Index: /issm/trunk/examples/Greenland/runme.m
===================================================================
--- /issm/trunk/examples/Greenland/runme.m (revision 20547)
+++ /issm/trunk/examples/Greenland/runme.m (revision 20548)
@@ -1,4 +1,4 @@
clear all;
-steps=[1 2 3 4 5];
+steps=[1];
%Location of SeaRISE dataset
@@ -146,5 +146,5 @@
lat = ncread(ncbox,'lat');
lon = ncread(ncbox,'lon');
- smbbox = ncread(ncbox,'SMB');
+ smbbox = ncread(ncbox,'MassFlux');
[x1 y1]=ll2xy(lat,lon,+1,45,70);
Index: /issm/trunk/examples/ISMIP/CheatyRunme.m
===================================================================
--- /issm/trunk/examples/ISMIP/CheatyRunme.m (revision 20547)
+++ /issm/trunk/examples/ISMIP/CheatyRunme.m (revision 20548)
@@ -3,5 +3,5 @@
%step 8 is specific to ISMIPF
-steps=[1:7];
+steps=[1];
% parameter file to be used, choose between CheatyIsmipA.par or CheatyIsmipF.par
Index: /issm/trunk/examples/IceBridge/Greenland.par
===================================================================
--- /issm/trunk/examples/IceBridge/Greenland.par (revision 20547)
+++ /issm/trunk/examples/IceBridge/Greenland.par (revision 20548)
@@ -62,6 +62,6 @@
disp(' Interpolating surface mass balance');
-md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0);
-md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice;
+md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0);
+md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice;
disp(' Construct basal friction parameters');
Index: /issm/trunk/examples/IceBridge/Greenland_cheatsheet.par
===================================================================
--- /issm/trunk/examples/IceBridge/Greenland_cheatsheet.par (revision 20547)
+++ /issm/trunk/examples/IceBridge/Greenland_cheatsheet.par (revision 20548)
@@ -66,6 +66,6 @@
disp(' Interpolating surface mass balance');
-md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0);
-md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice;
+md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0);
+md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice;
disp(' Construct basal friction parameters');
Index: /issm/trunk/examples/IceBridge/Greenland_noOIB.par
===================================================================
--- /issm/trunk/examples/IceBridge/Greenland_noOIB.par (revision 20547)
+++ /issm/trunk/examples/IceBridge/Greenland_noOIB.par (revision 20548)
@@ -40,6 +40,6 @@
disp(' Interpolating surface mass balance');
-md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0);
-md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice;
+md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0);
+md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice;
disp(' Construct basal friction parameters');
Index: /issm/trunk/examples/IceBridge/runme.m
===================================================================
--- /issm/trunk/examples/IceBridge/runme.m (revision 20547)
+++ /issm/trunk/examples/IceBridge/runme.m (revision 20548)
@@ -46,5 +46,5 @@
md = setmask(md,'','');
- md = parameterize(md,'./Greenland_cheatsheet.par');
+ md = parameterize(md,'./Greenland.par');
%md = parameterize(md,'./Greenland_noOIB.par');
md = setflowequation(md,'SSA','all');
@@ -108,5 +108,5 @@
smb = InterpFromGridToMesh(x1,y1,smb',md.mesh.x,md.mesh.y,0)*1000/md.materials.rho_ice;
smb = [smb smb smb-1.0];
- md.surfaceforcings.mass_balance = [smb;1 10 20];
+ md.smb.mass_balance = [smb;1 10 20];
%Set transient options, run for 20 years, saving every year
@@ -117,5 +117,5 @@
%Additional options
md.inversion.iscontrol=0;
- md.transient.requested_outputs={'IceVolume','TotalSmb','SurfaceforcingsMassBalance'};
+ md.transient.requested_outputs={'IceVolume','TotalSmb','SmbMassBalance'};
md.verbose=verbose('solution',true,'module',true,'convergence',true);
@@ -134,5 +134,5 @@
plotmodel(md,'data',md.results.TransientSolution(end).Vel,'caxis',[1e-1 6000],...
'log', 10, 'title', 'Velocity (m/y)','gridded',1, ...
- 'data', md.results.TransientSolution(end).SurfaceforcingsMassBalance, ...
+ 'data', md.results.TransientSolution(end).SmbMassBalance, ...
'title', 'Surface mass balance (m/y)','gridded',1, ...
'data',md.results.TransientSolution(end).Thickness,...
@@ -146,5 +146,5 @@
%Plot surface mass balance
surfmb=[]; for i=1:100; surfmb=[surfmb ...
- md.results.TransientSolution(i).SurfaceforcingsMassBalance]; end
+ md.results.TransientSolution(i).SmbMassBalance]; end
subplot(3,1,1); plot([0.2:0.2:20],mean(surfmb)); title('Mean Surface mass balance');
Index: /issm/trunk/examples/IceflowModels/EISMINT.par
===================================================================
--- /issm/trunk/examples/IceflowModels/EISMINT.par (revision 20547)
+++ /issm/trunk/examples/IceflowModels/EISMINT.par (revision 20548)
@@ -29,5 +29,5 @@
sb=10^-2/1000.; %m/yr/m
rel=450.*1000.; %m
-md.surfaceforcings.mass_balance=min(smb_max,sb*(rel-radius));
+md.smb.mass_balance=min(smb_max,sb*(rel-radius));
disp(' creating velocities');
Index: /issm/trunk/examples/Jakobshavn/Jks.par
===================================================================
--- /issm/trunk/examples/Jakobshavn/Jks.par (revision 20547)
+++ /issm/trunk/examples/Jakobshavn/Jks.par (revision 20548)
@@ -38,6 +38,6 @@
disp(' Interpolating surface mass balance');
-md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0);
-md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice;
+md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0);
+md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice;
disp(' Construct basal friction parameters');
Index: /issm/trunk/examples/Jakobshavn/runme.m
===================================================================
--- /issm/trunk/examples/Jakobshavn/runme.m (revision 20547)
+++ /issm/trunk/examples/Jakobshavn/runme.m (revision 20548)
@@ -1,3 +1,3 @@
-steps=[4];
+steps=[1];
if any(steps==1)
Index: /issm/trunk/examples/UncertaintyQuantification/runme.m
===================================================================
--- /issm/trunk/examples/UncertaintyQuantification/runme.m (revision 20547)
+++ /issm/trunk/examples/UncertaintyQuantification/runme.m (revision 20548)
@@ -1,4 +1,4 @@
%PIG Uncertainty Quantification Application
-steps=[1:3];
+steps=[1];
if any(steps==1)
@@ -140,8 +140,17 @@
md.stressbalance.restol=10^-5; %tighten tolerances for UQ analyses
+
+ %Turn off verbosity
+ md.verbose=verbose(0);
%solve
md.qmu.isdakota=1; md.inversion.iscontrol=0;
md.cluster=generic('name',oshostname,'np',4);
+
+ %Dakota runs in parallel with a master/slave configuration.
+ % At least 2 cpu's are needed to run the UQ
+ md.qmu.params.evaluation_scheduling='master';
+ md.qmu.params.processors_per_evaluation=md.cluster.np-1;
+
md=solve(md,StressbalanceSolutionEnum,'overwrite','y');
@@ -217,4 +226,10 @@
md.inversion.iscontrol=0;
md.cluster=generic('name',oshostname,'np',2);
+
+ %Dakota runs in parallel with a master/slave configuration.
+ % At least 2 cpu's are needed to run the UQ
+ md.qmu.params.evaluation_scheduling='master';
+ md.qmu.params.processors_per_evaluation=md.cluster.np-1
+
md.verbose=verbose('qmu',true);
md=solve(md,StressbalanceSolutionEnum,'overwrite','y');
Index: /issm/trunk/jenkins/jenkins.sh
===================================================================
--- /issm/trunk/jenkins/jenkins.sh (revision 20547)
+++ /issm/trunk/jenkins/jenkins.sh (revision 20548)
@@ -7,4 +7,7 @@
rm -rf $ISSM_DIR/nightlylog
mkdir $ISSM_DIR/nightlylog
+
+#Server URI
+SERVER='https://ross.ics.uci.edu:8080'
#Get configuration
@@ -44,5 +47,5 @@
#Get changes from jenkins itself (svn requires credentials)
rm -rf changes
- wget http://ross.ics.uci.edu:8080/job/$JOB_NAME/$BUILD_NUMBER/changes > /dev/null 2>&1
+ wget $SERVER/job/$JOB_NAME/$BUILD_NUMBER/changes > /dev/null 2>&1
#Process html page and get the list of files that has changed (tricky...)
@@ -60,8 +63,8 @@
if [ ! -z "$(cat $ISSM_DIR/TEMP | grep externalpackages)" ] ; then
echo " -- checking for changed externalpackages... yes";
- ISSM_EXTERNALPACKAGES="install"
+ ISSM_EXTERNALPACKAGES="yes"
else
echo " -- checking for changed externalpackages... no";
- ISSM_EXTERNALPACKAGES="none"
+ ISSM_EXTERNALPACKAGES="no"
fi
@@ -89,5 +92,5 @@
echo " -- checking for reconfiguration... yes";
echo " -- checking for recompilation... yes";
- ISSM_EXTERNALPACKAGES="install"
+ ISSM_EXTERNALPACKAGES="yes"
ISSM_RECONFIGURE="yes"
ISSM_COMPILATION="yes"
@@ -97,5 +100,5 @@
echo $SVN_REVISION_1 > $ISSM_DIR/svn_revision_old
#}}}
-#install/none external packages (ISSM_EXTERNALPACKAGES){{{
+#Install external packages (ISSM_EXTERNALPACKAGES){{{
#Jenkins xml files for individual packages
@@ -115,7 +118,6 @@
cd $ISSM_DIR/externalpackages/$PACKAGENAME
- #install if requested or if install does not exist
- if [ "$ISSM_EXTERNALPACKAGES" == "install" ] || [ ! -d install ] || [ ! "$(ls -A install)" ];
- then
+ #install if requested or if previous install has not been successful
+ if [ "$ISSM_EXTERNALPACKAGES" == "yes" ] || [ ! -f SUCCESS ]; then
echo "======================================================";
echo " Installing $PACKAGENAME ";
@@ -126,11 +128,11 @@
echo " ERROR: installation of $PACKAGENAME failed ";
echo "======================================================";
- #erase install directory, so that next time, we still try and compile this!
- rm -rf install
echo "" >> $EXTERNAL_TEST_FILE
echo 'External packages did not install right. Check it.' >> $EXTERNAL_TEST_FILE
echo '' >> $EXTERNAL_TEST_FILE
+ exit 1
else
echo "" >> $EXTERNAL_TEST_FILE
+ touch SUCCESS
fi
source $ISSM_DIR/etc/environment.sh
Index: /issm/trunk/src/c/Makefile.am
===================================================================
--- /issm/trunk/src/c/Makefile.am (revision 20547)
+++ /issm/trunk/src/c/Makefile.am (revision 20548)
@@ -534,5 +534,4 @@
./shared/TriMesh/SplitMeshForRifts.cpp\
./shared/TriMesh/TriMeshUtils.cpp\
- ./modules/TriaSearchx/TriaSearchx.cpp\
./modules/TriMeshx/TriMeshx.cpp\
./modules/TriMeshProcessRiftsx/TriMeshProcessRiftsx.cpp\
@@ -594,4 +593,7 @@
if !STANDALONE_LIBRARIES
libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB)
+if FORTRAN
+libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB)
+endif
endif
endif
@@ -645,5 +647,4 @@
libISSMOverload_la_CFLAGS = -D_C_ -fPIC $(COPTFLAGS) $(CFLAGS)
#}}}
-
#Executable {{{
if ANDROID
Index: /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 20547)
+++ /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 20548)
@@ -77,8 +77,4 @@
/*Finite element Analysis*/
void LevelsetAnalysis::Core(FemModel* femmodel){/*{{{*/
-
- #if !defined(_DEVELOPMENT_)
- _error_("Not implemented yet");
- #endif
/*parameters: */
Index: /issm/trunk/src/c/classes/Elements/PentaRef.cpp
===================================================================
--- /issm/trunk/src/c/classes/Elements/PentaRef.cpp (revision 20547)
+++ /issm/trunk/src/c/classes/Elements/PentaRef.cpp (revision 20548)
@@ -443,5 +443,5 @@
/*Get nodal functions derivatives in reference triangle*/
- IssmDouble* dbasis_ref=xNew(3*numnodes);
+ IssmDouble dbasis_ref[3*NUMNODESMAX];
GetNodalFunctionsDerivativesReference(dbasis_ref,gauss,finiteelement);
@@ -461,7 +461,4 @@
dbasis[numnodes*2+i]=Jinv[2][0]*dbasis_ref[0*numnodes+i]+Jinv[2][1]*dbasis_ref[1*numnodes+i]+Jinv[2][2]*dbasis_ref[2*numnodes+i];
}
-
- /*Clean up*/
- xDelete(dbasis_ref);
}
/*}}}*/
Index: /issm/trunk/src/c/classes/Elements/SegRef.cpp
===================================================================
--- /issm/trunk/src/c/classes/Elements/SegRef.cpp (revision 20547)
+++ /issm/trunk/src/c/classes/Elements/SegRef.cpp (revision 20548)
@@ -146,5 +146,5 @@
/*Get nodal functions derivatives in reference triangle*/
- IssmDouble* dbasis_ref=xNew(numnodes);
+ IssmDouble dbasis_ref[1*NUMNODESMAX];
GetNodalFunctionsDerivativesReference(dbasis_ref,gauss,finiteelement);
@@ -158,8 +158,4 @@
dbasis[i] = Jinv*dbasis_ref[i];
}
-
- /*Clean up*/
- xDelete(dbasis_ref);
-
}
/*}}}*/
Index: /issm/trunk/src/c/classes/Elements/TetraRef.cpp
===================================================================
--- /issm/trunk/src/c/classes/Elements/TetraRef.cpp (revision 20547)
+++ /issm/trunk/src/c/classes/Elements/TetraRef.cpp (revision 20548)
@@ -225,5 +225,5 @@
/*Get nodal functions derivatives in reference triangle*/
- IssmDouble* dbasis_ref=xNew(3*numnodes);
+ IssmDouble dbasis_ref[3*NUMNODESMAX];
GetNodalFunctionsDerivativesReference(dbasis_ref,gauss,finiteelement);
@@ -243,7 +243,4 @@
dbasis[numnodes*2+i]=Jinv[2][0]*dbasis_ref[0*numnodes+i]+Jinv[2][1]*dbasis_ref[1*numnodes+i]+Jinv[2][2]*dbasis_ref[2*numnodes+i];
}
-
- /*Clean up*/
- xDelete(dbasis_ref);
}
/*}}}*/
Index: /issm/trunk/src/c/classes/Elements/TriaRef.cpp
===================================================================
--- /issm/trunk/src/c/classes/Elements/TriaRef.cpp (revision 20547)
+++ /issm/trunk/src/c/classes/Elements/TriaRef.cpp (revision 20548)
@@ -197,5 +197,5 @@
/*Get nodal functions derivatives in reference triangle*/
- IssmDouble* dbasis_ref=xNew(2*numnodes);
+ IssmDouble dbasis_ref[2*NUMNODESMAX];
GetNodalFunctionsDerivativesReference(dbasis_ref,gauss,finiteelement);
@@ -211,7 +211,4 @@
dbasis[numnodes*1+i] = Jinv[1][0]*dbasis_ref[0*numnodes+i]+Jinv[1][1]*dbasis_ref[1*numnodes+i];
}
-
- /*Clean up*/
- xDelete(dbasis_ref);
}
Index: /issm/trunk/src/c/modules/modules.h
===================================================================
--- /issm/trunk/src/c/modules/modules.h (revision 20547)
+++ /issm/trunk/src/c/modules/modules.h (revision 20548)
@@ -89,5 +89,4 @@
#include "./SpcNodesx/SpcNodesx.h"
#include "./SurfaceAreax/SurfaceAreax.h"
-#include "./TriaSearchx/TriaSearchx.h"
#include "./TriMeshx/TriMeshx.h"
#include "./TriMeshProcessRiftsx/TriMeshProcessRiftsx.h"
Index: /issm/trunk/src/m/boundaryconditions/SetMarineIceSheetBC.m
===================================================================
--- /issm/trunk/src/m/boundaryconditions/SetMarineIceSheetBC.m (revision 20547)
+++ /issm/trunk/src/m/boundaryconditions/SetMarineIceSheetBC.m (revision 20548)
@@ -40,5 +40,5 @@
pos=find(md.mesh.vertexonboundary & ~vertexonicefront);
if isempty(pos),
- warning('SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually')
+ disp('SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet applied')
end
md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
Index: /issm/trunk/src/m/classes/calving.m
===================================================================
--- /issm/trunk/src/m/classes/calving.m (revision 20547)
+++ /issm/trunk/src/m/classes/calving.m (revision 20548)
@@ -39,6 +39,6 @@
if (solution~=TransientSolutionEnum() | md.transient.ismovingfront==0), return; end
- md = checkfield(md,'fieldname','calving.calvingrate(1:md.mesh.numberofvertices,:)','>=',0,'timeseries',1,'NaN',1,'Inf',1);
- md = checkfield(md,'fieldname','calving.meltingrate(1:md.mesh.numberofvertices,:)','>=',0,'timeseries',1,'NaN',1,'Inf',1);
+ md = checkfield(md,'fieldname','calving.calvingrate','>=',0,'timeseries',1,'NaN',1,'Inf',1);
+ md = checkfield(md,'fieldname','calving.meltingrate','>=',0,'timeseries',1,'NaN',1,'Inf',1);
end % }}}
function disp(self) % {{{
Index: /issm/trunk/src/m/classes/clusters/generic_static.m
===================================================================
--- /issm/trunk/src/m/classes/clusters/generic_static.m (revision 20547)
+++ /issm/trunk/src/m/classes/clusters/generic_static.m (revision 20548)
@@ -51,8 +51,26 @@
function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{
+ %Check that issm.exe exists in the right path
+ if ~exist([cluster.codepath '/issm.exe'],'file'),
+ error(['File ' cluster.codepath '/issm.exe does not exist']);
+ end
+
+ %Now process codepath and replace empty spaces with \ to avoid errors in queuing script
+ codepath2=strrep(cluster.codepath,' ','\ ');
+
+ %write queuing script
+ %what is the executable being called?
+ executable='issm.exe';
+ if isdakota,
+ version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3));
+ if (version>=6),
+ executable='issm_dakota.exe';
+ end
+ end
+
%write queuing script
fid=fopen([modelname '.queue'],'w');
fprintf(fid,'#!%s\n',cluster.shell);
- fprintf(fid,[cluster.codepath '/mpiexec -np %i %s/issm.exe %s %s %s \n'],cluster.np,cluster.codepath,EnumToString(solution),'./',modelname);
+ fprintf(fid,['%s/mpiexec -np %i %s/%s %s %s %s \n'],codepath2,cluster.np,codepath2,executable,EnumToString(solution),'./',modelname);
fclose(fid);
Index: /issm/trunk/src/m/classes/clusters/lonestar.m
===================================================================
--- /issm/trunk/src/m/classes/clusters/lonestar.m (revision 20547)
+++ /issm/trunk/src/m/classes/clusters/lonestar.m (revision 20548)
@@ -123,8 +123,14 @@
fprintf(fid,['module load ' cluster.modules{i} '\n']);
end
+
+ %fprintf(fid,'export KMP_AFFINITY="granularity=fine,compact,verbose" \n\n');
+
if length(find(cluster.email=='@'))>0
- fprintf(fid,'#SBATCH --mail-user=%s \n',cluster.email);
- fprintf(fid,'#SBATCH --mail-type=end \n\n');
+ %fprintf(fid,'#SBATCH --mail-user=%s \n',cluster.email);
+ %fprintf(fid,'#SBATCH --mail-type=end \n\n');
+
+ fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Began on Lonestar 5.'' %s <<< ''Job Started'' " \n\n',cluster.email);
end
+
fprintf(fid,'export PATH="$PATH:."\n\n');
fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
@@ -134,4 +140,9 @@
if ~io_gather, %concatenate the output files:
fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+ end
+
+ if length(find(cluster.email=='@'))>0
+ fprintf(fid,'\n');
+ fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Ended on Lonestar 5.'' %s <<< ''Job Ended'' " \n\n',cluster.email);
end
fclose(fid);
Index: /issm/trunk/src/m/classes/clusters/pfe.m
===================================================================
--- /issm/trunk/src/m/classes/clusters/pfe.m (revision 20547)
+++ /issm/trunk/src/m/classes/clusters/pfe.m (revision 20548)
@@ -92,5 +92,14 @@
end
end
-
+ elseif strcmpi(cluster.processor,'bro'),
+ if cluster.hyperthreading,
+ if ((cluster.cpuspernode>56 ) | (cluster.cpuspernode<1)),
+ md = checkmessage(md,'cpuspernode should be between 1 and 56 for ''bro'' processors in hyperthreading mode');
+ end
+ else
+ if ((cluster.cpuspernode>28 ) | (cluster.cpuspernode<1)),
+ md = checkmessage(md,'cpuspernode should be between 1 and 28 for ''bro'' processors');
+ end
+ end
elseif strcmpi(cluster.processor,'has'),
if cluster.hyperthreading,
Index: /issm/trunk/src/m/classes/independent.py
===================================================================
--- /issm/trunk/src/m/classes/independent.py (revision 20547)
+++ /issm/trunk/src/m/classes/independent.py (revision 20548)
@@ -2,4 +2,5 @@
from pairoptions import pairoptions
from fielddisplay import fielddisplay
+from checkfield import checkfield
from MatlabFuncs import *
from EnumDefinitions import *
@@ -52,5 +53,5 @@
raise TypeError("independent checkconsistency error: nods should be set to the size of the independent variable")
- if self.fov_forward_indices:
+ if len(self.fov_forward_indices) > 0:
if not strcmpi(driver,'fov_forward'):
raise TypeError("cannot declare an independent with fov_forward_indices when the driver is not fov_forward!")
Index: /issm/trunk/src/m/classes/miscellaneous.m
===================================================================
--- /issm/trunk/src/m/classes/miscellaneous.m (revision 20547)
+++ /issm/trunk/src/m/classes/miscellaneous.m (revision 20548)
@@ -39,9 +39,13 @@
end % }}}
function savemodeljs(self,fid,modelname) % {{{
-
+
writejsstring(fid,[modelname '.miscellaneous.notes'],self.notes);
writejsstring(fid,[modelname '.miscellaneous.name'],self.name);
if strcmpi(class(self.dummy),'double'),
- writejs1Darray(fid,[modelname '.miscellaneous.dummy'],self.dummy);
+ if size(self.dummy,2)==1,
+ writejs1Darray(fid,[modelname '.miscellaneous.dummy'],self.dummy);
+ else
+ writejs2Darray(fid,[modelname '.miscellaneous.dummy'],self.dummy);
+ end
end
Index: /issm/trunk/src/m/classes/model.m
===================================================================
--- /issm/trunk/src/m/classes/model.m (revision 20547)
+++ /issm/trunk/src/m/classes/model.m (revision 20548)
@@ -208,5 +208,4 @@
md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
end;
- if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
%results
Index: /issm/trunk/src/m/classes/model.py
===================================================================
--- /issm/trunk/src/m/classes/model.py (revision 20547)
+++ /issm/trunk/src/m/classes/model.py (revision 20548)
@@ -687,6 +687,4 @@
md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers)
- if not numpy.isnan(md.balancethickness.thickening_rate).all(): md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers)
-
#results
if not numpy.isnan(md.initialization.vx).all(): md.initialization.vx=DepthAverage(md,md.initialization.vx)
Index: /issm/trunk/src/m/coordsystems/gdaltransform.m
===================================================================
--- /issm/trunk/src/m/coordsystems/gdaltransform.m (revision 20547)
+++ /issm/trunk/src/m/coordsystems/gdaltransform.m (revision 20548)
@@ -6,10 +6,19 @@
%
% Example:
-% [x,y] = gdaltransform(md.mesh.lat,md.mesh.long,'EPSG:3184','EPSG:3411');
+% [x,y] = gdaltransform(md.mesh.long,md.mesh.lat,'EPSG:4326','EPSG:3031')
%
% For reference:
-% EPSG: 4326 (lat,long)
-% EPSG: 3411 (greenland, +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.449 +units=m +no_defs)
-% EPSG: 3031 (antarctica, +proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs)
+% EPSG: 4326 (lat,long)
+% EPSG: 3411 (Greenland, UPS 45W, 70N)
+% EPSG: 3031 (Antarctica, UPS 0E, 71S)
+%
+% ll2xy default projection Antarctica:
+% +proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs
+% ll2xy default projection Greenland:
+% +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs
+% Bamber's Greeland projection
+% +proj=stere +lat_0=90 +lat_ts=71 +lon_0=-39 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs
+%
+% To get proj.4 string from EPSG, use gdalsrsinfo. Example: gdalsrsinfo "EPSG:4326" | grep "PROJ.4"
%give ourselves a unique temporary directory:
@@ -17,11 +26,12 @@
fid=fopen([temproot '/.rand1234.txt'],'w');
- for i=1:length(x),
- fprintf(fid,'%g %g\n',x(i),y(i));
- end
+ fprintf(fid,'%8g %8g\n',[x(:) y(:)]');
fclose(fid);
[s,r]=system(['gdaltransform -s_srs ',proj_in,' -t_srs ',proj_out,' < ' temproot '/.rand1234.txt > ' temproot '/.rand1235.txt']);
- A=textread([temproot '/.rand1235.txt']);
- xout=A(:,1);
- yout=A(:,2);
+ if s~=0 | ~isempty(deblank(r)),
+ error(r);
+ end
+ A=load([temproot '/.rand1235.txt']);
+ xout=A(:,1); xout=reshape(xout,size(x));
+ yout=A(:,2); yout=reshape(yout,size(y));
Index: sm/trunk/src/m/exp/downstreamflowlines.m
===================================================================
--- /issm/trunk/src/m/exp/downstreamflowlines.m (revision 20547)
+++ (revision )
@@ -1,110 +1,0 @@
-function flowpath=downstreamflowlines(index,x,y,u,v,x0,y0,varargin)
-%DOWNSTREAMFLOWLINES - compute flowlines from a given set of seed points
-%
-% Usage:
-% flowpath=downstreamflowlines(index,x,y,u,v,x0,y0)
-%
-% the velocity field is given by the couple (u,v) and the coordinates
-% of the seed points are (x0,y0). One can use one or several seed
-% points
-%
-% Example:
-% flowpath=downstreamflowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.vx,md.initialization.vy,x0,y0)
-
-%check input size
-if nargin>9 | nargin<7,
- help flowlines
- error('flowlines error message: bad usage');
-end
-
-%check input
-if (length(x)~=length(y) | length(x)~=length(u) | length(x)~=length(v)),
- error('flowlines error message: x,y,u and v must have the same length');
-end
-if length(x)<3,
- error('flowlines error message: at least one element is required');
-end
-if length(x0)~=length(y0),
- error('flowlines error message: x0 and y0 do not have the same length');
-end
-
-%get maxiter and precision
-if nargin==9
- maxiter=varargin{1};%maximum number of iterations
- precision=varargin{2}; %division of each segment (higer precision increases number of segments)
-else
- maxiter=200; %maximum number of iterations
- precision=1; %division of each segment (higer precision increases number of segments)
-end
-
-%check seed points
-tria=TriaSearch(index,x,y,x0,y0);
-pos=find(isnan(tria));
-x0(pos)=[];
-y0(pos)=[];
-
-%initialize other variables
-N=length(x0);
-X=x0; Y=y0;
-flowpath=struct('x',cell(N,1),'y',cell(N,1),'name','','density',1);
-for i=1:N,
- flowpath(i).x=x0(i);
- flowpath(i).y=y0(i);
-end
-done=zeros(N,1);
-
-%get avegared length of each element
-length_tria=1/3*(sqrt( (x(index(:,1))-x(index(:,2))).^2+(y(index(:,1))-y(index(:,2))).^2 )+...
- sqrt((x(index(:,1))-x(index(:,3))).^2+(y(index(:,1))-y(index(:,3))).^2 )+...
- sqrt((x(index(:,2))-x(index(:,3))).^2+(y(index(:,2))-y(index(:,3))).^2 ));
-
-%take velocity for each element
-u=u(index)*[1;1;1]/3;
-v=v(index)*[1;1;1]/3;
-
-%initialization:
-counter=1;
-
-while any(~done)
-
- %find current triangle
- queue=find(~done);
- tria=TriaSearch(index,x,y,X(queue),Y(queue));
-
- %check that the point is actually inside a triangle of the mesh
- listnan=find(isnan(tria));
- for i=1:length(listnan)
- %remove the last point
- flowpath(queue(listnan(i))).x(end)=[];
- flowpath(queue(listnan(i))).y(end)=[];
- done(queue(listnan(i)))=1;
- end
- tria(listnan)=[];
- queue(listnan)=[];
-
- if isempty(tria),
- break;
- end
-
- %velocity of the current triangle and norm it
- ut=u(tria); vt=v(tria); normv=sqrt(ut.^2+vt.^2);
- ut=ut./normv;vt=vt./normv;
-
- %check counter
- if counter>maxiter
- disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going forward'])
- break
- end
- counter=counter+1;
-
- %remove stagnant point
- done(queue(find(ut==0 & vt==0)))=1;
-
- %build next point
- for i=1:length(queue)
- X(queue(i))=flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision;
- Y(queue(i))=flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision;
- flowpath(queue(i)).x=[flowpath(queue(i)).x;flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision];
- flowpath(queue(i)).y=[flowpath(queue(i)).y;flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision];
- end
-end
Index: /issm/trunk/src/m/exp/flowlines.m
===================================================================
--- /issm/trunk/src/m/exp/flowlines.m (revision 20547)
+++ /issm/trunk/src/m/exp/flowlines.m (revision 20548)
@@ -3,5 +3,5 @@
%
% Usage:
-% flowpath=flowlines(index,x,y,u,v,x0,y0)
+% flowpath=flowlines(index,x,y,u,v,x0,y0,varargin)
%
% the velocity field is given by the couple (u,v) and the coordinates
@@ -10,11 +10,11 @@
%
% Example:
-% flowpath=flowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.vx,md.initialization.vy,x0,y0)
-
-%check input size
-if nargin>8 | nargin<7,
- help flowlines
- error('flowlines error message: bad usage');
-end
+% flowpath=flowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.initialization.vx,md.initialization.vy,x0,y0)
+%
+% Options:
+% - 'maxiter': how many steps upstream and downstream of the seed points (default: 200)
+% - 'precision': division of each segment (higer precision increases number of segments, default: 1)
+% - 'downstream':flow line upstream of the seed points (default: 1)
+% - 'upstream': flow line upstream of the seed points (default: 1)
%check input
@@ -29,15 +29,14 @@
end
-%get maxiter and precision
-if nargin==8
- maxiter=varargin{1};
-else
- maxiter=200; %maximum number of iterations
-end
-precision=1; %division of each segment (higer precision increases number of segments)
+%process options
+options = pairoptions(varargin{:});
+maxiter = getfieldvalue(options,'maxiter',200);
+precision = getfieldvalue(options,'precision',1);
+downstream = getfieldvalue(options,'downstream',1);
+upstream = getfieldvalue(options,'upstream',1);
-%check seed points
-tria=TriaSearch(index,x,y,x0,y0);
-%tria=tsearch(x,y,index,x0,y0);
+%Create triangulation once for all and check seed points
+trep = triangulation(index,x,y);
+tria = pointLocation(trep,[x0 y0]);
pos=find(isnan(tria));
x0(pos)=[];
@@ -63,104 +62,106 @@
v=v(index)*[1;1;1]/3;
-%initialization:
-counter=1;
+if downstream,
+ %initialization:
+ counter=1;
-while any(~done)
+ while any(~done)
- %find current triangle
- queue=find(~done);
- tria=TriaSearch(index,x,y,X(queue),Y(queue));
- %tria=tsearch(x,y,index,X(queue),Y(queue));
+ %find current triangle
+ queue=find(~done);
+ tria = pointLocation(trep,[X(queue),Y(queue)]);
- %check that the point is actually inside a triangle of the mesh
- listnan=find(isnan(tria));
- for i=1:length(listnan)
- %remove the last point
- flowpath(queue(listnan(i))).x(end)=[];
- flowpath(queue(listnan(i))).y(end)=[];
- done(queue(listnan(i)))=1;
- end
- tria(listnan)=[];
- queue(listnan)=[];
+ %check that the point is actually inside a triangle of the mesh
+ listnan=find(isnan(tria));
+ for i=1:length(listnan)
+ %remove the last point
+ flowpath(queue(listnan(i))).x(end)=[];
+ flowpath(queue(listnan(i))).y(end)=[];
+ done(queue(listnan(i)))=1;
+ end
+ tria(listnan)=[];
+ queue(listnan)=[];
- if isempty(tria),
- break;
- end
+ if isempty(tria),
+ break;
+ end
- %velocity of the current triangle and norm it
- ut=u(tria); vt=v(tria); normv=sqrt(ut.^2+vt.^2);
- ut=ut./normv;vt=vt./normv;
+ %velocity of the current triangle and norm it
+ ut=u(tria); vt=v(tria); normv=max(eps,sqrt(ut.^2+vt.^2));
+ ut=ut./normv;vt=vt./normv;
- %check counter
- if counter>maxiter
- disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going forward'])
- break
- end
- counter=counter+1;
+ %check counter
+ if counter>maxiter
+ disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going forward'])
+ break
+ end
+ counter=counter+1;
- %remove stagnant point
- done(queue(find(ut==0 & vt==0)))=1;
+ %remove stagnant point
+ done(queue(find(ut==0 & vt==0)))=1;
- %build next point
- for i=1:length(queue)
- X(queue(i))=flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision;
- Y(queue(i))=flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision;
- flowpath(queue(i)).x=[flowpath(queue(i)).x;flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision];
- flowpath(queue(i)).y=[flowpath(queue(i)).y;flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision];
+ %build next point
+ for i=1:length(queue)
+ X(queue(i))=flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision;
+ Y(queue(i))=flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision;
+ flowpath(queue(i)).x=[flowpath(queue(i)).x;flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision];
+ flowpath(queue(i)).y=[flowpath(queue(i)).y;flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision];
+ end
end
end
%same process but reverse (vel=-vel) to have a vcomplete flow line
-queue=[];
-counter=1;
-X=x0; Y=y0;
-done=zeros(N,1);
+if upstream,
+ queue=[];
+ counter=1;
+ X=x0; Y=y0;
+ done=zeros(N,1);
-while any(~done)
+ while any(~done)
- %find current triangle
- queue=find(~done);
- tria=TriaSearch(index,x,y,X(queue),Y(queue));
- %tria=tsearch(x,y,index,X(queue),Y(queue));
+ %find current triangle
+ queue=find(~done);
+ tria = pointLocation(trep,[X(queue),Y(queue)]);
- %check that the point is actually inside a triangle of the mesh
- listnan=find(isnan(tria));
- for i=1:length(listnan)
- %remove the last point
- flowpath(queue(listnan(i))).x(1)=[];
- flowpath(queue(listnan(i))).y(1)=[];
- done(queue(listnan(i)))=1;
- end
- tria(listnan)=[];
- queue(listnan)=[];
+ %check that the point is actually inside a triangle of the mesh
+ listnan=find(isnan(tria));
+ for i=1:length(listnan)
+ %remove the last point
+ flowpath(queue(listnan(i))).x(1)=[];
+ flowpath(queue(listnan(i))).y(1)=[];
+ done(queue(listnan(i)))=1;
+ end
+ tria(listnan)=[];
+ queue(listnan)=[];
- if isempty(tria),
- break;
- end
+ if isempty(tria),
+ break;
+ end
- %velocity of the current triangle and norm it
- ut=-u(tria); vt=-v(tria); normv=sqrt(ut.^2+vt.^2);
- ut=ut./normv;vt=vt./normv;
+ %velocity of the current triangle and norm it
+ ut=-u(tria); vt=-v(tria); normv=max(eps,sqrt(ut.^2+vt.^2));
+ ut=ut./normv;vt=vt./normv;
- %check counter
- if counter>maxiter
- disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going backward'])
- break
- end
- counter=counter+1;
+ %check counter
+ if counter>maxiter
+ disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going backward'])
+ break
+ end
+ counter=counter+1;
- %remove stagnant point
- done(queue(find(ut==0 & vt==0)))=1;
+ %remove stagnant point
+ done(queue(find(ut==0 & vt==0)))=1;
- %build next point
- for i=1:length(queue)
- X(queue(i))=flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision;
- Y(queue(i))=flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision;
- flowpath(queue(i)).x=[flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision; flowpath(queue(i)).x];
- flowpath(queue(i)).y=[flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision; flowpath(queue(i)).y];
+ %build next point
+ for i=1:length(queue)
+ X(queue(i))=flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision;
+ Y(queue(i))=flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision;
+ flowpath(queue(i)).x=[flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision; flowpath(queue(i)).x];
+ flowpath(queue(i)).y=[flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision; flowpath(queue(i)).y];
+ end
end
end
-%EXP compatibility
+%EXP compatibility (add name)
for i=1:length(queue)
flowpath(queue(i)).name=['flowline' num2str(i)];
Index: /issm/trunk/src/m/mesh/patchglobe.m
===================================================================
--- /issm/trunk/src/m/mesh/patchglobe.m (revision 20547)
+++ /issm/trunk/src/m/mesh/patchglobe.m (revision 20548)
@@ -6,4 +6,12 @@
%recover basic options:
bandwidth=getfieldvalue(options,'bandwidth',100000);
+
+ %some checks on the mesh:
+ if (isempty(mh.x) | isempty(mh.y) | isempty(mh.z) | isempty(mh.lat) | isempty(mh.long) | isempty(mh.r) )
+ error('patchglobe error message: 3D planet mesh has one of the following empty: ''x'',''y'',''z'',''lat'',''long'' or ''r''');
+ end
+ if (isempty(mh2d.x) | isempty(mh2d.y) | isempty(mh2d.lat) | isempty(mh2d.long))
+ error('patchglobe error message: 3D planet mesh has one of the following empty: ''x'',''y'',''lat'' or ''long''');
+ end
%give ourselves a unique temporary directory:
Index: /issm/trunk/src/m/miscellaneous/transientrestart.m
===================================================================
--- /issm/trunk/src/m/miscellaneous/transientrestart.m (revision 20547)
+++ /issm/trunk/src/m/miscellaneous/transientrestart.m (revision 20548)
@@ -18,5 +18,5 @@
%Change time
-md.timestepping.start_time = results.time/md.constants.yts;
+md.timestepping.start_time = results.time;
%Change initialization fields
Index: /issm/trunk/src/m/plot/applyoptions.js
===================================================================
--- /issm/trunk/src/m/plot/applyoptions.js (revision 20547)
+++ /issm/trunk/src/m/plot/applyoptions.js (revision 20548)
@@ -11,5 +11,5 @@
if (options.getfieldvalue('colorbar')==1) {
//Handle movie data {{{
- if (typeof data == 'string') {
+ if (typeof data == 'string') {
//throw Error('plot error message: data of type string');
return;
@@ -25,7 +25,8 @@
})
});
- data = data[node['movieFrame']].slice(0,-1);
+ data = data[0].slice(0,-1);
} //}}}
//Variable options initialization {{{
+
var caxis = options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]);
var canvassize = options.getfieldvalue('canvassize',480);
@@ -47,12 +48,9 @@
var clabelitem;
var precision=options.getfieldvalue('colorbarprecision',3);
- if (options.exist('log')) {
+
+ if (options.getfieldvalue('log',10)!='off') {
for (var i = cdivisions; i >= 0; i--) {
- if (caxisdelta*i/cdivisions==min) {
- labels[i] = (caxis[0]).toPrecision(precision);
- }
- else {
- labels[i] = (Math.exp(Math.log(caxisdelta)*i/cdivisions)+caxis[0]).toPrecision(precision);
- }
+ var scale = Math.log(caxis[1])-Math.log(caxis[0]);
+ labels[i] = (Math.exp(Math.log(caxis[0])+scale*(cdivisions-i)/cdivisions)).toPrecision(precision);
}
} else {
@@ -228,8 +226,16 @@
var cmap = options.getfieldvalue('cmap','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)];
- tgradient.addColorStop(i/colorbar.length,'rgba('+color.toString()+',1.0)');
+ if (options.getfieldvalue('log',10)!='off') {
+ for (var i = 0; i < colorbar.length; i++) {
+ color = colorbar[colorbar.length-i-1];
+ color = [Math.round(color[0]*255),Math.round(color[1]*255),Math.round(color[2]*255)];
+ tgradient.addColorStop(1.0-Math.exp(Math.log((colorbar.length-i)/colorbar.length)/Math.log(options.getfieldvalue('log',10))*i/colorbar.length),'rgba('+color.toString()+',1.0)');
+ }
+ } else {
+ for (var i = 0; i < colorbar.length; i++) {
+ color = colorbar[colorbar.length-i-1];
+ color = [Math.round(color[0]*255),Math.round(color[1]*255),Math.round(color[2]*255)];
+ tgradient.addColorStop(i/colorbar.length,'rgba('+color.toString()+',1.0)');
+ }
}
Index: /issm/trunk/src/m/plot/manualcb.m
===================================================================
--- /issm/trunk/src/m/plot/manualcb.m (revision 20547)
+++ /issm/trunk/src/m/plot/manualcb.m (revision 20548)
@@ -62,6 +62,13 @@
ytick = (ztick-zmin)/(zmax-zmin);
else
- ztick = getfieldvalue(options,'tick',round(logspace(log(zmin)/log(10),log(zmax)/log(10),8)));
+ %old method
+ ztick = getfieldvalue(options,'tick',round( logspace(log10(zmin),log10(zmax),8) ));
ytick = linspace(0,1,numel(ztick));
+
+ %New method
+ test=logspace(-10,10,21);
+ pos=find(test>=zmin & test<=zmax);
+ ztick= test(pos);
+ ytick= (log(ztick) - log(zmin))/(log(zmax) - log(zmin));
end
@@ -69,16 +76,23 @@
hold on
numcolors=size(cmap,1);
-if strcmpi(getfieldvalue(options,'orientation','vertical'),'vertical'),
- image_rgb = ind2rgb(repmat((1:numcolors)',1,2),cmap);
-else
- image_rgb = ind2rgb(repmat((1:numcolors)',1,2)',cmap);
-end
if 1,
%disappears somtimes
- imagesc([0 1],[0 1],repmat(image_rgb,[1 10 1]));
+ if strcmpi(getfieldvalue(options,'orientation','vertical'),'vertical'),
+ image_rgb = ind2rgb(repmat((1:numcolors)',1,10),cmap);
+ else
+ image_rgb = ind2rgb(repmat((1:numcolors),10,1),cmap);
+ end
+
+ imagesc([0 1],[0 1],image_rgb);
else
%Creates triangles when exported as pdf
- for i=1:numcolors,
- patch([0,0,1,1],[(i-1)/numcolors,i/numcolors,i/numcolors,(i-1)/numcolors],'none','FaceColor',cmap(i,:),'Clipping','off','EdgeColor','none')
+ if strcmpi(getfieldvalue(options,'orientation','vertical'),'vertical'),
+ for i=1:numcolors,
+ patch([0,0,1,1],[(i-1)/numcolors,i/numcolors,i/numcolors,(i-1)/numcolors],0,'FaceColor',cmap(i,:),'Clipping','off','EdgeColor','none')
+ end
+ else
+ for i=1:numcolors,
+ patch([(i-1)/numcolors,i/numcolors,i/numcolors,(i-1)/numcolors],[0,0,1,1],0,'FaceColor',cmap(i,:),'Clipping','off','EdgeColor','none')
+ end
end
end
Index: /issm/trunk/src/m/plot/plot_overlay.js
===================================================================
--- /issm/trunk/src/m/plot/plot_overlay.js (revision 20547)
+++ /issm/trunk/src/m/plot/plot_overlay.js (revision 20548)
@@ -127,6 +127,12 @@
vertices[vertices.length] = vertex[2];
- texcoords[texcoords.length] = (x[i] - modelxlim[0]) / xrange;
- texcoords[texcoords.length] = (y[i] - modelylim[0]) / yrange;
+ if (md.mesh.classname() == 'mesh3dsurface') {
+ texcoords[texcoords.length] = degrees(Math.atan2(y[i], x[i])) / 360 + 0.5;
+ texcoords[texcoords.length] = degrees(Math.asin(z[i] / magnitude)) / 180 + 0.5;
+ }
+ else {
+ texcoords[texcoords.length] = (x[i] - modelxlim[0]) / xrange;
+ texcoords[texcoords.length] = (y[i] - modelylim[0]) / yrange;
+ }
}
Index: /issm/trunk/src/m/plot/plot_unit.js
===================================================================
--- /issm/trunk/src/m/plot/plot_unit.js (revision 20547)
+++ /issm/trunk/src/m/plot/plot_unit.js (revision 20548)
@@ -96,4 +96,5 @@
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];
@@ -196,13 +197,14 @@
})
});
-
- for(var i = 0; i < data.length; i++){
- //Prevent evaluation of datasubarray min/max if caxis exists
- if (options.exist('caxis')) {
- caxis = options.getfieldvalue('caxis');
- }
- else {
- caxis = [ArrayMin(data[i]),ArrayMax(data[i].slice(0,-1))];
- }
+ //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))];
+
+ for(var i = 0; i < data.length; i++){
datamin = caxis[0];
datamax = caxis[1];
Index: /issm/trunk/src/m/plot/processdata.js
===================================================================
--- /issm/trunk/src/m/plot/processdata.js (revision 20547)
+++ /issm/trunk/src/m/plot/processdata.js (revision 20548)
@@ -143,5 +143,5 @@
//log?
- if (options.exist('log')){
+ if (options.getfieldvalue('log','off')!='off'){
var bounds=options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]);
for(var i=0;ibounds[1])data[i][j]=bounds[1];
+ }
+ }
+ for(var i=0;i