85 @@ + ctx.stroke(); + } + } +- canvas.overlaycanvas = overlaycanvas; + } //}}} ++ if (options.exist('textlabels')) { ++ //Attatch new overlay handler to display text labels ++ var textLabels = options.getfieldvalue('textlabels',[]); ++ canvas.overlayHandlers['text'] = function(canvas) { ++ for (var i = 0; i < textLabels.length; i++) { ++ //Get text label to display ++ var textLabel = textLabels[i]; ++ textLabel = { ++ position: defaultFor(textLabel.position, vec3.create()), ++ text: defaultFor(textLabel.text, ''), ++ fontSize: defaultFor(textLabel.fontSize, 18), ++ fontColor: defaultFor(textLabel.fontColor, 'black'), ++ ++ }; ++ ++ // function declared in slr-gfm sim-front-end-controller.js ++ // if labels are behind the globe sphere then skip iteartion and do not display them ++ if (isLabelVisible(textLabel)) { ++ //Transform from world space to viewport space ++ var screenPoint = vec3.transformMat4(vec3.create(), textLabel.position, canvas.camera.vpMatrix); ++ var x = (screenPoint[0] + 1.0) * (canvas.width / 2) + canvas.selector.offset().left; ++ var y = (-screenPoint[1] + 1.0) * (canvas.height / 2) + canvas.selector.offset().top; ++ ++ //Draw text ++ ctx.font = 'bold ' + String(textLabel.fontSize) + 'px Arial Black, sans-serif'; ++ ctx.fillStyle = textLabel.fontColor; ++ ctx.strokeStyle = 'white'; ++ ctx.textAlign = 'center'; ++ ctx.textBaseline = 'middle'; ++ ctx.fillText(textLabel.text, x, y); ++ ctx.strokeText(textLabel.text, x, y); ++ } ++ } ++ } ++ } //}}} + //{{{ additional rendering nodes + if (options.exist('render')) { + var meshresults = processmesh(md, data, options); +- var x = meshresults[0]; +- var y = meshresults[1]; +- var z = meshresults[2]; ++ var x = meshresults[0]; ++ var y = meshresults[1]; ++ var z = meshresults[2]; + var elements = meshresults[3]; +- var is2d = meshresults[4]; ++ var is2d = meshresults[4]; + var isplanet = meshresults[5]; +- ++ + var xlim = options.getfieldvalue('xlim', [ArrayMin(x), ArrayMax(x)]); + var ylim = options.getfieldvalue('ylim', [ArrayMin(y), ArrayMax(y)]); + var zlim = options.getfieldvalue('zlim', [ArrayMin(z), ArrayMax(z)]); + +- var global = vec3.length([(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2]) < 6371000/10; //tolerance for global models = center is 637100 meters away from center of earth +- var translation = global ? [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2] : [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) - 6371000, (zlim[0] + zlim[1]) / 2]; +- ++ var global = vec3.length([(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2]) < 6371000/10; //tolerance for global models = center is 637100 meters away from center of earth ++ var translation = global ? [(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, (zlim[0] + zlim[1]) / 2] : canvas.view.position; ++ + var renderObjects = options.getfieldvalue('render',{}); +- if ('sky' in renderObjects && !('sky' in canvas.nodes)) { +- var object = renderObjects.sky; ++ for (var renderObject in renderObjects) { ++ //Modify renderObejct? ++ var object = renderObjects[renderObject]; + object = { +- enabled: defaultFor(object.enabled, true), +- scale: defaultFor(object.scale, 1), ++ enabled: defaultFor(object.enabled, true), //Toggle display of the render object node ++ scale: defaultFor(object.scale, 1), //Model matrix scaling ++ x: defaultFor(object.x, [0.0, 1.0, 0.0, 0.0, 0.0, 0.0]), //x coordinate array ++ y: defaultFor(object.y, [0.0, 0.0, 0.0, 1.0, 0.0, 0.0]), //y coordinate array ++ z: defaultFor(object.z, [0.0, 0.0, 0.0, 0.0, 0.0, 1.0]), //z coordinate array ++ indices: defaultFor(object.indices, []), //indices array ++ name: defaultFor(object.name, 'NY'), //Text to display for cities. ++ size: defaultFor(object.size, 1), //Physical size of the object in meters ++ color: defaultFor(object.color, 'black'), //Diffuse color of object ++ height: defaultFor(object.height, 25000), //Height of object along y axis, currently for clouds only ++ range: defaultFor(object.range, 120000), //Range of sz plane to spawn object, currently for clouds only ++ quantity: defaultFor(object.quantity, 15) //Quantity of objects to display, currently for clouds only + }; +- if (object.enabled) { +- var atmosphereScale = 1.25; +- var mesh = GL.Mesh.icosahedron({size: 6371000 * atmosphereScale, subdivisions: 5}); ++ if (!object.enabled) { continue; } ++ if ('sky' === renderObject && !('sky' in canvas.nodes)) { ++ var mesh = GL.Mesh.icosahedron({size: 6371000 * canvas.atmosphere.scaleHeight, subdivisions: 5}); + var texture = initTexture(gl, canvas.rootPath + 'textures/TychoSkymapII_t4_2k.jpg'); + node = new Node( + 'canvas', canvas, + 'options', options, ++ 'renderObject', object, + 'name', 'sky', + 'shaderName', 'SkyFromSpace', + 'cullFace', gl.FRONT, +@@ -285,19 +284,13 @@ + 'translation',translation + ); + } +- } +- if ('space' in renderObjects && !('space' in canvas.nodes)) { +- var object = renderObjects.space; +- object = { +- enabled: defaultFor(object.enabled, true), +- scale: defaultFor(object.scale, 1), +- }; +- if (object.enabled) { ++ if ('space' === renderObject && !('space' in canvas.nodes)) { + var mesh = GL.Mesh.sphere({size: 6371000 * 20}); + var texture = initTexture(gl, canvas.rootPath + 'textures/TychoSkymapII_t4_2k.jpg'); + node = new Node( + 'canvas', canvas, + 'options', options, ++ 'renderObject', object, + 'name', 'space', + 'shaderName', 'Textured', + 'cullFace', gl.FRONT, +@@ -307,20 +300,11 @@ + 'translation',translation + ); + } +- } +- if ('coastlines' in renderObjects && !('coastlines' in canvas.nodes)) { +- var object = renderObjects.coastlines; +- object = { +- enabled: defaultFor(object.enabled, false), +- scale: defaultFor(object.scale, 1), +- x: defaultFor(object.x, {}), +- y: defaultFor(object.y, {}), +- z: defaultFor(object.z, {}) +- }; +- if (object.enabled) { ++ if ('coastlines' === renderObject && !('coastlines' in canvas.nodes)) { + node = new Node( + 'canvas', canvas, + 'options', options, ++ 'renderObject', object, + 'name', 'coastlines', + 'shaderName', 'Colored', + 'drawMode', gl.LINE_STRIP, +@@ -330,49 +314,28 @@ + ); + node.patch('Vertices', [object.x, object.y, object.z], 'FaceColor', 'none'); + } +- } +- if ('graticule' in renderObjects && !('graticule' in canvas.nodes)) { +- var object = renderObjects.graticule; +- object = { +- enabled: defaultFor(object.enabled, false), +- scale: defaultFor(object.scale, 1), +- x: defaultFor(object.x, {}), +- y: defaultFor(object.y, {}), +- z: defaultFor(object.z, {}) +- }; +- if (object.enabled) { ++ if ('graticule' === renderObject && !('graticule' in canvas.nodes)) { + node = new Node( + 'canvas', canvas, + 'options', options, ++ 'renderObject', object, + 'name', 'graticule', + 'shaderName', 'Colored', + 'drawMode', gl.LINE_STRIP, + 'lineWidth', options.getfieldvalue('linewidth', 1), + 'scale', [object.scale, object.scale, object.scale], +- 'rotation', [-90, 0, 0] ++ 'rotation', [-90, 180, 0] + ); + node.patch('Vertices', [object.x, object.y, object.z], 'FaceColor', 'none'); + } +- } +- if ('cities' in renderObjects && !('cities' in canvas.nodes)) { +- var object = renderObjects.cities; +- object = { +- enabled: defaultFor(object.enabled, false), +- scale: defaultFor(object.scale, 1), +- size: defaultFor(object.size, 1.5), +- color: defaultFor(object.color, 'black'), +- x: defaultFor(object.x, {}), +- y: defaultFor(object.y, {}), +- z: defaultFor(object.z, {}), +- indices: defaultFor(object.indices, {}) +- }; +- if (object.enabled) { ++ if ('cities' === renderObject && !('cities' in canvas.nodes)) { + var mesh = GL.Mesh.icosahedron({size: object.size, subdivisions: 1}); + node = new Node( + 'canvas', canvas, + 'options', options, ++ 'renderObject', object, + 'name', 'cities', +- 'shaderName', 'Colored', ++ 'shaderName', 'ColoredDiffuse', + 'diffuseColor', object.color, + 'lineWidth', options.getfieldvalue('linewidth', 1), + 'scale', [object.scale, object.scale, object.scale], +@@ -380,46 +343,42 @@ + ); + node.geometryShader('Mesh', mesh, 'Vertices', [object.x, object.y, object.z], 'Indices', object.indices); + } +- } +- if ('city' in renderObjects) { +- var object = renderObjects.city; +- object = { +- enabled: defaultFor(object.enabled, false), +- name: defaultFor(object.name, 'NY'), +- size: defaultFor(object.size, 15000), +- color: defaultFor(object.color, 'magenta'), +- x: defaultFor(object.x, {}), +- y: defaultFor(object.y, {}), +- z: defaultFor(object.z, {}) +- }; +- if (object.enabled) { ++ if ('axis' === renderObject && !('axis' in canvas.nodes)) { ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'renderObject', object, ++ 'name', 'axis', ++ 'shaderName', 'Colored', ++ 'drawMode', gl.LINES, ++ 'lineWidth', options.getfieldvalue('linewidth', 1), ++ 'scale', [object.scale, object.scale, object.scale], ++ 'rotation', [0, 0, 0] ++ ); ++ node.patch('Vertices', [object.x, object.y, object.z], 'FaceColor', 'none'); ++ } ++ if ('city' === renderObject) { + //city + var mesh = GL.Mesh.sphere({size: object.size}); + node = new Node( + 'canvas', canvas, + 'options', options, ++ 'renderObject', object, + 'name', 'city', +- 'shaderName', 'Colored', ++ 'shaderName', 'ColoredDiffuse', + 'diffuseColor', object.color, + 'mesh', mesh, + 'translation', [object.x, object.z, -object.y] + ); +- +- var overlaycanvasid = options.getfieldvalue('overlayid', options.getfieldvalue('canvasid')+'-overlay'); +- var overlaycanvas = $('#'+overlaycanvasid)[0]; +- overlaycanvas.draw = function(canvas) { +- var rect = overlaycanvas.getBoundingClientRect(); +- overlaycanvas.width = rect.width; +- overlaycanvas.height = rect.height; +- var ctx = overlaycanvas.getContext('2d'); ++ //Attatch new overlay handler to display city name ++ canvas.overlayHandlers['city'] = function(canvas) { + var node = canvas.nodes['city']; +- node.translation = [object.x, object.z, -object.y]; +- node.updateModelMatrix(); ++ var object = node.renderObject; + var screenPoint = vec3.transformMat4(vec3.create(), node.translation, canvas.camera.vpMatrix); + var x = (screenPoint[0] + 1.0) * (canvas.width / 2) + canvas.selector.offset().left; + var y = (-screenPoint[1] + 1.0) * (canvas.height / 2) + canvas.selector.offset().top; + +- ctx.font = String(options.getfieldvalue('colorbarfontsize', 22))+'px Arial Black, sans-serif'; ++ ctx.font = 'bold ' + String(options.getfieldvalue('colorbarfontsize', 22))+'px Arial Black, sans-serif'; + ctx.fillStyle = options.getfieldvalue('colorbarfontcolor','black'); + ctx.strokeStyle = 'white'; + ctx.textAlign = 'center'; +@@ -427,25 +386,29 @@ + ctx.fillText(object.name, x, y); + ctx.strokeText(object.name, x, y); + } +- canvas.overlaycanvas = overlaycanvas; + } +- } +- if (canvas.clouds.enabled) { +- //clouds +- for (var i = 0; i < canvas.clouds.quantity; i++) { ++ if ('clouds' === renderObject && !('clouds0' in canvas.nodes)) { ++ //clouds + var mesh = GL.Mesh.fromURL(canvas.rootPath+'obj/cloud.obj'); +- translation = [translation[0] + Math.floor((Math.random() * (1 + 12000 - (-12000)) + (-12000))), translation[1] - 405000, translation[2] + Math.floor((Math.random() * (1 + 12000 - (-12000)) + (-12000)))]; +- node = new Node( +- 'canvas', canvas, +- 'options', options, +- 'name', 'clouds' + i, +- 'shaderName', 'Textured', +- 'animation', {'time': Date.now(),'target': translation,'current': translation}, +- 'diffuseColor', [0.7,0.7,0.7,1.0], +- 'mesh', mesh, +- 'scale', [2500, 2500, 2500], +- 'translation', translation +- ); ++ for (var i = 0; i < object.quantity; i++) { ++ //TODO: More options, less magic numbers. Add animation. Better shading. ++ var offset = [ translation[0] + (Math.random() - 0.5) * 2 * object.range, ++ translation[1] + object.height + (Math.random() - 0.5) * 0.2 * object.range, ++ translation[2] + (Math.random() - 0.5) * 2 * object.range]; ++ node = new Node( ++ 'canvas', canvas, ++ 'options', options, ++ 'renderObject', object, ++ 'name', 'clouds' + i, ++ 'shaderName', 'ColoredDiffuse', ++ 'animation', {'time': Date.now(),'target': translation,'current': translation}, ++ 'diffuseColor', [0.7,0.7,0.7,1.0], ++ 'specularColor', [0.0,0.0,0.0,1.0], ++ 'mesh', mesh, ++ 'scale', [object.scale, object.scale, object.scale], ++ 'translation', offset ++ ); ++ } + } + } + } //}}} +Index: ../trunk-jpl/src/m/array/arrayoperations.js +=================================================================== +--- ../trunk-jpl/src/m/array/arrayoperations.js (revision 21910) ++++ ../trunk-jpl/src/m/array/arrayoperations.js (revision 21911) +@@ -1,9 +1,17 @@ + function ArrayMax(array){ //{{{ +- return Math.max.apply(null,array); ++ //Calculate array max using for loop instead of Math.max.apply(null, array) to avoid recursive stack overflow in mobile browsers ++ ++ var max=-Infinity; ++ ++ for (var i=0;i(n); for (int i=0;i(n); for (int i=0;i(n); for (int i=0;i(n); for (int i=0;icounter << "\n"); + ds->counter++; + *pf=Js[ds->counter]; +- for(int i=0;i<*n;i++)X[i]=Xs[ds->priorn*i+ds->counter]; +- for(int i=0;i<*n;i++)G[i]=Gs[ds->priorn*i+ds->counter]; ++ for(int i=0;i<*n;i++) X[i]=Xs[ds->priorn*i+ds->counter]; ++ for(int i=0;i<*n;i++) G[i]=Gs[ds->priorn*i+ds->counter]; + } + ++ printf("J [i] = %g\n",*pf); + } + #endif +Index: ../trunk-jpl/src/wrappers/M1qn3/M1qn3.h +=================================================================== +--- ../trunk-jpl/src/wrappers/M1qn3/M1qn3.h (revision 21911) ++++ ../trunk-jpl/src/wrappers/M1qn3/M1qn3.h (revision 21912) +@@ -29,8 +29,6 @@ + #define XHANDLE prhs[0] + #define GHANDLE prhs[1] + #define JHANDLE prhs[2] +-#define MAXSTEPSHANDLE prhs[3] +-#define MAXITERHANDLE prhs[4] + /* serial output macros: */ + #define XOUT (mxArray**)&plhs[0] + #endif +@@ -38,10 +36,8 @@ + #ifdef _HAVE_PYTHON_MODULES_ + /* serial input macros: */ + #define XHANDLE PyTuple_GetItem(args,0) +-#define GHANDLE PyTuple_GetItem(args,1) +-#define JHANDLE PyTuple_GetItem(args,2) +-#define MAXSTEPSHANDLE PyTuple_GetItem(args,3) +-#define MAXITERHANDLE PyTuple_GetItem(args,4) ++#define GHANDLE PyTuple_GetItem(args,1) ++#define JHANDLE PyTuple_GetItem(args,2) + /* serial output macros: */ + #define XOUT output,0 + #endif Index: /issm/oecreview/Archive/21724-22754/ISSM-21912-21913.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21912-21913.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21912-21913.diff (revision 22755) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/src/wrappers/M1qn3/M1qn3.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/M1qn3/M1qn3.cpp (revision 21912) ++++ ../trunk-jpl/src/wrappers/M1qn3/M1qn3.cpp (revision 21913) +@@ -111,7 +111,7 @@ + &reverse,&indic,izs,rzs,(void*)&data_struct); + + switch(int(omode)){ +- case 0: _printf0_(" Stop requested\n"); break; ++ case 0: /* _printf0_(" Stop requested\n");*/ break; + case 1: _printf0_(" Convergence reached (gradient satisfies stopping criterion)\n"); break; + case 2: _printf0_(" Bad initialization\n"); break; + case 3: _printf0_(" Line search failure\n"); break; +@@ -163,7 +163,5 @@ + for(int i=0;i<*n;i++) X[i]=Xs[ds->priorn*i+ds->counter]; + for(int i=0;i<*n;i++) G[i]=Gs[ds->priorn*i+ds->counter]; + } +- +- printf("J [i] = %g\n",*pf); + } + #endif Index: /issm/oecreview/Archive/21724-22754/ISSM-21913-21914.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21913-21914.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21913-21914.diff (revision 22755) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/m/classes/clusters/pfe.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 21913) ++++ ../trunk-jpl/src/m/classes/clusters/pfe.m (revision 21914) +@@ -353,7 +353,6 @@ + fprintf(fid,'#PBS -e %s.errlog \n\n',modelname); + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); + fprintf(fid,'module load comp-intel/2016.2.181\n'); +- fprintf(fid,'module load mpi-sgi/mpt\n'); + fprintf(fid,'module load netcdf/4.4.1.1_mpt\n'); + fprintf(fid,'module load mpi-sgi/mpt.2.15r20\n'); + fprintf(fid,'export PATH="$PATH:."\n'); Index: /issm/oecreview/Archive/21724-22754/ISSM-21914-21915.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21914-21915.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21914-21915.diff (revision 22755) @@ -0,0 +1,188 @@ +Index: ../trunk-jpl/src/c/analyses/MeltingAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MeltingAnalysis.cpp (revision 21914) ++++ ../trunk-jpl/src/c/analyses/MeltingAnalysis.cpp (revision 21915) +@@ -38,8 +38,6 @@ + }/*}}}*/ + void MeltingAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ + +- int frictionlaw; +- + /*Now, is the model 3d? otherwise, do nothing: */ + if(iomodel->domaintype==Domain2DhorizontalEnum)return; + +Index: ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 21914) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 21915) +@@ -58,7 +58,6 @@ + void HydrologyDCInefficientAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ + + bool isefficientlayer; +- bool element_active; + int hydrology_model; + + /*Fetch data needed: */ +Index: ../trunk-jpl/src/c/bamg/BamgVertex.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/BamgVertex.cpp (revision 21914) ++++ ../trunk-jpl/src/c/bamg/BamgVertex.cpp (revision 21915) +@@ -193,7 +193,6 @@ + double detold = tria->det; + tria->det = bamg::det( (*tria)[0],(*tria)[1] ,(*tria)[2]); + if (loop) { +- BamgVertex *v0,*v1,*v2,*v3; + if (tria->det<0) ok =1; + else if ( (double)tria->det < detold/2 ) ok=1; + } +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21914) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21915) +@@ -132,7 +132,8 @@ + triangles[nbt].color = Tho.subdomains[reft[i]].ReferenceNumber; + nbt++; + } +- if (nbt==0 && nbv==0) { ++ if (nbt==0 && nbv==0){ ++ delete [] refv; + _error_("All triangles have been removed"); + } + delete [] kk; +Index: ../trunk-jpl/src/c/shared/Sorting/binary_search.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Sorting/binary_search.cpp (revision 21914) ++++ ../trunk-jpl/src/c/shared/Sorting/binary_search.cpp (revision 21915) +@@ -14,8 +14,8 @@ + int binary_search(int* poffset,int target,int* sorted_integers,int num_integers){ /*{{{*/ + + /*output: */ +- int offset; //offset, if found +- int found=0; //found=0 if target is not found, 1 otherwise. ++ int offset=0; //offset, if found ++ int found=0; //found=0 if target is not found, 1 otherwise. + + /*intermediary: */ + int *beg = NULL; +Index: ../trunk-jpl/src/c/modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp (revision 21914) ++++ ../trunk-jpl/src/c/modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp (revision 21915) +@@ -148,7 +148,8 @@ + int edge1,edge2,edge3; + + double xel[2],yel[2]; +- double coord1,coord2; ++ double coord1 = 0.; ++ double coord2 = 0.; + double xfinal[2],yfinal[2]; + + /*edge 1: */ +Index: ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp (revision 21914) ++++ ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp (revision 21915) +@@ -32,7 +32,6 @@ + IssmDouble* dzB=NULL; + + /*output: */ +- int m; + IssmDouble* dz=NULL; + + //----------------------Calculate Grid Lengths------------------------------ +Index: ../trunk-jpl/src/c/modules/ExpToLevelSetx/ExpToLevelSetx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ExpToLevelSetx/ExpToLevelSetx.cpp (revision 21914) ++++ ../trunk-jpl/src/c/modules/ExpToLevelSetx/ExpToLevelSetx.cpp (revision 21915) +@@ -11,12 +11,8 @@ + + int ExpToLevelSetx(double** pdistance,double* x, double* y, int nods, Contours* contours){ + +- /*Contour:*/ +- double value; +- + /*output: */ +- double* distance; +- distance = xNew(nods); ++ double* distance = xNew(nods); + for(int i=0;i inline void GenericExternalResult::Marshall(char** pmarshalled_data,int* pmarshalled_data_size, int marshall_direction){/*{{{*/ + +- int size; ++ int size = 0; + + if(marshall_direction==MARSHALLING_FORWARD || marshall_direction == MARSHALLING_SIZE)size=strlen(value)+1; + +Index: ../trunk-jpl/src/c/classes/Params/StringParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Params/StringParam.cpp (revision 21914) ++++ ../trunk-jpl/src/c/classes/Params/StringParam.cpp (revision 21915) +@@ -51,7 +51,7 @@ + /*}}}*/ + void StringParam::Marshall(char** pmarshalled_data,int* pmarshalled_data_size, int marshall_direction){ /*{{{*/ + +- int size; ++ int size = 0; + + if(marshall_direction==MARSHALLING_FORWARD || marshall_direction == MARSHALLING_SIZE)size=strlen(value)+1; + +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21914) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21915) +@@ -151,7 +151,7 @@ + + #ifndef _HAVE_JAVASCRIPT_ + if(this->parameters->Exist(OutputFileNameEnum)) this->parameters->FindParam(&outbinfilename,OutputFileNameEnum); +- if(this-parameters->Exist(LockFileNameEnum)) this->parameters->FindParam(&lockfilename,LockFileNameEnum); ++ if(this->parameters->Exist(LockFileNameEnum)) this->parameters->FindParam(&lockfilename,LockFileNameEnum); + #endif + + /*Delete all the datasets: */ +@@ -177,10 +177,7 @@ + + /*Now delete: */ + if(profiler)delete profiler; +- +- +-} +-/*}}}*/ ++}/*}}}*/ + + /*Object management*/ + void FemModel::CheckPoint(void){/*{{{*/ +Index: ../trunk-jpl/src/c/classes/kriging/Observations.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/Observations.cpp (revision 21914) ++++ ../trunk-jpl/src/c/classes/kriging/Observations.cpp (revision 21915) +@@ -256,6 +256,9 @@ + /*If radius is not provided or is 0, return all observations*/ + if(radius==0) radius=this->quadtree->root->length; + ++ /*For CPPcheck*/ ++ hmin = 2*radius; ++ + /*First, find closest point in Quadtree (fast but might not be the true closest obs)*/ + this->quadtree->ClosestObs(&index,x_interp,y_interp); + if(index>=0){ Index: /issm/oecreview/Archive/21724-22754/ISSM-21915-21916.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21915-21916.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21915-21916.diff (revision 22755) @@ -0,0 +1,40 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21915) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21916) +@@ -1069,6 +1069,7 @@ + f1=gl[1]/(gl[1]-gl[2]); + f2=gl[1]/(gl[1]-gl[0]); + } ++ else _error_("case not possible"); + } + *point1=point; + *fraction1=f1; +@@ -1179,6 +1180,7 @@ + xyz_bis[2][1]=*(xyz_list+3*1+1)+s2*(*(xyz_list+3*2+1)-*(xyz_list+3*1+1)); + xyz_bis[2][2]=*(xyz_list+3*1+2)+s2*(*(xyz_list+3*2+2)-*(xyz_list+3*1+2)); + } ++ else _error_("case not possible"); + + /*Compute fraction of grounded element*/ + GetJacobianDeterminant(&area_init, xyz_list,NULL); +Index: ../trunk-jpl/src/c/classes/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21915) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21916) +@@ -895,6 +895,7 @@ + f1=gl[1]/(gl[1]-gl[2]); + f2=gl[1]/(gl[1]-gl[0]); + } ++ else _error_("case not possible"); + } + *point1=point; + *fraction1=f1; +@@ -990,6 +991,7 @@ + xyz_bis[2][1]=*(xyz_list+3*1+1)+s2*(*(xyz_list+3*2+1)-*(xyz_list+3*1+1)); + xyz_bis[2][2]=*(xyz_list+3*1+2)+s2*(*(xyz_list+3*2+2)-*(xyz_list+3*1+2)); + } ++ else _error_("case not possible"); + + /*Compute fraction of grounded element*/ + GetTriaJacobianDeterminant(&area_init, xyz_list,NULL); Index: /issm/oecreview/Archive/21724-22754/ISSM-21916-21917.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21916-21917.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21916-21917.diff (revision 22755) @@ -0,0 +1,125 @@ +Index: ../trunk-jpl/src/m/classes/SMBd18opdd.py +=================================================================== +--- ../trunk-jpl/src/m/classes/SMBd18opdd.py (revision 21916) ++++ ../trunk-jpl/src/m/classes/SMBd18opdd.py (revision 21917) +@@ -96,8 +96,12 @@ + md = checkfield(md,'fieldname','smb.rlapslgm','>=',0,'numel',[1]) + + if self.isd18opd: +- md = checkfield(md,'fieldname','smb.temperatures_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) +- md = checkfield(md,'fieldname','smb.precipitations_presentday','size',[md.mesh.numberofvertices+1,12],'NaN',1,'Inf',1,'timeseries',1) ++ lent=float(np.size(self.temperatures_presentday,1)) ++ lenp=float(np.size(self.precipitations_presentday,1)) ++ multt=np.ceil(lent/12.)*12. ++ multp=np.ceil(lenp/12.)*12. ++ md = checkfield(md,'fieldname','smb.temperatures_presentday','size',[md.mesh.numberofvertices+1,multt],'NaN',1,'Inf',1,'timeseries',1) ++ md = checkfield(md,'fieldname','smb.precipitations_presentday','size',[md.mesh.numberofvertices+1,multp],'NaN',1,'Inf',1,'timeseries',1) + md = checkfield(md,'fieldname','smb.delta18o','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) + md = checkfield(md,'fieldname','smb.dpermil','>=',0,'numel',[1]) + md = checkfield(md,'fieldname','smb.f','>=',0,'numel',[1]) +Index: ../trunk-jpl/src/m/classes/SMBd18opdd.m +=================================================================== +--- ../trunk-jpl/src/m/classes/SMBd18opdd.m (revision 21916) ++++ ../trunk-jpl/src/m/classes/SMBd18opdd.m (revision 21917) +@@ -75,8 +75,12 @@ + md = checkfield(md,'fieldname','smb.rlaps','>=',0,'numel',1); + md = checkfield(md,'fieldname','smb.rlapslgm','>=',0,'numel',1); + if(self.isd18opd==1) +- md = checkfield(md,'fieldname','smb.temperatures_presentday','size',[md.mesh.numberofvertices+1 12],'NaN',1,'Inf',1,'timeseries',1); +- md = checkfield(md,'fieldname','smb.precipitations_presentday','size',[md.mesh.numberofvertices+1 12],'NaN',1,'Inf',1,'timeseries',1); ++ lent=size(self.temperatures_presentday,2); ++ lenp=size(self.precipitations_presentday,2); ++ multt=ceil(lent/12)*12; ++ multp=ceil(lenp/12)*12; ++ md = checkfield(md,'fieldname','smb.temperatures_presentday','size',[md.mesh.numberofvertices+1 multt],'NaN',1,'Inf',1,'timeseries',1); ++ md = checkfield(md,'fieldname','smb.precipitations_presentday','size',[md.mesh.numberofvertices+1 multp],'NaN',1,'Inf',1,'timeseries',1); + md = checkfield(md,'fieldname','smb.delta18o','NaN',1,'Inf',1,'size',[2,NaN],'singletimeseries',1); + md = checkfield(md,'fieldname','smb.dpermil','>=',0,'numel',1); + md = checkfield(md,'fieldname','smb.f','>=',0,'numel',1); +Index: ../trunk-jpl/src/c/classes/Inputs/TransientInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TransientInput.h (revision 21916) ++++ ../trunk-jpl/src/c/classes/Inputs/TransientInput.h (revision 21917) +@@ -69,7 +69,9 @@ + void GetInputValue(IssmDouble* pvalue,Gauss* gauss ,int index){_error_("not implemented yet");}; + void GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime); + int GetInputInterpolationType(){_error_("not implemented yet!");}; ++ IssmDouble GetTimeByOffset(int offset); + Input* GetTimeInput(IssmDouble time); ++ int GetTimeInputOffset(IssmDouble time); + void GetTimeValues(IssmDouble* values,IssmDouble time){_error_("not implemented yet");}; + void GetVectorFromInputs(Vector* vector,int* doflist); + IssmDouble InfinityNorm(void); +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21916) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21917) +@@ -538,11 +538,12 @@ + IssmDouble* tmp=xNew(numvertices); + IssmDouble Delta18oTime; + IssmDouble dpermil,f; +- IssmDouble time,yts,time_yr,month; ++ IssmDouble time,yts,time_yr,month,time_clim; + this->parameters->FindParam(&time,TimeEnum); + this->parameters->FindParam(&yts,ConstantsYtsEnum); + this->parameters->FindParam(&f,SmbFEnum); + time_yr=floor(time/yts)*yts; ++ time_clim=time_yr; + + /*Get some pdd parameters*/ + dpermil=this->matpar->GetMaterialParameter(SmbDpermilEnum); +@@ -550,13 +551,20 @@ + /*Recover present day temperature and precipitation*/ + Input* input=this->inputs->GetInput(SmbTemperaturesPresentdayEnum); _assert_(input); + Input* input2=this->inputs->GetInput(SmbPrecipitationsPresentdayEnum); _assert_(input2); ++ int offset; ++ ++ offset=dynamic_cast(input)->GetTimeInputOffset(time_yr); ++ if (fmod(offset,12)!=1){ ++ time_clim=floor(dynamic_cast(input)->GetTimeByOffset(offset-fmod(offset,12)+1)/yts)*yts; ++ } ++ + /*loop over vertices: */ + Gauss* gauss=this->NewGauss(); + for(int month=0;month<12;month++) { + for(int iv=0;ivGaussVertex(iv); +- input->GetInputValue(&TemperaturesPresentday[iv*12+month],gauss,month/12.*yts); +- input2->GetInputValue(&PrecipitationsPresentday[iv*12+month],gauss,month/12.*yts); ++ input->GetInputValue(&TemperaturesPresentday[iv*12+month],gauss,time_clim+month/12.*yts); ++ input2->GetInputValue(&PrecipitationsPresentday[iv*12+month],gauss,time_clim+month/12.*yts); + + PrecipitationsPresentday[iv*12+month]=PrecipitationsPresentday[iv*12+month]*yts; + } +Index: ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp (revision 21916) ++++ ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp (revision 21917) +@@ -247,6 +247,27 @@ + delete input; + } + /*}}}*/ ++int TransientInput::GetTimeInputOffset(IssmDouble time){/*{{{*/ ++ ++ int found; ++ int offset; ++ ++ /*go through the timesteps, and figure out which interval we ++ * *fall within. Then interpolate the values on this interval: */ ++ found=binary_search(&offset,time,this->timesteps,this->numtimesteps); ++ if(!found) _error_("Input not found (is TransientInput sorted ?)"); ++ ++ return offset; ++} ++/*}}}*/ ++IssmDouble TransientInput::GetTimeByOffset(int offset){/*{{{*/ ++ ++ if (offset < 0) offset=0; ++ _assert_(this->timesteps[offset]); ++ ++ return this->timesteps[offset]; ++} ++/*}}}*/ + void TransientInput::GetInputUpToCurrentTimeAverages(IssmDouble** pvalues, IssmDouble** ptimes, int* pnumtimes, IssmDouble currenttime){/*{{{*/ + + int i; Index: /issm/oecreview/Archive/21724-22754/ISSM-21917-21918.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21917-21918.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21917-21918.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/test/NightlyRun/test436.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test436.m (revision 21917) ++++ ../trunk-jpl/test/NightlyRun/test436.m (revision 21918) +@@ -22,7 +22,7 @@ + md=solve(md,'Steadystate'); + field_names ={field_names{:},['Vx' i{1}],['Vy' i{1}],['Vz' i{1}],['Vel' i{1}],['Pressure' i{1}],... + ['Temperature' i{1}],['Waterfraction' i{1}],['Enthalpy' i{1}]}; +- field_tolerances={field_tolerances{:},2e-09,1e-09,1e-09,1e-09,1e-13,1e-10,5e-10,5e-10}; ++ field_tolerances={field_tolerances{:},2e-09,1e-09,1e-09,1e-09,1e-13,1e-10,6e-10,5e-10}; + field_values={field_values{:},... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21918-21919.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21918-21919.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21918-21919.diff (revision 22755) @@ -0,0 +1,1445 @@ +Index: ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.h +=================================================================== +--- ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.h (revision 21918) ++++ ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.h (revision 21919) +@@ -11,7 +11,7 @@ + /*NeoPZ includes*/ + /*REAL and STATE definitions, NeoPZ variables itapopo should be read by NeoPZ's config.h*/ + #ifndef REFPATTERNDIR +- # define REFPATTERNDIR "/home/santos/trunk-jpl/externalpackages/neopz/install/include/refpatterns" ++ #define REFPATTERNDIR "/home/santos/trunk-jpl/externalpackages/neopz/install/include/refpatterns" + #endif + + #ifndef REALdouble +@@ -23,7 +23,6 @@ + #endif + + #include +-#include + #include + #include + #include +@@ -35,10 +34,15 @@ + #include + #include + #include ++#include + #include ++#include ++ ++#include "../shared/shared.h" ++ + /*}}}*/ + +-class AdaptiveMeshRefinement : public TPZSaveable { ++class AdaptiveMeshRefinement{ + + public: + +@@ -48,11 +52,6 @@ + AdaptiveMeshRefinement(const AdaptiveMeshRefinement &cp); + AdaptiveMeshRefinement & operator= (const AdaptiveMeshRefinement &cp); + virtual ~AdaptiveMeshRefinement(); +- +- /*Savable methods*/ +- virtual int ClassId() const; +- virtual void Read(TPZStream &buf,void *context); +- virtual void Write(TPZStream &buf,int withclassid); + + /*General methods*/ + void CleanUp(); +@@ -69,11 +68,15 @@ + + private: + /*Private attributes*/ +- int elementswidth; // Geometric nodes for element: 3 == Tria, 4 == Tetra, 6 == Penta ++ int elementswidth; // Geometric nodes for element: 3 == Tria, 4 == Tetra, 6 == Penta + int levelmax; // Max level of refinement + double regionlevel1; // Region which will be refined with level 1 + double regionlevelmax; // Region which will be refined with level max ++ int step; //itapopo testando ++ int smooth_frequency; //itapopo testando + std::vector sid2index; // Vector that keeps index of PZGeoMesh elements used in the ISSM mesh (sid) ++ std::vector index2sid; // Vector that keeps sid of issm mesh elements used in the neopz mesh (index) ++ std::vector specialelementsindex; // Vector that keeps index of the special elements (created to avoid haning nodes) + TPZGeoMesh *fathermesh; // Father Mesh is the entire mesh without refinement + TPZGeoMesh *currentmesh; // Current Mesh is the refined mesh + +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 21918) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 21919) +@@ -176,15 +176,18 @@ + void SmoothedGradThickness(IssmDouble** pdHdx,IssmDouble** pdHdy); + void ThicknessZZErrorEstimator(IssmDouble** pelementerror); + void MeanGroundedIceLevelSet(IssmDouble** pmasklevelset); ++ void GetElementCenterCoordinates(IssmDouble** pxc,IssmDouble** pyc); + #endif + + #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + void ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); + void InitializeAdaptiveRefinementBamg(void); ++ void GethmaxVerticesFromZeroLevelSetDistance(IssmDouble* hmaxvertices,int levelset_type); ++ void GethmaxVerticesFromEstimators(IssmDouble* hmaxvertices,int errorestimator_type); ++ void GetVerticeDistanceToZeroLevelSet(IssmDouble** pverticedistance,int leveset_type); + #endif + + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) +- /*Adaptive mesh refinement methods*/ + void ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); + void InitializeAdaptiveRefinementNeopz(void); + void SetRefPatterns(void); +Index: ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.cpp (revision 21918) ++++ ../trunk-jpl/src/c/classes/AdaptiveMeshRefinement.cpp (revision 21919) +@@ -9,10 +9,7 @@ + #endif + + #include "./AdaptiveMeshRefinement.h" +-#include "TPZVTKGeoMesh.h" +-#include "../shared/shared.h" +-#include "pzgeotriangle.h" +-#include "pzreftriangle.h" ++ + using namespace pzgeom; + + /*Constructor, copy, clean up and destructor*/ +@@ -39,25 +36,17 @@ + this->sid2index.clear(); + this->sid2index.resize(cp.sid2index.size()); + for(int i=0;isid2index[i]=cp.sid2index[i]; +- ++ this->index2sid.clear(); ++ this->index2sid.resize(cp.index2sid.size()); ++ for(int i=0;iindex2sid[i]=cp.index2sid[i]; ++ this->specialelementsindex.clear(); ++ this->specialelementsindex.resize(cp.specialelementsindex.size()); ++ for(int i=0;ispecialelementsindex[i]=cp.specialelementsindex[i]; ++ + return *this; +- + } + /*}}}*/ + AdaptiveMeshRefinement::~AdaptiveMeshRefinement(){/*{{{*/ +- +- bool ismismip = false; +- if(ismismip){//itapopo +- TPZFileStream fstr; +- std::stringstream ss; +- +- ss << this->levelmax; +- std::string AMRfile = "/home/santos/L" + ss.str() + "_amr.txt"; +- +- fstr.OpenWrite(AMRfile.c_str()); +- int withclassid = 1; +- this->Write(fstr,withclassid); +- } + this->CleanUp(); + gRefDBase.clear(); + } +@@ -72,6 +61,8 @@ + this->regionlevel1 = -1; + this->regionlevelmax = -1; + this->sid2index.clear(); ++ this->index2sid.clear(); ++ this->specialelementsindex.clear(); + } + /*}}}*/ + void AdaptiveMeshRefinement::Initialize(){/*{{{*/ +@@ -83,84 +74,14 @@ + this->elementswidth = -1; + this->regionlevel1 = -1; + this->regionlevelmax = -1; ++ this->step = 0; ++ this->smooth_frequency = 1; + this->sid2index.clear(); ++ this->index2sid.clear(); ++ this->specialelementsindex.clear(); + } + /*}}}*/ +-int AdaptiveMeshRefinement::ClassId() const{/*{{{*/ +- return 13829430; //Antartic area with ice shelves (km^2) +-} +-/*}}}*/ +-void AdaptiveMeshRefinement::Read(TPZStream &buf,void *context){/*{{{*/ + +- try +- { +- /* Read the id context*/ +- TPZSaveable::Read(buf,context); +- /* Read class id*/ +- int classid; +- buf.Read(&classid,1); +- /* Verify the class id*/ +- if(classid!=this->ClassId()) _error_("AdaptiveMeshRefinement::Read: Error in restoring AdaptiveMeshRefinement!\n"); +- /* Read simple attributes */ +- buf.Read(&this->levelmax,1); +- buf.Read(&this->elementswidth,1); +- buf.Read(&this->regionlevel1,1); +- buf.Read(&this->regionlevelmax,1); +- /* Read vector attributes*/ +- int size; +- buf.Read(&size,1); +- int* psid2index=xNew(size); +- buf.Read(psid2index,size); +- this->sid2index.clear(); +- this->sid2index.assign(psid2index,psid2index+size); +- /* Read geometric mesh (father)*/ +- TPZSaveable *sv1 = TPZSaveable::Restore(buf,0); +- this->fathermesh = dynamic_cast(sv1); +- /* Read geometric mesh (current)*/ +- TPZSaveable *sv2 = TPZSaveable::Restore(buf,0); +- this->currentmesh = dynamic_cast(sv2); +- /* Cleanup*/ +- xDelete(psid2index); +- } +- catch(const std::exception& e) +- { +- _error_("AdaptiveMeshRefinement::Read: Exception catched!\n"); +- } +- +-} +-/*}}}*/ +-template class TPZRestoreClass;/*{{{*/ +-/*}}}*/ +-void AdaptiveMeshRefinement::Write(TPZStream &buf,int withclassid){/*{{{*/ +- +- try +- { +- /* Write context (this class) class ID*/ +- TPZSaveable::Write(buf,withclassid); +- /* Write this class id*/ +- int classid = this->ClassId(); +- buf.Write(&classid,1); +- /* Write simple attributes */ +- buf.Write(&this->levelmax,1); +- buf.Write(&this->elementswidth,1); +- buf.Write(&this->regionlevel1,1); +- buf.Write(&this->regionlevelmax,1); +- /* Write vector attributes*/ +- int size=this->sid2index.size(); +- int* psid2index=&this->sid2index[0]; +- buf.Write(&size,1);//vector size +- buf.Write(psid2index,this->sid2index.size()); +- /* Write the geometric mesh*/ +- this->fathermesh->Write(buf,this->ClassId()); +- this->currentmesh->Write(buf,this->ClassId()); +- } +- catch(const std::exception& e) +- { +- _error_("AdaptiveMeshRefinement::Write: Exception catched!\n"); +- } +-} +-/*}}}*/ +- + /*Mesh refinement methods*/ + void AdaptiveMeshRefinement::Execute(bool &amr_verbose, + int &numberofelements, +@@ -175,29 +96,69 @@ + if(!this->fathermesh || !this->currentmesh) _error_("Impossible to execute refinement: fathermesh or currentmesh is NULL!\n"); + if(numberofelements!=this->sid2index.size()) _error_("Impossible to execute refinement: sid2index.size is not equal to numberofelements!\n"); + ++ /*Combine the fields*/ ++ double mean_mask = 0; ++ double mean_tauerror = 0; ++ double mean_Herror = 0; ++ int* fmask = xNew(numberofelements); ++ int* ftauerror = xNew(numberofelements); ++ int* fHerror = xNew(numberofelements); ++ int* phi = xNew(numberofelements); ++ /*Calculate mean values*/ ++ for(int i=0;isid2index.size();i++){ ++ mean_mask += masklevelset[i]; ++ mean_tauerror += deviatorictensorerror[i]; ++ mean_Herror += thicknesserror[i]; ++ } ++ mean_mask /= this->sid2index.size(); ++ mean_tauerror /= this->sid2index.size(); ++ mean_Herror /= this->sid2index.size(); ++ /*Filter to thickness*/ ++ for(int i=0;isid2index.size();i++){ ++ fmask[i]=0; ++ if(thicknesserror[i]>mean_Herror) fmask[i]=1; ++ } ++ /*Filter to tau*/ ++ for(int i=0;isid2index.size();i++){ ++ ftauerror[i]=0; ++ if(deviatorictensorerror[i]>mean_tauerror) ftauerror[i]=1; ++ } ++ /*Sum*/ ++ for(int i=0;isid2index.size();i++){ ++ phi[i]=ftauerror[i]+fmask[i]; ++ } ++ + /*Execute the refinement.*/ + this->RefinementProcess(amr_verbose,partiallyfloatedelements,masklevelset,deviatorictensorerror,thicknesserror); +- ++ + /*Get new geometric mesh in ISSM data structure*/ + this->GetMesh(newnumberofvertices,newnumberofelements,x,y,elementslist); +- ++ ++ std::ofstream file("/home/santos/mesh.vtk"); ++ TPZVTKGeoMesh::PrintGMeshVTK(this->currentmesh,file); ++ + /*Verify the new geometry*/ + this->CheckMesh(newnumberofvertices,newnumberofelements,this->elementswidth,x,y,elementslist); + + } + /*}}}*/ +-void AdaptiveMeshRefinement::RefinementProcess(bool &amr_verbose,double* partiallyfloatedelements,double* masklevelset, +- double* deviatorictensorerror,double* thicknesserror){/*{{{*/ ++void AdaptiveMeshRefinement::RefinementProcess(bool &amr_verbose,double* partiallyfloatedelements,double* masklevelset,double* deviatorictensorerror,double* thicknesserror){/*{{{*/ + + if(amr_verbose) _printf_("\n\trefinement process started (level max = " << this->levelmax << ")\n"); + + /*Intermediaries*/ + TPZGeoMesh* nohangingnodesmesh=NULL; ++ ++ //itapopo ++ this->step++; ++ + double mean_mask = 0; + double mean_tauerror = 0; + double mean_Herror = 0; +- double group_error = 0; +- ++ double group_Herror = 0; ++ int index,sid; ++ std::vector specialfatherindex; specialfatherindex.clear(); ++ + /*Calculate mean values*/ + for(int i=0;isid2index.size();i++){ + mean_mask += masklevelset[i]; +@@ -208,33 +169,129 @@ + mean_tauerror /= this->sid2index.size(); + mean_Herror /= this->sid2index.size(); + ++ if(amr_verbose) _printf_("\t\tdeal with special elements...\n"); ++ /*Deal with special elements*/ ++ for(int i=0;ispecialelementsindex.size();i++){ ++ if(this->specialelementsindex[i]==-1) continue; ++ /*Get special element and verify*/ ++ TPZGeoEl* geoel=this->currentmesh->Element(this->specialelementsindex[i]); ++ if(!geoel)_error_("special element (sid) "<HasSubElement())_error_("special element (sid) "<NSubElements()<<" subelements!\n"); ++ if(geoel->MaterialId()!=this->GetElemMaterialID()) _error_("geoel->MaterialId is not GetElemMaterialID!\n"); ++ if(!geoel->Father())_error_("father of special element (sid) "<Father(); ++ TPZVec siblings; ++ father->GetHigherSubElements(siblings); ++ std::vector sidvec; sidvec.resize(siblings.size()); ++ for (int j=0;jindex2sid[siblings[j]->Index()]; ++ } ++ ++ /*Now, reset the data strucure and verify if the siblings should be deleted*/ ++ if(siblings.size()<4){ ++ /*Reset subelements in the father*/ ++ father->ResetSubElements(); ++ }else{ ++ if(siblings.size()!=4) _error_("element (index) "<Index()<<" has "<NSubElements()<<" subelements!\n"); ++ } ++ for (int j=0;jspecialelementsindex.size();k++){ ++ if(this->specialelementsindex[k]==siblings[j]->Index()){ ++ index = siblings[j]->Index(); ++ if(index<0) _error_("index is null!\n"); ++ sid = this->index2sid[index]; ++ if(sid<0) _error_("sid is null!\n"); ++ this->specialelementsindex[k] = -1; ++ this->index2sid[index] = -1; ++ this->sid2index[sid] = -1; ++ } ++ } ++ if(siblings.size()<4){ ++ /*Ok, the special element can be deleted*/ ++ siblings[j]->ResetSubElements(); ++ this->currentmesh->DeleteElement(siblings[j],siblings[j]->Index()); ++ } ++ } ++ ++ /*Now, verify if the father should be refined with uniform pattern (smoother)*/ ++ this->smooth_frequency=10000000; ++ if(siblings.size()==3 || this->step%this->smooth_frequency==0){//it keeps the mesh with uniform elements ++ /*Father has uniform subelements now*/ ++ TPZVec sons; ++ father->Divide(sons); ++ this->smooth_frequency=this->step; ++ }else{ ++ specialfatherindex.push_back(father->Index()); ++ } ++ if(this->specialelementsindex[i]!=-1) _error_("special element "<currentmesh->BuildConnectivity(); ++ + if(amr_verbose) _printf_("\t\tuniform refinement...\n"); ++ /*Deal with uniform elemnts*/ + for(int i=0;isid2index.size();i++){ ++ if(this->sid2index[i]==-1) continue; ++ /*Get element and verify*/ + TPZGeoEl* geoel=this->currentmesh->Element(this->sid2index[i]); +- if(geoel->HasSubElement()) _error_("Impossible to refine: geoel (index) "<sid2index[i]<<" has subelements!\n"); +- if(geoel->MaterialId()!=this->GetElemMaterialID()) _error_("Impossible to refine: geoel->MaterialId is not GetElemMaterialID!\n"); +- /*Refine*/ +- if(thicknesserror[i]>mean_Herror){ ++ if(geoel->HasSubElement()) _error_("element (sid) "<NSubElements()<<" subelements!\n"); ++ if(geoel->MaterialId()!=this->GetElemMaterialID()) _error_("geoel->MaterialId is not GetElemMaterialID!\n"); ++ ++ /*Refine process*/ ++ if(thicknesserror[i]>mean_Herror) ++ { ++ int count=0; ++ TPZGeoEl* father=geoel->Father(); ++ if(father){ ++ for(int j=3;j<6;j++){ ++ index=father->Neighbour(j).Element()->Index(); ++ for(int k=0;k sons; +- if(geoel->Level()levelmax) geoel->Divide(sons); ++ if(geoel->Level()levelmax && count==0) geoel->Divide(sons); + } +- else if(geoel->Level()>0){ /*try to unrefine*/ +- TPZVec sons; +- geoel->Father()->GetHigherSubElements(sons); +- group_error=0; +- for(int j=0;jIndex(); ++ else if(geoel->Level()>0) ++ {/*Unrefine process*/ ++ ++ /*Get siblings and verify*/ ++ TPZVec siblings; ++ geoel->Father()->GetHigherSubElements(siblings); ++ //if(siblings.size()<4) _error_("Impossible to refine: geoel (index) "<sid2index[i]<<" has less than 3 siblings!\n"); ++ if(siblings.size()>4) continue;//Father has more then 4 sons, this group should not be unrefined. ++ ++ /*Compute the error of the group*/ ++ group_Herror=0; ++ for(int j=0;jIndex(); ++ sid = this->index2sid[index]; ++ if(sid==-1) continue; ++ group_Herror+=thicknesserror[sid]; + } +- } +- } ++ /*Verify if this group should be unrefined*/ ++ if(group_Herror>0 && group_Herror<0*mean_Herror){ //itapopo ++ /*Reset subelements in the father*/ ++ this->currentmesh->Element(geoel->Father()->Index())->ResetSubElements(); ++ /*Delete the elements and set their indexes in the index2sid and sid2index*/ ++ for (int j=0;jIndex(); ++ sid = this->index2sid[index]; ++ this->index2sid[index]=-1; ++ if(sid!=-1) this->sid2index[sid]=-1; ++ this->currentmesh->DeleteElement(siblings[j],siblings[j]->Index()); ++ }//for j ++ }//if ++ }/*Unrefine process*/ ++ }//for i + this->currentmesh->BuildConnectivity(); + + if(amr_verbose) _printf_("\t\trefine to avoid hanging nodes...\n"); + this->RefineMeshToAvoidHangingNodes(this->currentmesh); +- this->currentmesh->BuildConnectivity(); + + //nohangingnodesmesh = this->CreateRefPatternMesh(newmesh); itapopo tentar otimizar +- ++ + if(amr_verbose) _printf_("\trefinement process done!\n"); + } + /*}}}*/ +@@ -256,7 +313,8 @@ + /*}}}*/ + void AdaptiveMeshRefinement::RefineMeshToAvoidHangingNodes(TPZGeoMesh *gmesh){/*{{{*/ + +- /*Refine elements to avoid hanging nodes: non-uniform refinement*/ ++ /*Now, insert special elements to avoid hanging nodes*/ ++ this->specialelementsindex.clear(); + const int NElem = gmesh->NElements(); + for(int i=0;i refp=TPZRefPatternTools::PerfectMatchRefPattern(geoel); + if(refp){ ++ /*Non-uniform refinement*/ + TPZVec Sons; + geoel->SetRefPattern(refp); + geoel->Divide(Sons); +- } ++ /*Keep the index of the special elements*/ ++ for(int j=0;jspecialelementsindex.push_back(Sons[j]->Index()); ++ } + } +- gmesh->BuildConnectivity(); +- ++ gmesh->BuildConnectivity(); + } + /*}}}*/ + void AdaptiveMeshRefinement::GetMesh(int &nvertices,int &nelements,double** px,double** py, int** pelements){/*{{{*/ +@@ -280,8 +340,8 @@ + + /* IMPORTANT! pelements are in Matlab indexing + NEOPZ works only in C indexing. +- This method cleans up and updated the this->sid2index +- and fills in it with the new mesh. ++ This method cleans up and updated the this->sid2index ++ and this->index2sid and fills in it with the new mesh. + Avoid to call this method before Refinement Process.*/ + + /*Intermediaries */ +@@ -294,6 +354,7 @@ + double* newmeshY = NULL;//xNew(ntotalvertices); + TPZGeoEl* geoel = NULL; + long* vertex_index2sid = xNew(gmesh->NNodes()); ++ this->index2sid.clear(); this->index2sid.resize(gmesh->NElements()); + this->sid2index.clear(); + + /*Get mesh coords */ +@@ -307,6 +368,9 @@ + /*Fill in the vertex_index2sid vector with non usual index value*/ + for(int i=0;iNNodes();i++) vertex_index2sid[i]=-1; + ++ /*Fill in the this->index2sid vector with non usual index value*/ ++ for(int i=0;iNElements();i++) this->index2sid[i]=-1; ++ + /*Get elements without sons and fill in the vertex_index2sid with used vertices (indexes) */ + sid=0; + for(int i=0;iNElements();i++){//over gmesh elements index +@@ -315,6 +379,7 @@ + if(geoel->HasSubElement()) continue; + if(geoel->MaterialId() != this->GetElemMaterialID()) continue; + this->sid2index.push_back(i);//keep the element index ++ this->index2sid[i]=this->sid2index.size()-1;//keep the element sid + for(int j=0;jelementswidth;j++){ + nodeindex=geoel->NodeIndex(j); + if(vertex_index2sid[nodeindex]==-1){ +@@ -346,8 +411,29 @@ + sid = vertex_index2sid[geoel->NodeIndex(j)]; + newelements[i*this->elementswidth+j]=(int)sid+1;//C to Matlab indexing + } ++ /*Verify the Jacobian determinant. If detJ<0, swap the 2 first postions: ++ a -> b ++ b -> a */ ++ double detJ,xa,xb,xc,ya,yb,yc; ++ int a,b,c; ++ ++ a=newelements[i*this->elementswidth+0]-1; ++ b=newelements[i*this->elementswidth+1]-1; ++ c=newelements[i*this->elementswidth+2]-1; ++ ++ xa=newmeshX[a]; ya=newmeshY[a]; ++ xb=newmeshX[b]; yb=newmeshY[b]; ++ xc=newmeshX[c]; yc=newmeshY[c]; ++ ++ detJ=(xb-xa)*(yc-ya)-(xc-xa)*(yb-ya); ++ ++ /*verify and swap, if necessary*/ ++ if(detJ<0) { ++ newelements[i*this->elementswidth+0]=b+1;//a->b ++ newelements[i*this->elementswidth+1]=a+1;//b->a ++ } + } +- ++ + /*Setting outputs*/ + nvertices = nconformvertices; + nelements = nconformelements; +@@ -357,7 +443,6 @@ + + /*Cleanup*/ + xDelete(vertex_index2sid); +- + } + /*}}}*/ + void AdaptiveMeshRefinement::FindElements(int &numberofpoints,double* xp,double* yp,TPZGeoMesh *gmesh,int &hlevel,std::vector &elements){/*{{{*/ +Index: ../trunk-jpl/src/m/mesh/bamg.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.m (revision 21918) ++++ ../trunk-jpl/src/m/mesh/bamg.m (revision 21919) +@@ -24,9 +24,9 @@ + % - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) + % - maxsubdiv : maximum subdivision of exisiting elements (default is 10) + % - metric : matrix (numberofnodes x 3) used as a metric +-% - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) +-% 2 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) +-% 3 -> rescaled absolute error c/(err coeff^2) * Abs(H)/(smax-smin) ++% - Metrictype : 0 -> absolute error c/(err coeff^2) * Abs(H) (default) ++% 1 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) ++% 2 -> rescaled absolute error c/(err coeff^2) * Abs(H)/(smax-smin) + % - nbjacoby : correction used by Hessiantype=1 (default is 1) + % - nbsmooth : number of metric smoothing procedure (default is 3) + % - omega : relaxation parameter of the smoothing procedure (default is 1.8) +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21918) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21919) +@@ -113,6 +113,15 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.amr.hmin",AmrHminEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.hmax",AmrHmaxEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.err",AmrErrEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.keepmetric",AmrKeepMetricEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.groundingline_resolution",AmrGroundingLineResolutionEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.groundingline_distance",AmrGroundingLineDistanceEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.icefront_resolution",AmrIceFrontResolutionEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.icefront_distance",AmrIceFrontDistanceEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.thicknesserror_resolution",AmrThicknessErrorResolutionEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.thicknesserror_threshold",AmrThicknessErrorThresholdEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.deviatoricerror_resolution",AmrDeviatoricErrorResolutionEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.deviatoricerror_threshold",AmrDeviatoricErrorThresholdEnum)); + /*Convert fieldname to enum and put it in params*/ + iomodel->FindConstant(&fieldname,"md.amr.fieldname"); + parameters->AddObject(new IntParam(AmrFieldEnum,StringToEnumx(fieldname))); +Index: ../trunk-jpl/src/c/classes/AmrBamg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.h (revision 21918) ++++ ../trunk-jpl/src/c/classes/AmrBamg.h (revision 21919) +@@ -13,14 +13,27 @@ + + public: + int fieldenum; ++ int keepmetric; ++ IssmDouble groundingline_resolution; ++ IssmDouble groundingline_distance; ++ IssmDouble icefront_resolution; ++ IssmDouble icefront_distance; ++ IssmDouble thicknesserror_resolution; ++ IssmDouble thicknesserror_threshold; ++ IssmDouble deviatoricerror_resolution; ++ IssmDouble deviatoricerror_threshold; + + /* Constructor, destructor etc*/ +- AmrBamg(IssmDouble hmin, IssmDouble hmax,int fieldenum_in,IssmDouble err_in); ++ AmrBamg(IssmDouble hmin,IssmDouble hmax,int fieldenum_in,IssmDouble err_in,int keepmetric_in, ++ IssmDouble groundingline_resolution_in,IssmDouble groundingline_distance_in, ++ IssmDouble icefront_resolution_in,IssmDouble icefront_distance_in, ++ IssmDouble thicknesserror_resolution_in,IssmDouble thicknesserror_threshold_in, ++ IssmDouble deviatoricerror_resolution_in,IssmDouble deviatoricerror_threshold_in); + ~AmrBamg(); + + /*General methods*/ + void Initialize(int* elements,IssmDouble* x,IssmDouble* y,int numberofvertices,int numberofelements); +- void ExecuteRefinementBamg(IssmDouble* field,int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist); ++ void ExecuteRefinementBamg(IssmDouble* field,IssmDouble* hmaxVertices,int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist); + + private: + BamgGeom* geometry; +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21918) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21919) +@@ -2302,9 +2302,9 @@ + case AmrNeopzEnum: this->ReMeshNeopz(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; + #endif + +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) + case AmrBamgEnum: this->ReMeshBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; +- #endif ++ #endif + + default: _error_("not implemented yet"); + } +@@ -2719,11 +2719,9 @@ + /*}}}*/ + void FemModel::WriteMeshInResults(void){/*{{{*/ + +- //itapopo + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) + this->WriteErrorEstimatorsInResults(); + #endif +- //itapopo + + int step = -1; + int numberofelements = -1; +@@ -2754,30 +2752,6 @@ + this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshYEnum, + y,numberofvertices,1,step,time)); + +- //itapopo +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) +- if(IssmComm::GetRank()==0){ +- TPZFileStream fstr; +- std::stringstream ss; +- int frictionlaw,levelmax; +- this->parameters->FindParam(&frictionlaw,FrictionLawEnum); +- this->parameters->FindParam(&levelmax,AmrLevelMaxEnum); +- ss << levelmax; +- if(frictionlaw==1){ +- ss << "_viscous/amr.txt"; +- }else if(frictionlaw==7){ +- ss << "_tsai/amr.txt"; +- }else{ +- _error_("friction law not supported here."); +- } +- std::string AMRfile = "/home/santos/Misomip2/L" + ss.str(); +- fstr.OpenWrite(AMRfile.c_str()); +- int withclassid = 1; +- this->amr->Write(fstr,withclassid); +- } +- #endif +- //itapopo +- + /*Cleanup*/ + xDelete(x); + xDelete(y); +@@ -3613,6 +3587,47 @@ + + } + /*}}}*/ ++void FemModel::GetElementCenterCoordinates(IssmDouble** pxc,IssmDouble** pyc){/*{{{*/ ++ ++ /*Intermediaries*/ ++ int elementswidth = this->GetElementsWidth(); ++ int numberofelements = this->elements->NumberOfElements(); ++ int* elem_vertices = xNew(elementswidth); ++ Vector* vxc = new Vector(numberofelements); ++ Vector* vyc = new Vector(numberofelements); ++ IssmDouble *x = NULL; ++ IssmDouble *y = NULL; ++ IssmDouble *z = NULL; ++ ++ /*Get vertices coordinates*/ ++ VertexCoordinatesx(&x,&y,&z,this->vertices,false) ; ++ ++ /*Insert the element center coordinates*/ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=xDynamicCast(this->elements->GetObjectByOffset(i)); ++ element->GetVerticesSidList(elem_vertices); ++ int sid = element->Sid(); ++ vxc->SetValue(sid,(x[elem_vertices[0]]+x[elem_vertices[1]]+x[elem_vertices[2]])/3.,INS_VAL); ++ vyc->SetValue(sid,(y[elem_vertices[0]]+y[elem_vertices[1]]+y[elem_vertices[2]])/3.,INS_VAL); ++ } ++ ++ /*Assemble*/ ++ vxc->Assemble(); ++ vyc->Assemble(); ++ ++ /*Serialize and set output*/ ++ (*pxc)=vxc->ToMPISerial(); ++ (*pyc)=vyc->ToMPISerial(); ++ ++ /*Cleanup*/ ++ xDelete(x); ++ xDelete(y); ++ xDelete(z); ++ xDelete(elem_vertices); ++ delete vxc; ++ delete vyc; ++} ++/*}}}*/ + #endif + + #ifdef _HAVE_DAKOTA_ +@@ -4335,20 +4350,41 @@ + /*Get Rank*/ + int my_rank = IssmComm::GetRank(); + ++ /*Intermediaries*/ ++ int numberofvertices = this->vertices->NumberOfVertices(); ++ IssmDouble* vector_serial = NULL; ++ IssmDouble* hmaxvertices_serial = NULL; ++ Vector *vector = NULL; ++ + /*Get vector to create metric*/ +- int numberofvertices = this->vertices->NumberOfVertices(); +- Vector *vector = NULL; +- GetVectorFromInputsx(&vector,this,this->amrbamg->fieldenum,VertexSIdEnum); +- vector->Assemble(); +- IssmDouble* vector_serial = vector->ToMPISerial(); +- delete vector; ++ if(this->amrbamg->fieldenum!=NoneEnum){ ++ GetVectorFromInputsx(&vector,this,this->amrbamg->fieldenum,VertexSIdEnum); ++ vector->Assemble(); ++ vector_serial = vector->ToMPISerial(); ++ } + ++ /*Get hmaxVertices to create metric*/ ++ if(this->amrbamg->groundingline_distance>0||this->amrbamg->icefront_distance>0|| ++ this->amrbamg->thicknesserror_threshold>0||this->amrbamg->deviatoricerror_threshold>0){ ++ /*Initialize hmaxvertices with NAN*/ ++ hmaxvertices_serial=xNew(numberofvertices); ++ for(int i=0;iamrbamg->groundingline_distance>0) this->GethmaxVerticesFromZeroLevelSetDistance(hmaxvertices_serial,MaskGroundediceLevelsetEnum); ++ if(this->amrbamg->icefront_distance>0) this->GethmaxVerticesFromZeroLevelSetDistance(hmaxvertices_serial,MaskIceLevelsetEnum); ++ if(this->amrbamg->thicknesserror_threshold>0) this->GethmaxVerticesFromEstimators(hmaxvertices_serial,ThicknessErrorEstimatorEnum); ++ if(this->amrbamg->deviatoricerror_threshold>0) this->GethmaxVerticesFromEstimators(hmaxvertices_serial,DeviatoricStressErrorEstimatorEnum); ++ } ++ + if(my_rank==0){ +- this->amrbamg->ExecuteRefinementBamg(vector_serial,&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); ++ this->amrbamg->ExecuteRefinementBamg(vector_serial,hmaxvertices_serial,&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); + if(newnumberofvertices<=0 || newnumberofelements<=0) _error_("Error in the refinement process."); + } + ++ /*Cleanup*/ + xDelete(vector_serial); ++ xDelete(hmaxvertices_serial); ++ delete vector; + + /*Send new mesh to others CPU*/ + ISSM_MPI_Bcast(&newnumberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); +@@ -4378,14 +4414,14 @@ + /*Define variables*/ + int numberofvertices = this->vertices->NumberOfVertices(); + int numberofelements = this->elements->NumberOfElements(); +- int numberofsegments = 0; //used on matlab + IssmDouble* x = NULL; + IssmDouble* y = NULL; + IssmDouble* z = NULL; + int* elements = NULL; +- int elementswidth = this->GetElementsWidth(); //just tria elements in this version. Itapopo: + IssmDouble hmin,hmax,err; +- int fieldenum; ++ IssmDouble groundingline_resolution,groundingline_distance,icefront_resolution,icefront_distance; ++ IssmDouble thicknesserror_resolution,thicknesserror_threshold,deviatoricerror_resolution,deviatoricerror_threshold; ++ int fieldenum,keepmetric; + + /*Get rank*/ + int my_rank = IssmComm::GetRank(); +@@ -4401,9 +4437,22 @@ + this->parameters->FindParam(&hmax,AmrHmaxEnum); + this->parameters->FindParam(&fieldenum,AmrFieldEnum); + this->parameters->FindParam(&err,AmrErrEnum); ++ this->parameters->FindParam(&keepmetric,AmrKeepMetricEnum); ++ this->parameters->FindParam(&groundingline_resolution,AmrGroundingLineResolutionEnum); ++ this->parameters->FindParam(&groundingline_distance,AmrGroundingLineDistanceEnum); ++ this->parameters->FindParam(&icefront_resolution,AmrIceFrontResolutionEnum); ++ this->parameters->FindParam(&icefront_distance,AmrIceFrontDistanceEnum); ++ this->parameters->FindParam(&thicknesserror_resolution,AmrThicknessErrorResolutionEnum); ++ this->parameters->FindParam(&thicknesserror_threshold,AmrThicknessErrorThresholdEnum); ++ this->parameters->FindParam(&deviatoricerror_resolution,AmrDeviatoricErrorResolutionEnum); ++ this->parameters->FindParam(&deviatoricerror_threshold,AmrDeviatoricErrorThresholdEnum); + + /*Create bamg data structures for bamg*/ +- this->amrbamg = new AmrBamg(hmin,hmax,fieldenum,err); ++ this->amrbamg = new AmrBamg(hmin,hmax,fieldenum,err,keepmetric, ++ groundingline_resolution,groundingline_distance, ++ icefront_resolution,icefront_distance, ++ thicknesserror_resolution,thicknesserror_threshold, ++ deviatoricerror_resolution,deviatoricerror_threshold); + + /*Re-create original mesh and put it in bamg structure (only cpu 0)*/ + if(my_rank==0){ +@@ -4417,6 +4466,204 @@ + xDelete(elements); + } + /*}}}*/ ++void FemModel::GethmaxVerticesFromZeroLevelSetDistance(IssmDouble* hmaxvertices,int levelset_type){/*{{{*/ ++ ++ if(!hmaxvertices) _error_("hmaxvertices is NULL!\n"); ++ ++ /*Intermediaries*/ ++ int numberofvertices = this->vertices->NumberOfVertices(); ++ IssmDouble* verticedistance = NULL; ++ IssmDouble threshold,resolution; ++ ++ switch(levelset_type){ ++ case MaskGroundediceLevelsetEnum: ++ threshold = this->amrbamg->groundingline_distance; ++ resolution = this->amrbamg->groundingline_resolution; ++ break; ++ case MaskIceLevelsetEnum: ++ threshold = this->amrbamg->icefront_distance; ++ resolution = this->amrbamg->icefront_resolution; ++ break; ++ default: _error_("not implemented yet"); ++ } ++ ++ /*Get vertice distance to zero level set points*/ ++ this->GetVerticeDistanceToZeroLevelSet(&verticedistance,levelset_type); ++ if(!verticedistance) _error_("verticedistance is NULL!\n"); ++ ++ /*Fill hmaxVertices*/ ++ for(int i=0;i(hmaxvertices[i])) hmaxvertices[i]=resolution; ++ else hmaxvertices[i]=min(resolution,hmaxvertices[i]); ++ } ++ } ++ ++ /*Cleanup*/ ++ xDelete(verticedistance); ++} ++/*}}}*/ ++void FemModel::GethmaxVerticesFromEstimators(IssmDouble* hmaxvertices,int errorestimator_type){/*{{{*/ ++ ++ if(!hmaxvertices) _error_("hmaxvertices is NULL!\n"); ++ ++ /*Intermediaries*/ ++ int numberofelements = this->elements->NumberOfElements(); ++ int numberofvertices = this->vertices->NumberOfVertices(); ++ IssmDouble* error_elements = NULL; ++ IssmDouble* error_vertices = NULL; ++ IssmDouble *x = NULL; ++ IssmDouble *y = NULL; ++ IssmDouble *z = NULL; ++ int *index = NULL; ++ IssmDouble maxerror,threshold,resolution; ++ ++ switch(errorestimator_type){ ++ case ThicknessErrorEstimatorEnum: ++ threshold = this->amrbamg->thicknesserror_threshold; ++ resolution = this->amrbamg->thicknesserror_resolution; ++ this->ThicknessZZErrorEstimator(&error_elements); ++ break; ++ case DeviatoricStressErrorEstimatorEnum: ++ threshold = this->amrbamg->deviatoricerror_threshold; ++ resolution = this->amrbamg->deviatoricerror_resolution; ++ this->ZZErrorEstimator(&error_elements); ++ break; ++ default: _error_("not implemented yet"); ++ } ++ ++ if(!error_elements) _error_("error_elements is NULL!\n"); ++ ++ /*Get mesh*/ ++ this->GetMesh(this->vertices,this->elements,&x,&y,&z,&index); ++ ++ /*Sum the estimators over the vertices*/ ++ error_vertices=xNewZeroInit(numberofvertices); ++ for(int i=0;iGetElementsWidth();j++){ ++ int vid=index[i*this->GetElementsWidth()+j]-1;//Matlab to C indexing ++ error_vertices[vid]+=error_elements[i]; ++ } ++ } ++ ++ /*Find the max of the estimators (use error_elements)*/ ++ maxerror=error_elements[0]; ++ for(int i=0;ithreshold*maxerror){ ++ if(xIsNan(hmaxvertices[i])) hmaxvertices[i]=resolution; ++ else hmaxvertices[i]=min(resolution,hmaxvertices[i]); ++ } ++ } ++ ++ /*Cleanup*/ ++ xDelete(x); ++ xDelete(y); ++ xDelete(z); ++ xDelete(index); ++ xDelete(error_elements); ++ xDelete(error_vertices); ++} ++/*}}}*/ ++void FemModel::GetVerticeDistanceToZeroLevelSet(IssmDouble** pverticedistance,int levelset_type){/*{{{*/ ++ ++ /*Here, "zero level set" means grounding line or ice front, depending on the level set type*/ ++ /*pverticedistance is the minimal vertice distance to the grounding line or ice front*/ ++ if(levelset_type!=MaskGroundediceLevelsetEnum && levelset_type!=MaskIceLevelsetEnum){ ++ _error_("level set type not implemented yet!"); ++ } ++ ++ /*Output*/ ++ IssmDouble* verticedistance; ++ ++ /*Intermediaries*/ ++ int elementswidth = this->GetElementsWidth(); ++ int numberofvertices = this->vertices->NumberOfVertices(); ++ int numberofelements = this->elements->NumberOfElements(); ++ int* elem_vertices = xNew(elementswidth); ++ IssmDouble* levelset = xNew(elementswidth); ++ IssmDouble* xp = NULL; ++ IssmDouble* yp = NULL; ++ IssmDouble* x = NULL; ++ IssmDouble* y = NULL; ++ IssmDouble* z = NULL; ++ Vector* vx_zerolevelset = new Vector(numberofelements); ++ Vector* vy_zerolevelset = new Vector(numberofelements); ++ IssmDouble* x_zerolevelset = NULL; ++ IssmDouble* y_zerolevelset = NULL; ++ int count,sid,npoints; ++ IssmDouble xcenter,ycenter,distance; ++ ++ /*Get vertices coordinates*/ ++ VertexCoordinatesx(&x,&y,&z,this->vertices,false) ; ++ ++ /*Use the element center coordinate if level set is zero (grounding line or ice front), otherwise set NAN*/ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=xDynamicCast(this->elements->GetObjectByOffset(i)); ++ element->GetInputListOnVertices(levelset,levelset_type); ++ element->GetVerticesSidList(elem_vertices); ++ sid = element->Sid(); ++ xcenter = NAN; ++ ycenter = NAN; ++ Tria* tria = xDynamicCast(element); ++ if(tria->IsIceInElement()){/*verify if there is ice in the element*/ ++ if(levelset[0]*levelset[1]<0. || levelset[0]*levelset[2]<0. || ++ abs(levelset[0]*levelset[1])SetValue(sid,xcenter,INS_VAL); ++ vy_zerolevelset->SetValue(sid,ycenter,INS_VAL); ++ } ++ /*Assemble and serialize*/ ++ vx_zerolevelset->Assemble(); ++ vy_zerolevelset->Assemble(); ++ x_zerolevelset=vx_zerolevelset->ToMPISerial(); ++ y_zerolevelset=vy_zerolevelset->ToMPISerial(); ++ ++ /*keep just the element center coordinates with zero level set (compact the structure to save time in the next step)*/ ++ count = 0; ++ xp = xNewZeroInit(numberofelements); ++ yp = xNewZeroInit(numberofelements); ++ for(int i=0;i(x_zerolevelset[i])){ ++ xp[count]=x_zerolevelset[i]; ++ yp[count]=y_zerolevelset[i]; ++ count++; ++ } ++ } ++ npoints=count; ++ ++ /*Find the minimal vertice distance to the zero levelset (grounding line or ice front)*/ ++ verticedistance=xNew(numberofvertices); ++ for(int i=0;i(elem_vertices); ++ xDelete(levelset); ++ xDelete(x_zerolevelset); ++ xDelete(y_zerolevelset); ++ xDelete(xp); ++ xDelete(yp); ++ xDelete(x); ++ xDelete(y); ++ xDelete(z); ++ delete vx_zerolevelset; ++ delete vy_zerolevelset; ++} ++/*}}}*/ + #endif + + #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) +@@ -4479,7 +4726,6 @@ + xDelete(masklevelset); + xDelete(deviatorictensorerror); + xDelete(thicknesserror); +- + } + /*}}}*/ + void FemModel::InitializeAdaptiveRefinementNeopz(void){/*{{{*/ +@@ -4511,37 +4757,11 @@ + + /*Create initial mesh (coarse mesh) in neopz data structure*/ + /*Just CPU #0 should keep AMR object*/ +- this->SetRefPatterns(); ++ /*Initialize refinement pattern*/ ++ this->SetRefPatterns(); + if(my_rank==0){ +- bool ismisomip = false; +- if(ismisomip){//itapopo +- TPZFileStream fstr; +- std::stringstream ss; +- int frictionlaw; +- +- this->parameters->FindParam(&frictionlaw,FrictionLawEnum); +- +- ss << levelmax; +- if(frictionlaw==1){ +- ss << "_viscous/amr.txt"; +- }else if(frictionlaw==7){ +- ss << "_tsai/amr.txt"; +- }else{ +- _error_("friction law not supported here."); +- } +- +- std::string AMRfile = "/home/santos/Misomip2/L" + ss.str(); +- fstr.OpenRead(AMRfile.c_str()); +- +- TPZSaveable *sv = TPZSaveable::Restore(fstr,0); +- this->amr = dynamic_cast(sv); +- } +- else{ +- this->amr = new AdaptiveMeshRefinement(); +- //this->amr->SetLevelMax(levelmax); //Set max level of refinement +- //this->amr->SetRegions(regionlevel1,regionlevelmax); +- this->amr->CreateInitialMesh(numberofvertices,numberofelements,elementswidth,x,y,elements); +- } ++ this->amr = new AdaptiveMeshRefinement(); ++ this->amr->CreateInitialMesh(numberofvertices,numberofelements,elementswidth,x,y,elements); + this->amr->SetLevelMax(levelmax); //Set max level of refinement + this->amr->SetRegions(regionlevel1,regionlevelmax); + } +@@ -4558,15 +4778,17 @@ + /*Initialize the global variable of refinement patterns*/ + gRefDBase.InitializeUniformRefPattern(ETriangle); + +- /*Insert specifics patterns to ISSM core*/ ++ /*Insert specifics patterns to ISSM core*/ + std::string filepath = REFPATTERNDIR; + std::string filename1 = filepath + "/2D_Triang_Rib_3.rpt"; + std::string filename2 = filepath + "/2D_Triang_Rib_4.rpt"; +- std::string filename3 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4.rpt"; +- std::string filename4 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4_permuted.rpt"; +- std::string filename5 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5.rpt"; +- std::string filename6 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5_permuted.rpt"; +- std::string filename7 = filepath + "/2D_Triang_Rib_5.rpt"; ++ std::string filename3 = filepath + "/2D_Triang_Rib_5.rpt"; ++ std::string filename4 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4.rpt"; ++ std::string filename5 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4_permuted.rpt"; ++ std::string filename6 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5.rpt"; ++ std::string filename7 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5_permuted.rpt"; ++ std::string filename8 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_4_5.rpt"; ++ std::string filename9 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_4_5_permuted.rpt"; + + TPZAutoPointer refpat1 = new TPZRefPattern(filename1); + TPZAutoPointer refpat2 = new TPZRefPattern(filename2); +@@ -4575,6 +4797,8 @@ + TPZAutoPointer refpat5 = new TPZRefPattern(filename5); + TPZAutoPointer refpat6 = new TPZRefPattern(filename6); + TPZAutoPointer refpat7 = new TPZRefPattern(filename7); ++ TPZAutoPointer refpat8 = new TPZRefPattern(filename8); ++ TPZAutoPointer refpat9 = new TPZRefPattern(filename9); + + if(!gRefDBase.FindRefPattern(refpat1)) gRefDBase.InsertRefPattern(refpat1); + if(!gRefDBase.FindRefPattern(refpat2)) gRefDBase.InsertRefPattern(refpat2); +@@ -4583,6 +4807,8 @@ + if(!gRefDBase.FindRefPattern(refpat5)) gRefDBase.InsertRefPattern(refpat5); + if(!gRefDBase.FindRefPattern(refpat6)) gRefDBase.InsertRefPattern(refpat6); + if(!gRefDBase.FindRefPattern(refpat7)) gRefDBase.InsertRefPattern(refpat7); ++ if(!gRefDBase.FindRefPattern(refpat8)) gRefDBase.InsertRefPattern(refpat8); ++ if(!gRefDBase.FindRefPattern(refpat9)) gRefDBase.InsertRefPattern(refpat9); + } + /*}}}*/ + #endif +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21918) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21919) +@@ -1710,7 +1710,8 @@ + name==LevelsetfunctionSlopeXEnum || + name==LevelsetfunctionSlopeYEnum || + name==LevelsetfunctionPicardEnum || +- //name==CalvingCalvingrateEnum || ++ name==CalvingCalvingrateEnum || ++ name==CalvingMeltingrateEnum || + name==GradientEnum || + name==OldGradientEnum || + name==ConvergedEnum || +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21918) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21919) +@@ -16,12 +16,25 @@ + using namespace std; + + /*Constructor, copy, clean up and destructor*/ +-AmrBamg::AmrBamg(IssmDouble hmin, IssmDouble hmax,int fieldenum_in,IssmDouble err){/*{{{*/ ++AmrBamg::AmrBamg(IssmDouble hmin,IssmDouble hmax,int fieldenum_in,IssmDouble err_in,int keepmetric_in, ++ IssmDouble groundingline_resolution_in,IssmDouble groundingline_distance_in, ++ IssmDouble icefront_resolution_in,IssmDouble icefront_distance_in, ++ IssmDouble thicknesserror_resolution_in,IssmDouble thicknesserror_threshold_in, ++ IssmDouble deviatoricerror_resolution_in,IssmDouble deviatoricerror_threshold_in){/*{{{*/ + +- this->fieldenum = fieldenum_in; +- this->geometry = NULL; +- this->fathermesh = NULL; +- this->previousmesh = NULL; ++ this->fieldenum = fieldenum_in; ++ this->keepmetric = keepmetric_in; ++ this->groundingline_resolution = groundingline_resolution_in; ++ this->groundingline_distance = groundingline_distance_in; ++ this->icefront_resolution = icefront_resolution_in; ++ this->icefront_distance = icefront_distance_in; ++ this->thicknesserror_resolution = thicknesserror_resolution_in; ++ this->thicknesserror_threshold = thicknesserror_threshold_in; ++ this->deviatoricerror_resolution = deviatoricerror_resolution_in; ++ this->deviatoricerror_threshold = deviatoricerror_threshold_in; ++ this->geometry = NULL; ++ this->fathermesh = NULL; ++ this->previousmesh = NULL; + + /*Only initialize options for now (same as bamg.m)*/ + this->options = new BamgOpts(); +@@ -48,7 +61,7 @@ + this->options->err=xNew(1); + this->options->errSize[0]=1; + this->options->errSize[1]=1; +- this->options->err[0] = err; ++ this->options->err[0] = err_in; + } + /*}}}*/ + AmrBamg::~AmrBamg(){/*{{{*/ +@@ -82,7 +95,7 @@ + /*Cleanup and return*/ + delete Th; + }/*}}}*/ +-void AmrBamg::ExecuteRefinementBamg(IssmDouble* field,int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ ++void AmrBamg::ExecuteRefinementBamg(IssmDouble* field,IssmDouble* hmaxVertices,int* pnewnumberofvertices,int *pnewnumberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ + + /*Intermediaries*/ + BamgGeom* geomout=new BamgGeom(); +@@ -92,27 +105,42 @@ + _assert_(this->geometry); + _assert_(this->options); + _assert_(this->fathermesh); +- _assert_(field); ++ _assert_(field || hmaxVertices);//at least one is necessary + + /*Prepare field for metric*/ +- this->options->field = field; ++ this->options->field = field; ++ this->options->hmaxVertices = hmaxVertices; + + /*remesh*/ + if(this->previousmesh){ +- this->options->fieldSize[0] = this->previousmesh->VerticesSize[0]; +- this->options->fieldSize[1] = 1; ++ this->options->fieldSize[0] = this->previousmesh->VerticesSize[0]; ++ this->options->fieldSize[1] = 1; ++ this->options->hmaxVerticesSize[0] = this->previousmesh->VerticesSize[0]; ++ this->options->hmaxVerticesSize[1] = 1; + Bamgx(meshout,geomout,this->previousmesh,this->geometry,this->options); + } + else{ +- this->options->fieldSize[0] = this->fathermesh->VerticesSize[0]; +- this->options->fieldSize[1] = 1; ++ this->options->fieldSize[0] = this->fathermesh->VerticesSize[0]; ++ this->options->fieldSize[1] = 1; ++ this->options->hmaxVerticesSize[0] = this->fathermesh->VerticesSize[0]; ++ this->options->hmaxVerticesSize[1] = 1; + Bamgx(meshout,geomout,this->fathermesh,this->geometry,this->options); + } + +- /*remove field for memory management (FemModel is taking care of deleting it)*/ ++ /*remove field and hmaxVertices for memory management (FemModel is taking care of deleting it)*/ + this->options->field = NULL; + this->options->fieldSize[0] = 0; + this->options->fieldSize[1] = 0; ++ this->options->hmaxVertices = NULL; ++ this->options->hmaxVerticesSize[0] = 0; ++ this->options->hmaxVerticesSize[1] = 0; ++ ++ /*verify if the metric will be reseted or not*/ ++ if(!this->keepmetric){ ++ if(this->options->metric) xDelete(this->options->metric); ++ this->options->metricSize[0] = 0; ++ this->options->metricSize[1] = 0; ++ } + + /*Change previous mesh*/ + if(this->previousmesh) delete this->previousmesh; +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21918) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21919) +@@ -848,6 +848,15 @@ + AmrHmaxEnum, + AmrFieldEnum, + AmrErrEnum, ++ AmrKeepMetricEnum, ++ AmrGroundingLineResolutionEnum, ++ AmrGroundingLineDistanceEnum, ++ AmrIceFrontResolutionEnum, ++ AmrIceFrontDistanceEnum, ++ AmrThicknessErrorResolutionEnum, ++ AmrThicknessErrorThresholdEnum, ++ AmrDeviatoricErrorResolutionEnum, ++ AmrDeviatoricErrorThresholdEnum, + DeviatoricStressErrorEstimatorEnum, + ThicknessErrorEstimatorEnum, + /*}}}*/ +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21918) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21919) +@@ -824,6 +824,15 @@ + case AmrHmaxEnum : return "AmrHmax"; + case AmrFieldEnum : return "AmrField"; + case AmrErrEnum : return "AmrErr"; ++ case AmrKeepMetricEnum : return "AmrKeepMetric"; ++ case AmrGroundingLineResolutionEnum : return "AmrGroundingLineResolution"; ++ case AmrGroundingLineDistanceEnum : return "AmrGroundingLineDistance"; ++ case AmrIceFrontResolutionEnum : return "AmrIceFrontResolution"; ++ case AmrIceFrontDistanceEnum : return "AmrIceFrontDistance"; ++ case AmrThicknessErrorResolutionEnum : return "AmrThicknessErrorResolution"; ++ case AmrThicknessErrorThresholdEnum : return "AmrThicknessErrorThreshold"; ++ case AmrDeviatoricErrorResolutionEnum : return "AmrDeviatoricErrorResolution"; ++ case AmrDeviatoricErrorThresholdEnum : return "AmrDeviatoricErrorThreshold"; + case DeviatoricStressErrorEstimatorEnum : return "DeviatoricStressErrorEstimator"; + case ThicknessErrorEstimatorEnum : return "ThicknessErrorEstimator"; + case ParametersENDEnum : return "ParametersEND"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21918) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21919) +@@ -842,6 +842,15 @@ + else if (strcmp(name,"AmrHmax")==0) return AmrHmaxEnum; + else if (strcmp(name,"AmrField")==0) return AmrFieldEnum; + else if (strcmp(name,"AmrErr")==0) return AmrErrEnum; ++ else if (strcmp(name,"AmrKeepMetric")==0) return AmrKeepMetricEnum; ++ else if (strcmp(name,"AmrGroundingLineResolution")==0) return AmrGroundingLineResolutionEnum; ++ else if (strcmp(name,"AmrGroundingLineDistance")==0) return AmrGroundingLineDistanceEnum; ++ else if (strcmp(name,"AmrIceFrontResolution")==0) return AmrIceFrontResolutionEnum; ++ else if (strcmp(name,"AmrIceFrontDistance")==0) return AmrIceFrontDistanceEnum; ++ else if (strcmp(name,"AmrThicknessErrorResolution")==0) return AmrThicknessErrorResolutionEnum; ++ else if (strcmp(name,"AmrThicknessErrorThreshold")==0) return AmrThicknessErrorThresholdEnum; ++ else if (strcmp(name,"AmrDeviatoricErrorResolution")==0) return AmrDeviatoricErrorResolutionEnum; ++ else if (strcmp(name,"AmrDeviatoricErrorThreshold")==0) return AmrDeviatoricErrorThresholdEnum; + else if (strcmp(name,"DeviatoricStressErrorEstimator")==0) return DeviatoricStressErrorEstimatorEnum; + else if (strcmp(name,"ThicknessErrorEstimator")==0) return ThicknessErrorEstimatorEnum; + else if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; +@@ -865,7 +874,10 @@ + else if (strcmp(name,"Hook")==0) return HookEnum; + else if (strcmp(name,"ExternalResult")==0) return ExternalResultEnum; + else if (strcmp(name,"FileParam")==0) return FileParamEnum; +- else if (strcmp(name,"Input")==0) return InputEnum; ++ else stage=8; ++ } ++ if(stage==8){ ++ if (strcmp(name,"Input")==0) return InputEnum; + else if (strcmp(name,"IntInput")==0) return IntInputEnum; + else if (strcmp(name,"IntParam")==0) return IntParamEnum; + else if (strcmp(name,"IntVecParam")==0) return IntVecParamEnum; +@@ -874,10 +886,7 @@ + else if (strcmp(name,"Matdamageice")==0) return MatdamageiceEnum; + else if (strcmp(name,"Matenhancedice")==0) return MatenhancediceEnum; + else if (strcmp(name,"Matestar")==0) return MatestarEnum; +- else stage=8; +- } +- if(stage==8){ +- if (strcmp(name,"Matpar")==0) return MatparEnum; ++ else if (strcmp(name,"Matpar")==0) return MatparEnum; + else if (strcmp(name,"Node")==0) return NodeEnum; + else if (strcmp(name,"Numericalflux")==0) return NumericalfluxEnum; + else if (strcmp(name,"Neumannflux")==0) return NeumannfluxEnum; +@@ -988,7 +997,10 @@ + else if (strcmp(name,"MinVel")==0) return MinVelEnum; + else if (strcmp(name,"MaxVel")==0) return MaxVelEnum; + else if (strcmp(name,"MinVx")==0) return MinVxEnum; +- else if (strcmp(name,"MaxVx")==0) return MaxVxEnum; ++ else stage=9; ++ } ++ if(stage==9){ ++ if (strcmp(name,"MaxVx")==0) return MaxVxEnum; + else if (strcmp(name,"MaxAbsVx")==0) return MaxAbsVxEnum; + else if (strcmp(name,"MinVy")==0) return MinVyEnum; + else if (strcmp(name,"MaxVy")==0) return MaxVyEnum; +@@ -997,10 +1009,7 @@ + else if (strcmp(name,"MaxVz")==0) return MaxVzEnum; + else if (strcmp(name,"MaxAbsVz")==0) return MaxAbsVzEnum; + else if (strcmp(name,"FloatingArea")==0) return FloatingAreaEnum; +- else stage=9; +- } +- if(stage==9){ +- if (strcmp(name,"GroundedArea")==0) return GroundedAreaEnum; ++ else if (strcmp(name,"GroundedArea")==0) return GroundedAreaEnum; + else if (strcmp(name,"IceMass")==0) return IceMassEnum; + else if (strcmp(name,"IceVolume")==0) return IceVolumeEnum; + else if (strcmp(name,"IceVolumeAboveFloatation")==0) return IceVolumeAboveFloatationEnum; +Index: ../trunk-jpl/src/m/classes/amrbamg.m +=================================================================== +--- ../trunk-jpl/src/m/classes/amrbamg.m (revision 21918) ++++ ../trunk-jpl/src/m/classes/amrbamg.m (revision 21919) +@@ -9,6 +9,15 @@ + hmax = 0.; + fieldname = ''; + err = 0.; ++ keepmetric = 0; ++ groundingline_resolution = 0.; ++ groundingline_distance = 0.; ++ icefront_resolution = 0.; ++ icefront_distance = 0.; ++ thicknesserror_resolution = 0.; ++ thicknesserror_threshold = 0.; ++ deviatoricerror_resolution = 0.; ++ deviatoricerror_threshold = 0.; + end + methods + function self = amrbamg(varargin) % {{{ +@@ -29,6 +38,19 @@ + self.fieldname ='Vel'; + self.err=3.; + ++ %keep metric? ++ self.keepmetric=1; ++ ++ %other criterias ++ self.groundingline_resolution=500.; ++ self.groundingline_distance=0.; ++ self.icefront_resolution=500.; ++ self.icefront_distance=0.; ++ self.thicknesserror_resolution=500.; ++ self.thicknesserror_threshold=0.; ++ self.deviatoricerror_resolution=500.; ++ self.deviatoricerror_threshold=0.; ++ + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + +@@ -35,6 +57,15 @@ + md = checkfield(md,'fieldname','amr.hmax','numel',[1],'>',0,'NaN',1); + md = checkfield(md,'fieldname','amr.hmin','numel',[1],'>',0,'<',self.hmax,'NaN',1); + %md = checkfield(md,'fieldname','amr.fieldname','string',[1]); ++ md = checkfield(md,'fieldname','amr.keepmetric','numel',[1],'>=',0,'<=',1,'NaN',1); ++ md = checkfield(md,'fieldname','amr.groundingline_resolution','numel',[1],'>',0,'<',self.hmax,'NaN',1); ++ md = checkfield(md,'fieldname','amr.groundingline_distance','numel',[1],'>=',0,'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','amr.icefront_resolution','numel',[1],'>',0,'<',self.hmax,'NaN',1); ++ md = checkfield(md,'fieldname','amr.icefront_distance','numel',[1],'>=',0,'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','amr.thicknesserror_resolution','numel',[1],'>',0,'<',self.hmax,'NaN',1); ++ md = checkfield(md,'fieldname','amr.thicknesserror_threshold','numel',[1],'>=',0,'<=',1,'NaN',1); ++ md = checkfield(md,'fieldname','amr.deviatoricerror_resolution','numel',[1],'>',0,'<',self.hmax,'NaN',1); ++ md = checkfield(md,'fieldname','amr.deviatoricerror_threshold','numel',[1],'>=',0,'<=',1,'NaN',1); + end % }}} + function disp(self) % {{{ + disp(sprintf(' amrbamg parameters:')); +@@ -42,6 +73,15 @@ + fielddisplay(self,'hmin',['minimum element length']); + fielddisplay(self,'hmax',['maximum element length']); + fielddisplay(self,'fieldname',['name of input that will be used to compute the metric (should be an input of FemModel)']); ++ fielddisplay(self,'keepmetric',['indicates whether the metric should be kept every remeshing time']); ++ fielddisplay(self,'groundingline_resolution',['element length near the grounding line']); ++ fielddisplay(self,'groundingline_distance',['distance around the grounding line which elements will be refined']); ++ fielddisplay(self,'icefront_resolution',['element length near the ice front']); ++ fielddisplay(self,'icefront_distance',['distance around the ice front which elements will be refined']); ++ fielddisplay(self,'thicknesserror_resolution',['element length when thickness error estimator is used']); ++ fielddisplay(self,'thicknesserror_threshold',['maximum threshold thickness error permitted']); ++ fielddisplay(self,'deviatoricerror_resolution',['element length when deviatoric stress error estimator is used']); ++ fielddisplay(self,'deviatoricerror_threshold',['maximum threshold deviatoricstress error permitted']); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ +@@ -50,7 +90,16 @@ + WriteData(fid,prefix,'object',self,'class','amr','fieldname','hmin','format','Double'); + WriteData(fid,prefix,'object',self,'class','amr','fieldname','hmax','format','Double'); + WriteData(fid,prefix,'object',self,'class','amr','fieldname','fieldname','format','String'); +- WriteData(fid,prefix,'object',self,'class','err','fieldname','err','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','err','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','keepmetric','format','Integer'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','groundingline_resolution','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','groundingline_distance','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','icefront_resolution','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','icefront_distance','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','thicknesserror_resolution','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','thicknesserror_threshold','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','deviatoricerror_resolution','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','deviatoricerror_threshold','format','Double'); + + end % }}} + end Index: /issm/oecreview/Archive/21724-22754/ISSM-21919-21920.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21919-21920.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21919-21920.diff (revision 22755) @@ -0,0 +1,28 @@ +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21919) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 21920) +@@ -554,8 +554,8 @@ + int offset; + + offset=dynamic_cast(input)->GetTimeInputOffset(time_yr); +- if (fmod(offset,12)!=1){ +- time_clim=floor(dynamic_cast(input)->GetTimeByOffset(offset-fmod(offset,12)+1)/yts)*yts; ++ if (fmod(offset,12.)!=1){ ++ time_clim=floor(dynamic_cast(input)->GetTimeByOffset(offset-fmod(offset,12.)+1)/yts)*yts; + } + + /*loop over vertices: */ +Index: ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp (revision 21919) ++++ ../trunk-jpl/src/c/classes/Inputs/TransientInput.cpp (revision 21920) +@@ -263,7 +263,7 @@ + IssmDouble TransientInput::GetTimeByOffset(int offset){/*{{{*/ + + if (offset < 0) offset=0; +- _assert_(this->timesteps[offset]); ++ _assert_(offsetnumtimesteps); + + return this->timesteps[offset]; + } Index: /issm/oecreview/Archive/21724-22754/ISSM-21920-21921.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21920-21921.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21920-21921.diff (revision 22755) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test322.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test322.py (revision 21920) ++++ ../trunk-jpl/test/NightlyRun/test322.py (revision 21921) +@@ -35,7 +35,7 @@ + + #Fields and tolerances to track changes + field_names =['Gradient','Misfits','FrictionCoefficient','Pressure','Vel','Vx','Vy'] +-field_tolerances=[5e-05,1e-08,7e-08,5e-09,1e-08,1e-08,1e-08] ++field_tolerances=[5e-05,1e-08,7e-08,5e-09,5e-08,5e-08,5e-08] + field_values=[\ + md.results.StressbalanceSolution.Gradient1,\ + md.results.StressbalanceSolution.J,\ +Index: ../trunk-jpl/test/NightlyRun/test322.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test322.m (revision 21920) ++++ ../trunk-jpl/test/NightlyRun/test322.m (revision 21921) +@@ -23,7 +23,7 @@ + + %Fields and tolerances to track changes + field_names ={'Gradient','Misfits','FrictionCoefficient','Pressure','Vel','Vx','Vy'}; +-field_tolerances={5e-05,1e-08,7e-08,5e-09,1e-08,1e-08,1e-08}; ++field_tolerances={5e-05,1e-08,7e-08,5e-09,5e-08,5e-08,5e-08}; + field_values={... + (md.results.StressbalanceSolution.Gradient1),... + (md.results.StressbalanceSolution.J),... Index: /issm/oecreview/Archive/21724-22754/ISSM-21921-21922.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21921-21922.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21921-21922.diff (revision 22755) @@ -0,0 +1,29 @@ +Index: ../trunk-jpl/jenkins/windows +=================================================================== +--- ../trunk-jpl/jenkins/windows (revision 21921) ++++ ../trunk-jpl/jenkins/windows (revision 21922) +@@ -59,5 +59,5 @@ + #ex: "'id',[101 102 103]" + + #In Windows, we don't yet have MUMPS, can't do full stokes, so exclude all FS runs. Also exclude all runs with Dakota. And exclude higher order runs that have penalties. And 800+ tests because we don't want to have --with-development since we do the binaries with this version +-MATLAB_NROPTIONS="'exclude',[104,119, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440,444, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460,243]" ++MATLAB_NROPTIONS="'exclude',[104,119, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440,444, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460,243,430,441,442]" + PYTHON_NROPTIONS="" +Index: ../trunk-jpl/jenkins/linux64_ross_javascript +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_javascript (revision 21921) ++++ ../trunk-jpl/jenkins/linux64_ross_javascript (revision 21922) +@@ -23,10 +23,10 @@ + #-----------------------------------# + + #List of external pakages to be installed and their installation scripts +-EXTERNALPACKAGES="emscripten install.sh +- gsl install-javascript.sh ++EXTERNALPACKAGES="gsl install-javascript.sh + triangle install-javascript.sh +- shell2junit install.sh" ++ shell2junit install.sh ++ emscripten install.sh" + + #-----------------# + # 4: test options # Index: /issm/oecreview/Archive/21724-22754/ISSM-21922-21923.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21922-21923.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21922-21923.diff (revision 22755) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/test/NightlyRun/test3019.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3019.m (revision 21922) ++++ ../trunk-jpl/test/NightlyRun/test3019.m (revision 21923) +@@ -32,5 +32,5 @@ + + %Fields and tolerances to track changes + field_names ={'Jac Forward','Jac Reverse','Jac Forward - Reverse'}; +-field_tolerances={1e-8,1e-8,1e-6}; ++field_tolerances={1e-8,1e-8,5e-6}; + field_values={jac_forward,jac_reverse,jac_forward-jac_reverse}; +Index: ../trunk-jpl/test/NightlyRun/test3019.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3019.py (revision 21922) ++++ ../trunk-jpl/test/NightlyRun/test3019.py (revision 21923) +@@ -44,5 +44,5 @@ + + #Fields and tolerances to track changes + field_names =['Jac Forward','Jac Reverse','Jac Forward - Reverse'] +-field_tolerances=[1e-8,1e-8,1e-6] ++field_tolerances=[1e-8,1e-8,5e-6] + field_values=[jac_forward,jac_reverse,jac_forward-jac_reverse] Index: /issm/oecreview/Archive/21724-22754/ISSM-21923-21924.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21923-21924.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21923-21924.diff (revision 22755) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/test/Archives/Archive3015.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/NightlyRun/test3015.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3015.m (revision 21923) ++++ ../trunk-jpl/test/NightlyRun/test3015.m (revision 21924) +@@ -76,4 +76,4 @@ + %Fields and tolerances to track changes + field_names ={'dV/dh-dV/dh0'}; + field_tolerances={1e-13}; +-field_values={dVdh_ad-dVdh_an}; ++field_values={dVdh_ad}; Index: /issm/oecreview/Archive/21724-22754/ISSM-21924-21925.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21924-21925.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21924-21925.diff (revision 22755) @@ -0,0 +1,27 @@ +Index: ../trunk-jpl/test/NightlyRun/test3015.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3015.m (revision 21924) ++++ ../trunk-jpl/test/NightlyRun/test3015.m (revision 21925) +@@ -74,6 +74,6 @@ + disp(sprintf('dV/dh: analytical: %16.16g\n using adolc: %16.16g\n',dVdh_an,dVdh_ad)); + + %Fields and tolerances to track changes +-field_names ={'dV/dh-dV/dh0'}; +-field_tolerances={1e-13}; ++field_names ={'dV/dh'}; ++field_tolerances={1e-8}; + field_values={dVdh_ad}; +Index: ../trunk-jpl/test/NightlyRun/test3015.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3015.py (revision 21924) ++++ ../trunk-jpl/test/NightlyRun/test3015.py (revision 21925) +@@ -90,6 +90,6 @@ + print "dV/dh: analytical: %16.16g\n using adolc: %16.16g\n" % (dVdh_an,dVdh_ad) + + #Fields and tolerances to track changes +-field_names =['dV/dh-dV/dh0'] +-field_tolerances=[1e-13] +-field_values=[dVdh_ad-dVdh_an] ++field_names =['dV/dh'] ++field_tolerances=[1e-8] ++field_values=[dVdh_ad] Index: /issm/oecreview/Archive/21724-22754/ISSM-21925-21926.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21925-21926.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21925-21926.diff (revision 22755) @@ -0,0 +1,100 @@ +Index: ../trunk-jpl/src/m/Makefile.am +=================================================================== +--- ../trunk-jpl/src/m/Makefile.am (revision 21925) ++++ ../trunk-jpl/src/m/Makefile.am (revision 21926) +@@ -134,9 +134,7 @@ + ${ISSM_DIR}/src/m/io/fileptr.js \ + ${ISSM_DIR}/src/m/io/savemodel.js \ + ${ISSM_DIR}/src/m/io/loadmodel.js \ +- ${ISSM_DIR}/src/m/io/saveAsFile.js \ + ${ISSM_DIR}/src/m/io/writetofile.js \ +- ${ISSM_DIR}/src/m/io/download.js \ + ${ISSM_DIR}/src/m/io/writetofile.js \ + ${ISSM_DIR}/src/m/materials/paterson.js \ + ${ISSM_DIR}/src/m/mesh/triangle.js \ +Index: ../trunk-jpl/jenkins/linux64_ross_javascript +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_javascript (revision 21925) ++++ ../trunk-jpl/jenkins/linux64_ross_javascript (revision 21926) +@@ -23,10 +23,12 @@ + #-----------------------------------# + + #List of external pakages to be installed and their installation scripts +-EXTERNALPACKAGES="gsl install-javascript.sh ++EXTERNALPACKAGES="autotools install.sh ++ cmake install.sh ++ emscripten install.sh ++ gsl install-javascript.sh + triangle install-javascript.sh +- shell2junit install.sh +- emscripten install.sh" ++ shell2junit install.sh" + + #-----------------# + # 4: test options # +Index: ../trunk-jpl/externalpackages/emscripten/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/emscripten/install.sh (revision 21925) ++++ ../trunk-jpl/externalpackages/emscripten/install.sh (revision 21926) +@@ -19,3 +19,9 @@ + ./emsdk update + ./emsdk install latest + ./emsdk activate latest ++ ++cd ../ ++mv src install ++cd install ++ ++source ./emsdk_env.sh +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 21925) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 21926) +@@ -29,6 +29,7 @@ + EXAMPLES_TEST=0 + MATLAB_TEST=0 + PYTHON_TEST=0 ++JAVASCRIPT_TEST=0 + + #source configuration script + source $1; +@@ -140,7 +141,7 @@ + cd $ISSM_DIR/externalpackages/$PACKAGENAME + + #install if requested or if previous install has not been successful +- if [ "$ISSM_EXTERNALPACKAGES" == "yes" ] || [ ! -d ./install ] || [ ! "$(ls -A ./install)" ]; then ++ if [ "$ISSM_EXTERNALPACKAGES" == "yes" ] || [ ! -d ./install -a ! -d ./install-javascript ] || ([ -d ./install ] && [ ! "$(ls -A ./install)" ]) || ([ -d ./install-javascript ] && [ ! "$(ls -A ./install-javascript)" ]); then + echo "======================================================"; + echo " Installing $PACKAGENAME "; + echo "======================================================"; +@@ -180,10 +181,17 @@ + exit 1; + fi + ++#Set CXX/CC flags for JS runs after exnteralpackages to avoid conflicts during their compilation ++CXX_PREVIOUS=$CXX ++CC_PREVIOUS=$CC ++if [ $JAVASCRIPT_TEST -eq 1 ]; then ++ export CXX=em++ ++ export CC=emcc ++fi ++ + source $ISSM_DIR/etc/environment.sh + +-if [ "$OS" == "win" ] +-then ++if [ "$OS" == "win" ]; then + echo " == WINDOWS ENVIRONMENT DETECTED ==" + source $ISSM_DIR/externalpackages/windows/windows_environment.sh + fi +@@ -237,6 +245,10 @@ + fi + #}}} + ++#Restore CXX/CC to their previous values ++export CXX=$CXX_PREVIOUS ++export CC=$CC_PREVIOUS ++ + #matlab tests + # {{{ + if [ $MATLAB_TEST -eq 1 ]; then Index: /issm/oecreview/Archive/21724-22754/ISSM-21926-21927.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21926-21927.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21926-21927.diff (revision 22755) @@ -0,0 +1,48 @@ +Index: ../trunk-jpl/test/NightlyRun/test444.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test444.m (revision 21926) ++++ ../trunk-jpl/test/NightlyRun/test444.m (revision 21927) +@@ -19,7 +19,7 @@ + regionalmask=zeros(md.mesh.numberofvertices,1); + in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'../Exp/SquareHalfRight.exp','node',1); + regionalmask(find(in))=1; +-md.transient.requested_outputs={'default','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1',... ++md.transient.requested_outputs={'default','GroundedArea','FloatingArea','IceVolumeAboveFloatation','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1',... + 'IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation'}; + md.outputdefinition.definitions{1}=regionaloutput('name','GroundedArea1','outputnamestring','GroundedArea','mask',regionalmask,... + 'definitionstring','Outputdefinition1'); +@@ -37,6 +37,8 @@ + 'definitionstring','Outputdefinition7'); + md.outputdefinition.definitions{8}=regionaloutput('name','TotalSmb1','outputnamestring','TotalSmb','mask',regionalmask,... + 'definitionstring','Outputdefinition8'); ++md.outputdefinition.definitions{9}=regionaloutput('name','TotalSmb2','outputnamestring','TotalSmb','mask',regionalmask,... ++ 'definitionstring','Outputdefinition9'); + + md=extrude(md,3,1); + md=collapse(md); +@@ -57,6 +59,8 @@ + md.qmu.responses.TotalFloatingBmb1=response_function('Outputdefinition3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.TotalGroundedBmb1=response_function('Outputdefinition4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.TotalSmb1=response_function('Outputdefinition8',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.TotalSmb2=response_function('Outputdefinition9',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); ++md.qmu.responses.FloatingArea=response_function('FloatingArea',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + + md.qmu.method =dakota_method('nond_samp'); + md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),... +@@ -93,10 +97,10 @@ + + %we put all the mean and stdev data in the montecarlo field, which we will use to test for success. + md.results.dakota.montecarlo=[]; +-for i=1:8, ++for i=1:11, + md.results.dakota.montecarlo=[md.results.dakota.montecarlo md.results.dakota.dresp_out(i).mean]; + end +-for i=1:8, ++for i=1:11, + md.results.dakota.montecarlo=[md.results.dakota.montecarlo md.results.dakota.dresp_out(i).stddev]; + end + field_names ={'montecarlo'}; +Index: ../trunk-jpl/test/Archives/Archive444.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21927-21928.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21927-21928.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21927-21928.diff (revision 22755) @@ -0,0 +1,52 @@ +Index: ../trunk-jpl/externalpackages/emscripten/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/emscripten/install.sh (revision 21927) ++++ ../trunk-jpl/externalpackages/emscripten/install.sh (revision 21928) +@@ -11,7 +11,7 @@ + tar -zxvf emsdk-portable.tar.gz + mv emsdk_portable src + +-cd src ++cd src + + export CXX=g++ + export CC=gcc +@@ -20,8 +20,6 @@ + ./emsdk install latest + ./emsdk activate latest + +-cd ../ +-mv src install +-cd install +- +-source ./emsdk_env.sh ++#Related to moving the install path after installation - However, not safe to install in dir named "install" since a failure would not be noticed by jenkins when triggering ++#Not reliable - when executed in subshell without sourcing the install file, this has no effect. Safer to explicitly source for each dependent externalpackage. ++source emsdk_env.sh +Index: ../trunk-jpl/externalpackages/triangle/install-javascript.sh +=================================================================== +--- ../trunk-jpl/externalpackages/triangle/install-javascript.sh (revision 21927) ++++ ../trunk-jpl/externalpackages/triangle/install-javascript.sh (revision 21928) +@@ -8,6 +8,9 @@ + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + ++#Source emscripten to ensure emcc/em++ compiler are in env ++source $ISSM_DIR/externalpackages/emscripten/src/emsdk_env.sh ++ + #Untar + cd install-javascript + cp ../triangle.zip ./ +Index: ../trunk-jpl/externalpackages/gsl/install-javascript.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gsl/install-javascript.sh (revision 21927) ++++ ../trunk-jpl/externalpackages/gsl/install-javascript.sh (revision 21928) +@@ -20,6 +20,8 @@ + + export CC=emcc + export CXX=em++ ++#Source emscripten to ensure emcc/em++ compiler are in env ++source $ISSM_DIR/externalpackages/emscripten/src/emsdk_env.sh + + # Issue with variadic function signatures. + export CFLAGS=-DSTDC_HEADERS Index: /issm/oecreview/Archive/21724-22754/ISSM-21928-21929.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21928-21929.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21928-21929.diff (revision 22755) @@ -0,0 +1,35 @@ +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 21928) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 21929) +@@ -181,6 +181,14 @@ + exit 1; + fi + ++ ++source $ISSM_DIR/etc/environment.sh ++ ++if [ "$OS" == "win" ]; then ++ echo " == WINDOWS ENVIRONMENT DETECTED ==" ++ source $ISSM_DIR/externalpackages/windows/windows_environment.sh ++fi ++ + #Set CXX/CC flags for JS runs after exnteralpackages to avoid conflicts during their compilation + CXX_PREVIOUS=$CXX + CC_PREVIOUS=$CC +@@ -187,14 +195,8 @@ + if [ $JAVASCRIPT_TEST -eq 1 ]; then + export CXX=em++ + export CC=emcc ++ source $ISSM_DIR/externalpackages/emscripten/src/emsdk_env.sh + fi +- +-source $ISSM_DIR/etc/environment.sh +- +-if [ "$OS" == "win" ]; then +- echo " == WINDOWS ENVIRONMENT DETECTED ==" +- source $ISSM_DIR/externalpackages/windows/windows_environment.sh +-fi + #}}} + #ISSM compilation yes/no (ISSM_COMPILATION) {{{ + if [ "$ISSM_COMPILATION" == "yes" ] Index: /issm/oecreview/Archive/21724-22754/ISSM-21929-21930.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21929-21930.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21929-21930.diff (revision 22755) @@ -0,0 +1,198 @@ +Index: ../trunk-jpl/src/m/classes/amrbamg.m +=================================================================== +--- ../trunk-jpl/src/m/classes/amrbamg.m (revision 21929) ++++ ../trunk-jpl/src/m/classes/amrbamg.m (revision 21930) +@@ -10,6 +10,7 @@ + fieldname = ''; + err = 0.; + keepmetric = 0; ++ gradation = 0.; + groundingline_resolution = 0.; + groundingline_distance = 0.; + icefront_resolution = 0.; +@@ -41,6 +42,9 @@ + %keep metric? + self.keepmetric=1; + ++ %control of element lengths ++ self.gradation=1.5; ++ + %other criterias + self.groundingline_resolution=500.; + self.groundingline_distance=0.; +@@ -58,6 +62,7 @@ + md = checkfield(md,'fieldname','amr.hmin','numel',[1],'>',0,'<',self.hmax,'NaN',1); + %md = checkfield(md,'fieldname','amr.fieldname','string',[1]); + md = checkfield(md,'fieldname','amr.keepmetric','numel',[1],'>=',0,'<=',1,'NaN',1); ++ md = checkfield(md,'fieldname','amr.gradation','numel',[1],'>=',1.1,'<=',5,'NaN',1); + md = checkfield(md,'fieldname','amr.groundingline_resolution','numel',[1],'>',0,'<',self.hmax,'NaN',1); + md = checkfield(md,'fieldname','amr.groundingline_distance','numel',[1],'>=',0,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','amr.icefront_resolution','numel',[1],'>',0,'<',self.hmax,'NaN',1); +@@ -74,6 +79,7 @@ + fielddisplay(self,'hmax',['maximum element length']); + fielddisplay(self,'fieldname',['name of input that will be used to compute the metric (should be an input of FemModel)']); + fielddisplay(self,'keepmetric',['indicates whether the metric should be kept every remeshing time']); ++ fielddisplay(self,'gradation',['maximum ratio between two adjacent edges']); + fielddisplay(self,'groundingline_resolution',['element length near the grounding line']); + fielddisplay(self,'groundingline_distance',['distance around the grounding line which elements will be refined']); + fielddisplay(self,'icefront_resolution',['element length near the ice front']); +@@ -92,6 +98,7 @@ + WriteData(fid,prefix,'object',self,'class','amr','fieldname','fieldname','format','String'); + WriteData(fid,prefix,'object',self,'class','amr','fieldname','err','format','Double'); + WriteData(fid,prefix,'object',self,'class','amr','fieldname','keepmetric','format','Integer'); ++ WriteData(fid,prefix,'object',self,'class','amr','fieldname','gradation','format','Double'); + WriteData(fid,prefix,'object',self,'class','amr','fieldname','groundingline_resolution','format','Double'); + WriteData(fid,prefix,'object',self,'class','amr','fieldname','groundingline_distance','format','Double'); + WriteData(fid,prefix,'object',self,'class','amr','fieldname','icefront_resolution','format','Double'); +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21929) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21930) +@@ -849,6 +849,7 @@ + AmrFieldEnum, + AmrErrEnum, + AmrKeepMetricEnum, ++ AmrGradationEnum, + AmrGroundingLineResolutionEnum, + AmrGroundingLineDistanceEnum, + AmrIceFrontResolutionEnum, +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21929) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21930) +@@ -825,6 +825,7 @@ + case AmrFieldEnum : return "AmrField"; + case AmrErrEnum : return "AmrErr"; + case AmrKeepMetricEnum : return "AmrKeepMetric"; ++ case AmrGradationEnum : return "AmrGradation"; + case AmrGroundingLineResolutionEnum : return "AmrGroundingLineResolution"; + case AmrGroundingLineDistanceEnum : return "AmrGroundingLineDistance"; + case AmrIceFrontResolutionEnum : return "AmrIceFrontResolution"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21929) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21930) +@@ -843,6 +843,7 @@ + else if (strcmp(name,"AmrField")==0) return AmrFieldEnum; + else if (strcmp(name,"AmrErr")==0) return AmrErrEnum; + else if (strcmp(name,"AmrKeepMetric")==0) return AmrKeepMetricEnum; ++ else if (strcmp(name,"AmrGradation")==0) return AmrGradationEnum; + else if (strcmp(name,"AmrGroundingLineResolution")==0) return AmrGroundingLineResolutionEnum; + else if (strcmp(name,"AmrGroundingLineDistance")==0) return AmrGroundingLineDistanceEnum; + else if (strcmp(name,"AmrIceFrontResolution")==0) return AmrIceFrontResolutionEnum; +@@ -873,11 +874,11 @@ + else if (strcmp(name,"ElementHook")==0) return ElementHookEnum; + else if (strcmp(name,"Hook")==0) return HookEnum; + else if (strcmp(name,"ExternalResult")==0) return ExternalResultEnum; +- else if (strcmp(name,"FileParam")==0) return FileParamEnum; + else stage=8; + } + if(stage==8){ +- if (strcmp(name,"Input")==0) return InputEnum; ++ if (strcmp(name,"FileParam")==0) return FileParamEnum; ++ else if (strcmp(name,"Input")==0) return InputEnum; + else if (strcmp(name,"IntInput")==0) return IntInputEnum; + else if (strcmp(name,"IntParam")==0) return IntParamEnum; + else if (strcmp(name,"IntVecParam")==0) return IntVecParamEnum; +@@ -996,11 +997,11 @@ + else if (strcmp(name,"NearestInterp")==0) return NearestInterpEnum; + else if (strcmp(name,"MinVel")==0) return MinVelEnum; + else if (strcmp(name,"MaxVel")==0) return MaxVelEnum; +- else if (strcmp(name,"MinVx")==0) return MinVxEnum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"MaxVx")==0) return MaxVxEnum; ++ if (strcmp(name,"MinVx")==0) return MinVxEnum; ++ else if (strcmp(name,"MaxVx")==0) return MaxVxEnum; + else if (strcmp(name,"MaxAbsVx")==0) return MaxAbsVxEnum; + else if (strcmp(name,"MinVy")==0) return MinVyEnum; + else if (strcmp(name,"MaxVy")==0) return MaxVyEnum; +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21929) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21930) +@@ -114,6 +114,7 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.amr.hmax",AmrHmaxEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.err",AmrErrEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.keepmetric",AmrKeepMetricEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.amr.gradation",AmrGradationEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.groundingline_resolution",AmrGroundingLineResolutionEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.groundingline_distance",AmrGroundingLineDistanceEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.icefront_resolution",AmrIceFrontResolutionEnum)); +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21929) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 21930) +@@ -2719,9 +2719,8 @@ + /*}}}*/ + void FemModel::WriteMeshInResults(void){/*{{{*/ + +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ /*Write the erros estimators*/ + this->WriteErrorEstimatorsInResults(); +- #endif + + int step = -1; + int numberofelements = -1; +@@ -4418,7 +4417,7 @@ + IssmDouble* y = NULL; + IssmDouble* z = NULL; + int* elements = NULL; +- IssmDouble hmin,hmax,err; ++ IssmDouble hmin,hmax,err,gradation; + IssmDouble groundingline_resolution,groundingline_distance,icefront_resolution,icefront_distance; + IssmDouble thicknesserror_resolution,thicknesserror_threshold,deviatoricerror_resolution,deviatoricerror_threshold; + int fieldenum,keepmetric; +@@ -4438,6 +4437,7 @@ + this->parameters->FindParam(&fieldenum,AmrFieldEnum); + this->parameters->FindParam(&err,AmrErrEnum); + this->parameters->FindParam(&keepmetric,AmrKeepMetricEnum); ++ this->parameters->FindParam(&gradation,AmrGradationEnum); + this->parameters->FindParam(&groundingline_resolution,AmrGroundingLineResolutionEnum); + this->parameters->FindParam(&groundingline_distance,AmrGroundingLineDistanceEnum); + this->parameters->FindParam(&icefront_resolution,AmrIceFrontResolutionEnum); +@@ -4448,7 +4448,7 @@ + this->parameters->FindParam(&deviatoricerror_threshold,AmrDeviatoricErrorThresholdEnum); + + /*Create bamg data structures for bamg*/ +- this->amrbamg = new AmrBamg(hmin,hmax,fieldenum,err,keepmetric, ++ this->amrbamg = new AmrBamg(hmin,hmax,fieldenum,err,keepmetric,gradation, + groundingline_resolution,groundingline_distance, + icefront_resolution,icefront_distance, + thicknesserror_resolution,thicknesserror_threshold, +Index: ../trunk-jpl/src/c/classes/AmrBamg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.h (revision 21929) ++++ ../trunk-jpl/src/c/classes/AmrBamg.h (revision 21930) +@@ -24,7 +24,7 @@ + IssmDouble deviatoricerror_threshold; + + /* Constructor, destructor etc*/ +- AmrBamg(IssmDouble hmin,IssmDouble hmax,int fieldenum_in,IssmDouble err_in,int keepmetric_in, ++ AmrBamg(IssmDouble hmin,IssmDouble hmax,int fieldenum_in,IssmDouble err_in,int keepmetric_in,IssmDouble gradation_in, + IssmDouble groundingline_resolution_in,IssmDouble groundingline_distance_in, + IssmDouble icefront_resolution_in,IssmDouble icefront_distance_in, + IssmDouble thicknesserror_resolution_in,IssmDouble thicknesserror_threshold_in, +Index: ../trunk-jpl/src/c/classes/AmrBamg.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21929) ++++ ../trunk-jpl/src/c/classes/AmrBamg.cpp (revision 21930) +@@ -16,7 +16,7 @@ + using namespace std; + + /*Constructor, copy, clean up and destructor*/ +-AmrBamg::AmrBamg(IssmDouble hmin,IssmDouble hmax,int fieldenum_in,IssmDouble err_in,int keepmetric_in, ++AmrBamg::AmrBamg(IssmDouble hmin,IssmDouble hmax,int fieldenum_in,IssmDouble err_in,int keepmetric_in,IssmDouble gradation_in, + IssmDouble groundingline_resolution_in,IssmDouble groundingline_distance_in, + IssmDouble icefront_resolution_in,IssmDouble icefront_distance_in, + IssmDouble thicknesserror_resolution_in,IssmDouble thicknesserror_threshold_in, +@@ -42,7 +42,7 @@ + this->options->cutoff = 10.e-5; + this->options->coeff = 1; + this->options->errg = 0.1; +- this->options->gradation = 1.5; ++ this->options->gradation = gradation_in; + this->options->Hessiantype = 0; + this->options->maxnbv = 1e6; + this->options->maxsubdiv = 10; Index: /issm/oecreview/Archive/21724-22754/ISSM-21930-21931.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21930-21931.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21930-21931.diff (revision 22755) @@ -0,0 +1,804 @@ +Index: ../trunk-jpl/src/c/bamg/GeomEdge.h +=================================================================== +--- ../trunk-jpl/src/c/bamg/GeomEdge.h (revision 21930) ++++ ../trunk-jpl/src/c/bamg/GeomEdge.h (revision 21931) +@@ -26,7 +26,6 @@ + + //Methods + R2 F(double theta) const ; // parametrization of the curve edge +- double R1tg(double theta,R2 &t) const ; // 1/radius of curvature + tangente + int Cracked() const; + int TgA() const; + int TgB() const; +Index: ../trunk-jpl/src/c/bamg/GeomEdge.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/GeomEdge.cpp (revision 21930) ++++ ../trunk-jpl/src/c/bamg/GeomEdge.cpp (revision 21931) +@@ -62,77 +62,6 @@ + int GeomEdge::Mark() const {/*{{{*/ + return type &16; + }/*}}}*/ +- double GeomEdge::R1tg(double theta,R2 & t) const{/*{{{*/ +- /*Original code from Frederic Hecht (BAMG v1.01, MeshGeom.cpp/R1tg)*/ +- // 1/R of radius of cuvature +- +- R2 A=v[0]->r,B=v[1]->r; +- double dca,dcb,dcta,dctb; +- double ddca,ddcb,ddcta,ddctb; +- double tt = theta*theta; +- +- //check theta +- _assert_(theta>=0 && theta<=1); +- +- if (TgA()){ +- if (TgB()){ +- // Tangent A and B provided: +- // interpolation d'hermite +- dcb = 6*theta*(1-theta); +- ddcb = 6*(1-2*theta); +- dca = -dcb; +- ddca = -ddcb; +- dcta = (3*theta - 4)*theta + 1; +- ddcta=6*theta-4; +- dctb = 3*tt - 2*theta; +- ddctb = 6*theta-2; +- } +- else { +- //Tangent A provided but tangent B not provided +- // 1-t*t, t-t*t, t*t +- double t = theta; +- dcb = 2*t; +- ddcb = 2; +- dca = -dcb; +- ddca = -2; +- dcta = 1-dcb; +- ddcta = -ddcb; +- dctb=0; +- ddctb=0; +- } +- } +- else{ +- if (TgB()){ +- //Tangent B provided but tangent A not provided +- double t = 1-theta; +- dca = -2*t; +- ddca = 2; +- dcb = -dca; +- ddcb = -2; +- dctb = 1+dca; +- ddctb= ddca; +- dcta =0; +- ddcta =0; +- } +- else { +- //Neither thangent A nor tangent B provided +- // lagrange P1 +- t=B-A; +- return 0; +- } +- } +- R2 d = A*dca + B*dcb + tg[0]* dcta + tg[1] * dctb; +- R2 dd = A*ddca + B*ddcb + tg[0]* ddcta + tg[1] * ddctb; +- double d2=(d,d); +- double sd2 = sqrt(d2); +- t=d; +- if(d2>1.0e-20){ +- t/=sd2; +- return Abs(Det(d,dd))/(d2*sd2); +- } +- else return 0; +- } +- /*}}}*/ + int GeomEdge::Required() {/*{{{*/ + return type &64; + }/*}}}*/ +Index: ../trunk-jpl/src/c/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21930) ++++ ../trunk-jpl/src/c/bamg/Mesh.cpp (revision 21931) +@@ -1593,7 +1593,10 @@ + long i0 = GetId(triangles[it][VerticesOfTriangularEdge[j][0]]); + long i1 = GetId(triangles[it][VerticesOfTriangularEdge[j][1]]); + k = edge4->SortAndFind(i0,i1); +- _assert_(k>=0); ++ if(k<0){ ++ delete [] colorV; ++ _error_("This should not happen"); ++ } + subdomains[i].direction = (vertices + i0 == edges[k].v[0]) ? 1 : -1; + subdomains[i].edge = edges+k; + Gh.subdomains[i].edge = Gh.edges + k; +@@ -2053,7 +2056,15 @@ + if (xy==0) dd=dxdx; + else if (xy==1) dd=dxdy; + else if (xy==2) dd=dydy; +- else _error_("not supported yet"); ++ else{ ++ delete [] detT; ++ delete [] Mmass; ++ delete [] workT; ++ delete [] workV; ++ delete [] Mmassxx; ++ delete [] OnBoundary; ++ _error_("not supported yet"); ++ } + // do leat 2 iteration for boundary problem + for (int ijacobi=0;ijacobi= maxnbv){ ++ delete [] bcurve; + _error_("too many vertices on geometry: " << NbVerticesOnGeomVertex << " >= " << maxnbv); + } + +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21930) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 21931) +@@ -984,7 +984,6 @@ + GiaIvinsAnalysisEnum, + EsaSolutionEnum, + EsaAnalysisEnum, +- MeshdeformationAnalysisEnum, + LevelsetAnalysisEnum, + ExtrapolationAnalysisEnum, + /*}}}*/ +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21930) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 21931) +@@ -952,7 +952,6 @@ + case GiaIvinsAnalysisEnum : return "GiaIvinsAnalysis"; + case EsaSolutionEnum : return "EsaSolution"; + case EsaAnalysisEnum : return "EsaAnalysis"; +- case MeshdeformationAnalysisEnum : return "MeshdeformationAnalysis"; + case LevelsetAnalysisEnum : return "LevelsetAnalysis"; + case ExtrapolationAnalysisEnum : return "ExtrapolationAnalysis"; + case ApproximationEnum : return "Approximation"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21930) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 21931) +@@ -973,7 +973,6 @@ + else if (strcmp(name,"GiaIvinsAnalysis")==0) return GiaIvinsAnalysisEnum; + else if (strcmp(name,"EsaSolution")==0) return EsaSolutionEnum; + else if (strcmp(name,"EsaAnalysis")==0) return EsaAnalysisEnum; +- else if (strcmp(name,"MeshdeformationAnalysis")==0) return MeshdeformationAnalysisEnum; + else if (strcmp(name,"LevelsetAnalysis")==0) return LevelsetAnalysisEnum; + else if (strcmp(name,"ExtrapolationAnalysis")==0) return ExtrapolationAnalysisEnum; + else if (strcmp(name,"Approximation")==0) return ApproximationEnum; +@@ -997,11 +996,11 @@ + else if (strcmp(name,"NearestInterp")==0) return NearestInterpEnum; + else if (strcmp(name,"MinVel")==0) return MinVelEnum; + else if (strcmp(name,"MaxVel")==0) return MaxVelEnum; ++ else if (strcmp(name,"MinVx")==0) return MinVxEnum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"MinVx")==0) return MinVxEnum; +- else if (strcmp(name,"MaxVx")==0) return MaxVxEnum; ++ if (strcmp(name,"MaxVx")==0) return MaxVxEnum; + else if (strcmp(name,"MaxAbsVx")==0) return MaxAbsVxEnum; + else if (strcmp(name,"MinVy")==0) return MinVyEnum; + else if (strcmp(name,"MaxVy")==0) return MaxVyEnum; +Index: ../trunk-jpl/src/c/shared/Numerics/GaussPoints.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/GaussPoints.cpp (revision 21930) ++++ ../trunk-jpl/src/c/shared/Numerics/GaussPoints.cpp (revision 21931) +@@ -1690,20 +1690,3 @@ + xDelete(work); + + }/*}}}*/ +- +-/*Element Gauss points TO BE REMOVED*/ +-void gaussQuad( IssmPDouble** pxgaus, IssmPDouble** pxwgt, IssmPDouble** pegaus, IssmPDouble** pewgt, int nigaus, int njgaus ) {/*{{{*/ +- /*Gauss quadrature points for the quadrilaterial.*/ +- +- /*get the gauss points using the product of two line rules */ +- GaussLegendreLinear(pxgaus, pxwgt, nigaus); +- GaussLegendreLinear(pegaus, pewgt, njgaus); +-}/*}}}*/ +-void gaussHexa( IssmPDouble** pxgaus, IssmPDouble** pxwgt, IssmPDouble** pegaus, IssmPDouble** pewgt, IssmPDouble** pzgaus, IssmPDouble ** pzwgt, int nigaus, int njgaus, int nkgaus ) {/*{{{*/ +- /*Gauss quadrature points for the hexahedron.*/ +- +- /* get the gauss points using the product of three line rules */ +- GaussLegendreLinear(pxgaus, pxwgt, nigaus); +- GaussLegendreLinear(pegaus, pewgt, njgaus); +- GaussLegendreLinear(pzgaus, pzwgt, nkgaus); +-}/*}}}*/ +Index: ../trunk-jpl/src/c/shared/Numerics/GaussPoints.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/GaussPoints.h (revision 21930) ++++ ../trunk-jpl/src/c/shared/Numerics/GaussPoints.h (revision 21931) +@@ -17,7 +17,4 @@ + #define MAX_GAUS_ITER 30 + void GaussRecur(IssmPDouble* zero, IssmPDouble* weight, int n, IssmPDouble* alpha, IssmPDouble* beta); + +-void gaussQuad(IssmPDouble** pxgaus, IssmPDouble** pxwgt, IssmPDouble** pegaus, IssmPDouble** pewgt, int nigaus, int njgaus); +-void gaussHexa(IssmPDouble** pxgaus, IssmPDouble** pxwgt, IssmPDouble** pegaus, IssmPDouble** pewgt, IssmPDouble** pzgaus, IssmPDouble ** pzwgt, int nigaus, int njgaus, int nkgaus); +- + #endif +Index: ../trunk-jpl/src/c/modules/ExpToLevelSetx/ExpToLevelSetxt.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ExpToLevelSetx/ExpToLevelSetxt.cpp (revision 21930) ++++ ../trunk-jpl/src/c/modules/ExpToLevelSetx/ExpToLevelSetxt.cpp (revision 21931) +@@ -67,18 +67,8 @@ + } + + } +-double ddistance(double x1,double y1,double x2,double y2){ +- return sqrt(pow(x2-x1,2)+pow(y2-y1,2)); +-} +-double ddot(double x1, double y1, double x2, double y2){ +- return x1*x2+y1*y2; +-} +- +-bool isPointLeftOfRay(double x, double y, double raySx, double raySy, double rayEx, double rayEy) { +- return (y-raySy)*(rayEx-raySx) +- > (x-raySx)*(rayEy-raySy); +-} +- ++double ddistance(double x1,double y1,double x2,double y2){ return sqrt(pow(x2-x1,2)+pow(y2-y1,2)); } ++double ddot(double x1, double y1, double x2, double y2){ return x1*x2+y1*y2; } + double minimum_distance(double x1, double y1, double x2, double y2, double x0, double y0){ + + // Return minimum distance between line segment [(x1,y1) (x2,y2)] and point (x0,y0) (v=(x1,y1), w=(x2,y2) and p=(x0,y0) +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 21930) ++++ ../trunk-jpl/src/c/Makefile.am (revision 21931) +@@ -293,7 +293,6 @@ + ./cores/dummy_core.cpp\ + ./cores/surfaceslope_core.cpp\ + ./cores/bedslope_core.cpp\ +- ./cores/meshdeformation_core.cpp\ + ./cores/damage_core.cpp\ + ./cores/levelsetfunctionslope_core.cpp\ + ./cores/movingfront_core.cpp\ +@@ -447,9 +446,6 @@ + if SMOOTH + issm_sources += ./analyses/SmoothAnalysis.cpp + endif +-if MESHDEFORMATION +-issm_sources += ./analyses/MeshdeformationAnalysis.cpp +-endif + if LEVELSET + issm_sources += ./analyses/LevelsetAnalysis.cpp + issm_sources += ./modules/Calvingx/Calvingx.cpp +Index: ../trunk-jpl/src/c/cores/meshdeformation_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/meshdeformation_core.cpp (revision 21930) ++++ ../trunk-jpl/src/c/cores/meshdeformation_core.cpp (nonexistent) +@@ -1,30 +0,0 @@ +-/*!\file: meshdeformation_core.cpp +- * \brief: core of the slope solution +- */ +- +-#include "./cores.h" +-#include "../toolkits/toolkits.h" +-#include "../classes/classes.h" +-#include "../shared/shared.h" +-#include "../solutionsequences/solutionsequences.h" +-#include "../modules/modules.h" +- +-void meshdeformation_core(FemModel* femmodel){ +- +- /*parameters: */ +- bool save_results; +- +- /*Recover some parameters: */ +- femmodel->parameters->FindParam(&save_results,SaveResultsEnum); +- +- if(VerboseSolution()) _printf0_("computing mesh deformation (elasticity)...\n"); +- +- /*Call on core computations: */ +- femmodel->SetCurrentConfiguration(MeshdeformationAnalysisEnum); +- solutionsequence_linear(femmodel); +- +- if(save_results){ +- if(VerboseSolution()) _printf0_("saving results:\n"); +- } +- +-} +Index: ../trunk-jpl/src/c/classes/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21930) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.cpp (revision 21931) +@@ -1221,49 +1221,6 @@ + return base*(surface - bed + min( rho_water/rho_ice * bathymetry, 0.) ); + } + /*}}}*/ +-void Penta::InputControlUpdate(IssmDouble scalar,bool save_parameter){/*{{{*/ +- +- /*Intermediary*/ +- int num_controls; +- int* control_type=NULL; +- Input* input=NULL; +- +- /*retrieve some parameters: */ +- this->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); +- this->parameters->FindParam(&control_type,NULL,InversionControlParametersEnum); +- +- for(int i=0;iinputs->GetInput(MaterialsRheologyBEnum); _assert_(input); +- } +- else if(control_type[i]==DamageDbarEnum){ +- if (!IsOnBase()) goto cleanup_and_return; +- input=(Input*)this->inputs->GetInput(DamageDEnum); _assert_(input); +- } +- else{ +- input=(Input*)this->inputs->GetInput(control_type[i]); _assert_(input); +- } +- if(input->ObjectEnum()!=ControlInputEnum) _error_("input " << EnumToStringx(control_type[i]) << " is not a ControlInput"); +- +- ((ControlInput*)input)->UpdateValue(scalar); +- ((ControlInput*)input)->Constrain(); +- if (save_parameter) ((ControlInput*)input)->SaveValue(); +- +- if(control_type[i]==MaterialsRheologyBbarEnum){ +- this->InputExtrude(MaterialsRheologyBEnum,-1); +- } +- else if(control_type[i]==DamageDbarEnum){ +- this->InputExtrude(DamageDEnum,-1); +- } +- } +- +- /*Clean up and return*/ +-cleanup_and_return: +- xDelete(control_type); +-} +-/*}}}*/ + void Penta::InputDepthAverageAtBase(int original_enum,int average_enum){/*{{{*/ + + IssmDouble Jdet,value; +@@ -1367,18 +1324,6 @@ + } + } + /*}}}*/ +-void Penta::InputScale(int enum_type,IssmDouble scale_factor){/*{{{*/ +- +- Input* input=NULL; +- +- /*Make a copy of the original input: */ +- input=(Input*)this->inputs->GetInput(enum_type); +- if(!input)_error_("could not find old input with enum: " << EnumToStringx(enum_type)); +- +- /*Scale: */ +- input->Scale(scale_factor); +-} +-/*}}}*/ + void Penta::InputUpdateFromIoModel(int index,IoModel* iomodel){ /*{{{*/ + + /*Intermediaries*/ +Index: ../trunk-jpl/src/c/classes/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21930) ++++ ../trunk-jpl/src/c/classes/Elements/Penta.h (revision 21931) +@@ -90,10 +90,8 @@ + IssmDouble GroundedArea(void); + IssmDouble IceVolume(void); + IssmDouble IceVolumeAboveFloatation(void); +- void InputControlUpdate(IssmDouble scalar,bool save_parameter); + void InputDepthAverageAtBase(int enum_type,int average_enum_type); + void InputExtrude(int enum_type,int start); +- void InputScale(int enum_type,IssmDouble scale_factor); + void InputUpdateFromIoModel(int index, IoModel* iomodel); + void InputUpdateFromSolutionOneDof(IssmDouble* solutiong,int enum_type); + void InputUpdateFromSolutionOneDofCollapsed(IssmDouble* solutiong,int enum_type); +Index: ../trunk-jpl/src/c/classes/Elements/Seg.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21930) ++++ ../trunk-jpl/src/c/classes/Elements/Seg.h (revision 21931) +@@ -78,10 +78,8 @@ + IssmDouble GroundedArea(void){_error_("not implemented yet");}; + IssmDouble IceVolume(void){_error_("not implemented yet");}; + IssmDouble IceVolumeAboveFloatation(void){_error_("not implemented yet");}; +- void InputControlUpdate(IssmDouble scalar,bool save_parameter){_error_("not implemented yet");}; + void InputDepthAverageAtBase(int enum_type,int average_enum_type){_error_("not implemented yet");}; + void InputExtrude(int enum_type,int start){_error_("not implemented"); /*For penta only*/}; +- void InputScale(int enum_type,IssmDouble scale_factor){_error_("not implemented yet");}; + void InputUpdateFromIoModel(int index, IoModel* iomodel){_error_("not implemented yet");}; + void InputUpdateFromSolutionOneDof(IssmDouble* solution,int inputenum){_error_("not implemented yet");}; + void InputUpdateFromSolutionOneDofCollapsed(IssmDouble* solution,int inputenum){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Elements/Tetra.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21930) ++++ ../trunk-jpl/src/c/classes/Elements/Tetra.h (revision 21931) +@@ -92,10 +92,8 @@ + bool IsOnBase(); + bool IsOnSurface(); + bool IsZeroLevelset(int levelset_enum){_error_("not implemented");}; +- void InputControlUpdate(IssmDouble scalar,bool save_parameter){_error_("not implemented yet");}; + void InputDepthAverageAtBase(int enum_type,int average_enum_type){_error_("not implemented yet");}; + void InputExtrude(int enum_type,int start){_error_("not implemented"); /*For penta only*/}; +- void InputScale(int enum_type,IssmDouble scale_factor){_error_("not implemented yet");}; + void InputUpdateFromIoModel(int index, IoModel* iomodel); + void InputUpdateFromSolutionOneDof(IssmDouble* solution,int inputenum); + void InputUpdateFromSolutionOneDofCollapsed(IssmDouble* solution,int inputenum){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21930) ++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 21931) +@@ -221,10 +221,8 @@ + virtual IssmDouble GroundedArea(void)=0; + virtual IssmDouble IceVolume(void)=0; + virtual IssmDouble IceVolumeAboveFloatation(void)=0; +- virtual void InputControlUpdate(IssmDouble scalar,bool save_parameter)=0; + virtual void InputDepthAverageAtBase(int enum_type,int average_enum_type)=0; + virtual void InputExtrude(int input_enum,int start)=0; +- virtual void InputScale(int enum_type,IssmDouble scale_factor)=0; + virtual void InputUpdateFromSolutionOneDofCollapsed(IssmDouble* solution,int inputenum)=0; + virtual void InputUpdateFromSolutionOneDof(IssmDouble* solution,int inputenum)=0; + virtual bool IsFaceOnBoundary(void)=0; +Index: ../trunk-jpl/src/c/classes/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21930) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.cpp (revision 21931) +@@ -1366,7 +1366,7 @@ + /*Computeportion of the element that has a positive levelset*/ + + bool negative=true; +- int point; ++ int point=0; + const IssmPDouble epsilon= 1.e-15; + IssmDouble f1,f2; + +@@ -1404,6 +1404,9 @@ + f1=gl[1]/(gl[1]-gl[2]); + f2=gl[1]/(gl[1]-gl[0]); + } ++ else{ ++ _error_("This case should NOT be happening"); ++ } + } + *point1=point; + *fraction1=f1; +@@ -1660,33 +1663,6 @@ + return base*(surface-bed+min(rho_water/rho_ice*bathymetry,0.)); + } + /*}}}*/ +-void Tria::InputControlUpdate(IssmDouble scalar,bool save_parameter){/*{{{*/ +- +- /*Intermediary*/ +- int num_controls; +- int* control_type=NULL; +- Input* input=NULL; +- +- /*retrieve some parameters: */ +- this->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); +- this->parameters->FindParam(&control_type,NULL,InversionControlParametersEnum); +- +- for(int i=0;iinputs->GetInput(control_type[i]); _assert_(input); +- if (input->ObjectEnum()!=ControlInputEnum){ +- _error_("input " << EnumToStringx(control_type[i]) << " is not a ControlInput"); +- } +- +- ((ControlInput*)input)->UpdateValue(scalar); +- ((ControlInput*)input)->Constrain(); +- if (save_parameter) ((ControlInput*)input)->SaveValue(); +- +- } +- +- /*Clean up and return*/ +- xDelete(control_type); +-} +-/*}}}*/ + void Tria::InputDepthAverageAtBase(int enum_type,int average_enum_type){/*{{{*/ + + /*New input*/ +@@ -1705,18 +1681,6 @@ + this->inputs->AddInput((Input*)newinput); + } + /*}}}*/ +-void Tria::InputScale(int enum_type,IssmDouble scale_factor){/*{{{*/ +- +- Input* input=NULL; +- +- /*Make a copy of the original input: */ +- input=(Input*)this->inputs->GetInput(enum_type); +- if(!input)_error_("could not find old input with enum: " << EnumToStringx(enum_type)); +- +- /*Scale: */ +- input->Scale(scale_factor); +-} +-/*}}}*/ + void Tria::InputUpdateFromIoModel(int index, IoModel* iomodel){ //i is the element index/*{{{*/ + + /*Intermediaries*/ +Index: ../trunk-jpl/src/c/classes/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21930) ++++ ../trunk-jpl/src/c/classes/Elements/Tria.h (revision 21931) +@@ -90,10 +90,8 @@ + bool HasEdgeOnSurface(); + IssmDouble IceVolume(void); + IssmDouble IceVolumeAboveFloatation(void); +- void InputControlUpdate(IssmDouble scalar,bool save_parameter); + void InputDepthAverageAtBase(int enum_type,int average_enum_type); + void InputExtrude(int enum_type,int start){_error_("not implemented"); /*For penta only*/}; +- void InputScale(int enum_type,IssmDouble scale_factor); + bool IsFaceOnBoundary(void); + bool IsIcefront(void); + bool IsNodeOnShelfFromFlags(IssmDouble* flags); +Index: ../trunk-jpl/src/c/classes/Inputs/ControlInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/ControlInput.h (revision 21930) ++++ ../trunk-jpl/src/c/classes/Inputs/ControlInput.h (revision 21931) +@@ -80,7 +80,6 @@ + void ResultToPatch(IssmDouble* values,int nodesperelement,int sid){_error_("not supported yet");}; + void SaveValue(void); + void Scale(IssmDouble scale_factor){_error_("not implemented yet");}; +- void ScaleGradient(IssmDouble scale); + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; + void SetGradient(Input* gradient_in); + void SetInput(Input* in_input); +Index: ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h (revision 21930) ++++ ../trunk-jpl/src/c/classes/Inputs/DatasetInput.h (revision 21931) +@@ -76,7 +76,6 @@ + void ResultToPatch(IssmDouble* values,int nodesperelement,int sid){_error_("not supported yet");}; + void SaveValue(void){_error_("not implemented yet");}; + void Scale(IssmDouble scale_factor){_error_("not implemented yet");}; +- void ScaleGradient(IssmDouble scale){_error_("not implemented yet");}; + void Set(IssmDouble setvalue){_error_("Set not implemented yet");}; + void SetGradient(Input* gradient_in){_error_("not implemented yet");}; + void UpdateValue(IssmDouble scalar){_error_("not implemented yet");}; +Index: ../trunk-jpl/src/c/classes/Inputs/ControlInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Inputs/ControlInput.cpp (revision 21930) ++++ ../trunk-jpl/src/c/classes/Inputs/ControlInput.cpp (revision 21931) +@@ -235,10 +235,6 @@ + if(savedvalues) delete this->savedvalues; + this->savedvalues=xDynamicCast(this->values->copy()); + }/*}}}*/ +-void ControlInput::ScaleGradient(IssmDouble scaling_factor){/*{{{*/ +- if(!gradient) _error_("Gradient of ControlInput " << EnumToStringx(enum_type) << " not found"); +- gradient->Scale(scaling_factor); +-}/*}}}*/ + void ControlInput::SetGradient(Input* gradient_in){/*{{{*/ + + /*Get enum for current gradient*/ +Index: ../trunk-jpl/src/c/analyses/MeshdeformationAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MeshdeformationAnalysis.cpp (revision 21930) ++++ ../trunk-jpl/src/c/analyses/MeshdeformationAnalysis.cpp (nonexistent) +@@ -1,56 +0,0 @@ +-#include "./MeshdeformationAnalysis.h" +-#include "../toolkits/toolkits.h" +-#include "../classes/classes.h" +-#include "../shared/shared.h" +-#include "../modules/modules.h" +- +-/*Model processing*/ +-void MeshdeformationAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ +- _error_("not implemented yet"); +-}/*}}}*/ +-void MeshdeformationAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/ +- _error_("not implemented yet"); +-}/*}}}*/ +-void MeshdeformationAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel){/*{{{*/ +- _error_("not implemented yet"); +-}/*}}}*/ +-int MeshdeformationAnalysis::DofsPerNode(int** doflist,int domaintype,int approximation){/*{{{*/ +- _error_("not implemented"); +-}/*}}}*/ +-void MeshdeformationAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ +- _error_("not implemented yet"); +-}/*}}}*/ +-void MeshdeformationAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ +- _error_("not implemented yet"); +-}/*}}}*/ +- +-/*Finite Element Analysis*/ +-void MeshdeformationAnalysis::Core(FemModel* femmodel){/*{{{*/ +- _error_("not implemented"); +-}/*}}}*/ +-ElementVector* MeshdeformationAnalysis::CreateDVector(Element* element){/*{{{*/ +- /*Default, return NULL*/ +- return NULL; +-}/*}}}*/ +-ElementMatrix* MeshdeformationAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/ +-_error_("Not implemented"); +-}/*}}}*/ +-ElementMatrix* MeshdeformationAnalysis::CreateKMatrix(Element* element){/*{{{*/ +- _error_("not implemented yet"); +-}/*}}}*/ +-ElementVector* MeshdeformationAnalysis::CreatePVector(Element* element){/*{{{*/ +-_error_("not implemented yet"); +-}/*}}}*/ +-void MeshdeformationAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ +- _error_("not implemented yet"); +-}/*}}}*/ +-void MeshdeformationAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_index){/*{{{*/ +- _error_("Not implemented yet"); +-}/*}}}*/ +-void MeshdeformationAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ +- _error_("not implemented yet"); +-}/*}}}*/ +-void MeshdeformationAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ +- /*Default, do nothing*/ +- return; +-}/*}}}*/ +Index: ../trunk-jpl/src/c/analyses/MeshdeformationAnalysis.h +=================================================================== +--- ../trunk-jpl/src/c/analyses/MeshdeformationAnalysis.h (revision 21930) ++++ ../trunk-jpl/src/c/analyses/MeshdeformationAnalysis.h (nonexistent) +@@ -1,33 +0,0 @@ +-/*! \file MeshdeformationAnalysis.h +- * \brief: header file for generic external result object +- */ +- +-#ifndef _MeshdeformationAnalysis_ +-#define _MeshdeformationAnalysis_ +- +-/*Headers*/ +-#include "./Analysis.h" +- +-class MeshdeformationAnalysis: public Analysis{ +- +- public: +- /*Model processing*/ +- void CreateConstraints(Constraints* constraints,IoModel* iomodel); +- void CreateLoads(Loads* loads, IoModel* iomodel); +- void CreateNodes(Nodes* nodes,IoModel* iomodel); +- int DofsPerNode(int** doflist,int domaintype,int approximation); +- void UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type); +- void UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum); +- +- /*Finite element Analysis*/ +- void Core(FemModel* femmodel); +- ElementVector* CreateDVector(Element* element); +- ElementMatrix* CreateJacobianMatrix(Element* element); +- ElementMatrix* CreateKMatrix(Element* element); +- ElementVector* CreatePVector(Element* element); +- void GetSolutionFromInputs(Vector* solution,Element* element); +- void GradientJ(Vector* gradient,Element* element,int control_type,int control_index); +- void InputUpdateFromSolution(IssmDouble* solution,Element* element); +- void UpdateConstraints(FemModel* femmodel); +-}; +-#endif +Index: ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp (revision 21930) ++++ ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp (revision 21931) +@@ -551,62 +551,6 @@ + default: _error_("mesh "<vertices->NumberOfVertices(); +- Element* element; +- +- Vector* vec_dist_zerolevelset = NULL; +- GetVectorFromInputsx(&vec_dist_zerolevelset, femmodel, MaskIceLevelsetEnum, VertexPIdEnum); +- +- /* set NaN on elements intersected by zero levelset */ +- for(i=0;ielements->Size();i++){ +- element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); +- if(element->IsZeroLevelset(MaskIceLevelsetEnum)) +- for(k=0;kGetNumberOfVertices();k++) +- vec_dist_zerolevelset->SetValue(element->vertices[k]->Sid(),NAN,INS_VAL); +- } +- +- /* set distance on elements intersected by zero levelset */ +- for(i=0;ielements->Size();i++){ +- element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); +- if(element->IsZeroLevelset(MaskIceLevelsetEnum)){ +- SetDistanceToZeroLevelsetElement(vec_dist_zerolevelset, element); +- +- /* Get maximum distance to interface along vertices */ +- for(k=0;kGetNumberOfVertices();k++){ +- vec_dist_zerolevelset->GetValue(&val,element->vertices[k]->Sid()); +- if((val>0.) && (val>dmaxp)) +- dmaxp=val; +- else if((val<0.) && (valGetValue(&val,i); +- if(val==1.) //FIXME: improve check +- vec_dist_zerolevelset->SetValue(i,3.*dmaxp,INS_VAL); +- else if(val==-1.) +- vec_dist_zerolevelset->SetValue(i,3.*dmaxm,INS_VAL); +- } +- +- /*Assemble vector and serialize */ +- vec_dist_zerolevelset->Assemble(); +- IssmDouble* dist_zerolevelset=vec_dist_zerolevelset->ToMPISerial(); +- InputUpdateFromVectorx(femmodel,dist_zerolevelset,MaskIceLevelsetEnum,VertexSIdEnum); +- +- /*Clean up and return*/ +- delete vec_dist_zerolevelset; +- delete dist_zerolevelset; +-}/*}}}*/ + void LevelsetAnalysis::SetDistanceToZeroLevelsetElement(Vector* vec_signed_dist, Element* element){/*{{{*/ + + if(!element->IsZeroLevelset(MaskIceLevelsetEnum)) +Index: ../trunk-jpl/src/c/analyses/analyses.h +=================================================================== +--- ../trunk-jpl/src/c/analyses/analyses.h (revision 21930) ++++ ../trunk-jpl/src/c/analyses/analyses.h (revision 21931) +@@ -33,7 +33,6 @@ + #include "./SmbAnalysis.h" + #include "./SealevelriseAnalysis.h" + #include "./MeltingAnalysis.h" +-#include "./MeshdeformationAnalysis.h" + #include "./SmoothAnalysis.h" + #include "./StressbalanceAnalysis.h" + #include "./StressbalanceSIAAnalysis.h" +Index: ../trunk-jpl/src/c/analyses/LevelsetAnalysis.h +=================================================================== +--- ../trunk-jpl/src/c/analyses/LevelsetAnalysis.h (revision 21930) ++++ ../trunk-jpl/src/c/analyses/LevelsetAnalysis.h (revision 21931) +@@ -31,7 +31,6 @@ + void GetSolutionFromInputs(Vector* solution,Element* element); + void GradientJ(Vector* gradient,Element* element,int control_type,int control_index); + void InputUpdateFromSolution(IssmDouble* solution,Element* element); +- void SetDistanceOnIntersectedElements(FemModel* femmodel); + void SetDistanceToZeroLevelsetElement(Vector* vec_signed_dist, Element* element); + void UpdateConstraints(FemModel* femmodel); + }; +Index: ../trunk-jpl/src/c/analyses/EnumToAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/EnumToAnalysis.cpp (revision 21930) ++++ ../trunk-jpl/src/c/analyses/EnumToAnalysis.cpp (revision 21931) +@@ -109,9 +109,6 @@ + #ifdef _HAVE_ESA_ + case EsaAnalysisEnum : return new EsaAnalysis(); + #endif +- #ifdef _HAVE_MESHDEFORMATION_ +- case MeshdeformationAnalysisEnum : return new MeshdeformationAnalysis(); +- #endif + #ifdef _HAVE_LEVELSET_ + case LevelsetAnalysisEnum : return new LevelsetAnalysis(); + #endif Index: /issm/oecreview/Archive/21724-22754/ISSM-21931-21932.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21931-21932.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21931-21932.diff (revision 22755) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/wrappers/MeshPartition/MeshPartition.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/MeshPartition/MeshPartition.cpp (revision 21931) ++++ ../trunk-jpl/src/wrappers/MeshPartition/MeshPartition.cpp (revision 21932) +@@ -24,8 +24,8 @@ + int *elements = NULL; + int elements_width; + +- int numberofelements2d; +- int numberofvertices2d; ++ int numberofelements2d=0; ++ int numberofvertices2d=0; + int* elements2d=NULL; + + int numberoflayers; Index: /issm/oecreview/Archive/21724-22754/ISSM-21932-21933.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21932-21933.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21932-21933.diff (revision 22755) @@ -0,0 +1,44 @@ +Index: ../trunk-jpl/src/m/plot/plot_scatter.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_scatter.m (revision 21932) ++++ ../trunk-jpl/src/m/plot/plot_scatter.m (revision 21933) +@@ -7,6 +7,7 @@ + % Available options: + % 'caxis' : default is full range + % 'MarkerSize' : default is 3 ++% 'subset' : only plot the indices provided + % 'Line' : use line instead of circles + % 'Cutoff' : cut the line if the distance between 2 points is + % greater than Cutoff (default is 1000) +@@ -22,6 +23,13 @@ + error('x, y and data should have the same size'); + end + ++if exist(options,'subset'), ++ pos=getfieldvalue(options,'subset'); ++ x=x(pos); ++ y=y(pos); ++ level=level(pos); ++end ++ + %Some processing + Min=min(level); + Max=max(level); +@@ -58,6 +66,7 @@ + levels=round_ice(linspace(ylim(1),ylim(2),numcolors+1),2); + else + palette=getcolormap(options); ++ colormap(palette); + numcolors=size(palette,1); + levels=round_ice(linspace(Min,Max,numcolors+1),2); + end +@@ -75,7 +84,8 @@ + if ~exist(options,'line'), + for i=1:numcolors + pos=find(colorind==i); +- hprime=plot3(x(pos),y(pos),ones(size(x(pos))),... ++ % hprime=plot3(x(pos),y(pos),ones(size(x(pos))),... ++ hprime=plot(x(pos),y(pos),... + 'o','MarkerSize',getfieldvalue(options,'MarkerSize',3),'MarkerEdgeColor',palette(i,:),... + 'MarkerFaceColor',palette(i,:)); + hp=[hp;hprime]; Index: /issm/oecreview/Archive/21724-22754/ISSM-21933-21934.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21933-21934.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21933-21934.diff (revision 22755) @@ -0,0 +1,32 @@ +Index: ../trunk-jpl/src/m/classes/clusters/generic.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/generic.m (revision 21933) ++++ ../trunk-jpl/src/m/classes/clusters/generic.m (revision 21934) +@@ -111,11 +111,11 @@ + fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib); + if ismac, + if IssmConfig('_HAVE_MPI_'), +- fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --dsymutil=yes --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',... +- cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,solution,[cluster.executionpath '/' dirname], modelname,modelname,modelname); ++ fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --dsymutil=yes --suppressions=%s %s/%s %s %s %s 2> %s.errlog >%s.outlog ',... ++ cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname], modelname,modelname,modelname); + else +- fprintf(fid,'%s --leak-check=full --dsymutil=yes --error-limit=no --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',... +- cluster.valgrind,cluster.valgrindsup,cluster.codepath,solution,[cluster.executionpath '/' dirname], modelname,modelname,modelname); ++ fprintf(fid,'%s --leak-check=full --dsymutil=yes --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog >%s.outlog ',... ++ cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname], modelname,modelname,modelname); + end + else + if IssmConfig('_HAVE_MPI_'), +@@ -143,9 +143,9 @@ + end + + if cluster.np>1, +- fprintf(fid,'"C:\\Program Files\\MPICH2\\bin\\mpiexec.exe" -n %i "%s/issm.exe" %s ./ %s ',cluster.np,cluster.codepath,solution,modelname); ++ fprintf(fid,'"C:\\Program Files\\MPICH2\\bin\\mpiexec.exe" -n %i "%s/%s" %s ./ %s ',cluster.np,cluster.codepath,executable,solution,modelname); + else +- fprintf(fid,'"%s/issm.exe" %s ./ %s ',cluster.codepath,solution,modelname); ++ fprintf(fid,'"%s/%s" %s ./ %s ',cluster.codepath,executable,solution,modelname); + end + fclose(fid); + end Index: /issm/oecreview/Archive/21724-22754/ISSM-21934-21935.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21934-21935.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21934-21935.diff (revision 22755) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/src/m/classes/friction.m +=================================================================== +--- ../trunk-jpl/src/m/classes/friction.m (revision 21934) ++++ ../trunk-jpl/src/m/classes/friction.m (revision 21935) +@@ -30,6 +30,8 @@ + switch nargin + case 0 + self=setdefaultparameters(self); ++ case 1 ++ self=structtoobj(friction(),varargin{1}); + otherwise + error('constructor not supported'); + end +Index: ../trunk-jpl/src/m/classes/timestepping.m +=================================================================== +--- ../trunk-jpl/src/m/classes/timestepping.m (revision 21934) ++++ ../trunk-jpl/src/m/classes/timestepping.m (revision 21935) +@@ -15,6 +15,8 @@ + switch nargin + case 0 + self=setdefaultparameters(self); ++ case 1 ++ self=structtoobj(timestepping(),varargin{1}); + otherwise + error('constructor not supported'); + end Index: /issm/oecreview/Archive/21724-22754/ISSM-21935-21936.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21935-21936.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21935-21936.diff (revision 22755) @@ -0,0 +1,38 @@ +Index: ../trunk-jpl/src/c/classes/Params/StringArrayParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Params/StringArrayParam.cpp (revision 21935) ++++ ../trunk-jpl/src/c/classes/Params/StringArrayParam.cpp (revision 21936) +@@ -21,23 +21,21 @@ + /*}}}*/ + StringArrayParam::StringArrayParam(int in_enum_type,char** in_values, int in_numstrings){/*{{{*/ + +- int i; +- int size; ++ this->enum_type=in_enum_type; ++ this->numstrings=in_numstrings; + +- enum_type=in_enum_type; +- numstrings=in_numstrings; +- + if(numstrings){ +- value=xNew(numstrings); +- for(i=0;i(size); ++ this->value=xNew(numstrings); ++ for(int i=0;i(size); + xMemCpy(string,in_values[i],size); +- value[i]=string; ++ this->value[i]=string; + } + } +- else value=NULL; ++ else{ ++ this->value=NULL; ++ } + + } + /*}}}*/ Index: /issm/oecreview/Archive/21724-22754/ISSM-21936-21937.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21936-21937.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21936-21937.diff (revision 22755) @@ -0,0 +1,17 @@ +Index: ../trunk-jpl/test/NightlyRun/test444.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test444.m (revision 21936) ++++ ../trunk-jpl/test/NightlyRun/test444.m (revision 21937) +@@ -83,7 +83,7 @@ + end + + %partitioning +-md.qmu.numberofpartitions=20; ++md.qmu.numberofpartitions=10; + md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); + md.qmu.partition=md.qmu.partition-1; + md.qmu.isdakota=1; +Index: ../trunk-jpl/test/Archives/Archive444.arch +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/21724-22754/ISSM-21937-21938.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21937-21938.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21937-21938.diff (revision 22755) @@ -0,0 +1,51 @@ +Index: ../trunk-jpl/test/NightlyRun/test224.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test224.py (revision 21937) ++++ ../trunk-jpl/test/NightlyRun/test224.py (revision 21938) +@@ -22,9 +22,9 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', \ + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] + field_tolerances=[\ +- 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,\ +- 1e-09,5e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06,\ +- 1e-09,5e-09,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05] ++ 2e-09,2e-09,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,\ ++ 2e-09,5e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06,\ ++ 2e-09,5e-09,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05] + field_values=[\ + md.results.TransientSolution[0].Vx,\ + md.results.TransientSolution[0].Vy,\ +Index: ../trunk-jpl/test/NightlyRun/test224.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test224.m (revision 21937) ++++ ../trunk-jpl/test/NightlyRun/test224.m (revision 21938) +@@ -13,9 +13,9 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', ... + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'}; + field_tolerances={... +- 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,... +- 1e-09,5e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06,... +- 1e-09,5e-09,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05}; ++ 2e-09,2e-09,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,... ++ 2e-09,5e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06,... ++ 2e-09,5e-09,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05}; + field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... +Index: ../trunk-jpl/test/NightlyRun/test224.js +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test224.js (revision 21937) ++++ ../trunk-jpl/test/NightlyRun/test224.js (revision 21938) +@@ -14,9 +14,9 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3']; + field_tolerances=[ +- 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, +- 1e-09,5e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06, +- 1e-09,5e-09,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05]; ++ 2e-09,2e-09,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ++ 2e-09,5e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06, ++ 2e-09,5e-09,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05]; + field_values=[ + (md.results.TransientSolution[0](1).Vx), + (md.results.TransientSolution[0](1).Vy), Index: /issm/oecreview/Archive/21724-22754/ISSM-21938-21939.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21938-21939.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21938-21939.diff (revision 22755) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/m/classes/slr.m +=================================================================== +--- ../trunk-jpl/src/m/classes/slr.m (revision 21938) ++++ ../trunk-jpl/src/m/classes/slr.m (revision 21939) +@@ -146,8 +146,8 @@ + + end % }}} + function marshall(self,prefix,md,fid) % {{{ +- WriteData(fid,prefix,'object',self,'fieldname','deltathickness','format','DoubleMat','mattype',2); +- %WriteData(fid,prefix,'object',self,'fieldname','deltathickness','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofelements+1); ++ %WriteData(fid,prefix,'object',self,'fieldname','deltathickness','format','DoubleMat','mattype',2); ++ WriteData(fid,prefix,'object',self,'fieldname','deltathickness','format','DoubleMat','mattype',2,'timeserieslength',md.mesh.numberofelements+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'fieldname','sealevel','mattype',1,'format','DoubleMat','timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'fieldname','reltol','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','abstol','format','Double'); Index: /issm/oecreview/Archive/21724-22754/ISSM-21939-21940.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21939-21940.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21939-21940.diff (revision 22755) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_se +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_se (revision 21939) ++++ ../trunk-jpl/jenkins/linux64_ross_se (revision 21940) +@@ -62,8 +62,8 @@ + #safer as some packages are very sensitive to parallel compilation) + NUMCPUS_INSTALL=5 + +-#number of cpus used in the nightly runs. +-NUMCPUS_RUN=4 ++#number of cpus used in the nightly runs. (pb of access to all_vertices.txt if more than 1) ++NUMCPUS_RUN=1 + + #Nightly run options. The matlab routine runme.m will be called + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable Index: /issm/oecreview/Archive/21724-22754/ISSM-21940-21941.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21940-21941.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21940-21941.diff (revision 22755) @@ -0,0 +1,32 @@ +Index: ../trunk-jpl/src/m/coordsystems/gmtmask.m +=================================================================== +--- ../trunk-jpl/src/m/coordsystems/gmtmask.m (revision 21940) ++++ ../trunk-jpl/src/m/coordsystems/gmtmask.m (revision 21941) +@@ -30,8 +30,10 @@ + + %First, write our lat,long file for gmt: + nv=length(lat); +- dlmwrite('./all_vertices.txt',[long lat (1:nv)'],'delimiter','\t','precision',10); ++ filename = ['all_vertices-' num2str(feature('GetPid')) '.txt'] ++ dlmwrite(filename,[long lat (1:nv)'],'delimiter','\t','precision',10); + ++ + %Avoid bypassing of the ld library path by Matlab (:() + if ismac, + dyld_library_path_old=getenv('DYLD_LIBRARY_PATH'); +@@ -39,7 +41,7 @@ + end + + %figure out which vertices are on the ocean, which one on the continent: +- [status,result] = system('gmt gmtselect ./all_vertices.txt -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices.txt'); ++ [status,result] = system(['gmt gmtselect ./' filename ' -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices.txt']); + if status~=0, + error(result); + end +@@ -63,5 +65,5 @@ + mask=zeros(nv,1); + mask(oce_vertices)=1; + +- system('rm -rf ./all_vertices.txt ./oce_vertices.txt ./gmt.history'); ++ system(['rm -rf ./' filename ' ./oce_vertices.txt ./gmt.history']); + if ~recursive, disp(sprintf('gmtmask: done')); end; Index: /issm/oecreview/Archive/21724-22754/ISSM-21941-21942.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21941-21942.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21941-21942.diff (revision 22755) @@ -0,0 +1,43 @@ +Index: ../trunk-jpl/src/m/coordsystems/gmtmask.m +=================================================================== +--- ../trunk-jpl/src/m/coordsystems/gmtmask.m (revision 21941) ++++ ../trunk-jpl/src/m/coordsystems/gmtmask.m (revision 21942) +@@ -30,10 +30,10 @@ + + %First, write our lat,long file for gmt: + nv=length(lat); +- filename = ['all_vertices-' num2str(feature('GetPid')) '.txt'] +- dlmwrite(filename,[long lat (1:nv)'],'delimiter','\t','precision',10); ++ filename_all = ['all_vertices-' num2str(feature('GetPid')) '.txt']; ++ filename_oce = ['oce_vertices-' num2str(feature('GetPid')) '.txt']; ++ dlmwrite(filename_all,[long lat (1:nv)'],'delimiter','\t','precision',10); + +- + %Avoid bypassing of the ld library path by Matlab (:() + if ismac, + dyld_library_path_old=getenv('DYLD_LIBRARY_PATH'); +@@ -41,7 +41,7 @@ + end + + %figure out which vertices are on the ocean, which one on the continent: +- [status,result] = system(['gmt gmtselect ./' filename ' -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices.txt']); ++ [status,result] = system(['gmt gmtselect ./' filename_all ' -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./' filename_oce]); + if status~=0, + error(result); + end +@@ -51,7 +51,7 @@ + setenv('DYLD_LIBRARY_PATH',dyld_library_path_old); + end + %read the con_vertices.txt file and flag our mesh vertices on the continent +- fid=fopen('./oce_vertices.txt','r'); ++ fid=fopen(['./' filename_oce],'r'); + line=fgets(fid); + line=fgets(fid); + oce_vertices=[]; +@@ -65,5 +65,5 @@ + mask=zeros(nv,1); + mask(oce_vertices)=1; + +- system(['rm -rf ./' filename ' ./oce_vertices.txt ./gmt.history']); ++ system(['rm -rf ./' filename_all ' ./' filename_oce ' ./gmt.history']); + if ~recursive, disp(sprintf('gmtmask: done')); end; Index: /issm/oecreview/Archive/21724-22754/ISSM-21942-21943.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21942-21943.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21942-21943.diff (revision 22755) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/test/NightlyRun/test2002.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2002.py (revision 21942) ++++ ../trunk-jpl/test/NightlyRun/test2002.py (revision 21943) +@@ -18,6 +18,8 @@ + #slr loading: + md.slr.deltathickness=np.zeros((md.mesh.numberofelements)) + md.slr.sealevel=np.zeros((md.mesh.numberofvertices)) ++md.slr.steric_rate=np.zeros((md.mesh.numberofvertices)) ++ + #antarctica + late=np.sum(md.mesh.lat[md.mesh.elements-1],axis=1)/3 + longe=np.sum(md.mesh.long[md.mesh.elements-1],axis=1)/3 Index: /issm/oecreview/Archive/21724-22754/ISSM-21943-21944.diff =================================================================== --- /issm/oecreview/Archive/21724-22754/ISSM-21943-21944.diff (revision 22755) +++ /issm/oecreview/Archive/21724-22754/ISSM-21943-21944.diff (revision 22755) @@ -0,0 +1,15142 @@ +Index: ../trunk-jpl/jenkins/javascript/karma/lib/Par/SquareShelfConstrained.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/Par/SquareShelfConstrained.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/Par/SquareShelfConstrained.js (nonexistent) +@@ -1,70 +0,0 @@ +-function parameterize(md){ +- +- //Geometry +- var hmin=300; +- var hmax=1000; +- var ymin=ArrayMin(md.mesh.y); +- var ymax=ArrayMax(md.mesh.y); +- var xmin=ArrayMin(md.mesh.x); +- var xmax=ArrayMax(md.mesh.x); +- +- md.geometry.thickness=NewArrayFill(md.mesh.numberofvertices,0); +- md.geometry.base=NewArrayFill(md.mesh.numberofvertices,0); +- md.geometry.surface=NewArrayFill(md.mesh.numberofvertices,0); +- md.geometry.bed=NewArrayFill(md.mesh.numberofvertices,0); +- +- for(i=0;inods) { +- console.error(['GetAreas error message: index should not have values above ' + nods.toString() ]); +- } +- if ((arguments.length===3 && index[0].length!==3)) { +- console.error('GetAreas error message: index should have 3 columns for 2d meshes.') +- } +- if ((arguments.length===4 && index[0].length!==6)) { +- console.error('GetAreas error message: index should have 6 columns for 3d meshes.') +- } +- +- //initialization +- areas=zeros(nels,1); +- +- var getColumnArray = function(arr, col) { +- return arr.map(function(value,index) { return value[col]; }); +- }; +- +- x1=getColumnArray(index, 0).map(function(value) { return x[value]; }).map(function(v) { return v === undefined ? 0 : v; }); +- x2=getColumnArray(index, 1).map(function(value) { return x[value]; }).map(function(v) { return v === undefined ? 0 : v; }); +- x3=getColumnArray(index, 2).map(function(value) { return x[value]; }).map(function(v) { return v === undefined ? 0 : v; }); +- y1=getColumnArray(index, 0).map(function(value) { return y[value]; }).map(function(v) { return v === undefined ? 0 : v; }); +- y2=getColumnArray(index, 1).map(function(value) { return y[value]; }).map(function(v) { return v === undefined ? 0 : v; }); +- y3=getColumnArray(index, 2).map(function(value) { return y[value]; }).map(function(v) { return v === undefined ? 0 : v; }); +- +- //compute the volume of each element +- if (arguments.length===3) { +- //compute the surface of the triangle +- areas=math.multiply(0.5, math.subtract(math.multiply(math.subtract(x2,x1), math.subtract(y3,y1)), math.multiply(math.subtract(y2,y1), math.subtract(x3,x1)))); +- } else { +- //V=area(triangle)*1/3(z1+z2+z3) +- +- var tempind1 = []; +- index.forEach(function(value, idx) { +- tempind1.push(value[3]); +- tempind1.push(value[4]); +- tempind1.push(value[5]); +- }); +- +- var tempind2 = []; +- index.forEach(function(value, idx) { +- tempind2.push(value[0]); +- tempind2.push(value[1]); +- tempind2.push(value[2]); +- }); +- +- var tempz1 = tempind1.map(function(value, idx) { +- return z[value][2]; +- }); +- +- var tempz2 = tempind2.map(function(value, idx) { +- return z[value][2]; +- }) +- +- thickness = math.subtract(math.mean(tempz1), math.mean(tempz2)); +- +- areas=math.multiply(math.multiply(0.5, math.subtract(math.multiply(math.subtract(x2,x1), math.subtract(y3,y1)), math.multiply(math.subtract(y2,y1), math.subtract(x3,x1)))), thickness); +- } +- +- return areas; +-}; +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/geometry.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/geometry.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/geometry.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/geometry.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/geometry.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/thermal.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/thermal.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/thermal.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/thermal.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/thermal.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/DepthAverage.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/DepthAverage.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/DepthAverage.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/extrusion/DepthAverage.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/DepthAverage.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/partitioner.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/partitioner.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/partitioner.js (nonexistent) +@@ -1,116 +0,0 @@ +-partitioner = function(md,...args) { +-function zeros(...args) { +- var array = []; +- for (var i = 0; i < args[0]; ++i) { +- array.push(args.length == 1 ? 0 : zeros(args.slice(1))); +- } +- return array; +-} +-//PARTITIONER - partition mesh +-// +-// List of options to partitioner: +-// +-// package: 'chaco', 'metis' or 'scotch' +-// npart: number of partitions. +-// weighting: 'on' or 'off': default off +-// section: 1 by defaults(1=bisection, 2=quadrisection, 3=octasection) +-// recomputeadjacency: 'on' by default (set to 'off' to compute existing one) +-// Output: md.qmu.partition recover the partition vector +-// +-// Usage: +-// md=partitioner(md,'package','chaco','npart',100,'weighting','on'); +-// +- +-//get options: +-options= new pairoptions(args.slice()); +- +-//set defaults +-options.addfielddefault('package','chaco'); +-options.addfielddefault('npart',10); +-options.addfielddefault('weighting','on'); +-options.addfielddefault('section',1); +-options.addfielddefault('recomputeadjacency','on'); +- +-//get package: +-package=options.getfieldvalue('package'); +-npart=options.getfieldvalue('npart'); +-recomputeadjacency=options.getfieldvalue('recomputeadjacency'); +- +-if(md.mesh.dimension()===3) { +- //partitioning essentially happens in 2D. So partition in 2D, then +- //extrude the partition vector vertically. +- md3d=md; //save for later +- md.mesh.elements=md.mesh.elements2d; +- md.mesh.x=md.mesh.x2d; +- md.mesh.y=md.mesh.y2d; +- md.mesh.numberofvertices=md.mesh.numberofvertices2d; +- md.mesh.numberofelements=md.mesh.numberofelements2d; +- md.qmu.vertex_weight=[]; +- md.mesh.vertexconnectivity=[]; +-} +- +-//adjacency matrix if needed: +-if (recomputeadjacency.toLowerCase() === 'on') { +- md=adjacency(md); +-} else { +- disp('skipping adjacency matrix computation as requested in the options'); +-} +- +-if (package.toLowerCase() === 'chaco') { +- +- // default method (from chaco.m) +- method=[[1], [1], [0], [0], [1], [1], [50], [0], [.001], [7654321]]; +- method[0]=3; // global method (3=inertial (geometric)) +- method[2]=0; // vertex weights (0=off, 1=on) +- +- //specify bisection +- method[5]=options.getfieldvalue('section');// ndims (1=bisection, 2=quadrisection, 3=octasection) +- +- //are we using weights? +- if (options.getfieldvalue('weighting').toLowerCase() === 'on') { +- weights=Math.floor(md.qmu.vertex_weight/math.min(md.qmu.vertex_weight)); +- method[2]=1; +- } else { +- weights=[]; +- } +- +- // partition into nparts +- if (md.mesh.classname() === 'mesh2d') { +- //TODO convert to column +- part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y,zeros(md.mesh.numberofvertices,1),method,npart,[])+1; //index partitions from 1 up. like metis. +- } else { +- //TODO convert to column +- part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y,md.mesh.z,method,npart,[])+1; //index partitions from 1 up. like metis. +- } +-} else if (package.toLowerCase() === 'scotch') { +- //are we using weights? +- if (options.getfieldvalue('weighting').toLowerCase() === 'on') { +- weights=floor(md.qmu.vertex_weight/min(md.qmu.vertex_weight)); +- } +- maptab=Scotch(md.qmu.adjacency,[],weights,[],'cmplt',[npart]); +- +- part=maptab.filter(function(x, idx) { return idx });//index partitions from 1 up. like metis. +-} else if (package.toLowerCase() === 'linear') { +- +- part = part.slice(0, md.mesh.numberofvertices); +-} else if (package.toLowerCase() === 'metis') { +- [element_partitioning,part]=MeshPartition(md.mesh,md.qmu.numberofpartitions); +-} else { +- console.error(['partitioner error message: could not find ' + package + ' partitioner']); +- //help partitioner +-} +- +-//extrude if we are in 3d +-if (md.mesh.dimension() === 3) { +- md3d.qmu.vertex_weight=md.qmu.vertex_weight; +- md3d.qmu.adjacency=md.qmu.adjacency; +- md=md3d; +- +- //TODO convert to column vec +- part=project3d(md,'vector',part,'type','node'); +-} +- +-md.qmu.partition=part; +- +-return md; +-}; +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/model.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/model.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/model.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/model.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/model.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/matice.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/matice.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/matice.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/matice.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/matice.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/issm-extlibraries.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/issm-extlibraries.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/issm-extlibraries.js (nonexistent) +@@ -1,119 +0,0 @@ +-/** +- * @fileoverview gl-matrix - High performance matrix and vector operations +- * @author Brandon Jones +- * @author Colin MacKenzie IV +- * @version 2.3.2 +- */ +- +-/* Copyright (c) 2015, Brandon Jones, Colin MacKenzie IV. +- +-Permission is hereby granted, free of charge, to any person obtaining a copy +-of this software and associated documentation files (the "Software"), to deal +-in the Software without restriction, including without limitation the rights +-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +-copies of the Software, and to permit persons to whom the Software is +-furnished to do so, subject to the following conditions: +- +-The above copyright notice and this permission notice shall be included in +-all copies or substantial portions of the Software. +- +-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +-THE SOFTWARE. */ +- +-!function(t,a){if("object"==typeof exports&&"object"==typeof module)module.exports=a();else if("function"==typeof define&&define.amd)define(a);else{var n=a();for(var r in n)("object"==typeof exports?exports:t)[r]=n[r]}}(this,function(){return function(t){function a(r){if(n[r])return n[r].exports;var o=n[r]={exports:{},id:r,loaded:!1};return t[r].call(o.exports,o,o.exports,a),o.loaded=!0,o.exports}var n={};return a.m=t,a.c=n,a.p="",a(0)}([function(t,a,n){a.glMatrix=n(1),a.mat2=n(2),a.mat2d=n(3),a.mat3=n(4),a.mat4=n(5),a.quat=n(6),a.vec2=n(9),a.vec3=n(7),a.vec4=n(8)},function(t,a){var n={};n.EPSILON=1e-6,n.ARRAY_TYPE="undefined"!=typeof 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t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=1,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=1,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},o.clone=function(t){var a=new r.ARRAY_TYPE(16);return a[0]=t[0],a[1]=t[1],a[2]=t[2],a[3]=t[3],a[4]=t[4],a[5]=t[5],a[6]=t[6],a[7]=t[7],a[8]=t[8],a[9]=t[9],a[10]=t[10],a[11]=t[11],a[12]=t[12],a[13]=t[13],a[14]=t[14],a[15]=t[15],a},o.copy=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t[9]=a[9],t[10]=a[10],t[11]=a[11],t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.identity=function(t){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=1,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=1,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},o.scalar.transpose=function(t,a){if(t===a){var n=a[1],r=a[2],o=a[3],l=a[6],u=a[7],e=a[11];t[1]=a[4],t[2]=a[8],t[3]=a[12],t[4]=n,t[6]=a[9],t[7]=a[13],t[8]=r,t[9]=l,t[11]=a[14],t[12]=o,t[13]=u,t[14]=e}else t[0]=a[0],t[1]=a[4],t[2]=a[8],t[3]=a[12],t[4]=a[1],t[5]=a[5],t[6]=a[9],t[7]=a[13],t[8]=a[2],t[9]=a[6],t[10]=a[10],t[11]=a[14],t[12]=a[3],t[13]=a[7],t[14]=a[11],t[15]=a[15];return t},o.SIMD.transpose=function(t,a){var n,r,o,l,u,e,M,i,s,c;return n=SIMD.Float32x4.load(a,0),r=SIMD.Float32x4.load(a,4),o=SIMD.Float32x4.load(a,8),l=SIMD.Float32x4.load(a,12),u=SIMD.Float32x4.shuffle(n,r,0,1,4,5),e=SIMD.Float32x4.shuffle(o,l,0,1,4,5),M=SIMD.Float32x4.shuffle(u,e,0,2,4,6),i=SIMD.Float32x4.shuffle(u,e,1,3,5,7),SIMD.Float32x4.store(t,0,M),SIMD.Float32x4.store(t,4,i),u=SIMD.Float32x4.shuffle(n,r,2,3,6,7),e=SIMD.Float32x4.shuffle(o,l,2,3,6,7),s=SIMD.Float32x4.shuffle(u,e,0,2,4,6),c=SIMD.Float32x4.shuffle(u,e,1,3,5,7),SIMD.Float32x4.store(t,8,s),SIMD.Float32x4.store(t,12,c),t},o.transpose=r.USE_SIMD?o.SIMD.transpose:o.scalar.transpose,o.scalar.invert=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15],m=n*e-r*u,h=n*M-o*u,d=n*i-l*u,v=r*M-o*e,z=r*i-l*e,p=o*i-l*M,w=s*x-c*I,A=s*f-D*I,R=s*F-S*I,b=c*f-D*x,Y=c*F-S*x,q=D*F-S*f,y=m*q-h*Y+d*b+v*R-z*A+p*w;return y?(y=1/y,t[0]=(e*q-M*Y+i*b)*y,t[1]=(o*Y-r*q-l*b)*y,t[2]=(x*p-f*z+F*v)*y,t[3]=(D*z-c*p-S*v)*y,t[4]=(M*R-u*q-i*A)*y,t[5]=(n*q-o*R+l*A)*y,t[6]=(f*d-I*p-F*h)*y,t[7]=(s*p-D*d+S*h)*y,t[8]=(u*Y-e*R+i*w)*y,t[9]=(r*R-n*Y-l*w)*y,t[10]=(I*z-x*d+F*m)*y,t[11]=(c*d-s*z-S*m)*y,t[12]=(e*A-u*b-M*w)*y,t[13]=(n*b-r*A+o*w)*y,t[14]=(x*h-I*v-f*m)*y,t[15]=(s*v-c*h+D*m)*y,t):null},o.SIMD.invert=function(t,a){var n,r,o,l,u,e,M,i,s,c,D=SIMD.Float32x4.load(a,0),S=SIMD.Float32x4.load(a,4),I=SIMD.Float32x4.load(a,8),x=SIMD.Float32x4.load(a,12);return u=SIMD.Float32x4.shuffle(D,S,0,1,4,5),r=SIMD.Float32x4.shuffle(I,x,0,1,4,5),n=SIMD.Float32x4.shuffle(u,r,0,2,4,6),r=SIMD.Float32x4.shuffle(r,u,1,3,5,7),u=SIMD.Float32x4.shuffle(D,S,2,3,6,7),l=SIMD.Float32x4.shuffle(I,x,2,3,6,7),o=SIMD.Float32x4.shuffle(u,l,0,2,4,6),l=SIMD.Float32x4.shuffle(l,u,1,3,5,7),u=SIMD.Float32x4.mul(o,l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),e=SIMD.Float32x4.mul(r,u),M=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(SIMD.Float32x4.mul(r,u),e),M=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),M),M=SIMD.Float32x4.swizzle(M,2,3,0,1),u=SIMD.Float32x4.mul(r,o),u=SIMD.Float32x4.swizzle(u,1,0,3,2),e=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),e),s=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(e,SIMD.Float32x4.mul(l,u)),s=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),u=SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(r,2,3,0,1),l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),o=SIMD.Float32x4.swizzle(o,2,3,0,1),e=SIMD.Float32x4.add(SIMD.Float32x4.mul(o,u),e),i=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(e,SIMD.Float32x4.mul(o,u)),i=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),i),i=SIMD.Float32x4.swizzle(i,2,3,0,1),u=SIMD.Float32x4.mul(n,r),u=SIMD.Float32x4.swizzle(u,1,0,3,2),i=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),i),s=SIMD.Float32x4.sub(SIMD.Float32x4.mul(o,u),s),u=SIMD.Float32x4.swizzle(u,2,3,0,1),i=SIMD.Float32x4.sub(SIMD.Float32x4.mul(l,u),i),s=SIMD.Float32x4.sub(s,SIMD.Float32x4.mul(o,u)),u=SIMD.Float32x4.mul(n,l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),M=SIMD.Float32x4.sub(M,SIMD.Float32x4.mul(o,u)),i=SIMD.Float32x4.add(SIMD.Float32x4.mul(r,u),i),u=SIMD.Float32x4.swizzle(u,2,3,0,1),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(o,u),M),i=SIMD.Float32x4.sub(i,SIMD.Float32x4.mul(r,u)),u=SIMD.Float32x4.mul(n,o),u=SIMD.Float32x4.swizzle(u,1,0,3,2),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),M),s=SIMD.Float32x4.sub(s,SIMD.Float32x4.mul(r,u)),u=SIMD.Float32x4.swizzle(u,2,3,0,1),M=SIMD.Float32x4.sub(M,SIMD.Float32x4.mul(l,u)),s=SIMD.Float32x4.add(SIMD.Float32x4.mul(r,u),s),c=SIMD.Float32x4.mul(n,e),c=SIMD.Float32x4.add(SIMD.Float32x4.swizzle(c,2,3,0,1),c),c=SIMD.Float32x4.add(SIMD.Float32x4.swizzle(c,1,0,3,2),c),u=SIMD.Float32x4.reciprocalApproximation(c),c=SIMD.Float32x4.sub(SIMD.Float32x4.add(u,u),SIMD.Float32x4.mul(c,SIMD.Float32x4.mul(u,u))),(c=SIMD.Float32x4.swizzle(c,0,0,0,0))?(SIMD.Float32x4.store(t,0,SIMD.Float32x4.mul(c,e)),SIMD.Float32x4.store(t,4,SIMD.Float32x4.mul(c,M)),SIMD.Float32x4.store(t,8,SIMD.Float32x4.mul(c,i)),SIMD.Float32x4.store(t,12,SIMD.Float32x4.mul(c,s)),t):null},o.invert=r.USE_SIMD?o.SIMD.invert:o.scalar.invert,o.scalar.adjoint=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15];return t[0]=e*(D*F-S*f)-c*(M*F-i*f)+x*(M*S-i*D),t[1]=-(r*(D*F-S*f)-c*(o*F-l*f)+x*(o*S-l*D)),t[2]=r*(M*F-i*f)-e*(o*F-l*f)+x*(o*i-l*M),t[3]=-(r*(M*S-i*D)-e*(o*S-l*D)+c*(o*i-l*M)),t[4]=-(u*(D*F-S*f)-s*(M*F-i*f)+I*(M*S-i*D)),t[5]=n*(D*F-S*f)-s*(o*F-l*f)+I*(o*S-l*D),t[6]=-(n*(M*F-i*f)-u*(o*F-l*f)+I*(o*i-l*M)),t[7]=n*(M*S-i*D)-u*(o*S-l*D)+s*(o*i-l*M),t[8]=u*(c*F-S*x)-s*(e*F-i*x)+I*(e*S-i*c),t[9]=-(n*(c*F-S*x)-s*(r*F-l*x)+I*(r*S-l*c)),t[10]=n*(e*F-i*x)-u*(r*F-l*x)+I*(r*i-l*e),t[11]=-(n*(e*S-i*c)-u*(r*S-l*c)+s*(r*i-l*e)),t[12]=-(u*(c*f-D*x)-s*(e*f-M*x)+I*(e*D-M*c)),t[13]=n*(c*f-D*x)-s*(r*f-o*x)+I*(r*D-o*c),t[14]=-(n*(e*f-M*x)-u*(r*f-o*x)+I*(r*M-o*e)),t[15]=n*(e*D-M*c)-u*(r*D-o*c)+s*(r*M-o*e),t},o.SIMD.adjoint=function(t,a){var n,r,o,l,u,e,M,i,s,c,D,S,I,n=SIMD.Float32x4.load(a,0),r=SIMD.Float32x4.load(a,4),o=SIMD.Float32x4.load(a,8),l=SIMD.Float32x4.load(a,12);return s=SIMD.Float32x4.shuffle(n,r,0,1,4,5),e=SIMD.Float32x4.shuffle(o,l,0,1,4,5),u=SIMD.Float32x4.shuffle(s,e,0,2,4,6),e=SIMD.Float32x4.shuffle(e,s,1,3,5,7),s=SIMD.Float32x4.shuffle(n,r,2,3,6,7),i=SIMD.Float32x4.shuffle(o,l,2,3,6,7),M=SIMD.Float32x4.shuffle(s,i,0,2,4,6),i=SIMD.Float32x4.shuffle(i,s,1,3,5,7),s=SIMD.Float32x4.mul(M,i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),c=SIMD.Float32x4.mul(e,s),D=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(SIMD.Float32x4.mul(e,s),c),D=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),D),D=SIMD.Float32x4.swizzle(D,2,3,0,1),s=SIMD.Float32x4.mul(e,M),s=SIMD.Float32x4.swizzle(s,1,0,3,2),c=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),c),I=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(c,SIMD.Float32x4.mul(i,s)),I=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),I),I=SIMD.Float32x4.swizzle(I,2,3,0,1),s=SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,2,3,0,1),i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),M=SIMD.Float32x4.swizzle(M,2,3,0,1),c=SIMD.Float32x4.add(SIMD.Float32x4.mul(M,s),c),S=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(c,SIMD.Float32x4.mul(M,s)),S=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),S),S=SIMD.Float32x4.swizzle(S,2,3,0,1),s=SIMD.Float32x4.mul(u,e),s=SIMD.Float32x4.swizzle(s,1,0,3,2),S=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),S),I=SIMD.Float32x4.sub(SIMD.Float32x4.mul(M,s),I),s=SIMD.Float32x4.swizzle(s,2,3,0,1),S=SIMD.Float32x4.sub(SIMD.Float32x4.mul(i,s),S),I=SIMD.Float32x4.sub(I,SIMD.Float32x4.mul(M,s)),s=SIMD.Float32x4.mul(u,i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),D=SIMD.Float32x4.sub(D,SIMD.Float32x4.mul(M,s)),S=SIMD.Float32x4.add(SIMD.Float32x4.mul(e,s),S),s=SIMD.Float32x4.swizzle(s,2,3,0,1),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(M,s),D),S=SIMD.Float32x4.sub(S,SIMD.Float32x4.mul(e,s)),s=SIMD.Float32x4.mul(u,M),s=SIMD.Float32x4.swizzle(s,1,0,3,2),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),D),I=SIMD.Float32x4.sub(I,SIMD.Float32x4.mul(e,s)),s=SIMD.Float32x4.swizzle(s,2,3,0,1),D=SIMD.Float32x4.sub(D,SIMD.Float32x4.mul(i,s)),I=SIMD.Float32x4.add(SIMD.Float32x4.mul(e,s),I),SIMD.Float32x4.store(t,0,c),SIMD.Float32x4.store(t,4,D),SIMD.Float32x4.store(t,8,S),SIMD.Float32x4.store(t,12,I),t},o.adjoint=r.USE_SIMD?o.SIMD.adjoint:o.scalar.adjoint,o.determinant=function(t){var a=t[0],n=t[1],r=t[2],o=t[3],l=t[4],u=t[5],e=t[6],M=t[7],i=t[8],s=t[9],c=t[10],D=t[11],S=t[12],I=t[13],x=t[14],f=t[15],F=a*u-n*l,m=a*e-r*l,h=a*M-o*l,d=n*e-r*u,v=n*M-o*u,z=r*M-o*e,p=i*I-s*S,w=i*x-c*S,A=i*f-D*S,R=s*x-c*I,b=s*f-D*I,Y=c*f-D*x;return F*Y-m*b+h*R+d*A-v*w+z*p},o.SIMD.multiply=function(t,a,n){var r=SIMD.Float32x4.load(a,0),o=SIMD.Float32x4.load(a,4),l=SIMD.Float32x4.load(a,8),u=SIMD.Float32x4.load(a,12),e=SIMD.Float32x4.load(n,0),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,3,3,3,3),u))));SIMD.Float32x4.store(t,0,M);var i=SIMD.Float32x4.load(n,4),s=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,3,3,3,3),u))));SIMD.Float32x4.store(t,4,s);var c=SIMD.Float32x4.load(n,8),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,3,3,3,3),u))));SIMD.Float32x4.store(t,8,D);var S=SIMD.Float32x4.load(n,12),I=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,3,3,3,3),u))));return SIMD.Float32x4.store(t,12,I),t},o.scalar.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=a[9],S=a[10],I=a[11],x=a[12],f=a[13],F=a[14],m=a[15],h=n[0],d=n[1],v=n[2],z=n[3];return t[0]=h*r+d*e+v*c+z*x,t[1]=h*o+d*M+v*D+z*f,t[2]=h*l+d*i+v*S+z*F,t[3]=h*u+d*s+v*I+z*m,h=n[4],d=n[5],v=n[6],z=n[7],t[4]=h*r+d*e+v*c+z*x,t[5]=h*o+d*M+v*D+z*f,t[6]=h*l+d*i+v*S+z*F,t[7]=h*u+d*s+v*I+z*m,h=n[8],d=n[9],v=n[10],z=n[11],t[8]=h*r+d*e+v*c+z*x,t[9]=h*o+d*M+v*D+z*f,t[10]=h*l+d*i+v*S+z*F,t[11]=h*u+d*s+v*I+z*m,h=n[12],d=n[13],v=n[14],z=n[15],t[12]=h*r+d*e+v*c+z*x,t[13]=h*o+d*M+v*D+z*f,t[14]=h*l+d*i+v*S+z*F,t[15]=h*u+d*s+v*I+z*m,t},o.multiply=r.USE_SIMD?o.SIMD.multiply:o.scalar.multiply,o.mul=o.multiply,o.scalar.translate=function(t,a,n){var r,o,l,u,e,M,i,s,c,D,S,I,x=n[0],f=n[1],F=n[2];return 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SIMD.Float32x4.store(t,12,M),t},o.translate=r.USE_SIMD?o.SIMD.translate:o.scalar.translate,o.scalar.scale=function(t,a,n){var r=n[0],o=n[1],l=n[2];return t[0]=a[0]*r,t[1]=a[1]*r,t[2]=a[2]*r,t[3]=a[3]*r,t[4]=a[4]*o,t[5]=a[5]*o,t[6]=a[6]*o,t[7]=a[7]*o,t[8]=a[8]*l,t[9]=a[9]*l,t[10]=a[10]*l,t[11]=a[11]*l,t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.SIMD.scale=function(t,a,n){var r,o,l,u=SIMD.Float32x4(n[0],n[1],n[2],0);return r=SIMD.Float32x4.load(a,0),SIMD.Float32x4.store(t,0,SIMD.Float32x4.mul(r,SIMD.Float32x4.swizzle(u,0,0,0,0))),o=SIMD.Float32x4.load(a,4),SIMD.Float32x4.store(t,4,SIMD.Float32x4.mul(o,SIMD.Float32x4.swizzle(u,1,1,1,1))),l=SIMD.Float32x4.load(a,8),SIMD.Float32x4.store(t,8,SIMD.Float32x4.mul(l,SIMD.Float32x4.swizzle(u,2,2,2,2))),t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.scale=r.USE_SIMD?o.SIMD.scale:o.scalar.scale,o.rotate=function(t,a,n,o){var l,u,e,M,i,s,c,D,S,I,x,f,F,m,h,d,v,z,p,w,A,R,b,Y,q=o[0],y=o[1],E=o[2],g=Math.sqrt(q*q+y*y+E*E);return Math.abs(g)M?(l.cross(t,a,o),l.length(t)<1e-6&&l.cross(t,n,o),l.normalize(t,t),e.setAxisAngle(r,t,Math.PI),r):M>.999999?(r[0]=0,r[1]=0,r[2]=0,r[3]=1,r):(l.cross(t,o,u),r[0]=t[0],r[1]=t[1],r[2]=t[2],r[3]=1+M,e.normalize(r,r))}}(),e.setAxes=function(){var t=o.create();return function(a,n,r,o){return t[0]=r[0],t[3]=r[1],t[6]=r[2],t[1]=o[0],t[4]=o[1],t[7]=o[2],t[2]=-n[0],t[5]=-n[1],t[8]=-n[2],e.normalize(a,e.fromMat3(a,t))}}(),e.clone=u.clone,e.fromValues=u.fromValues,e.copy=u.copy,e.set=u.set,e.identity=function(t){return t[0]=0,t[1]=0,t[2]=0,t[3]=1,t},e.setAxisAngle=function(t,a,n){n=.5*n;var r=Math.sin(n);return t[0]=r*a[0],t[1]=r*a[1],t[2]=r*a[2],t[3]=Math.cos(n),t},e.add=u.add,e.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=n[0],M=n[1],i=n[2],s=n[3];return t[0]=r*s+u*e+o*i-l*M,t[1]=o*s+u*M+l*e-r*i,t[2]=l*s+u*i+r*M-o*e,t[3]=u*s-r*e-o*M-l*i,t},e.mul=e.multiply,e.scale=u.scale,e.rotateX=function(t,a,n){n*=.5;var r=a[0],o=a[1],l=a[2],u=a[3],e=Math.sin(n),M=Math.cos(n);return t[0]=r*M+u*e,t[1]=o*M+l*e,t[2]=l*M-o*e,t[3]=u*M-r*e,t},e.rotateY=function(t,a,n){n*=.5;var r=a[0],o=a[1],l=a[2],u=a[3],e=Math.sin(n),M=Math.cos(n);return t[0]=r*M-l*e,t[1]=o*M+u*e,t[2]=l*M+r*e,t[3]=u*M-o*e,t},e.rotateZ=function(t,a,n){n*=.5;var r=a[0],o=a[1],l=a[2],u=a[3],e=Math.sin(n),M=Math.cos(n);return t[0]=r*M+o*e,t[1]=o*M-r*e,t[2]=l*M+u*e,t[3]=u*M-l*e,t},e.calculateW=function(t,a){var n=a[0],r=a[1],o=a[2];return t[0]=n,t[1]=r,t[2]=o,t[3]=Math.sqrt(Math.abs(1-n*n-r*r-o*o)),t},e.dot=u.dot,e.lerp=u.lerp,e.slerp=function(t,a,n,r){var o,l,u,e,M,i=a[0],s=a[1],c=a[2],D=a[3],S=n[0],I=n[1],x=n[2],f=n[3];return l=i*S+s*I+c*x+D*f,0>l&&(l=-l,S=-S,I=-I,x=-x,f=-f),1-l>1e-6?(o=Math.acos(l),u=Math.sin(o),e=Math.sin((1-r)*o)/u,M=Math.sin(r*o)/u):(e=1-r,M=r),t[0]=e*i+M*S,t[1]=e*s+M*I,t[2]=e*c+M*x,t[3]=e*D+M*f,t},e.sqlerp=function(){var t=e.create(),a=e.create();return function(n,r,o,l,u,M){return e.slerp(t,r,u,M),e.slerp(a,o,l,M),e.slerp(n,t,a,2*M*(1-M)),n}}(),e.invert=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=n*n+r*r+o*o+l*l,e=u?1/u:0; +-return t[0]=-n*e,t[1]=-r*e,t[2]=-o*e,t[3]=l*e,t},e.conjugate=function(t,a){return t[0]=-a[0],t[1]=-a[1],t[2]=-a[2],t[3]=a[3],t},e.length=u.length,e.len=e.length,e.squaredLength=u.squaredLength,e.sqrLen=e.squaredLength,e.normalize=u.normalize,e.fromMat3=function(t,a){var n,r=a[0]+a[4]+a[8];if(r>0)n=Math.sqrt(r+1),t[3]=.5*n,n=.5/n,t[0]=(a[5]-a[7])*n,t[1]=(a[6]-a[2])*n,t[2]=(a[1]-a[3])*n;else{var o=0;a[4]>a[0]&&(o=1),a[8]>a[3*o+o]&&(o=2);var l=(o+1)%3,u=(o+2)%3;n=Math.sqrt(a[3*o+o]-a[3*l+l]-a[3*u+u]+1),t[o]=.5*n,n=.5/n,t[3]=(a[3*l+u]-a[3*u+l])*n,t[l]=(a[3*l+o]+a[3*o+l])*n,t[u]=(a[3*u+o]+a[3*o+u])*n}return t},e.str=function(t){return"quat("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+")"},t.exports=e},function(t,a,n){var r=n(1),o={};o.create=function(){var t=new r.ARRAY_TYPE(3);return t[0]=0,t[1]=0,t[2]=0,t},o.clone=function(t){var a=new r.ARRAY_TYPE(3);return a[0]=t[0],a[1]=t[1],a[2]=t[2],a},o.fromValues=function(t,a,n){var o=new 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u=l*l,e=u*(2*l-3)+1,M=u*(l-2)+l,i=u*(l-1),s=u*(3-2*l);return t[0]=a[0]*e+n[0]*M+r[0]*i+o[0]*s,t[1]=a[1]*e+n[1]*M+r[1]*i+o[1]*s,t[2]=a[2]*e+n[2]*M+r[2]*i+o[2]*s,t},o.bezier=function(t,a,n,r,o,l){var u=1-l,e=u*u,M=l*l,i=e*u,s=3*l*e,c=3*M*u,D=M*l;return t[0]=a[0]*i+n[0]*s+r[0]*c+o[0]*D,t[1]=a[1]*i+n[1]*s+r[1]*c+o[1]*D,t[2]=a[2]*i+n[2]*s+r[2]*c+o[2]*D,t},o.random=function(t,a){a=a||1;var n=2*r.RANDOM()*Math.PI,o=2*r.RANDOM()-1,l=Math.sqrt(1-o*o)*a;return t[0]=Math.cos(n)*l,t[1]=Math.sin(n)*l,t[2]=o*a,t},o.transformMat4=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=n[3]*r+n[7]*o+n[11]*l+n[15];return u=u||1,t[0]=(n[0]*r+n[4]*o+n[8]*l+n[12])/u,t[1]=(n[1]*r+n[5]*o+n[9]*l+n[13])/u,t[2]=(n[2]*r+n[6]*o+n[10]*l+n[14])/u,t},o.transformMat3=function(t,a,n){var r=a[0],o=a[1],l=a[2];return t[0]=r*n[0]+o*n[3]+l*n[6],t[1]=r*n[1]+o*n[4]+l*n[7],t[2]=r*n[2]+o*n[5]+l*n[8],t},o.transformQuat=function(t,a,n){var 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a?cancelAnimationFrame(AnimationUpdater.animId):AnimationUpdater.animId=requestAnimationFrame(AnimationUpdater.run)}},"function"==typeof window.define&&null!=window.define.amd?define(function(){return{Gauge:g,Donut:f,BaseDonut:d,TextRenderer:i}}):"undefined"!=typeof module&&null!=module.exports?module.exports={Gauge:g,Donut:f,BaseDonut:d,TextRenderer:i}:(window.Gauge=g,window.Donut=f,window.BaseDonut=d,window.TextRenderer=i)}).call(this); +\ No newline at end of file +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/supportedcontrols.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/supportedcontrols.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/supportedcontrols.js (nonexistent) +@@ -1,16 +0,0 @@ +-function supportedcontrols() { +- var list = [ +- 'BalancethicknessThickeningRate', +- 'FrictionCoefficient', +- 'FrictionAs', +- 'MaterialsRheologyBbar', +- 'DamageDbar', +- 'Vx', +- 'Vy', +- 'Thickness', +- 'BalancethicknessOmega', +- 'BalancethicknessApparentMassbalance', +- 'MaterialsRheologyB']; +- +- return list; +-} +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/flowequation.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/flowequation.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/flowequation.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/flowequation.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/flowequation.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/friction.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/friction.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/friction.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/friction.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/friction.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/masstransport.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/masstransport.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/masstransport.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/masstransport.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/masstransport.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/adjacency.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/adjacency.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/adjacency.js (nonexistent) +@@ -1,61 +0,0 @@ +-adjacency = function(md) { +- //ADJACENCY - compute adjacency matrix, list of vertices and list of weights. +- // +- // function to create the adjacency matrix from the connectivity table. +- // +- // the required output is: +- // md.adj_mat (double [sparse nv x nv], vertex adjacency matrix) +- // md.qmu.vertex_weight (double [nv], vertex weights) +- +- var indi=[[md.mesh.elements.map(function(x) { return x[0]; })], [md.mesh.elements.map(function(x) { return x[1]; })], [md.mesh.elements.map(function(x) { return x[2]; })]]; +- var indj=[md.mesh.elements.map(function(x) { return x[1]; }), [md.mesh.elements.map(function(x) { return x[2]; })], [md.mesh.elements.map(function(x) { return x[0]; })]]; +- var values=1; +- +- md.qmu.adjacency=math.eye(md.mesh.numberofvertices, md.mesh.numberofvertices, 'sparse'); +- +- for (var i = 0; i < indi.length; ++i) { +- for (var j = 0; j < indj.length; ++j) { +- //md.qmu.adjacency[indi[i]][indj[j]] = values; +- md.qmu.adjacency.subset(math.index(i, j), values); +- } +- } +- +- var tempadj = math.subset(md.qmu.adjacency, math.index(0,math.range(0, math.size(md.qmu.adjacency)._data[1]))) +- +- //var tempadj = md.qmu.adjacency[0].map(function(col, i) { return md.qmu.adjacency.map(function(row) { return row[i]; }); }); +- //md.qmu.adjacency=[md.qmu.adjacency[0].map(function(x, idx) { return md.qmu.adjacency.map(function(row, jdx) { return md.qmu.adjacency[idx][jdx] | tempadj[i][j]; })})]; +- //md.qmu.adjacency=[tempadj.map(function(x, idx) { return md.qmu.adjacency.map(function(row, jdx) { return md.qmu.adjacency.subset(math.index(idx, jdx), md.qmu.adjacency.get([idx, jdx]) | tempadj.get([idx,jdx]));})})]; +- +- for (var i = 0; i < math.size(md.qmu.adjacency)._data[0]; ++i) { +- for (var j = 0; j < math.size(md.qmu.adjacency)._data[1]; ++j) { +- md.qmu.adjacency.subset(math.index(i,j), md.qmu.adjacency.subset(math.index(i,j)) | md.qmu.adjacency.subset(math.index(j,i))); +- } +- } +- //[tempadj.forEach(function(x, idx) { md.qmu.adjacency.forEach(function(y, jdx) { console.log(idx, jdx); return md.qmu.adjacency.subset(math.index(idx, jdx), md.qmu.adjacency.subset(math.index(idx, jdx)) );})})]; +- +- //now, build vwgt: +- areas=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y); +- +- //get node connectivity +- md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +- +- connectivity=md.mesh.vertexconnectivity.map(function(row) { return row.slice(0,row.length-1); }); +- pos=[]; +- for (var i = 0; i < connectivity.length; ++i) { +- if ((connectivity[i] !== 0)) { +- pos.push(i); +- } +- } +- +- console.log(areas); +- +- var tempconn = pos.map(function(val, idx) { return connectivity[val]; }); +- +- pos.forEach(function(val, idx) { +- connectivity[val] = areas[connectivity[val]]/3; +- }); +- +- md.qmu.vertex_weight=math.sum(connectivity); +- +- return md; +-}; +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/link-libs.sh +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/link-libs.sh (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/link-libs.sh (nonexistent) +@@ -1,7 +0,0 @@ +-# Create hard links for lib files +-ln $ISSM_DIR/src/m/enum/EnumDefinitions.js . +-ln $ISSM_DIR/src/m/classes/levelset.js . +-ln $ISSM_DIR/src/m/classes/mask.js . +-ln $ISSM_DIR/src/m/classes/mesh2d.js . +-ln $ISSM_DIR/src/m/classes/mesh3dprisms.js . +-ln $ISSM_DIR/src/m/classes/model.js . + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/link-libs.sh +___________________________________________________________________ +Deleted: svn:executable +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/mesh2d.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/mesh2d.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/mesh2d.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/mesh2d.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/mesh2d.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/calving.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/calving.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/calving.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/calving.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/calving.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/contourenvelope.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/contourenvelope.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/contourenvelope.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/parameterization/contourenvelope.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/contourenvelope.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/initialization.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/initialization.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/initialization.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/initialization.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/initialization.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/stressbalance.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/stressbalance.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/stressbalance.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/stressbalance.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/stressbalance.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/SMBforcing.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/SMBforcing.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/SMBforcing.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/SMBforcing.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/SMBforcing.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/mask.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/mask.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/mask.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/mask.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/mask.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/project2d.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/project2d.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/project2d.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/extrusion/project2d.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/project2d.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/project3d.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/project3d.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/project3d.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/extrusion/project3d.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/project3d.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/hydrologyshreve.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/hydrologyshreve.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/hydrologyshreve.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/hydrologyshreve.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/hydrologyshreve.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/EnumDefinitions.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/EnumDefinitions.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/EnumDefinitions.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/enum/EnumDefinitions.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/EnumDefinitions.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/qmu.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/qmu.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/qmu.js (nonexistent) +@@ -1 +0,0 @@ +-link /home/andy/Programming/Research/trunk-jpl/src/m/classes/qmu.js +\ No newline at end of file + +Property changes on: ../trunk-jpl/jenkins/javascript/karma/lib/bin/qmu.js +___________________________________________________________________ +Deleted: svn:special +## -1 +0,0 ## +-* +\ No newline at end of property +Index: ../trunk-jpl/jenkins/javascript/karma/lib/bin/issm-binaries.js +=================================================================== +--- ../trunk-jpl/jenkins/javascript/karma/lib/bin/issm-binaries.js (revision 21943) ++++ ../trunk-jpl/jenkins/javascript/karma/lib/bin/issm-binaries.js (nonexistent) +@@ -1,12024 +0,0 @@ +-function ArrayMax(array){ //{{{ +- return Math.max.apply(null,array); +-} //}}} +-function ArrayMax2D(array){ //{{{ +- +- var max=0; +- +- for (var i=0;i=value)return 1; +- } +- return 0; +-} //}}} +-function ArrayAnyAboveStrict(array,value) { //{{{ +- +- for(var i=0;ivalue)return 1; +- } +- return 0; +-} //}}} +-function ArrayAnd(array1,array2) { //{{{ +- +- var array=array1; +- for (var i=0;i=',16); +- checkfield(md,'fieldname','autodiff.lbufsize','>=',16); +- checkfield(md,'fieldname','autodiff.cbufsize','>=',16); +- checkfield(md,'fieldname','autodiff.tbufsize','>=',16); +- checkfield(md,'fieldname','autodiff.gcTriggerRatio','>=',0); +- checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',65536); +- +- //go through our dependents and independents and check consistency: +- for (var i=0;i=',0); +- } //}}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- var yts=365.0*24.0*3600.0; +- +- WriteData(fid,prefix,'object',this,'fieldname','spcthickness','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','thickening_rate','format','DoubleMat','mattype',1,'scale',1/yts); +- WriteData(fid,prefix,'object',this,'fieldname','stabilization','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','omega','format','DoubleMat','mattype',1); +- +- }//}}} +- this.fix=function() { //{{{ +- this.spcthickness=NullFix(this.spcthickness,NaN); +- this.thicknening_rate=NullFix(this.thicknening_rate,NaN); +- this.omega=NullFix(this.omega,NaN); +- }//}}} +- //properties +- // {{{ +- this.spcthickness = NaN; +- this.thickening_rate = NaN; +- this.stabilization = 0; +- this.omega = NaN; +- this.setdefaultparameters(); +- //}}} +-} +-//BASAL FORCINGS class definition +-// +-// Usage: +-// basalforcings=basalforcings(); +- +-function basalforcings(){ +- //methods +- this.setdefaultparameters = function() {//{{{ +- +- } // }}} +- this.disp = function(){ // {{{ +- console.log(sprintf(' basal forcings parameters:')); +- +- fielddisplay(this,'groundedice_melting_rate','basal melting rate (positive if melting) [m/yr]'); +- fielddisplay(this,'floatingice_melting_rate','basal melting rate (positive if melting) [m/yr]'); +- fielddisplay(this,'geothermalflux','geothermal heat flux [W/m^2]'); +- +- } // }}} +- this.classname = function(){ // {{{ +- return "basalforcings"; +- } // }}} +- this.initialize = function (md){ // {{{ +- +- if (isNaN(this.groundedice_melting_rate)){ +- this.groundedice_melting_rate=NewArrayFill(md.mesh.numberofvertices,0); +- console.log(' no basalforcings.groundedice_melting_rate specified: values set as zero'); +- } +- +- if (isNaN(this.floatingice_melting_rate)){ +- this.floatingice_melting_rate=NewArrayFill(md.mesh.numberofvertices,0); +- console.log(' no basalforcings.floatingice_melting_rate specified: values set as zero'); +- } +- +- } // }}} +- this.checkconsistency = function(md,solution,analyses) { //{{{ +- +- if(ArrayAnyEqual(ArrayIsMember(MasstransportAnalysisEnum(),analyses),1)){ +- if (!(solution==TransientSolutionEnum() & md.trans.ismasstransport==0)){ +- checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1); +- checkfield(md,'fieldname','basalforcings.floatingice_melting_rate','NaN',1,'Inf',1,'timeseries',1); +- } +- } +- +- if(ArrayAnyEqual(ArrayIsMember(BalancethicknessAnalysisEnum(),analyses),1)){ +- checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','basalforcings.floatingice_melting_rate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- } +- if(ArrayAnyEqual(ArrayIsMember(ThermalAnalysisEnum(),analyses),1)){ +- if (!(solution==TransientSolutionEnum() & md.trans.isthermal==0)){ +- checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1); +- checkfield(md,'fieldname','basalforcings.floatingice_melting_rate','NaN',1,'Inf',1,'timeseries',1); +- checkfield(md,'fieldname','basalforcings.geothermalflux','NaN',1,'Inf',1,'timeseries',1,'>=',0); +- } +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- var yts=365.0*24.0*3600.0; +- +- WriteData(fid,prefix,'name','md.basalforcings.model','data',FloatingMeltRateEnum(),'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','groundedice_melting_rate','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) +- WriteData(fid,prefix,'object',this,'fieldname','floatingice_melting_rate','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1) +- WriteData(fid,prefix,'object',this,'fieldname','geothermalflux','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); +- }//}}} +- this.fix=function() { //{{{ +- }//}}} +- //properties +- //{{{ +- this.groundedice_melting_rate = NaN; +- this.floatingice_melting_rate = NaN; +- this.geothermalflux = NaN; +- this.setdefaultparameters(); +- //}}} +-} +-//CALVING class definition +-// +-// Usage: +-// calving=new calving(); +- +-function calving (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- +- }// }}} +- this.disp= function(){// {{{ +- +- console.log(sprintf(' Calving parameters:')); +- fielddisplay(this,'calvingrate','calving rate at given location [m/a]'); +- fielddisplay(this,'meltingrate','melting rate at given location [m/a]'); +- +- }// }}} +- this.classname= function(){// {{{ +- return "calving"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { // {{{ +- //Early return +- if (solution!=TransientSolutionEnum() | md.trans.ismovingfront==0) return; +- +- checkfield(md,'fieldname','calving.calvingrate(1:md.mesh.numberofvertices,:)','>=',0,'timeseries',1,'NaN',1,'Inf',1); +- checkfield(md,'fieldname','calving.meltingrate(1:md.mesh.numberofvertices,:)','>=',0,'timeseries',1,'NaN',1,'Inf',1); +- } //}}} +- this.marshall=function(md,prefix,fid) { //{{{ +- var yts=365.0*24.0*3600.0; +- WriteData(fid,prefix,'name','md.calving.law','data',DefaultCalvingEnum(),'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','calvingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'scale',1./yts); +- WriteData(fid,prefix,'object',this,'fieldname','meltingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'scale',1./yts); +- }//}}} +- this.fix=function() { //{{{ +- this.calvingrate=NullFix(this.calvingrate,NaN); +- this.meltingrate=NullFix(this.meltingrate,NaN); +- }//}}} +- //properties +- // {{{ +- +- this.calvingrate = NaN; +- this.meltingrate = NaN; +- +- this.setdefaultparameters(); +- //}}} +-} +-//GENERIC class definition +-// +-// Usage: +-// generic=new generic(); +- +-function generic (){ +- //properties +- // {{{ +- var args = Array.prototype.slice.call(arguments); +- var options = new pairoptions(args.slice(0,args.length)); +- +- this.url=options.getfieldvalue('url',''); +- this.np=options.getfieldvalue('np',3); +- this.codeversion=options.getfieldvalue('codeversion',20486); +- this.codepath=options.getfieldvalue('codepath','issmdir/bin'); +- this.executionpath=options.getfieldvalue('executionpath','issmdir/execution'); +- //}}} +- //methods +- this.disp= function(){// {{{ +- console.log(sprintf(' generic class echo:')); +- console.log(sprintf(' url: "%s"',this.url)); +- console.log(sprintf(' np: %i',this.np)); +- console.log(sprintf(' codepath: "%s"',this.codepath)); +- console.log(sprintf(' executionpath: "%s"',this.executionpath)); +- }// }}} +- this.classname= function(){// {{{ +- return "generic"; +- }// }}} +- this.checkconsistency = function (md,solution,analyses) { //{{{ +- if (cluster.np<1){ +- md.checkmessage('number of processors should be at least 1'); +- } +- if (isNaN(cluster.np)){ +- md.checkmessage('number of processors should not be NaN!'); +- } +- } //}}} +- this.BuildQueueScript = function (cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) { // {{{ +- +- //write queuing script +- //what is the executable being called? +- executable='issm.exe'; +- +- fid=fopen(modelname+'.queue','w'); +- fprintf(fid,'#!%s\n',cluster.shell); +- fprintf(fid,'mpiexec -np %i %s/%s %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,executable,EnumToString(solution),cluster.executionpath+'/'+dirname,modelname,modelname,modelname); +- fclose(fid); +- } //}}} +- this.UploadAndRun = function (md,callbackfunction,fid,toolkitsstring,solutionstring,name,runtimename) { //{{{ +- +- var request = new XMLHttpRequest(); +- $(".run-button").html(sprintf("%-16s", "CONNECTING...")).prop("disabled", true); +- request.position = 0; //Keep track of current parsing position in repsonseText +- request.timeout = 30000; +- request.ontimeout = function (event) { //{{{ +- $(".run-button").html(sprintf("%-16s", "RUN")).prop("disabled", false); +- } //}}} +- request.upload.onprogress = function(event) { //{{{ +- var progress = (event.loaded / event.total * 100).toFixed(0); +- $(".run-button").html(sprintf("%-20s", "UPLOADING: " + progress + "%")); +- } //}}} +- request.onprogress = function (event) { //{{{ +- //Receive updates by parsing message length as a 32-bit hex string of form 0x*09ABCDEF)) +- var startIndex = request.position; +- var endIndex = request.position + 10; +- if (request.responseText.length >= endIndex) { //Ensure entire hex string is loaded +- var chunkSize = parseInt(request.responseText.slice(startIndex, endIndex)); +- startIndex = endIndex; +- endIndex = startIndex + chunkSize; +- if (chunkSize >= 1024) { //Arbitrary maximium size of message (Must be below minimium size of model results) +- $(".run-button").html(sprintf("%-20s", "DOWNLOADING: " + ((request.responseText.length - request.position) / chunkSize * 100).toFixed(0) + "%")).prop("disabled", true); +- } +- else if (request.responseText.length >= endIndex) { //Ensure entire chunk is loaded +- var responseChunk = request.responseText.slice(startIndex, endIndex); +- $(".run-button").html(responseChunk); +- request.position = endIndex; +- } +- } +- }; //}}} +- request.onload = function (event) { //{{{ +- //get context to this.str2ab to avoid duplciation +- function str2ab(str) { +- var buf = new Uint8Array(str.length); +- for (var i=0, strLen=str.length; i < strLen; i++) { +- buf[i] = str.charCodeAt(i); +- } +- return buf; +- } +- var responseText = request.responseText.slice(request.position + 10).replace(/\s/g, ''); +- var buffer = str2ab(window.atob(responseText)); +- var returnBuffer = new Uint8Array(buffer); +- var returnBuffer_size = returnBuffer.byteLength; +- try { +- md.results = parseresultsfrombuffer(returnBuffer,returnBuffer_size); +- } +- catch (e) { +- console.log(e); +- } +- $(".run-button").html(sprintf("%-16s", "RUN")).prop("disabled", false); +- callbackfunction(); +- }; //}}} +- +- var npbuffer = this.str2ab(md.cluster.np.toString()); +- var nplength = new Uint32Array(1); +- nplength[0] = npbuffer.byteLength; +- +- var codeversionbuffer = this.str2ab(md.cluster.codeversion.toString()); +- var codeversionlength = new Uint32Array(1); +- codeversionlength[0] = codeversionbuffer.byteLength; +- +- var runtimenamebuffer = this.str2ab(runtimename); +- var runtimenamelength = new Uint32Array(1); +- runtimenamelength[0] = runtimenamebuffer.byteLength; +- +- var namebuffer = this.str2ab(name); +- var namelength = new Uint32Array(1); +- namelength[0] = namebuffer.byteLength; +- +- var toolkitsbuffer = this.str2ab(toolkitsstring); +- var toolkitslength = new Uint32Array(1); +- toolkitslength[0] = toolkitsbuffer.byteLength; +- +- var solutionbuffer = this.str2ab(solutionstring); +- var solutionlength = new Uint32Array(1); +- solutionlength[0] = solutionbuffer.byteLength; +- +- var binbuffer = new Uint8Array(fid.rawbuffer()); //seems that 16 array bytes length could be incompatible. +- var binlength = new Uint32Array(1); +- binlength[0] = binbuffer.byteLength; +- +- var data = new Blob([nplength,npbuffer,codeversionlength,codeversionbuffer,runtimenamelength,runtimenamebuffer,namelength,namebuffer,toolkitslength,toolkitsbuffer,solutionlength,solutionbuffer,binlength,binbuffer]); +- +- request.open("POST", this.url, true); +- request.responseType = 'application/octet-stream'; +- request.send(data); +- +- } //}}} +- this.ab2str = function(buf) { //{{{ +- return String.fromCharCode.apply(null, new Uint16Array(buf)); +- } //}}} +- this.str2ab = function(str) { //{{{ +- var buf = new Uint8Array(str.length); +- for (var i=0, strLen=str.length; i < strLen; i++) { +- buf[i] = str.charCodeAt(i); +- } +- return buf; +- } //}}} +-} +-//LOCAL cluster class definition +-// +-// Usage: +-// local=new local(); +- +-function local (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- }// }}} +- this.disp= function(){// {{{ +- console.log(sprintf(' local cluster class echo: []')); +- }// }}} +- this.classname= function(){// {{{ +- return "local"; +- }// }}} +- this.checkconsistency = function (md,solution,analyses) { //{{{ +- } //}}} +- //properties +- // {{{ +- this.setdefaultparameters(); +- //}}} +-} +-//CONSTANTS class definition +-// +-// Usage: +-// constants=constants(); +- +-function constants() { +- //methods +- this.setdefaultparameters = function (){ //{{{ +- +- //acceleration due to gravity (m/s^2) +- this.g=9.81; +- +- //Earth's rotation speed +- this.omega = 7.292*1e-5; +- +- //converstion from year to seconds +- this.yts=365*24*3600; +- +- //the reference temperature for enthalpy model (cf Aschwanden) +- this.referencetemperature=223.15; +- }// }}} +- this.disp = function () { //{{{ +- console.log(sprintf(" Constants parameters:")); +- +- fielddisplay(this,'g','gravitational acceleration [m/s^2]'); +- fielddisplay(this,'omega','angular velocity of Earth [rad/s]'); +- fielddisplay(this,'yts','number of seconds in a year [s/yr]'); +- fielddisplay(this,'referencetemperature','reference temperature used in the enthalpy model [K]'); +- +- } //}}} +- this.classname = function () { //{{{ +- return "constants"; +- +- } //}}} +- this.checkconsistency = function(md,solution,analyses) {//% {{{ +- +- checkfield(md,'fieldname','constants.g','>=',0,'size',[1,1]); //We allow 0 for validation tests +- checkfield(md,'fieldname','constants.omega','>=',0,'size',[1,1]); +- checkfield(md,'fieldname','constants.yts','>',0,'size',[1,1]); +- checkfield(md,'fieldname','constants.referencetemperature','size',[1,1]); +- +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'object',this,'fieldname','g','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','yts','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','referencetemperature','format','Double'); +- }//}}} +- this.fix=function() { //{{{ +- }//}}} +- //properties +- // {{{ +- this.g = 0.; +- this.omega = 0.; +- this.yts = 0.; +- this.referencetemperature = 0.; +- this.setdefaultparameters(); +- //}}} +-} +-//DAMAGE class definition +-// +-// Usage: +-// damage=new damage(); +- +-function damage (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- +- //damage parameters: +- this.isdamage=0; +- this.D=0; +- this.law=0; +- +- this.max_damage=1-1e-5; //if damage reaches 1, solve becomes singular, as viscosity becomes nil +- +- //Type of stabilization used +- this.stabilization=4; +- +- //Maximum number of iterations +- this.maxiter=100; +- +- //finite element interpolation +- this.elementinterp='P1'; +- +- //damage evolution parameters +- this.stress_threshold=1.3e5; +- this.kappa=2.8; +- this.healing=0; +- this.c1=0; +- this.c2=0; +- this.c3=0; +- this.c4=0; +- this.equiv_stress=0; +- +- //output default: +- this.requested_outputs=['default']; +- +- }// }}} +- this.disp= function(){// {{{ +- console.log(sprintf(' Damage:\n')); +- +- fielddisplay(this,'isdamage','is damage mechanics being used? {true,false}'); +- if (this.isdamage){ +- fielddisplay(this,'law',"damage law ['0: analytical','1: pralong']"); +- fielddisplay(this,'D','damage tensor (scalar)'); +- fielddisplay(this,'spcdamage','damage constraints (NaN means no constraint)'); +- fielddisplay(this,'max_damage','maximum possible damage (0<=max_damage<1)'); +- +- fielddisplay(this,'stabilization','0: no, 1: artificial_diffusivity, 2: SUPG (not working), 4: flux corrected transport'); +- fielddisplay(this,'maxiter','maximum number of non linear iterations'); +- fielddisplay(this,'elementinterp',"interpolation scheme for finite elements {'P1','P2'}"); +- fielddisplay(this,'stress_threshold','stress threshold for damage initiation [Pa]'); +- fielddisplay(this,'kappa','ductility parameter for stress softening and damage'); +- fielddisplay(this,'c1','damage parameter 1'); +- fielddisplay(this,'c2','damage parameter 2'); +- fielddisplay(this,'c3','damage parameter 3'); +- fielddisplay(this,'c4','damage parameter 4'); +- fielddisplay(this,'healing','damage healing parameter'); +- fielddisplay(this,'equiv_stress','0: von Mises, 1: max principal'); +- fielddisplay(this,'requested_outputs','additional outputs requested'); +- } +- }// }}} +- this.classname= function(){// {{{ +- return "damage"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { //{{{ +- +- checkfield(md,'fieldname','damage.isdamage','values',[1,0]); +- if (this.isdamage){ +- checkfield(md,'fieldname','damage.law','numel',[1],'values',[0,1,2]); +- checkfield(md,'fieldname','damage.D','>=',0,'<=',this.max_damage,'size',[md.mesh.numberofvertices ,1]); +- checkfield(md,'fieldname','damage.spcdamage','Inf',1,'timeseries',1); +- checkfield(md,'fieldname','damage.max_damage','<',1,'>=',0); +- checkfield(md,'fieldname','damage.stabilization','numel',[1],'values',[0, 1, 2, 4]); +- checkfield(md,'fieldname','damage.maxiter','>=0',0); +- checkfield(md,'fieldname','damage.elementinterp','values',['P1','P2']); +- checkfield(md,'fieldname','damage.stress_threshold','>=',0); +- checkfield(md,'fieldname','damage.kappa','>',1); +- checkfield(md,'fieldname','damage.healing','>=',0); +- checkfield(md,'fieldname','damage.c1','>=',0); +- checkfield(md,'fieldname','damage.c2','>=',0); +- checkfield(md,'fieldname','damage.c3','>=',0); +- checkfield(md,'fieldname','damage.c4','>=',0); +- checkfield(md,'fieldname','damage.equiv_stress','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','damage.requested_outputs','stringrow',1); +- } +- else if (this.law!=0){ +- if (solution==DamageEvolutionSolutionEnum()){ +- throw Error('Invalid evolution law (md.damage.law) for a damage solution'); +- } +- } +- } //}}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- WriteData(fid,prefix,'object',this,'fieldname','isdamage','format','Boolean'); +- if (this.isdamage){ +- WriteData(fid,prefix,'object',this,'fieldname','law','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','D','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','spcdamage','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'fieldname','max_damage','format','Double'); +- +- WriteData(fid,prefix,'object',this,'fieldname','stabilization','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','maxiter','format','Integer'); +- WriteData(fid,prefix,'name','md.damage.elementinterp','data',StringToEnum(this.elementinterp),'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','stress_threshold','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','kappa','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','c1','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','c2','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','c3','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','c4','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','healing','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','equiv_stress','format','Integer'); +- } +- +- //process requested outputs +- var outputs = this.requested_outputs; +- for (var i=0;i 1 results in directions equally spaced from [0, 2*PI] being tested.', 'For example, 4 would result in directions [0, PI/2, PI, 3PI/2].']); +- fielddisplay(this,'opt_dist' ,'specifies the distance in km (default 25) to move a randomly selected path point on each iteration'); +- fielddisplay(this,'opt_niter' ,['number of iterations (default 30,000) to run for flightplan optimization', 'i.e. the number of times to randomly select a point and move it.']); +- +- console.log(sprintf('\n Output:')); +- fielddisplay(this,'solution' ,'name of kml solution file'); +- fielddisplay(this,'quality' ,'quality of kml solution'); +- +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { // {{{ +- +- //Early return +- if (solution!=FlaimSolutionEnum()) return; +- +- checkfield(md,'fieldname','flaim.tracks','file',1); +- if (isNaN(md.flaim.criterion) | md.flaim.criterion.length==0){ +- checkfield(md,'fieldname','flaim.targets','file',1); +- } +- else{ +- checkfield(md,'fieldname','flaim.criterion','numel',[md.mesh.numberofvertices, md.mesh.numberofelements]); +- } +- } //}}} +- //properties +- // {{{ +- +- this.targets = ''; +- this.tracks = ''; +- this.flightreqs = {}; +- this.criterion = NaN; +- this.gridsatequator = 200000; +- this.usevalueordering = true; +- this.split_antimeridian = true; +- this.solution = ''; +- this.quality = 0; +- this.path_optimize = false; +- this.opt_ndir = 1; +- this.opt_dist = 25; +- this.opt_niter = 30000; +- +- this.setdefaultparameters(); +- //}}} +-} +-//FLOWEQUATION class definition +-// +-// Usage: +-// flowequation=new flowequation(); +- +-function flowequation (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- //P1 for SSA +- this.fe_SSA= 'P1'; +- +- //P1 for HO +- this.fe_HO= 'P1'; +- +- //MINI condensed element for FS by default +- this.fe_FS = 'MINIcondensed'; +- }// }}} +- this.disp= function(){// {{{ +- console.log(sprintf(' flow equation parameters:')); +- +- fielddisplay(this,'isSIA','is the Shallow Ice Approximation (SIA) used ?'); +- fielddisplay(this,'isSSA','is the Shelfy-Stream Approximation (SSA) used ?'); +- fielddisplay(this,'isL1L2','is the L1L2 approximation used ?'); +- fielddisplay(this,'isHO','is the Higher-Order (HO) approximation used ?'); +- fielddisplay(this,'isFS','are the Full-FS (FS) equations used ?'); +- fielddisplay(this,'fe_SSA',"Finite Element for SSA 'P1', 'P1bubble' 'P1bubblecondensed' 'P2'"); +- fielddisplay(this,'fe_HO', "Finite Element for HO 'P1' 'P1bubble' 'P1bubblecondensed' 'P1xP2' 'P2xP1' 'P2'"); +- fielddisplay(this,'fe_FS', "Finite Element for FS 'P1P1' (debugging only) 'P1P1GLS' 'MINIcondensed' 'MINI' 'TaylorHood' 'XTaylorHood'"); +- fielddisplay(this,'vertex_equation','flow equation for each vertex'); +- fielddisplay(this,'element_equation','flow equation for each element'); +- fielddisplay(this,'borderSSA',"vertices on SSA's border (for tiling)"); +- fielddisplay(this,'borderHO',"vertices on HO's border (for tiling)"); +- fielddisplay(this,'borderFS',"vertices on FS' border (for tiling)"); +- +- }// }}} +- this.classname= function(){// {{{ +- return "flowequation"; +- +- }// }}} +- this.checkconsistency = function(md,solution,analyses) {//{{{ +- +- //Early return +- if ( ((!ArrayAnyEqual(ArrayIsMember(StressbalanceAnalysisEnum(),analyses),1)) & (!ArrayAnyEqual(ArrayIsMember(StressbalanceSIAAnalysisEnum(),analyses),1))) | +- (solution==TransientSolutionEnum() & md.trans.isstressbalance==0) +- ) return ; +- +- checkfield(md,'fieldname','flowequation.isSIA','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','flowequation.isSSA','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','flowequation.isL1L2','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','flowequation.isHO','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','flowequation.isFS','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','flowequation.fe_SSA','values',['P1','P1bubble','P1bubblecondensed','P2','P2bubble']); +- checkfield(md,'fieldname','flowequation.fe_HO' ,'values',['P1','P1bubble','P1bubblecondensed','P1xP2','P2xP1','P2','P2bubble','P1xP3','P2xP4']); +- checkfield(md,'fieldname','flowequation.fe_FS' ,'values',['P1P1','P1P1GLS','MINIcondensed','MINI','TaylorHood','LATaylorHood','XTaylorHood','OneLayerP4z','CrouzeixRaviart','LACrouzeixRaviart']); +- checkfield(md,'fieldname','flowequation.augmented_lagrangian_r','numel',[1],'>=',0.); +- checkfield(md,'fieldname','flowequation.augmented_lagrangian_rlambda','numel',[1],'>=',0.); +- checkfield(md,'fieldname','flowequation.augmented_lagrangian_rhop','numel',[1],'>=',0.); +- checkfield(md,'fieldname','flowequation.augmented_lagrangian_rholambda','numel',[1],'>=',0.); +- checkfield(md,'fieldname','flowequation.XTH_theta','numel',[1],'>=',0.,'<',0.5); +- checkfield(md,'fieldname','flowequation.borderSSA','size',[md.mesh.numberofvertices, 1],'values',[0, 1]); +- checkfield(md,'fieldname','flowequation.borderHO','size',[md.mesh.numberofvertices, 1],'values',[0, 1]); +- checkfield(md,'fieldname','flowequation.borderFS','size',[md.mesh.numberofvertices, 1],'values',[0, 1]); +- if (md.mesh.domaintype() == '2Dhorizontal'){ +- checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices, 1],'values',[1,2]); +- checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements, 1],'values',[1,2]); +- } +- else if (md.mesh.domaintype() == '3Dsurface'){ +- checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices, 1],'values',[1,2]); +- checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements, 1],'values',[1,2]); +- } +- else if (md.mesh.domaintype() =='2Dvertical'){ +- checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices, 1],'values',[2,4,5]); +- checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements, 1],'values',[2,4,5]); +- } +- else if (md.mesh.domaintype() =='3D'){ +- checkfield(md,'fieldname','flowequation.vertex_equation','size',[md.mesh.numberofvertices, 1],'values',[0,1,2,3,4,5,6,7,8]); +- checkfield(md,'fieldname','flowequation.element_equation','size',[md.mesh.numberofelements, 1],'values',[0,1,2,3,4,5,6,7,8]); +- } +- else throw Error('Case not supported yet'); +- +- if (!(this.isSIA | this.isSSA | this.isL1L2 | this.isHO | this.isFS)){ +- md = checkmessage(md,['no element types set for this model']); +- } +- if(ArrayAnyEqual(ArrayIsMember(StressbalanceSIAAnalysisEnum(), analyses),1)){ +- if (ArrayAnyEqual(this.element_equation,1)){ +- if(this.vertex_equation & ArrayAnyBelowStrict(md.mask.groundedice_levelset)){ +- console.log(sprintf("\n !!! Warning: SIA's model is not consistent on ice shelves !!!\n")); +- } +- } +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'object',this,'fieldname','isSIA','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isSSA','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isL1L2','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isHO','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isFS','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','fe_SSA','data',StringToEnum(this.fe_SSA),'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','fe_HO','data',StringToEnum(this.fe_HO) ,'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','fe_FS','data',StringToEnum(this.fe_FS) ,'format','Integer'); +- +- WriteData(fid,prefix,'object',this,'fieldname','augmented_lagrangian_r','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','augmented_lagrangian_rhop','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','augmented_lagrangian_rlambda','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','augmented_lagrangian_rholambda','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','XTH_theta','data',this.XTH_theta ,'format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','borderSSA','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','borderHO','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','borderFS','format','DoubleMat','mattype',1); +- +- //convert approximations to enums +- data=this.vertex_equation; +- +- //some optimization: +- var noneap=NoneApproximationEnum(); +- var siaap=SIAApproximationEnum(); +- var ssaap=SSAApproximationEnum(); +- var l1l2ap=L1L2ApproximationEnum(); +- var hoap=HOApproximationEnum(); +- var fsap=FSApproximationEnum(); +- var ssahoap=SSAHOApproximationEnum(); +- var hofsaap=HOFSApproximationEnum(); +- var ssafsap=SSAFSApproximationEnum(); +- +- for(var i=0;i=',0); +- } +- else{ +- checkfield(md,'fieldname','geometry.surface' ,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','geometry.base' ,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','geometry.thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1],'>',0); +- for(var i=0;iMath.pow(10,9)){ +- md = checkmessage(md,'equality thickness=surface-base violated'); +- break; +- } +- } +- if (solution==TransientSolutionEnum() & md.trans.isgroundingline){ +- checkfield(md,'fieldname','geometry.bed','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- } +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'object',this,'fieldname','surface','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','thickness','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'fieldname','base','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','bed','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','hydrostatic_ratio','format','DoubleMat','mattype',1); +- }//}}} +- this.fix=function() { //{{{ +- this.hydrostatic_ratio=NullFix(this.hydrostatic_ratio,NaN); +- }//}}} +- //properties +- // {{{ +- this.surface = NaN; +- this.thickness = NaN; +- this.base = NaN; +- this.bed = NaN; +- this.hydrostatic_ratio = NaN; +- this.setdefaultparameters(); +- //}}} +-} +-//GIA class definition +-// +-// Usage: +-// gia=new gia(); +- +-function gia (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- +- this.cross_section_shape=1; //square as default (see iedge in GiaDeflectionCorex) +- +- }// }}} +- this.disp= function(){// {{{ +- +- console.log(sprintf(' gia parameters:')); +- +- fielddisplay(this,'mantle_viscosity','mantle viscosity[Pa s]'); +- fielddisplay(this,'lithosphere_thickness','lithosphere thickness (km)'); +- fielddisplay(this,'cross_section_shape','1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore'); +- +- }// }}} +- this.classname= function(){// {{{ +- return "gia"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { // {{{ +- +- if(!ArrayAnyEqual(ArrayIsMember(GiaAnalysisEnum(),analyses),1))return; +- +- checkfield(md,'fieldname','gia.mantle_viscosity','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1],'>',0); +- checkfield(md,'fieldname','gia.lithosphere_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1],'>',0); +- checkfield(md,'fieldname','gia.cross_section_shape','numel',[1],'values',[1,2]); +- +- //be sure that if we are running a masstransport ice flow model coupled with gia, that thickness forcings +- //are not provided into the future. +- if (solution==TransientSolutionEnum() & md.trans.ismasstransport & md.trans.isgia){ +- //figure out if thickness is a transient forcing: +- if (md.geometry.thickness.length == (md.mesh.numberofvertices+1)){ +- //recover the furthest time "in time": +- t=md.geometry.thickness[0].length; +- if(md.geometry.thickness[md.geometry.thickness.length-1][t-1]!=md.timestepping.start_time){ +- md.checkmessage('if ismasstransport is on, transient thickness forcing for the gia model should not be provided in the future. Synchronize your start_time to correspond to the most recent transient thickness forcing timestep'); +- } +- } +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'object',this,'fieldname','mantle_viscosity','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','lithosphere_thickness','format','DoubleMat','mattype',1,'scale',Math.pow(10,3)); //from km to m +- WriteData(fid,prefix,'object',this,'fieldname','cross_section_shape','format','Integer'); +- }//}}} +- this.fix=function() { //{{{ +- this.mantle_viscosity=NullFix(this.mantle_viscosity,NaN); +- this.lithosphere_thickness=NullFix(this.lithosphere_thickness,NaN); +- }//}}} +- //properties +- // {{{ +- +- this.mantle_viscosity = NaN; +- this.lithosphere_thickness = NaN; +- this.cross_section_shape = 0; +- +- this.setdefaultparameters(); +- //}}} +-} +-//GROUNDINGLINE class definition +-// +-// Usage: +-// groundingline=new groundingline(); +- +-function groundingline (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- //Type of migration +- this.migration='None'; +- +- }// }}} +- this.disp= function(){// {{{ +- console.log(sprintf(' grounding line migration parameters:')); +- fielddisplay(this,'migration',"type of grounding line migration: 'SoftMigration','AggressiveMigration','SubelementMigration','SubelementMigration2' or 'None'"); +- +- +- }// }}} +- this.classname= function(){// {{{ +- return "groundingline"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) {// {{{ +- +- checkfield(md,'fieldname','groundingline.migration','values',['None', 'AggressiveMigration', 'SoftMigration', 'SubelementMigration', 'SubelementMigration2', 'Contact', 'None', 'GroundingOnly']); +- +- if (this.migration !='None'){ +- if (isNaN(md.geometry.bed)){ +- md.checkmessage('requesting grounding line migration, but bathymetry is absent!'); +- } +- for (var i=0;i0){ +- md.checkmessage('base not equal to bed on grounded ice!'); +- break; +- } +- if(md.geometry.bed[i] - md.geometry.base[i] > Math.pow(10,-9)){ +- md = checkmessage(md,'bed superior to base on floating ice!'); +- break; +- } +- } +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'data',StringToEnum(this.migration),'name','md.groundingline.migration','format','Integer'); +- }//}}} +- this.fix=function() { //{{{ +- }//}}} +- //properties +- // {{{ +- this.migration = ''; +- this.setdefaultparameters(); +- //}}} +-} +-//HYDROLOGYSHREVE class definition +-// +-// Usage: +-// hydrologyshreve=new hydrologyshreve(); +- +-function hydrologyshreve (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- +- //Type of stabilization to use 0:nothing 1:artificial_diffusivity +- this.stabilization=1; +- +- }// }}} +- this.disp= function(){// {{{ +- +- console.log(sprintf(' hydrologyshreve solution parameters:')); +- fielddisplay(this,'spcwatercolumn','water thickness constraints (NaN means no constraint) [m]'); +- fielddisplay(this,'stabilization','artificial diffusivity (default is 1). can be more than 1 to increase diffusivity.'); +- +- }// }}} +- this.classname= function(){// {{{ +- return "hydrologyshreve"; +- +- }// }}} +- this.type= function(){// {{{ +- +- return "hydrologyshreve"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { //{{{ +- +- //Early return +- if(!ArrayAnyEqual(ArrayIsMember(HydrologyShreveAnalysisEnum(),analyses),1)) return; +- +- checkfield(md,'fieldname','hydrology.spcwatercolumn','Inf',1,'timeseries',1); +- checkfield(md,'fieldname','hydrology.stabilization','>=',0); +- +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'name','md.hydrology.model','data',HydrologyshreveEnum(),'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','spcwatercolumn','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'fieldname','stabilization','format','Double'); +- }//}}} +- this.fix=function() { //{{{ +- this.spcwatercolumn=NullFix(this.spcwatercolumn,NaN); +- }//}}} +- //properties +- // {{{ +- this.spcwatercolumn = NaN; +- this.stabilization = 0; +- this.setdefaultparameters(); +- //}}} +-} +-//INITIALIZATION class definition +-// +-// Usage: +-// initialization=new initialization(); +- +-function initialization (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- }// }}} +- this.disp= function(){// {{{ +- console.log(sprintf(' initial field values:')); +- +- fielddisplay(this,'vx','x component of velocity [m/yr]'); +- fielddisplay(this,'vy','y component of velocity [m/yr]'); +- fielddisplay(this,'vz','z component of velocity [m/yr]'); +- fielddisplay(this,'vel','velocity norm [m/yr]'); +- fielddisplay(this,'pressure','pressure field [Pa]'); +- fielddisplay(this,'temperature','temperature [K]'); +- fielddisplay(this,'waterfraction','fraction of water in the ice'); +- fielddisplay(this,'sediment_head','sediment water head of subglacial system [m]'); +- fielddisplay(this,'epl_head','epl water head of subglacial system [m]'); +- fielddisplay(this,'epl_thickness','epl layer thickness [m]'); +- fielddisplay(this,'watercolumn','thickness of subglacial water [m]'); +- +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { //{{{ +- if(ArrayAnyEqual(ArrayIsMember(StressbalanceAnalysisEnum(),analyses),1)){ +- if (!(isNaN(md.initialization.vx) | isNaN(md.initialization.vy))){ +- checkfield(md,'fieldname','initialization.vx','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- } +- } +- if(ArrayAnyEqual(ArrayIsMember(MasstransportAnalysisEnum(),analyses),1)){ +- checkfield(md,'fieldname','initialization.vx','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- } +- if(ArrayAnyEqual(ArrayIsMember(BalancethicknessSolutionEnum(),analyses),1) & (solution==BalancethicknessSolutionEnum())){ +- checkfield(md,'fieldname','initialization.vx','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- //Triangle with zero velocity +- for(var i=0;i=',0,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','initialization.watercolumn' ,'>=',0,'size',[md.mesh.numberofvertices, 1]); +- } +- if(ArrayAnyEqual(ArrayIsMember(HydrologyShreveAnalysisEnum(),analyses),1)){ +- if (md.hydrology.type() == 'hydrologyshreve'){ +- checkfield(md,'fieldname','initialization.watercolumn','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices ,1]); +- } +- } +- if(ArrayAnyEqual(ArrayIsMember(HydrologyDCInefficientAnalysisEnum(),analyses),1)){ +- if (md.hydrology.type() == 'hydrologydc'){ +- checkfield(md,'fieldname','initialization.sediment_head','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- } +- } +- if(ArrayAnyEqual(ArrayIsMember(HydrologyDCEfficientAnalysisEnum(),analyses),1)){ +- if (md.hydrology.type() == 'hydrologydc'){ +- if (md.hydrology.isefficientlayer==1){ +- checkfield(md,'fieldname','initialization.epl_head','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices ,1]); +- checkfield(md,'fieldname','initialization.epl_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices ,1]); +- } +- } +- } +- } //}}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- var yts=365.0*24.0*3600.0; +- +- WriteData(fid,prefix,'object',this,'fieldname','vx','format','DoubleMat','mattype',1,'scale',1./yts); +- WriteData(fid,prefix,'object',this,'fieldname','vy','format','DoubleMat','mattype',1,'scale',1./yts); +- WriteData(fid,prefix,'object',this,'fieldname','vz','format','DoubleMat','mattype',1,'scale',1./yts); +- WriteData(fid,prefix,'object',this,'fieldname','pressure','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','temperature','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','waterfraction','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','sediment_head','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','epl_head','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','epl_thickness','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','watercolumn','format','DoubleMat','mattype',1); +- +- if (md.thermal.isenthalpy){ +- tpmp=NewArrayFill(md.mesh.numberofvertices,0); +- for (var i=0;i=tpmp[i]){ +- enthalpy[i] = md.materials.heatcapacity*(tpmp[i] - md.constants.referencetemperature) + md.materials.latentheat*md.initialization.waterfraction[i]; +- } +- WriteData(fid,prefix,'data',enthalpy,'format','DoubleMat','mattype',1,'name','md.initialization.enthalpy'); +- } +- }//}}} +- this.fix=function(md) { //{{{ +- this.vx=FloatFix(this.vx,md.mesh.numberofvertices); +- this.vy=FloatFix(this.vx,md.mesh.numberofvertices); +- this.vy=FloatFix(this.vx,md.mesh.numberofvertices); +- this.waterfraction=NullFix(this.waterfraction,NaN); +- this.sediment_head=NullFix(this.sediment_head,NaN); +- this.epl_head=NullFix(this.epl_head,NaN); +- this.epl_thickness=NullFix(this.epl_thickness,NaN); +- this.watercolumn=NullFix(this.watercolumn,NaN); +- }//}}} +- //properties +- // {{{ +- this.vx = NaN; +- this.vy = NaN; +- this.vz = NaN; +- this.vel = NaN; +- this.pressure = NaN; +- this.temperature = NaN; +- this.waterfraction = NaN; +- this.sediment_head = NaN; +- this.epl_head = NaN; +- this.epl_thickness = NaN; +- this.watercolumn = NaN; +- this.setdefaultparameters(); +- +- //}}} +-} +-//INVERSION class definition +-// +-// Usage: +-// inversion=new inversion(); +- +-function inversion (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- +- //default is incomplete adjoint for now +- this.incomplete_adjoint=1; +- +- //parameter to be inferred by control methods (only +- //drag and B are supported yet) +- this.control_parameters=['FrictionCoefficient']; +- +- //number of steps in the control methods +- this.nsteps=20; +- +- //maximum number of iteration in the optimization algorithm for +- //each step +- this.maxiter_per_step=20*NewArrayFill(this.nsteps,1); +- +- //the inversed parameter is updated as follows: +- //new_par=old_par + gradient_scaling(n)*C*gradient with C in [0 1]; +- //usually the gradient_scaling must be of the order of magnitude of the +- //inversed parameter (10^8 for B, 50 for drag) and can be decreased +- //after the first iterations +- this.gradient_scaling=NewArrayFill(this.nsteps,50); +- +- //several responses can be used: +- this.cost_functions=101; +- +- //step_threshold is used to speed up control method. When +- //misfit(1)/misfit(0) < this.step_threshold, we go directly to +- //the next step +- this.step_threshold=NewArrayFill(this.nsteps,.7); //30 per cent decrement. +- +- //cost_function_threshold is a criteria to stop the control methods. +- //if J[n]-J[n-1]/J[n] < criteria, the control run stops +- //NaN if not applied +- this.cost_function_threshold=NaN; //not activated +- +- }// }}} +- this.disp= function(){// {{{ +- +- console.log(sprintf(' inversion parameters:')); +- fielddisplay(this,'iscontrol','is inversion activated?'); +- fielddisplay(this,'incomplete_adjoint','1: linear viscosity, 0: non-linear viscosity'); +- fielddisplay(this,'control_parameters',"ex: {'FrictionCoefficient'}, or {'MaterialsRheologyBbar'}"); +- fielddisplay(this,'nsteps','number of optimization searches'); +- fielddisplay(this,'cost_functions','indicate the type of response for each optimization step'); +- fielddisplay(this,'cost_functions_coefficients','cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter'); +- fielddisplay(this,'cost_function_threshold','misfit convergence criterion. Default is 1%, NaN if not applied'); +- fielddisplay(this,'maxiter_per_step','maximum iterations during each optimization step'); +- fielddisplay(this,'gradient_scaling','scaling factor on gradient direction during optimization, for each optimization step'); +- fielddisplay(this,'step_threshold','decrease threshold for misfit, default is 30%'); +- fielddisplay(this,'min_parameters','absolute minimum acceptable value of the inversed parameter on each vertex'); +- fielddisplay(this,'max_parameters','absolute maximum acceptable value of the inversed parameter on each vertex'); +- fielddisplay(this,'vx_obs','observed velocity x component [m/yr]'); +- fielddisplay(this,'vy_obs','observed velocity y component [m/yr]'); +- fielddisplay(this,'vel_obs','observed velocity magnitude [m/yr]'); +- fielddisplay(this,'thickness_obs','observed thickness [m]'); +- fielddisplay(this,'surface_obs','observed surface elevation [m]'); +- console.log('Available cost functions:'); +- console.log(' 101: SurfaceAbsVelMisfit'); +- console.log(' 102: SurfaceRelVelMisfit'); +- console.log(' 103: SurfaceLogVelMisfit'); +- console.log(' 104: SurfaceLogVxVyMisfit'); +- console.log(' 105: SurfaceAverageVelMisfit'); +- console.log(' 201: ThicknessAbsMisfit'); +- console.log(' 501: DragCoefficientAbsGradient'); +- console.log(' 502: RheologyBbarAbsGradient'); +- console.log(' 503: ThicknessAbsGradient'); +- +- }// }}} +- this.extrude = function(md) {//{{{ +- this.vx_obs=project3d(md, 'vector', this.vx_obs, 'type', 'node'); +- this.vy_obs=project3d(md,'vector',this.vy_obs,'type','node'); +- this.vel_obs=project3d(md,'vector',this.vel_obs,'type','node'); +- this.thickness_obs=project3d(md,'vector',this.thickness_obs,'type','node'); +- +- if (numel(this.cost_functions_coefficients)>1) { +- this.cost_functions_coefficients=project3d(md,'vector',this.cost_functions_coefficients,'type','node'); +- } +- if (numel(this.min_parameters)>1) { +- this.min_parameters=project3d(md,'vector',this.min_parameters,'type','node'); +- } +- if (numel(this.max_parameters)>1) { +- this.max_parameters=project3d(md,'vector',this.max_parameters,'type','node'); +- } +- }//}}} +- this.classname= function(){// {{{ +- return "inversion"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { //{{{ +- +- //Early return +- if (!this.iscontrol) return; +- +- num_controls=md.inversion.control_parameters.length; +- num_costfunc=md.inversion.control_parameters[0].length; +- +- checkfield(md,'fieldname','inversion.iscontrol','values',[0, 1]); +- checkfield(md,'fieldname','inversion.incomplete_adjoint','values',[0 ,1]); +- checkfield(md,'fieldname','inversion.control_parameters','cell',1,'values',supportedcontrols()); +- checkfield(md,'fieldname','inversion.nsteps','numel',1,'>=',0); +- checkfield(md,'fieldname','inversion.maxiter_per_step','size',[md.inversion.nsteps, 1],'>=',0); +- checkfield(md,'fieldname','inversion.step_threshold','size',[md.inversion.nsteps, 1]); +- checkfield(md,'fieldname','inversion.cost_functions','size',[1, num_costfunc],'values',supportedcostfunctions()); +- checkfield(md,'fieldname','inversion.cost_functions_coefficients','size',[md.mesh.numberofvertices, num_costfunc],'>=',0); +- checkfield(md,'fieldname','inversion.gradient_scaling','size',[md.inversion.nsteps, num_controls]); +- checkfield(md,'fieldname','inversion.min_parameters','size',[md.mesh.numberofvertices , num_controls]); +- checkfield(md,'fieldname','inversion.max_parameters','size',[md.mesh.numberofvertices ,num_controls]); +- +- //Only SSA, HO and FS are supported right now +- if (solution==StressbalanceSolutionEnum()){ +- if (!(md.flowequation.isSSA | md.flowequation.isHO | md.flowequation.isFS | md.flowequation.isL1L2)){ +- md.checkmessage('inversion can only be performed for SSA, HO or FS ice flow models'); +- } +- } +- +- if (solution==BalancethicknessSolutionEnum()){ +- checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices ,1],'NaN',1,'Inf',1); +- } +- else if (solution==BalancethicknessSoftSolutionEnum()){ +- checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices, 1],'NaN',1,'Inf',1); +- } +- else{ +- checkfield(md,'fieldname','inversion.vx_obs','size',[md.mesh.numberofvertices ,1],'NaN',1,'Inf',1); +- checkfield(md,'fieldname','inversion.vy_obs','size',[md.mesh.numberofvertices ,1],'NaN',1,'Inf',1); +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- var yts=365.0*24.0*3600.0; +- +- WriteData(fid,prefix,'name','md.inversion.type','data',0,'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','iscontrol','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','incomplete_adjoint','format','Boolean'); +- if (!this.iscontrol) return; +- WriteData(fid,prefix,'object',this,'fieldname','nsteps','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','maxiter_per_step','format','IntMat','mattype',3); +- WriteData(fid,prefix,'object',this,'fieldname','cost_functions_coefficients','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','gradient_scaling','format','DoubleMat','mattype',3); +- WriteData(fid,prefix,'object',this,'fieldname','cost_function_threshold','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','min_parameters','format','DoubleMat','mattype',3); +- WriteData(fid,prefix,'object',this,'fieldname','max_parameters','format','DoubleMat','mattype',3); +- WriteData(fid,prefix,'object',this,'fieldname','step_threshold','format','DoubleMat','mattype',3); +- WriteData(fid,prefix,'object',this,'fieldname','vx_obs','format','DoubleMat','mattype',1,'scale',1./yts); +- WriteData(fid,prefix,'object',this,'fieldname','vy_obs','format','DoubleMat','mattype',1,'scale',1./yts); +- WriteData(fid,prefix,'object',this,'fieldname','vz_obs','format','DoubleMat','mattype',1,'scale',1./yts); +- if(this.thickness_obs.length==md.mesh.numberofelements) mattype=2; +- else mattype=1; +- WriteData(fid,prefix,'object',this,'class','inversion','fieldname','thickness_obs','format','DoubleMat','mattype',mattype); +- WriteData(fid,prefix,'object',this,'class','inversion','fieldname','surface_obs','format','DoubleMat','mattype',mattype); +- +- //process control parameters +- num_control_parameters=this.control_parameters.length; +- WriteData(fid,prefix,'object',this,'fieldname','control_parameters','format','StringArray'); +- WriteData(fid,prefix,'data',num_control_parameters,'name','md.inversion.num_control_parameters','format','Integer'); +- +- //process cost functions +- num_cost_functions=this.cost_functions[0].length; +- data=marshallcostfunctions(this.cost_functions); +- WriteData(fid,prefix,'data',data,'name','md.inversion.cost_functions','format','DoubleMat','mattype',3); +- WriteData(fid,prefix,'data',num_cost_functions,'name','md.inversion.num_cost_functions','format','Integer'); +- }//}}} +- this.fix=function() { //{{{ +- this.control_parameters=NullFix(this.control_parameters,NaN); +- this.maxiter_per_step=NullFix(this.maxiter_per_step,NaN); +- this.cost_functions=NullFix(this.cost_functions,NaN); +- this.cost_functions_coefficients=NullFix(this.cost_functions_coefficients,NaN); +- this.cost_function_threshold=NullFix(this.cost_function_threshold,NaN); +- this.gradient_scaling=NullFix(this.gradient_scaling,NaN); +- this.min_parameters=NullFix(this.min_parameters,NaN); +- this.max_parameters=NullFix(this.max_parameters,NaN); +- this.step_threshold=NullFix(this.step_threshold,NaN); +- this.vx_obs=NullFix(this.vx_obs,NaN); +- this.vy_obs=NullFix(this.vy_obs,NaN); +- this.vz_obs=NullFix(this.vz_obs,NaN); +- this.vel_obs=NullFix(this.vel_obs,NaN); +- this.thickness_obs=NullFix(this.thickness_obs,NaN); +- this.surface_obs=NullFix(this.surface_obs,NaN); +- }//}}} +- //properties +- // {{{ +- +- this.iscontrol = 0; +- this.incomplete_adjoint = 0; +- this.control_parameters = NaN; +- this.nsteps = 0; +- this.maxiter_per_step = NaN; +- this.cost_functions = NaN; +- this.cost_functions_coefficients = NaN; +- this.gradient_scaling = NaN; +- this.cost_function_threshold = 0; +- this.min_parameters = NaN; +- this.max_parameters = NaN; +- this.step_threshold = NaN; +- this.vx_obs = NaN; +- this.vy_obs = NaN; +- this.vz_obs = NaN; +- this.vel_obs = NaN; +- this.thickness_obs = NaN; +- this.surface_obs = NaN; +- +- this.setdefaultparameters(); +- //}}} +-} +-//MASK class definition +-// +-// Usage: +-// mask= new mask(); +- +-function mask () { +- //properties +- // {{{ +- this.groundedice_levelset = NaN; +- this.ice_levelset = NaN; +- //}}} +- //methods +- this.setdefaultparameters = function (){ //{{{ +- } // }}} +- this.disp = function () { //{{{ +- console.log(sprintf(" mask:")); +- +- fielddisplay(this,"groundedice_levelset","is ice grounded ? grounded ice if > 0, grounding line position if = 0, floating ice if < 0"); +- fielddisplay(this,"ice_levelset","presence of ice if < 0, icefront position if = 0, no ice if > 0"); +- } //}}} +- this.classname = function () { //{{{ +- return "mask"; +- } //}}} +- this.checkconsistency = function(md,solution,analyses){ //{{{ +- +- checkfield(md,'fieldname','mask.groundedice_levelset','size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mask.ice_levelset' ,'size',[md.mesh.numberofvertices, 1]); +- var isice=NewArrayFill(md.mesh.numberofvertices,0); +- for(var i=0;i 0, grounding line position if = 0, floating ice if < 0"); +- fielddisplay(this,"ice_levelset","presence of ice if < 0, icefront position if = 0, no ice if > 0"); +- fielddisplay(this,"ocean_levelset","is the vertex on the ocean? yes if = 1, no if = 0"); +- fielddisplay(this,"land_levelset","is the vertex on land? yes if = 1, no if = 0"); +- } //}}} +- this.classname = function () { //{{{ +- return "maskpsl"; +- } //}}} +- this.checkconsistency = function(md,solution,analyses){ //{{{ +- +- checkfield(md,'fieldname','mask.groundedice_levelset','size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mask.ice_levelset' ,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mask.ocean_levelset' ,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mask.land_levelset' ,'size',[md.mesh.numberofvertices, 1]); +- +- var isice=NewArrayFill(md.mesh.numberofvertices,0); +- for(var i=0;i',0); +- checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1); +- +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- var yts=365.*24.*3600.; +- +- WriteData(fid,prefix,'object',this,'fieldname','spcthickness','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'fieldname','isfreesurface','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','min_thickness','format','Double'); +- WriteData(fid,prefix,'data',StringToEnum(this.hydrostatic_adjustment),'format','Integer','name','md.masstransport.hydrostatic_adjustment'); +- WriteData(fid,prefix,'object',this,'fieldname','stabilization','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','vertex_pairing','format','DoubleMat','mattype',3); +- WriteData(fid,prefix,'object',this,'fieldname','penalty_factor','format','Double'); +- +- //process requested outputs +- var outputs = this.requested_outputs; +- for (var i=0;i',0); +- checkfield(md,'fieldname','materials.rho_water','>',0); +- checkfield(md,'fieldname','materials.rho_freshwater','>',0); +- checkfield(md,'fieldname','materials.mu_water','>',0); +- checkfield(md,'fieldname','materials.rheology_B','>',0,'timeseries',1,'NaN',1,'Inf',1); +- checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements,1]); +- checkfield(md,'fieldname','materials.rheology_law','values',['None','Cuffey','CuffeyTemperate','Paterson','Arrhenius','LliboutryDuval']); +- +- if(ArrayAnyEqual(ArrayIsMember(GiaAnalysisEnum(),analyses),1)){ +- checkfield(md,'fieldname','materials.lithosphere_shear_modulus','>',0,'numel',1); +- checkfield(md,'fieldname','materials.lithosphere_density','>',0,'numel',1); +- checkfield(md,'fieldname','materials.mantle_shear_modulus','>',0,'numel',1); +- checkfield(md,'fieldname','materials.mantle_density','>',0,'numel',1); +- } +- if (ArrayAnyEqual(ArrayIsMember(SealevelriseAnalysisEnum(),analyses),1)){ +- checkfield(md,'fieldname','materials.earth_density','>',0,'numel',1); +- } +- +- +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'name','md.materials.type','data',MaticeEnum(),'format','Integer'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','rho_ice','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','rho_water','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','rho_freshwater','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','mu_water','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','heatcapacity','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','latentheat','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','thermalconductivity','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','temperateiceconductivity','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','meltingpoint','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','beta','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','mixed_layer_capacity','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','thermal_exchange_velocity','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2); +- WriteData(fid,prefix,'data',StringToEnum(this.rheology_law),'name','md.materials.rheology_law','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','lithosphere_shear_modulus','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','lithosphere_density','format','Double','scale',10^3); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','mantle_shear_modulus','format','Double'); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','mantle_density','format','Double','scale',10^3); +- WriteData(fid,prefix,'object',this,'class','materials','fieldname','earth_density','format','Double'); +- +- }//}}} +- this.fix=function() { //{{{ +- }//}}} +- //properties +- // {{{ +- this.rho_ice = 0.; +- this.rho_water = 0.; +- this.rho_freshwater = 0.; +- this.mu_water = 0.; +- this.heatcapacity = 0.; +- this.latentheat = 0.; +- this.thermalconductivity = 0.; +- this.temperateiceconductivity = 0.; +- this.meltingpoint = 0.; +- this.beta = 0.; +- this.mixed_layer_capacity = 0.; +- this.thermal_exchange_velocity = 0.; +- this.rheology_B = NaN; +- this.rheology_n = NaN; +- this.rheology_law = ''; +- +- //gia: +- this.lithosphere_shear_modulus = 0.; +- this.lithosphere_density = 0.; +- this.mantle_shear_modulus = 0.; +- this.mantle_density = 0.; +- +- //SLR +- this.earth_density= 5512; // average density of the Earth, (kg/m^3) +- +- this.setdefaultparameters(); +- //}}} +-} +-//MESH2D class definition +-// +-// Usage: +-// mesh2d= new mesh2d(); +- +-function mesh2d () { +- //methods +- this.setdefaultparameters = function (){ //{{{ +- +- //the connectivity is the averaged number of nodes linked to a +- //given node through an edge. This connectivity is used to initially +- //allocate memory to the stiffness matrix. A value of 16 seems to +- //give a good memory/time ration. This value can be checked in +- //trunk/test/Miscellaneous/runme.m +- this.average_vertex_connectivity=25; +- } +- // }}} +- this.disp = function () { //{{{ +- console.log(sprintf(" 2D tria Mesh (horizontal):")); +- +- console.log(sprintf("\n Elements and vertices:")); +- fielddisplay(this,"numberofelements","number of elements"); +- fielddisplay(this,"numberofvertices","number of vertices"); +- fielddisplay(this,"elements","vertex indices of the mesh elements"); +- fielddisplay(this,"x","vertices x coordinate [m]"); +- fielddisplay(this,"y","vertices y coordinate [m]"); +- fielddisplay(this,"edges","edges of the 2d mesh (vertex1 vertex2 element1 element2)"); +- fielddisplay(this,"numberofedges","number of edges of the 2d mesh"); +- +- console.log(sprintf("\n Properties:")); +- fielddisplay(this,"vertexonboundary","vertices on the boundary of the domain flag list"); +- fielddisplay(this,"segments","edges on domain boundary (vertex1 vertex2 element)"); +- fielddisplay(this,"segmentmarkers","number associated to each segment"); +- fielddisplay(this,"vertexconnectivity","list of vertices connected to vertex_i"); +- fielddisplay(this,"elementconnectivity","list of vertices connected to element_i"); +- fielddisplay(this,"average_vertex_connectivity","average number of vertices connected to one vertex"); +- +- console.log(sprintf("\n Extracted model:")); +- fielddisplay(this,"extractedvertices","vertices extracted from the model"); +- fielddisplay(this,"extractedelements","elements extracted from the model"); +- +- console.log(sprintf("\n Projection:")); +- fielddisplay(this,"lat","vertices latitude [degrees]"); +- fielddisplay(this,"long","vertices longitude [degrees]"); +- fielddisplay(this,"epsg","EPSG code (ex: 3413 for UPS Greenland, 3031 for UPS Antarctica)"); +- } //}}} +- this.classname = function () { //{{{ +- return "mesh2d"; +- } //}}} +- this.domaintype=function (){ // {{{ +- return '2Dhorizontal'; +- } // }}} +- this.dimension = function () { //{{{ +- return 2; +- } //}}} +- this.elementtype = function() {//{{{ +- return 'Tria'; +- } // }}} +- this.checkconsistency = function(md,solution,analyses){ //{{{ +- +- checkfield(md,'fieldname','mesh.x','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mesh.y','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mesh.elements','NaN',1,'Inf',1,'>',0,'values',NewArrayFillIncrement(md.mesh.numberofvertices,1,1)); +- checkfield(md,'fieldname','mesh.elements','size',[md.mesh.numberofelements, 3]); +- if(ArrayAnyEqual(ArrayIsMember(NewArrayFillIncrement(md.mesh.numberofvertices,1,1),ArraySort(ArrayUnique(MatrixToList(md.mesh.elements)))),0)){ +- md.checkmessage('orphan nodes have been found. Check the mesh outline'); +- } +- checkfield(md,'fieldname','mesh.numberofelements','>',0); +- checkfield(md,'fieldname','mesh.numberofvertices','>',0); +- checkfield(md,'fieldname','mesh.average_vertex_connectivity','>=',9,'message',"'mesh.average_vertex_connectivity' should be at least 9 in 2d"); +- checkfield(md,'fieldname','mesh.segments','NaN',1,'Inf',1,'>',0,'size',[NaN, 3]); +- +- switch(solution){ +- case ThermalSolutionEnum(): +- checkmessage(md,'thermal not supported for 2d mesh'); +- break; +- default: +- break +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'name','md.mesh.domain_type','data',StringToEnum('Domain' + this.domaintype()),'format','Integer'); +- WriteData(fid,prefix,'name','md.mesh.domain_dimension','data',this.dimension(),'format','Integer'); +- WriteData(fid,prefix,'name','md.mesh.elementtype','data',StringToEnum(this.elementtype()),'format','Integer'); +- WriteData(fid,prefix,'object',this,'class','mesh','fieldname','x','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'class','mesh','fieldname','y','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'name','md.mesh.z','data',NewArrayFill(this.numberofvertices,0),'format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'class','mesh','fieldname','elements','format','DoubleMat','mattype',2); +- WriteData(fid,prefix,'object',this,'class','mesh','fieldname','numberofelements','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','mesh','fieldname','numberofvertices','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','mesh','fieldname','average_vertex_connectivity','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','mesh','fieldname','vertexonboundary','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'class','mesh','fieldname','segments','format','DoubleMat','mattype',3); +- }//}}} +- this.fix=function() { //{{{ +- //Transform objects into Float64Arrays: +- this.x=FloatFix(this.x,this.numberofvertices); +- this.y=FloatFix(this.y,this.numberofvertices); +- this.edges=NullFix(this.edges,NaN); +- this.vertexonboundary=FloatFix(this.vertexonboundary,this.numberofvertices); +- this.segmentmarkers=FloatFix(this.segmentmarkers,this.segments.length); +- this.extractedvertices=NullFix(this.extractedvertices,NaN); +- this.extractedelements=NullFix(this.extractedelements,NaN); +- this.lat=NullFix(this.lat,NaN); +- this.long=NullFix(this.long,NaN); +- }//}}} +- +- //properties +- // {{{ +- this.x = NaN; +- this.y = NaN; +- this.elements = NaN; +- this.numberofelements = 0; +- this.numberofvertices = 0; +- this.numberofedges = 0; +- +- this.lat = NaN; +- this.long = NaN; +- this.epsg = 0; +- +- this.vertexonboundary = NaN; +- +- this.edges = NaN; +- this.segments = NaN; +- this.segmentmarkers = NaN; +- this.vertexconnectivity = NaN; +- this.elementconnectivity = NaN; +- this.average_vertex_connectivity = 0; +- +- this.extractedvertices = NaN; +- this.extractedelements = NaN; +- +- this.setdefaultparameters(); +- //}}} +-} +-//MESH3DSURFACE class definition +-// +-// Usage: +-// mesh3dsurface= new mesh3dsurface(); +- +-function mesh3dsurface () { +- //methods +- this.setdefaultparameters = function (){ //{{{ +- +- //the connectivity is the averaged number of nodes linked to a +- //given node through an edge. This connectivity is used to initially +- //allocate memory to the stiffness matrix. A value of 16 seems to +- //give a good memory/time ration. This value can be checked in +- //trunk/test/Miscellaneous/runme.m +- this.average_vertex_connectivity=25; +- } +- // }}} +- this.disp = function () { //{{{ +- console.log(sprintf(" 2D tria Mesh (3D surface):")); +- +- console.log(sprintf("\n Elements and vertices:")); +- fielddisplay(this,"numberofelements","number of elements"); +- fielddisplay(this,"numberofvertices","number of vertices"); +- fielddisplay(this,"elements","vertex indices of the mesh elements"); +- fielddisplay(this,"x","vertices x coordinate [m]"); +- fielddisplay(this,"y","vertices y coordinate [m]"); +- fielddisplay(this,"z","vertices z coordinate [m]"); +- fielddisplay(this,"edges","edges of the 2d mesh (vertex1 vertex2 element1 element2)"); +- fielddisplay(this,"numberofedges","number of edges of the 2d mesh"); +- +- console.log(sprintf("\n Properties:")); +- fielddisplay(this,"vertexonboundary","vertices on the boundary of the domain flag list"); +- fielddisplay(this,"segments","edges on domain boundary (vertex1 vertex2 element)"); +- fielddisplay(this,"segmentmarkers","number associated to each segment"); +- fielddisplay(this,"vertexconnectivity","list of vertices connected to vertex_i"); +- fielddisplay(this,"elementconnectivity","list of vertices connected to element_i"); +- fielddisplay(this,"average_vertex_connectivity","average number of vertices connected to one vertex"); +- +- console.log(sprintf("\n Extracted model:")); +- fielddisplay(this,"extractedvertices","vertices extracted from the model"); +- fielddisplay(this,"extractedelements","elements extracted from the model"); +- +- console.log(sprintf("\n Projection:")); +- fielddisplay(this,"lat","vertices latitude [degrees]"); +- fielddisplay(this,"long","vertices longitude [degrees]"); +- fielddisplay(this,"r","vertices radius [m]"); +- } //}}} +- this.classname = function () { //{{{ +- return "mesh3dsurface"; +- } //}}} +- this.domaintype=function (){ // {{{ +- return '3Dsurface'; +- } // }}} +- this.dimension = function () { //{{{ +- return 2; +- } //}}} +- this.elementtype = function() {//{{{ +- return 'Tria'; +- } // }}} +- this.checkconsistency = function(md,solution,analyses){ //{{{ +- +- checkfield(md,'fieldname','mesh.x','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mesh.y','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mesh.z','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mesh.lat','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mesh.long','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mesh.r','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices, 1]); +- checkfield(md,'fieldname','mesh.elements','NaN',1,'Inf',1,'>',0,'values',NewArrayFillIncrement(md.mesh.numberofvertices,1,1)); +- checkfield(md,'fieldname','mesh.elements','size',[md.mesh.numberofelements, 3]); +- if(ArrayAnyEqual(ArrayIsMember(NewArrayFillIncrement(md.mesh.numberofvertices,1,1),ArraySort(ArrayUnique(MatrixToList(md.mesh.elements)))),0)){ +- md.checkmessage('orphan nodes have been found. Check the mesh outline'); +- } +- checkfield(md,'fieldname','mesh.numberofelements','>',0); +- checkfield(md,'fieldname','mesh.numberofvertices','>',0); +- checkfield(md,'fieldname','mesh.average_vertex_connectivity','>=',9,'message',"'mesh.average_vertex_connectivity' should be at least 9 in 2d"); +- checkfield(md,'fieldname','mesh.segments','NaN',1,'Inf',1,'>',0,'size',[NaN, 3]); +- +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'name','md.mesh.domain_type','data',StringToEnum('Domain' + this.domaintype()),'format','Integer'); +- WriteData(fid,prefix,'name','md.mesh.domain_dimension','data',this.dimension(),'format','Integer'); +- WriteData(fid,prefix,'name','md.mesh.elementtype','data',StringToEnum(this.elementtype()),'format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','x','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','y','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','z','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','lat','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','long','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','r','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','elements','format','DoubleMat','mattype',2); +- WriteData(fid,prefix,'object',this,'fieldname','numberofelements','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','numberofvertices','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','average_vertex_connectivity','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','vertexonboundary','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','segments','format','DoubleMat','mattype',3); +- }//}}} +- this.fix=function() { //{{{ +- //Transform objects into Float64Arrays: +- this.x=FloatFix(this.x,this.numberofvertices); +- this.y=FloatFix(this.y,this.numberofvertices); +- this.z=FloatFix(this.y,this.numberofvertices); +- this.r=FloatFix(this.y,this.numberofvertices); +- this.edges=NullFix(this.edges,NaN); +- this.vertexonboundary=FloatFix(this.vertexonboundary,this.numberofvertices); +- this.segmentmarkers=FloatFix(this.segmentmarkers,this.segments.length); +- this.extractedvertices=NullFix(this.extractedvertices,NaN); +- this.extractedelements=NullFix(this.extractedelements,NaN); +- this.lat=NullFix(this.lat,NaN); +- this.long=NullFix(this.long,NaN); +- }//}}} +- +- //properties +- // {{{ +- this.x = NaN; +- this.y = NaN; +- this.z = NaN; +- this.elements = NaN; +- this.numberofelements = 0; +- this.numberofvertices = 0; +- this.numberofedges = 0; +- +- this.lat = NaN; +- this.long = NaN; +- this.r = NaN; +- +- this.vertexonboundary = NaN; +- this.edges = NaN; +- this.segments = NaN; +- this.segmentmarkers = NaN; +- this.vertexconnectivity = NaN; +- this.elementconnectivity = NaN; +- this.average_vertex_connectivity = 0; +- +- this.extractedvertices = NaN; +- this.extractedelements = NaN; +- +- this.setdefaultparameters(); +- //}}} +-} +-//MISCELLANEOUS class definition +-// +-// Usage: +-// miscellaneous=new miscellaneous(); +- +-function miscellaneous (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- }// }}} +- this.disp= function(){// {{{ +- +- console.log(sprintf(' miscellaneous parameters:')); +- +- fielddisplay(this,'notes','notes in a cell of strings'); +- fielddisplay(this,'name','model name'); +- fielddisplay(this,'dummy','empty field to store some data'); +- +- }// }}} +- this.classname= function(){// {{{ +- return "miscellaneous"; +- }// }}} +- this.checkconsistency= function(md,solution,analyses) {// {{{ +- +- checkfield(md,'fieldname','miscellaneous.name','empty',1); +- }// }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'object',this,'fieldname','name','format','String'); +- }//}}} +- this.fix=function() { //{{{ +- }//}}} +- //properties +- // {{{ +- this.notes = ''; +- this.name = ''; +- this.dummy = []; +- +- this.setdefaultparameters(); +- //}}} +-} +-//MODEL class definition +-// +-// Usage: +-// md = new model() +- +-function model () { +- //methods +- this.disp = function() { //{{{ +- console.log(sprintf("class model echo: ")); +- console.log(sprintf("%19s: %-22s -- %s","mesh" ,"[1x1 " + typeof(this.mesh) + "]","mesh properties")); +- console.log(sprintf("%19s: %-22s -- %s","mask" ,"[1x1 " + typeof(this.mask) + "]","defines grounded and floating elements")); +- console.log(sprintf("%19s: %-22s -- %s","geometry" ,"[1x1 " + typeof(this.geometry) + "]","surface elevation, bedrock topography, ice thickness,...")); +- console.log(sprintf("%19s: %-22s -- %s","constants" ,"[1x1 " + typeof(this.constants) + "]","physical constants")); +- console.log(sprintf("%19s: %-22s -- %s","smb" ,"[1x1 " + typeof(this.smb) + "]","surface mass balance")); +- console.log(sprintf("%19s: %-22s -- %s","basalforcings" ,"[1x1 " + typeof(this.basalforcings) + "]","bed forcings")); +- console.log(sprintf("%19s: %-22s -- %s","materials" ,"[1x1 " + typeof(this.materials) + "]","material properties")); +- console.log(sprintf("%19s: %-22s -- %s","damage" ,"[1x1 " + typeof(this.damage) + "]","parameters for damage evolution solution")); +- console.log(sprintf("%19s: %-22s -- %s","friction" ,"[1x1 " + typeof(this.friction) + "]","basal friction/drag properties")); +- console.log(sprintf("%19s: %-22s -- %s","flowequation" ,"[1x1 " + typeof(this.flowequation) + "]","flow equations")); +- console.log(sprintf("%19s: %-22s -- %s","timestepping" ,"[1x1 " + typeof(this.timestepping) + "]","time stepping for trans models")); +- console.log(sprintf("%19s: %-22s -- %s","initialization" ,"[1x1 " + typeof(this.initialization) + "]","initial guess/state")); +- console.log(sprintf("%19s: %-22s -- %s","rifts" ,"[1x1 " + typeof(this.rifts) + "]","rifts properties")); +- console.log(sprintf("%19s: %-22s -- %s","slr" ,"[1x1 " + typeof(this.slr) + "]","slr forcings")); +- console.log(sprintf("%19s: %-22s -- %s","debug" ,"[1x1 " + typeof(this.debug) + "]","debugging tools (valgrind, gprof)")); +- console.log(sprintf("%19s: %-22s -- %s","verbose" ,"[1x1 " + typeof(this.verbose) + "]","verbosity level in solve")); +- console.log(sprintf("%19s: %-22s -- %s","settings" ,"[1x1 " + typeof(this.settings) + "]","settings properties")); +- console.log(sprintf("%19s: %-22s -- %s","toolkits" ,"[1x1 " + typeof(this.toolkits) + "]","PETSc options for each solution")); +- console.log(sprintf("%19s: %-22s -- %s","cluster" ,"[1x1 " + typeof(this.cluster) + "]","cluster parameters (number of cpus...)")); +- console.log(sprintf("%19s: %-22s -- %s","balancethickness","[1x1 " + typeof(this.balancethickness) + "]","parameters for balancethickness solution")); +- console.log(sprintf("%19s: %-22s -- %s","stressbalance" ,"[1x1 " + typeof(this.stressbalance) + "]","parameters for stressbalance solution")); +- console.log(sprintf("%19s: %-22s -- %s","groundingline" ,"[1x1 " + typeof(this.groundingline) + "]","parameters for groundingline solution")); +- console.log(sprintf("%19s: %-22s -- %s","hydrology" ,"[1x1 " + typeof(this.hydrology) + "]","parameters for hydrology solution")); +- console.log(sprintf("%19s: %-22s -- %s","masstransport" ,"[1x1 " + typeof(this.masstransport) + "]","parameters for masstransport solution")); +- console.log(sprintf("%19s: %-22s -- %s","thermal" ,"[1x1 " + typeof(this.thermal) + "]","parameters for thermal solution")); +- console.log(sprintf("%19s: %-22s -- %s","steadystate" ,"[1x1 " + typeof(this.steadystate) + "]","parameters for steadystate solution")); +- console.log(sprintf("%19s: %-22s -- %s","trans" ,"[1x1 " + typeof(this.trans) + "]","parameters for trans solution")); +- console.log(sprintf("%19s: %-22s -- %s","levelset" ,"[1x1 " + typeof(this.levelset) + "]","parameters for moving boundaries (level-set method)")); +- console.log(sprintf("%19s: %-22s -- %s","calving" ,"[1x1 " + typeof(this.calving) + "]","parameters for calving")); +- console.log(sprintf("%19s: %-22s -- %s","gia" ,"[1x1 " + typeof(this.gia) + "]","parameters for gia solution")); +- console.log(sprintf("%19s: %-22s -- %s","autodiff" ,"[1x1 " + typeof(this.autodiff) + "]","automatic differentiation parameters")); +- console.log(sprintf("%19s: %-22s -- %s","flaim" ,"[1x1 " + typeof(this.flaim) + "]","flaim parameters")); +- console.log(sprintf("%19s: %-22s -- %s","inversion" ,"[1x1 " + typeof(this.inversion) + "]","parameters for inverse methods")); +- console.log(sprintf("%19s: %-22s -- %s","qmu" ,"[1x1 " + typeof(this.qmu) + "]","dakota properties")); +- console.log(sprintf("%19s: %-22s -- %s","outputdefinition","[1x1 " + typeof(this.outputdefinition) + "]","output definition")); +- console.log(sprintf("%19s: %-22s -- %s","results" ,"[1x1 " + typeof(this.results) + "]","model results")); +- console.log(sprintf("%19s: %-22s -- %s","radaroverlay" ,"[1x1 " + typeof(this.radaroverlay) + "]","radar image for plot overlay")); +- console.log(sprintf("%19s: %-22s -- %s","miscellaneous" ,"[1x1 " + typeof(this.miscellaneous) + "]","miscellaneous fields")); +- } //}}} +- this.setdefaultparameters = function () { // {{{ +- +- //initialize subclasses +- this.mesh = new mesh2d(); +- this.mask = new mask(); +- this.constants = new constants(); +- this.geometry = new geometry(); +- this.initialization = new initialization(); +- this.smb = new SMBforcing(); +- this.basalforcings = new basalforcings(); +- this.friction = new friction(); +- this.rifts = new rifts(); +- this.slr = new slr(); +- this.timestepping = new timestepping(); +- this.groundingline = new groundingline(); +- this.materials = new matice(); +- this.damage = new damage(); +- this.flowequation = new flowequation(); +- this.debug = new debug(); +- this.verbose = new verbose(); +- this.settings = new settings(); +- this.toolkits = new toolkits(); +- this.cluster = new local(); +- this.balancethickness = new balancethickness(); +- this.stressbalance = new stressbalance(); +- this.hydrology = new hydrologyshreve(); +- this.masstransport = new masstransport(); +- this.thermal = new thermal(); +- this.steadystate = new steadystate(); +- this.trans = new trans(); +- this.levelset = new levelset(); +- this.calving = new calving(); +- this.gia = new gia(); +- this.autodiff = new autodiff(); +- this.flaim = new flaim(); +- this.inversion = new inversion(); +- this.qmu = new qmu(); +- this.radaroverlay = new radaroverlay(); +- this.results = {}; +- this.outputdefinition = new outputdefinition(); +- this.miscellaneous = new miscellaneous(); +- this.priv = new priv(); +- } //}}} +- this.checkmessage = function(string){ //{{{ +- console.log('model not consistent: ' + string); +- md.private.isconsistent=false; +- } //}}} +- this.fix = function(){ //{{{ +- +- for (var field in this){ +- +- //Some properties do not need to be fixed +- if (field == 'results' | field =='radaroverlay' | field == 'toolkits' | field =='cluster' | field == 'flaim' | field == 'priv') continue; +- +- //Check that current field is a class +- if(typeof this[field] == 'function'){ +- continue; +- } +- +- //Fix current object +- this[field].fix(this); +- } +- +- } //}}} +- //properties +- // {{{ +- //Careful here: no other class should be used as default value this is a bug of matlab +- this.mesh = 0; +- this.mask = 0; +- +- this.geometry = 0; +- this.constants = 0; +- this.smb = 0; +- this.basalforcings = 0; +- this.materials = 0; +- this.damage = 0; +- this.friction = 0; +- this.flowequation = 0; +- this.timestepping = 0; +- this.initialization = 0; +- this.rifts = 0; +- this.slr = 0; +- +- this.debug = 0; +- this.verbose = 0; +- this.settings = 0; +- this.toolkits = 0; +- this.cluster = 0; +- +- this.balancethickness = 0; +- this.stressbalance = 0; +- this.groundingline = 0; +- this.hydrology = 0; +- this.masstransport = 0; +- this.thermal = 0; +- this.steadystate = 0; +- this.trans = 0; +- this.levelset = 0; +- this.calving = 0; +- this.gia = 0; +- +- this.autodiff = 0; +- this.flaim = 0; +- this.inversion = 0; +- this.qmu = 0; +- +- this.results = 0; +- this.outputdefinition = 0; +- this.radaroverlay = 0; +- this.miscellaneous = 0; +- this.priv = 0; +- +- //set default values for fields +- this.setdefaultparameters(); +- +- //}}} +-} +-//OUTPUTDEFINITION class definition +-// +-// Usage: +-// outputdefinition=new outputdefinition(); +- +-function outputdefinition (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- this.definitions=[]; +- }// }}} +- this.disp= function(){// {{{ +- console.log(sprintf(' outputdefinition:')); +- fielddisplay(this,'definitions','list of potential outputs that can be requested, but which need additional data to be defined'); +- +- +- }// }}} +- this.classname= function(){// {{{ +- return "outputdefinition"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { //{{{ +- +- checkfield(md,'fieldname','outputdefinition.definitions','cell',1); +- +- for (var i=0;inumberofplots){ +- throw Error(sprintf("%s%s%s%i%s\n",'plotoptions error message: ',field,' cannot be assigned (',plotnum,' exceeds maximum number of plot)')); +- } +- list[Number(plotnum)-1].addfield(field,rawlist[i][1]); +- } +- } +- } +- else{ //assign option field to corresponding subplot +- +- +- //go through all subplot and assign to the first one free +- var inc=0; +- +- while (incnumberofplots-1){ +- console.log(sprintf("%s%s%s\n",'plot info message: too many ',rawlist[i][0],' options')); +- } +- } +- } +- +- //check that there is no duplicates +- for (var i=0;i=2){ +- //We have segments with rift markers, but no rift structure! +- md.checkmessage(['model should be processed for rifts (run meshprocessrifts)!']); +- break; +- } +- } +- for (var i=0;i=',1); +- md = checkfield(md,'fieldname','slr.degacc','size',[1, 1],'>=',1e-10); +- md = checkfield(md,'fieldname','slr.requested_outputs','stringrow',1); +- +- //check that love numbers are provided at the same level of accuracy: +- if (this.love_h.length != this.love_k.length){ +- throw Error('slr error message: love numbers should be provided at the same level of accuracy'); +- } +- +- } // }}} +- this.defaultoutputs = function(md){ // {{{ +- return ['Sealevel']; +- }//}}} +- this.classname= function(){// {{{ +- return "slr"; +- }// }}} +- this.disp= function(){// {{{ +- +- console.log(sprintf(' Sealevelrise solution parameters:')); +- +- fielddisplay(this,'deltathickness','thickness change (main loading of the slr solution core [m]'); +- fielddisplay(this,'sealevel','current sea level (prior to computation) [m]'); +- fielddisplay(this,'reltol','sea level rise relative convergence criterion, (default, NaN: not applied)'); +- fielddisplay(this,'abstol','sea level rise absolute convergence criterion, NaN: not applied'); +- fielddisplay(this,'maxiter','maximum number of nonlinear iterations'); +- fielddisplay(this,'love_h','love load number for radial displacement'); +- fielddisplay(this,'love_k','love load number for gravitational potential perturbation'); +- fielddisplay(this,'tide_love_h','tidal love number (degree 2)'); +- fielddisplay(this,'tide_love_k','tidal love number (degree 2)'); +- fielddisplay(this,'rigid','rigid earth graviational potential perturbation'); +- fielddisplay(this,'elastic','elastic earth graviational potential perturbation'); +- fielddisplay(this,'rotation','rotational earth potential perturbation'); +- fielddisplay(this,'degacc',"accuracy (default .01 deg) for numerical discretization of the Green's functions"); +- fielddisplay(this,'transitions','indices into parts of the mesh that will be icecaps'); +- fielddisplay(this,'requested_outputs','additional outputs requested'); +- } //}}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- WriteData(fid,prefix,'object',this,'fieldname','deltathickness','format','DoubleMat','mattype',2); +- WriteData(fid,prefix,'object',this,'fieldname','sealevel','mattype',1,'format','DoubleMat','enum',SealevelEnum(),'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'fieldname','reltol','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','abstol','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','maxiter','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','love_h','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','love_k','format','DoubleMat','mattype',1); +- WriteData(fid,prefix,'object',this,'fieldname','tide_love_h','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','tide_love_k','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','rigid','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','elastic','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','rotation','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','degacc','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','transitions','format','MatArray'); +- +- //process requested outputs +- var outputs = this.requested_outputs; +- for (var i=0;i=',1); +- checkfield(md,'fieldname','settings.recording_frequency','numel',[1],'>=',0); +- checkfield(md,'fieldname','settings.waitonlock','numel',[1]); +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'object',this,'fieldname','results_on_nodes','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','io_gather','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','lowmem','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','output_frequency','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','recording_frequency','format','Integer'); +- if (this.waitonlock>0) WriteData(fid,prefix,'name','md.settings.waitonlock','data',true,'format','Boolean'); +- else WriteData(fid,prefix,'name','md.settings.waitonlock','data',false,'format','Boolean'); +- }//}}} +- this.fix=function() { //{{{ +- }//}}} +- //properties +- // {{{ +- this.results_on_nodes = 0; +- this.io_gather = 0; +- this.lowmem = 0; +- this.output_frequency = 0; +- this.recording_frequency = 0; +- this.waitonlock = 0; +- this.upload_server = ''; +- this.upload_path = ''; +- this.upload_login = ''; +- this.upload_port = 0; +- this.upload_filename = ''; +- this.setdefaultparameters(); +- //}}} +-} +-//SMBforcing Class definition +-// +-// Usage: +-// SMB=SMBforcing(); +- +-function SMBforcing(){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- this.requested_outputs=['default']; +- } // }}} +- this.disp = function(){ // {{{ +- console.log(sprintf(' surface forcings parameters:')); +- fielddisplay(this,'mass_balance','surface mass balance [m/yr ice eq]'); +- fielddisplay(this,'requested_outputs','additional outputs requested'); +- } // }}} +- this.defaultoutputs = function(){ // {{{ +- return ''; +- }//}}} +- this.classname = function(){ // {{{ +- return "SMBforcing"; +- } // }}} +- this.extrude = function(md) {//{{{ +- this.mass_balance=project3d(md,'vector',this.mass_balance,'type','node'); +- }//}}} +- this.initialize = function(md) {// {{{ +- +- if (isNaN(this.mass_balance)){ +- this.mass_balance=NewArrayFill(md.mesh.numberofvertices,0); +- console.log(' no smb.mass_balance specified: values set as zero'); +- } +- +- } // }}} +- this.checkconsistency = function(md,solution,analyses) { //{{{ +- +- if(ArrayAnyEqual(ArrayIsMember(MasstransportAnalysisEnum(),analyses),1)){ +- checkfield(md,'fieldname','smb.mass_balance','timeseries',1,'NaN',1,'Inf',1); +- } +- if(ArrayAnyEqual(ArrayIsMember(BalancethicknessAnalysisEnum(),analyses),1)){ +- checkfield(md,'fieldname','smb.mass_balance','size',[md.mesh.numberofvertices,1],'NaN',1,'Inf',1); +- } +- checkfield(md,'fieldname','smb.requested_outputs','stringrow',1); +- +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- var yts=365.0*24.0*3600.0; +- +- WriteData(fid,prefix,'name','md.smb.model','data',SMBforcingEnum(),'format','Integer'); +- WriteData(fid,prefix,'object',this,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1); +- +- //process requested outputs +- var outputs = this.requested_outputs.slice(); +- for (var i=0;i',0,'NaN',1,'Inf',1); +- checkfield(md,'fieldname','stressbalance.reltol','size',[1, 1]); +- checkfield(md,'fieldname','stressbalance.abstol','size',[1, 1]); +- checkfield(md,'fieldname','stressbalance.isnewton','numel',[1],'values',[0, 1, 2]); +- checkfield(md,'fieldname','stressbalance.FSreconditioning','size',[1, 1],'NaN',1,'Inf',1); +- checkfield(md,'fieldname','stressbalance.viscosity_overshoot','size',[1, 1],'NaN',1,'Inf',1); +- checkfield(md,'fieldname','stressbalance.maxiter','size',[1, 1],'>=',1); +- checkfield(md,'fieldname','stressbalance.referential','size',[md.mesh.numberofvertices, 6]); +- checkfield(md,'fieldname','stressbalance.loadingforce','size',[md.mesh.numberofvertices, 3]); +- checkfield(md,'fieldname','stressbalance.requested_outputs','stringrow',1); +- +- //singular solution +- if(!ArrayAnyNaN(md.stressbalance.spcvx) | !ArrayAnyNaN(md.stressbalance.spcvy) | !ArrayAnyAboveStrict(md.mask.groundedice_levelset,0)){ +- md = checkmessage(md,'model is not well posed (singular). You need at least one node with fixed velocity!'); +- console.log(sprintf('\n !!! Warning: no spc applied, model might not be well posed if no basal friction is applied, check for solution crash\n')); +- } +- //CHECK THAT EACH LINES CONTAINS ONLY NAN VALUES OR NO NAN VALUES +- for(var i=0;iMath.pow(10,-18)){ +- md.checkmessage('Vectors in stressbalance.referential (columns 1 to 3 and 4 to 6) must be orthogonal'); +- break; +- } +- } +- } +- //CHECK THAT NO rotation specified for FS Grounded ice at base +- if (md.mesh.domaintype() == '3D' & md.flowequation.isFS){ +- for(var i=0;i0 & md.mesh.vertexonbase[i]){ +- if(!ArrayIsNan(md.stressbalance.referential[i])){ +- md.checkmessage('no referential should be specified for basal vertices of grounded ice'); +- break; +- } +- } +- } +- checkfield(md,'fieldname','stressbalance.FSreconditioning','>',0); +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','vertex_pairing','format','DoubleMat','mattype',3); +- +- var yts=365.0*24.0*3600.0; +- +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','spcvx','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','spcvy','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','spcvz','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','restol','format','Double'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','reltol','format','Double'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','abstol','format','Double','scale',1./yts); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','isnewton','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','FSreconditioning','format','Double'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','viscosity_overshoot','format','Double'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','maxiter','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','shelf_dampening','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','penalty_factor','format','Double'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','rift_penalty_lock','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','rift_penalty_threshold','format','Integer'); +- WriteData(fid,prefix,'object',this,'class','stressbalance','fieldname','referential','format','DoubleMat','mattype',1); +- +- var lx=NewArrayFill(this.loadingforce.length,0); for(var i=0;i',0.,'message','reltol must be larger than zero'); +- } +- checkfield(md,'fieldname','thermal.requested_outputs','stringrow',1); +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'object',this,'fieldname','spctemperature','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'fieldname','penalty_threshold','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','stabilization','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','reltol','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','maxiter','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','penalty_lock','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','penalty_factor','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','isenthalpy','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isdynamicbasalspc','format','Boolean'); +- +- //process requested outputs +- var outputs = this.requested_outputs; +- for (var i=0;i=',0,'NaN',1,'Inf',1); +- checkfield(md,'fieldname','timestepping.time_adapt','numel',[1],'values',[0,1]); +- checkfield(md,'fieldname','timestepping.cfl_coefficient','numel',[1],'>',0,'<=',1); +- checkfield(md,'fieldname','timestepping.interp_forcings','numel',[1],'values',[0,1]); +- if (this.final_time-this.start_time<0){ +- md.checkmessage('timestepping.final_time should be larger than timestepping.start_time'); +- } +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- var scale; +- scale = 365.0*24.0*3600.0; +- +- WriteData(fid,prefix,'object',this,'fieldname','start_time','format','Double','scale',scale); +- WriteData(fid,prefix,'object',this,'fieldname','final_time','format','Double','scale',scale); +- WriteData(fid,prefix,'object',this,'fieldname','time_step','format','Double','scale',scale); +- WriteData(fid,prefix,'object',this,'fieldname','time_adapt','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','cfl_coefficient','format','Double'); +- WriteData(fid,prefix,'object',this,'fieldname','interp_forcings','format','Boolean'); +- +- }//}}} +- this.fix=function() { //{{{ +- }//}}} +- //properties +- // {{{ +- this.start_time = 0.; +- this.final_time = 0.; +- this.time_step = 0.; +- this.time_adapt = 0; +- this.cfl_coefficient = 0.; +- this.interp_forcings = 1; +- +- this.setdefaultparameters(); +- //}}} +-} +-//TOOLKITS class definition +-// +-// Usage: +-// toolkits=new toolkits(); +- +-function toolkits (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- +- //default toolkits: +- if (IssmConfig('_HAVE_PETSC_')){ +- //MUMPS is the default toolkits +- if (IssmConfig('_HAVE_MUMPS_')){ +- this.DefaultAnalysis = mumpsoptions(); +- } +- else{ +- this.DefaultAnalysis = iluasmoptions(); +- } +- } +- else{ +- if (IssmConfig('_HAVE_MUMPS_')){ +- this.DefaultAnalysis = issmmumpssolver(); +- } +- else if (IssmConfig('_HAVE_GSL_')){ +- this.DefaultAnalysis = issmgslsolver(); +- } +- else{ +- console.warn('toolkits setdefaultparameters message: need at least Mumps or Gsl to define an issm solver type, no default solver assigned'); +- } +- } +- }// }}} +- this.disp = function(){// {{{ +- console.log(sprintf('List of toolkits options per analysis:\n')); +- for(var prop in this){ +- if(typeof this[prop] == 'object'){ +- console.log(prop+ ':',this[prop]); +- } +- } +- }// }}} +- this.checkconsistency = function (md,solution,analyses) { // {{{ +- for(var prop in this){ +- if(typeof this[prop] == 'object'){ +- if (this[prop] == ''){ +- md.checkmessage(sprintf("md.toolkits.%s is empty",prop)); +- } +- } +- } +- } // }}} +- this.ToolkitsFile = function(filename) { //{{{ +- //TOOLKITSFILE - build toolkits file (in string format) +- // +- // Build a Petsc compatible options string, from the toolkits model field + return options string. +- // This file string will also be used when the toolkit used is 'issm' instead of 'petsc' +- // +- // Usage: var toolkitsstring = toolkits.ToolkitsFile(); +- +- var string = ''; +- +- //write header +- string += sprintf('%s%s%s\n','\%Toolkits options file: ',filename,' written from Javascript toolkits array'); +- +- //start writing options +- for (var analysis in this){ +- var options; +- +- if(typeof this[analysis] == 'object') options=this[analysis]; else continue; +- +- //first write analysis: +- string += sprintf('\n+%s\n',analysis); //append a + to recognize it's an analysis enum +- +- //now, write options +- +- for(var optionname in options){ +- var optionvalue=options[optionname]; +- +- if (optionvalue.length==0){ +- //this option has only one argument +- string+=sprintf('-%s\n',optionname); +- } +- else{ +- //option with value. value can be string or scalar +- if (typeof optionvalue == 'number'){ +- string+=sprintf('-%s %g\n',optionname,optionvalue); +- } +- else if (typeof optionvalue == 'string'){ +- string+=sprintf('-%s %s\n',optionname,optionvalue); +- } +- else throw Error(sprintf("ToolkitsFile error: option '%s' is not well formatted",optionname)); +- } +- } +- } +- return string; +- } //}}} +- //properties +- // {{{ +- this.DefaultAnalysis = []; +- //The other properties are dynamic +- this.setdefaultparameters(); +- //}}} +-} +-//LEVELSET class definition +-// +-// Usage: +-// levelset=new levelset(); +- +-function levelset (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- +- //stabilization = 2 by default +- this.stabilization = 2; +- this.reinit_frequency = NaN; +- +- }// }}} +- this.disp= function(){// {{{ +- +- console.log(sprintf(' Level-set parameters:')); +- fielddisplay(this,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding'); +- fielddisplay(this,'spclevelset','Levelset constraints (NaN means no constraint)'); +- fielddisplay(this,'reinit_frequency','Amount of time steps after which the levelset function in re-initialized (NaN: no re-initialization).'); +- +- }// }}} +- this.classname= function(){// {{{ +- return "levelset"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { // {{{ +- //Early return +- if (solution!=TransientSolutionEnum() | md.trans.ismovingfront==0) return; +- +- checkfield(md,'fieldname','levelset.spclevelset','Inf',1,'timeseries',1); +- checkfield(md,'fieldname','levelset.stabilization','values',[0,1,2]); +- } //}}} +- this.marshall=function(md,prefix,fid) { //{{{ +- WriteData(fid,prefix,'object',this,'fieldname','stabilization','format','Integer'); +- WriteData(fid,prefix,'object',this,'fieldname','spclevelset','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1); +- WriteData(fid,prefix,'object',this,'fieldname','reinit_frequency','format','Integer'); +- +- }//}}} +- this.fix=function() { //{{{ +- this.spclevelset=NullFix(this.spclevelset,NaN); +- }//}}} +- //properties +- // {{{ +- +- this.stabilization = 0; +- this.spclevelset = NaN; +- this.reinit_frequency = NaN; +- +- this.setdefaultparameters(); +- //}}} +-} +-//TRANS class definition +-// +-// Usage: +-// trans =new trans(); +- +-function trans (){ +- //methods +- this.setdefaultparameters = function(){// {{{ +- +- //full analysis: Stressbalance, Masstransport and Thermal but no groundingline migration for now +- this.issmb = 1; +- this.ismasstransport = 1; +- this.isstressbalance = 1; +- this.isthermal = 1; +- this.isgroundingline = 0; +- this.isgia = 0; +- this.isdamageevolution = 0; +- this.ismovingfront = 0; +- this.ishydrology = 0; +- this.isslr = 0; +- this.iscoupler = 0; +- +- //default output +- this.requested_outputs=['default']; +- +- }// }}} +- this.disp= function(){// {{{ +- +- console.log(sprintf(' transient solution parameters:')); +- +- fielddisplay(this,'issmb','indicates whether a surface mass balance solution is used in the transient'); +- fielddisplay(this,'ismasstransport','indicates whether a masstransport solution is used in the transient'); +- fielddisplay(this,'isstressbalance','indicates whether a stressbalance solution is used in the transient'); +- fielddisplay(this,'isthermal','indicates whether a thermal solution is used in the transient'); +- fielddisplay(this,'isgroundingline','indicates whether a groundingline migration is used in the transient'); +- fielddisplay(this,'isgia','indicates whether a postglacial rebound model is used in the transient'); +- fielddisplay(this,'isdamageevolution','indicates whether damage evolution is used in the transient'); +- fielddisplay(this,'ismovingfront','indicates whether a moving front capability is used in the transient'); +- fielddisplay(this,'ishydrology','indicates whether an hydrology model is used'); +- fielddisplay(this,'isslr','indicates whether a sea-level rise model is used'); +- fielddisplay(this,'iscoupler','indicates whether different models are being run with need for coupling'); +- fielddisplay(this,'requested_outputs','list of additional outputs requested'); +- +- +- }// }}} +- this.classname= function(){// {{{ +- return "transient"; +- }// }}} +- this.checkconsistency = function(md,solution,analyses) { // {{{ +- +- //Early return +- if (solution!=TransientSolutionEnum()) return; +- +- checkfield(md,'fieldname','trans.issmb','numel',[1],'values',[0 ,1]); +- checkfield(md,'fieldname','trans.ismasstransport','numel',[1],'values',[0 ,1]); +- checkfield(md,'fieldname','trans.isstressbalance','numel',[1],'values',[0 ,1]); +- checkfield(md,'fieldname','trans.isthermal','numel',[1],'values',[0 ,1]); +- checkfield(md,'fieldname','trans.isgroundingline','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','trans.isgia','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','trans.isdamageevolution','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','trans.ismovingfront','numel',[1],'values',[0, 1]); +- checkfield(md,'fieldname','trans.ishydrology','numel',[1],'values',[0 ,1]); +- checkfield(md,'fieldname','trans.iscoupler','numel',[1],'values',[0 ,1]); +- checkfield(md,'fieldname','trans.isslr','numel',[1],'values',[0 ,1]); +- checkfield(md,'fieldname','trans.requested_outputs','stringrow',1); +- } // }}} +- this.marshall=function(md,prefix,fid) { //{{{ +- +- prefix='md.transient'; +- WriteData(fid,prefix,'object',this,'fieldname','issmb','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','ismasstransport','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isstressbalance','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isthermal','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isgroundingline','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isgia','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isdamageevolution','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','ishydrology','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','ismovingfront','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','isslr','format','Boolean'); +- WriteData(fid,prefix,'object',this,'fieldname','iscoupler','format','Boolean'); +- +- //process requested outputs +- var outputs = this.requested_outputs; +- for (var i=0;i: greater than provided value +-// - >=: greater or equal to provided value +-// - <: smallerthan provided value +-// - <=: smaller or equal to provided value +-// - < vec: smallerthan provided values on each vertex +-// - timeseries: 1 if check time series consistency (size and time) +-// - values: array of strings or vector of acceptable values +-// - numel: list of acceptable number of elements +-// - array: 1 if check that is array +-// - empty: 1 if check that non empty +-// - message: overloaded error message +-// +-// Usage: +-// checkfield(md,fieldname,options); +- +- //get options +- var args = Array.prototype.slice.call(arguments); +- var options = new pairoptions(args.slice(1,args.length)); +- +- //get field: +- if (options.exist('field')){ +- field=options.getfieldvalue('field'); +- fieldname=options.getfieldvalue('fieldname','no fieldname'); +- } +- else{ +- fieldname=options.getfieldvalue('fieldname'); +- eval("field=md." + fieldname + ";"); +- } +- +- //check empty +- if (options.exist('empty')){ +- if (field.length == 0){ +- md.checkmessage(options.getfieldvalue('message','field ' + "'" + fieldname + "'" + 'is empty')); +- } +- } +- +- //Check size +- if (options.exist('size')){ +- fieldsize=options.getfieldvalue('size'); +- if (isNaN(fieldsize[0])){ +- if (field[0].length !=fieldsize[1]){ +- md.checkmessage(options.getfieldvalue('message', sprintf("field '%s' should have %i columns",fieldname,fieldsize[1]))); +- } +- } +- else if (isNaN(fieldsize[1])){ +- if (field.length!= fieldsize[0]){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' should have %i lines",fieldname,fieldsize[0]))); +- } +- } +- else{ +- if (IsArray(field)){ +- if ((field.length!=fieldsize[0])){ +- md.checkmessage(options.getfieldvalue('message', sprintf("field '%s' should be %ix%i",fieldname,fieldsize[0],fieldsize[1]))); +- } +- } +- if (IsArray(field[0])){ +- if(field[0].length!=fieldsize[1]){ +- md.checkmessage(options.getfieldvalue('message', sprintf("field '%s' should be %ix%i",fieldname,fieldsize[0],fieldsize[1]))); +- } +- } +- } +- } +- +- //Check numel +- if (options.exist('numel')){ +- fieldnumel=options.getfieldvalue('numel'); +- if (!ArrayIsMember(fieldnumel,[field.length])){ +- if (fieldnumel.length==1){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' size should be %i",fieldname,fieldnumel[0]))); +- } +- else if (fieldnumel.length==2){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' size should be %i or %i",fieldname,fieldnumel[0],fieldnumel[1]))); +- } +- else{ +- var string=''; +- for (var i=0;i=')){ +- lowerbound=options.getfieldvalue('>='); +- field2=MatrixToList(field); +- if (options.getfieldvalue('timeseries',0)) field2=MatrixToList(ArrayCopy(field).splice(-1,1)); +- +- if (ArrayAnyBelowStrict(field2,lowerbound)){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' should have values above %g",fieldname,lowerbound))); +- } +- } +- if (options.exist('>')){ +- lowerbound=options.getfieldvalue('>'); +- field2=MatrixToList(field); +- if (options.getfieldvalue('timeseries',0)) field2=MatrixToList(ArrayCopy(field).splice(-1,1)); +- +- if (ArrayAnyBelowOrEqual(field2,lowerbound)){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' should have values above %g",fieldname,lowerbound))); +- } +- } +- +- //check smaller +- if (options.exist('<=')){ +- upperbound=options.getfieldvalue('<='); +- field2=MatrixToList(field); +- if (options.getfieldvalue('timeseries',0)) field2=MatrixToList(ArrayCopy(field).splice(-1,1)); +- +- if (ArrayAnyAboveOrEqual(field2,upperbound)){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' should have values below %g",fieldname,upperbound))); +- } +- } +- +- +- if (options.exist('<')){ +- upperbound=options.getfieldvalue('<'); +- field2=MatrixToList(field); +- if (options.getfieldvalue('timeseries',0)) field2=MatrixToList(ArrayCopy(field).splice(-1,1)); +- if (ArrayAnyAboveStrict(field2,upperbound)){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' should have values below %g",fieldname,upperbound))); +- } +- } +- +- //Check row of stringrow +- if (options.getfieldvalue('stringrow',0)){ +- if (IsArray(field[0])){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' should have only one row",field))); +- } +- if (!IsArray(field)){ +- md.checkmessage(options.getfieldvalue('message',sprintf("field '%s' should be an array of string",fieldname))); +- } +- else{ +- for(var i=0;i=this.buffer.byteLength)this.resize(); +- this.view.setUint32(this.ptr,value,true); this.ptr+=4; +- } +- else if(format == 'char'){ +- if(this.ptr+value.length>=this.buffer.byteLength)this.resize(); +- for(var i=0;i=this.buffer.byteLength)this.resize(); +- if (!IsArray(value)){ +- this.view.setFloat64(this.ptr,value,true); +- this.ptr+=8; +- } +- else{ +- if (!IsArray(value[0])){ +- if(this.ptr+value.length*8>=this.buffer.byteLength){ +- this.resize(); +- if(this.ptr+value.length*8>=this.buffer.byteLength)throw Error('fileptr.fwrite error: need to increase increment size!'); +- } +- for(var i=0;i=this.buffer.byteLength)this.resize(); +- for(var i=0;i 30){ +- displayunit(offset,name,"not displayed",comment); +- } +- else{ +- displayunit(offset,name,"'"+field+"'",comment); +- } +- } +- //numeric +- else if (typeof(field) == "number"){ +- +- displayunit(offset,name,sprintf("%g",field),comment); +- +- } +- //logical +- else if (typeof(field) == "boolean") { +- +- if (field){ +- displayunit(offset,name,"true",comment); +- } +- else{ +- displayunit(offset,name,"false",comment); +- } +- +- } +- //object +- else if (typeof(field) == "object"){ +- +- if(field.length == 0) displayunit(offset,name,sprintf("(%i)",field.length),comment); +- else if ((field[0].length==0) | (typeof field[0].length =='undefined')){ +- displayunit(offset,name,sprintf("(%i)",field.length),comment); +- } +- else{ +- displayunit(offset,name,sprintf("(%i,%i)",field.length,field[0].length),comment); +- } +- +- } +- else{ +- displayunit(offset,name,"not displayed",comment); +- } +-} //}}} +- +-function displayunit(offset,name,characterization,comment){ // {{{ +- +- //take care of name +- if (name.length>23){ +- name=name.slice(0,21) + "..."; +- } +- +- //take care of characterization +- if ( characterization == "\" \"" || characterization == "NaN" ){ +- +- characterization="N/A"; +- } +- if (characterization.length>15){ +- characterization=characterization.slice(0,13) + "..."; +- } +- +- //print +- if (comment.length==0){ +- console.log(sprintf("%s%-23s: %-15s",offset,name,characterization)); +- } +- else{ +- if (typeof(comment) == "string"){ +- //console.log(sprintf("%s%-23s: %-15s -- %s",offset,name,characterization,comment)); +- console.log(sprintf("%s%s: %-15s -- %s",offset,name,characterization,comment)); +- } +- else{ +- throw Error("fielddisplay error message: format for comment not supported yet"); +- } +- } +-} //}}} +-/** +- * A class to parse color values +- * @author Stoyan Stefanov +- * @link http://www.phpied.com/rgb-color-parser-in-javascript/ +- * @license Use it if you like it +- */ +-function RGBColor(color_string) +-{ +- this.ok = false; +- +- // strip any leading # +- if (color_string.charAt(0) == '#') { // remove # if any +- color_string = color_string.substr(1,6); +- } +- +- color_string = color_string.replace(/ /g,''); +- color_string = color_string.toLowerCase(); +- +- // before getting into regexps, try simple matches +- // and overwrite the input +- var simple_colors = { +- aliceblue: 'f0f8ff', +- antiquewhite: 'faebd7', +- aqua: '00ffff', +- aquamarine: '7fffd4', +- azure: 'f0ffff', +- beige: 'f5f5dc', +- bisque: 'ffe4c4', +- black: '000000', +- blanchedalmond: 'ffebcd', +- blue: '0000ff', +- blueviolet: '8a2be2', +- brown: 'a52a2a', +- burlywood: 'deb887', +- cadetblue: '5f9ea0', +- chartreuse: '7fff00', +- chocolate: 'd2691e', +- coral: 'ff7f50', +- cornflowerblue: '6495ed', +- cornsilk: 'fff8dc', +- crimson: 'dc143c', +- cyan: '00ffff', +- darkblue: '00008b', +- darkcyan: '008b8b', +- darkgoldenrod: 'b8860b', +- darkgray: 'a9a9a9', +- darkgreen: '006400', +- darkkhaki: 'bdb76b', +- darkmagenta: '8b008b', +- darkolivegreen: '556b2f', +- darkorange: 'ff8c00', +- darkorchid: '9932cc', +- darkred: '8b0000', +- darksalmon: 'e9967a', +- darkseagreen: '8fbc8f', +- darkslateblue: '483d8b', +- darkslategray: '2f4f4f', +- darkturquoise: '00ced1', +- darkviolet: '9400d3', +- deeppink: 'ff1493', +- deepskyblue: '00bfff', +- dimgray: '696969', +- dodgerblue: '1e90ff', +- feldspar: 'd19275', +- firebrick: 'b22222', +- floralwhite: 'fffaf0', +- forestgreen: '228b22', +- fuchsia: 'ff00ff', +- gainsboro: 'dcdcdc', +- ghostwhite: 'f8f8ff', +- gold: 'ffd700', +- goldenrod: 'daa520', +- gray: '808080', +- green: '008000', +- greenyellow: 'adff2f', +- honeydew: 'f0fff0', +- hotpink: 'ff69b4', +- indianred : 'cd5c5c', +- indigo : '4b0082', +- ivory: 'fffff0', +- khaki: 'f0e68c', +- lavender: 'e6e6fa', +- lavenderblush: 'fff0f5', +- lawngreen: '7cfc00', +- lemonchiffon: 'fffacd', +- lightblue: 'add8e6', +- lightcoral: 'f08080', +- lightcyan: 'e0ffff', +- lightgoldenrodyellow: 'fafad2', +- lightgrey: 'd3d3d3', +- lightgreen: '90ee90', +- lightpink: 'ffb6c1', +- lightsalmon: 'ffa07a', +- lightseagreen: '20b2aa', +- lightskyblue: '87cefa', +- lightslateblue: '8470ff', +- lightslategray: '778899', +- lightsteelblue: 'b0c4de', +- lightyellow: 'ffffe0', +- lime: '00ff00', +- limegreen: '32cd32', +- linen: 'faf0e6', +- magenta: 'ff00ff', +- maroon: '800000', +- mediumaquamarine: '66cdaa', +- mediumblue: '0000cd', +- mediumorchid: 'ba55d3', +- mediumpurple: '9370d8', +- mediumseagreen: '3cb371', +- mediumslateblue: '7b68ee', +- mediumspringgreen: '00fa9a', +- mediumturquoise: '48d1cc', +- mediumvioletred: 'c71585', +- midnightblue: '191970', +- mintcream: 'f5fffa', +- mistyrose: 'ffe4e1', +- moccasin: 'ffe4b5', +- navajowhite: 'ffdead', +- navy: '000080', +- oldlace: 'fdf5e6', +- olive: '808000', +- olivedrab: '6b8e23', +- orange: 'ffa500', +- orangered: 'ff4500', +- orchid: 'da70d6', +- palegoldenrod: 'eee8aa', +- palegreen: '98fb98', +- paleturquoise: 'afeeee', +- palevioletred: 'd87093', +- papayawhip: 'ffefd5', +- peachpuff: 'ffdab9', +- peru: 'cd853f', +- pink: 'ffc0cb', +- plum: 'dda0dd', +- powderblue: 'b0e0e6', +- purple: '800080', +- red: 'ff0000', +- rosybrown: 'bc8f8f', +- royalblue: '4169e1', +- saddlebrown: '8b4513', +- salmon: 'fa8072', +- sandybrown: 'f4a460', +- seagreen: '2e8b57', +- seashell: 'fff5ee', +- sienna: 'a0522d', +- silver: 'c0c0c0', +- skyblue: '87ceeb', +- slateblue: '6a5acd', +- slategray: '708090', +- snow: 'fffafa', +- springgreen: '00ff7f', +- steelblue: '4682b4', +- tan: 'd2b48c', +- teal: '008080', +- thistle: 'd8bfd8', +- tomato: 'ff6347', +- turquoise: '40e0d0', +- violet: 'ee82ee', +- violetred: 'd02090', +- wheat: 'f5deb3', +- white: 'ffffff', +- whitesmoke: 'f5f5f5', +- yellow: 'ffff00', +- yellowgreen: '9acd32' +- }; +- for (var key in simple_colors) { +- if (color_string == key) { +- color_string = simple_colors[key]; +- } +- } +- // emd of simple type-in colors +- +- // array of color definition objects +- var color_defs = [ +- { +- re: /^rgb\((\d{1,3}),\s*(\d{1,3}),\s*(\d{1,3})\)$/, +- example: ['rgb(123, 234, 45)', 'rgb(255,234,245)'], +- process: function (bits){ +- return [ +- parseInt(bits[1]), +- parseInt(bits[2]), +- parseInt(bits[3]) +- ]; +- } +- }, +- { +- re: /^(\w{2})(\w{2})(\w{2})$/, +- example: ['#00ff00', '336699'], +- process: function (bits){ +- return [ +- parseInt(bits[1], 16), +- parseInt(bits[2], 16), +- parseInt(bits[3], 16) +- ]; +- } +- }, +- { +- re: /^(\w{1})(\w{1})(\w{1})$/, +- example: ['#fb0', 'f0f'], +- process: function (bits){ +- return [ +- parseInt(bits[1] + bits[1], 16), +- parseInt(bits[2] + bits[2], 16), +- parseInt(bits[3] + bits[3], 16) +- ]; +- } +- } +- ]; +- +- // search through the definitions to find a match +- for (var i = 0; i < color_defs.length; i++) { +- var re = color_defs[i].re; +- var processor = color_defs[i].process; +- var bits = re.exec(color_string); +- if (bits) { +- channels = processor(bits); +- this.r = channels[0]; +- this.g = channels[1]; +- this.b = channels[2]; +- this.ok = true; +- } +- +- } +- +- // validate/cleanup values +- this.r = (this.r < 0 || isNaN(this.r)) ? 0 : ((this.r > 255) ? 255 : this.r); +- this.g = (this.g < 0 || isNaN(this.g)) ? 0 : ((this.g > 255) ? 255 : this.g); +- this.b = (this.b < 0 || isNaN(this.b)) ? 0 : ((this.b > 255) ? 255 : this.b); +- +- // some getters +- this.toRGB = function () { +- return 'rgb(' + this.r + ', ' + this.g + ', ' + this.b + ')'; +- } +- this.toHex = function () { +- var r = this.r.toString(16); +- var g = this.g.toString(16); +- var b = this.b.toString(16); +- if (r.length == 1) r = '0' + r; +- if (g.length == 1) g = '0' + g; +- if (b.length == 1) b = '0' + b; +- return '#' + r + g + b; +- } +- +- // help +- this.getHelpXML = function () { +- +- var examples = new Array(); +- // add regexps +- for (var i = 0; i < color_defs.length; i++) { +- var example = color_defs[i].example; +- for (var j = 0; j < example.length; j++) { +- examples[examples.length] = example[j]; +- } +- } +- // add type-in colors +- for (var sc in simple_colors) { +- examples[examples.length] = sc; +- } +- +- var xml = document.createElement('ul'); +- xml.setAttribute('id', 'rgbcolor-examples'); +- for (var i = 0; i < examples.length; i++) { +- try { +- var list_item = document.createElement('li'); +- var list_color = new RGBColor(examples[i]); +- var example_div = document.createElement('div'); +- example_div.style.cssText = +- 'margin: 3px; ' +- + 'border: 1px solid black; ' +- + 'background:' + list_color.toHex() + '; ' +- + 'color:' + list_color.toHex() +- ; +- example_div.appendChild(document.createTextNode('test')); +- var list_item_value = document.createTextNode( +- ' ' + examples[i] + ' -> ' + list_color.toRGB() + ' -> ' + list_color.toHex() +- ); +- list_item.appendChild(example_div); +- list_item.appendChild(list_item_value); +- xml.appendChild(list_item); +- +- } catch(e){} +- } +- return xml; +- +- } +- +-} +- +-function setflowequation(md){ +-//SETFLOWEQUATION - associate a solution type to each element +-// +-// This routine works like plotmodel: it works with an even number of inputs +-// 'SIA','SSA','L1L2','HO','FS' and 'fill' are the possible options +-// that must be followed by the corresponding exp file or flags list +-// It can either be a domain file (argus type, .exp extension), or an array of element flags. +-// If user wants every element outside the domain to be +-// setflowequationd, add '~' to the name of the domain file (ex: '~HO.exp'); +-// an empty string '' will be considered as an empty domain +-// a string 'all' will be considered as the entire domain +-// You can specify the type of coupling, 'penalties' or 'tiling', to use with the input 'coupling' +-// NB: L1L2 cannot currently be coupled to any other ice flow model +-// +-// Usage: +-// setflowequation(md,varargin) +-// +-// Example: +-// setflowequation(md,'HO',HO,'fill','SIA','coupling','tiling'); +- +- //some checks on list of arguments +- if(arguments.length<3) throw Error('setflowequation error message'); +- +- //Process options +- var args = Array.prototype.slice.call(arguments); +- var options = new pairoptions(args.slice(1,args.length)); +- options.deleteduplicates(1); +- +- //Find_out what kind of coupling to use +- coupling_method=options.getfieldvalue('coupling','tiling'); +- if ((coupling_method != 'tiling') & !(coupling_method != 'penalties')){ +- throw error('coupling type can only be: tiling or penalties'); +- } +- +- //recover elements distribution +- SIAflag = FlagElements(md,options.getfieldvalue('SIA','')); +- SSAflag = FlagElements(md,options.getfieldvalue('SSA','')); +- HOflag = FlagElements(md,options.getfieldvalue('HO','')); +- L1L2flag = FlagElements(md,options.getfieldvalue('L1L2','')); +- FSflag = FlagElements(md,options.getfieldvalue('FS','')); +- filltype = options.getfieldvalue('fill','none'); +- options.displayunused(); +- +- //Flag the elements that have not been flagged as filltype +- if (filltype === 'SIA'){ +- for(var i=0;i3){ +- if (arguments[3]=='icedomain'){ +- icedomain=arguments[4]; +- } +- else{ +- throw Error('mask error message: wrong field specified. Only icedomain allowed for now.'); +- } +- if (IsArray(icedomain)){ +- throw Error('setmask error message: icedomain should be an array!'); +- } +- } +- +- //Get assigned fields +- var x=md.mesh.x; +- var y=md.mesh.y; +- var elements=md.mesh.elements; +- +- //Assign elementonfloatingice, elementongroundedice, vertexongroundedice and vertexonfloatingice. +- //Only change at your own peril! This is synchronized heavily with the GroundingLineMigration module. +- elementonfloatingice=FlagElements(md,floatingice); +- elementongroundedice=FlagElements(md,groundedice); +- +- //Because groundedice nodes and elements can be included into an floatingice, we need to update. Remember, all the previous +- //arrays come from domain outlines that can intersect one another: +- elementonfloatingice=ArrayAnd(elementonfloatingice,ArrayNot(elementongroundedice)); +- elementongroundedice=ArrayNot(elementonfloatingice); +- +- //the order here is important. we choose vertexongroundedice as default on the grounding line. +- vertexonfloatingice=NewArrayFill(md.mesh.numberofvertices,0); +- vertexongroundedice=NewArrayFill(md.mesh.numberofvertices,0); +- pos=ArrayFind(elementongroundedice,1); for (var i=0;i3){ +- md.mask.ice_levelset = NewArrayFill(md.mesh.numberofvertices,1.0); +- //use contourtomesh to set ice values inside ice domain +- //[vertexinsideicedomain,elementinsideicedomain]=ContourToMesh(elements,x,y,icedomain,'node',1); +- pos=ArrayFind(vertexinsideicedomain,1.0);for(var i=0;i