Index: sm/trunk/src/m/utils/Mesh/BuildAdaptedMeshYams.m
===================================================================
--- /issm/trunk/src/m/utils/Mesh/BuildAdaptedMeshYams.m	(revision 1330)
+++ 	(revision )
@@ -1,82 +1,0 @@
-function md=BuildAdaptedMeshYams
-%BUILDADAPTEDMESHYAMS - Build model of Antarctica by refining according to observed velocity error estimator
-%
-%   Usage:
-%      md=BuildAdaptedMeshYams
-
-%PIG settings
-%{
-nsteps=4;
-resolution=10000;
-hmin=1500;
-hmax=10^7;
-gradation=3*ones(nsteps,1);
-epsilon=10^-0;
-domainoutline='DomainOutline.exp';
-%}
-
-%%{
-%Antarctica settings
-nsteps=6;
-resolution=8000;
-hmin=50;
-hmax=3*10^5;
-gradation=[1.5*ones(2,1);3*ones(nsteps-2,1)];
-epsilon=2*10^-0;
-domainoutline='EnvDomainOutline200km.exp';
-%%}
-
-velpath='/u/wilkes-r1b/larour/ModelData/RignotAntarcticaVelMosaicRampErsAlos/RignotAntVelSmooth.mat'; scale=1;
-%velpath='/u/wilkes-r1b/larour/ModelData/RignotAntarcticaVel1km/RignotAntVel.mat'; scale=365*24*3600; %(from m/s to m/yr)
-%velpath='/u/wilkes-r1b/larour/ModelData/RignotPigVel1996/RignotPig1996_HoleFree.mat'; scale=1;
-%velpath='/proj/ice/larour/Glaciology/Model_Data/RignotAntarcticaVel1km/RignotAntVel';
-%velpath='/proj/ice/larour/Glaciology/Model_Data/BamberAntarcticaVel1km/velocity';
-%velpath='/proj/ice/larour/Glaciology/Model_Data/mosaicAnt1km_ramp_ers_alos/RignotAntVel';
-
-groundingline='GroundingLine.exp';
-icestreams='Icestream.exp';
-parameterfile='Basins.par';
-
-%clear data
-clear md
-
-%build new model
-md=model;
-
-%mesh with initial resolution
-md=mesh(md,domainoutline,resolution);
-disp(['First mesh, number of elements: ' num2str(md.numberofelements)]);
-
-%load velocities 
-load(velpath);
-
-%start mesh adaptation
-for i=1:nsteps,
-	disp(['Iteration #' num2str(i) '/' num2str(nsteps)]);
-
-	%interpolate velocities onto mesh
-	disp('   interpolating velocities');
-	md.vx_obs=InterpFromGrid(x_m,y_m,vx,md.x,md.y,0)*scale;
-	md.vy_obs=InterpFromGrid(x_m,y_m,vy,md.x,md.y,0)*scale;
-	md.vel_obs=averaging(md,sqrt(md.vx_obs.^2+md.vy_obs.^2),2);
-
-	%adapt according to velocities
-	disp('   adapting');
-	md=YamsCall(md,md.vel_obs,hmin,hmax,gradation(i),epsilon);
-end
-	
-disp(['Final mesh, number of elements: ' num2str(md.numberofelements)]);
-md.vx_obs=InterpFromGrid(x_m,y_m,vx,md.x,md.y,0);
-md.vy_obs=InterpFromGrid(x_m,y_m,vy,md.x,md.y,0);
-md.vel_obs=sqrt(md.vx_obs.^2+md.vy_obs.^2);
-return;
-
-%parameterize model
-disp('Parameterizing');
-md=geography(md,groundingline,icestreams);
-md=parameterize(md,parameterfile);
-
-%md.vx_obs=DataInterp(x_m,y_m,vx*md.yts,md.x,md.y);
-%md.vy_obs=DataInterp(x_m,y_m,vy*md.yts,md.x,md.y);
-%md.vel_obs=sqrt(md.vx_obs.^2+md.vy_obs.^2);
-%return;
Index: /issm/trunk/src/m/utils/Mesh/MeshYams.m
===================================================================
--- /issm/trunk/src/m/utils/Mesh/MeshYams.m	(revision 1331)
+++ /issm/trunk/src/m/utils/Mesh/MeshYams.m	(revision 1331)
@@ -0,0 +1,82 @@
+function md=MeshYams
+%MESHYAMS - Build model of Antarctica by refining according to observed velocity error estimator
+%
+%   Usage:
+%      md=MeshYams;
+
+%PIG settings
+%{
+nsteps=4;
+resolution=10000;
+hmin=1500;
+hmax=10^7;
+gradation=3*ones(nsteps,1);
+epsilon=10^-0;
+domainoutline='DomainOutline.exp';
+%}
+
+%%{
+%Antarctica settings
+nsteps=6;
+resolution=5000;
+hmin=300;        %300m
+hmax=150*10^3;   %150km
+gradation=[1.5*ones(2,1);3*ones(nsteps-2,1)];
+epsilon=3*10^-0; %3m/a interpolation error
+domainoutline='EnvDomainOutline200km.exp';
+%%}
+
+velpath='/u/wilkes-r1b/larour/ModelData/RignotAntarcticaVelMosaicRampErsAlos/RignotAntVelSmooth.mat'; scale=1;
+%velpath='/u/wilkes-r1b/larour/ModelData/RignotAntarcticaVel1km/RignotAntVel.mat'; scale=365*24*3600; %(from m/s to m/yr)
+%velpath='/u/wilkes-r1b/larour/ModelData/RignotPigVel1996/RignotPig1996_HoleFree.mat'; scale=1;
+%velpath='/proj/ice/larour/Glaciology/Model_Data/RignotAntarcticaVel1km/RignotAntVel';
+%velpath='/proj/ice/larour/Glaciology/Model_Data/BamberAntarcticaVel1km/velocity';
+%velpath='/proj/ice/larour/Glaciology/Model_Data/mosaicAnt1km_ramp_ers_alos/RignotAntVel';
+
+groundingline='GroundingLine.exp';
+icestreams='Icestream.exp';
+parameterfile='Basins.par';
+
+%clear data
+clear md
+
+%build new model
+md=model;
+
+%mesh with initial resolution
+md=mesh(md,domainoutline,resolution);
+disp(['First mesh, number of elements: ' num2str(md.numberofelements)]);
+
+%load velocities 
+load(velpath);
+
+%start mesh adaptation
+for i=1:nsteps,
+	disp(['Iteration #' num2str(i) '/' num2str(nsteps)]);
+
+	%interpolate velocities onto mesh
+	disp('   interpolating velocities');
+	md.vx_obs=InterpFromGrid(x_m,y_m,vx,md.x,md.y,0)*scale;
+	md.vy_obs=InterpFromGrid(x_m,y_m,vy,md.x,md.y,0)*scale;
+	md.vel_obs=averaging(md,sqrt(md.vx_obs.^2+md.vy_obs.^2),2);
+
+	%adapt according to velocities
+	disp('   adapting');
+	md=YamsCall(md,md.vel_obs,hmin,hmax,gradation(i),epsilon);
+end
+	
+disp(['Final mesh, number of elements: ' num2str(md.numberofelements)]);
+md.vx_obs=InterpFromGrid(x_m,y_m,vx,md.x,md.y,0);
+md.vy_obs=InterpFromGrid(x_m,y_m,vy,md.x,md.y,0);
+md.vel_obs=sqrt(md.vx_obs.^2+md.vy_obs.^2);
+return;
+
+%parameterize model
+disp('Parameterizing');
+md=geography(md,groundingline,icestreams);
+md=parameterize(md,parameterfile);
+
+%md.vx_obs=DataInterp(x_m,y_m,vx*md.yts,md.x,md.y);
+%md.vy_obs=DataInterp(x_m,y_m,vy*md.yts,md.x,md.y);
+%md.vel_obs=sqrt(md.vx_obs.^2+md.vy_obs.^2);
+%return;
Index: /issm/trunk/src/m/utils/Mesh/YamsCall.m
===================================================================
--- /issm/trunk/src/m/utils/Mesh/YamsCall.m	(revision 1330)
+++ /issm/trunk/src/m/utils/Mesh/YamsCall.m	(revision 1331)
@@ -133,5 +133,4 @@
 system(['yams2-linux -O 1 -v 1 -ecp -hgrad ' num2str(gradation)  ' carre0 carre1']);
 rmpath([ISSM_DIR '/externalpackages/yams']);
-t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']);
 
 %plug new mesh
@@ -146,4 +145,5 @@
 md.numberofgrids=size(Coor,1);
 md.numberofelements=size(Tria,1);
+t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']);
 
 %clean up: