Index: /issm/trunk/test/Validation/MacAyealVsPattyn/test1_iceshelf/Square.par
===================================================================
--- /issm/trunk/test/Validation/MacAyealVsPattyn/test1_iceshelf/Square.par	(revision 908)
+++ /issm/trunk/test/Validation/MacAyealVsPattyn/test1_iceshelf/Square.par	(revision 909)
@@ -1,122 +1,35 @@
-
 %Ok, start defining model parameters here
 
-%material parameters
-	md.g=9.8;
-	md.rho_ice=917;
-	md.rho_water=1023;
-	di=md.rho_ice/md.rho_water;
-	md.yts=365*24*3600;
-	md.heatcapacity=2009;
-	md.thermalconductivity=2.2; %W/mK
-	md.beta=9.8*10^-8;
+disp('      creating thickness');
+hmin=300;
+hmax=1000;
+ymin=min(md.y);
+ymax=max(md.y);
+md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin);
+md.firn_layer=10*ones(md.numberofgrids,1);
+md.bed=-md.rho_ice/md.rho_water*md.thickness;
+md.surface=md.bed+md.thickness;
 
-%Solution parameters
-	%parallelization 
-	md.cluster='none';
-	md.np=2;
-	md.time=1;
-	md.exclusive=0;
+disp('      creating temperature');
+md.observed_temperature=(273-20)*ones(md.numberofgrids,1);
 
-	%statics
-	md.eps_rel=0.01;
-	md.eps_abs=10;
-	md.lowmem=1;
-	if md.numberofgrids<1000000,
-	md.sparsity=.001;
-	else
-	md.sparsity=.0001;
-	end
+disp('      creating drag');
+md.drag_type=2; %0 none 1 plastic 2 viscous
+md.drag=200*ones(md.numberofgrids,1); %q=1.
+%Take care of iceshelves: no basal drag
+pos=find(md.elementoniceshelf);
+md.drag(md.elements(pos,:))=0;
+md.p=ones(md.numberofelements,1);
+md.q=ones(md.numberofelements,1);
 
-	%dynamics
-	md.dt=1*md.yts; %1 year
-	md.ndt=md.dt*10; 
-	md.artificial_diffusivity=1;
+disp('      creating flow law paramter');
+md.B=paterson(md.observed_temperature);
+md.n=3*ones(md.numberofelements,1);
 
-	%control
-	md.control_type={'drag'}; %'drag', 'B'
-	md.nsteps=5;
-	md.tolx=10^-4;
-	md.maxiter=20;
-	md.optscal=10;
-	md.fit='logarithmic'; %'absolute','relative','logarithmic'
-	md.meanvel=1000/md.yts; %1000 meters/year
-	md.epsvel=eps;
+disp('      boundary conditions for diagnostic model: ');
+md=SetMarineIceSheetBC(md,'Front.exp');
 
-
-	disp('      creating thickness');
-	hmin=300;
-	hmax=1000;
-	ymin=min(md.y);
-	ymax=max(md.y);
-	md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin);
-	md.firn_layer=10*ones(md.numberofgrids,1);
-	md.bed=-di*md.thickness+10;
-	md.surface=md.bed+md.thickness;
-
-	disp('      creating velocities');
-	md.vx_obs=zeros(md.numberofgrids,1);
-	md.vy_obs=zeros(md.numberofgrids,1);
-	md.vel_obs=sqrt(md.vx_obs.^2+md.vy_obs.^2);
-	
-	disp('      creating drag');
-	md.drag_type=2; %0 none 1 plastic 2 viscous
-	md.drag=200*ones(md.numberofgrids,1); %q=1.
-	%Take care of iceshelves: no basal drag
-	pos=find(md.elementoniceshelf);
-	md.drag(md.elements(pos,:))=0;
-	md.p=ones(md.numberofelements,1);
-	md.q=ones(md.numberofelements,1);
-
-	disp('      creating temperature');
-	md.observed_temperature=(273-20)*ones(md.numberofgrids,1);
-
-	disp('      creating flow law paramter');
-	md.B=paterson(md.observed_temperature);
-	md.n=3*ones(md.numberofelements,1);
-
-	disp('      creating accumulation rates');
-	md.accumulation=ones(md.numberofgrids,1)/md.yts; %1m/a
-	md.melting=0*ones(md.numberofgrids,1)/md.yts; %1m/a
-
-	%Deal with boundary conditions:
-	
-	disp('      boundary conditions for diagnostic model: ');
-	%Build gridonicefront, array of boundary grids belonging to the icefront:
-	gridinsideicefront=ArgusContourToMesh(md.elements,md.x,md.y,expread('Front.exp',1),'node',2);
-	gridonicefront=double(md.gridonboundary & gridinsideicefront);
-
-	md.gridondirichlet_diag=zeros(md.numberofgrids,1);
-	pos=find(md.gridonboundary & ~gridonicefront);md.gridondirichlet_diag(pos)=1;
-	md.dirichletvalues_diag=zeros(md.numberofgrids,2);
-
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_diag=md.segments(pos,:);
-	md.neumannvalues_diag=NaN*ones(length(md.segmentonneumann_diag),1); %dynamic boundary conditions (water pressure)
-
-	disp('      boundary conditions for prognostic model: ');
-	md.gridondirichlet_prog=zeros(md.numberofgrids,1);
-	md.dirichletvalues_prog=zeros(md.numberofgrids,1);
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_prog=md.segments(pos,:);
-	md.neumannvalues_prog=zeros(size(md.segmentonneumann_prog,1),1);
-	md.neumannvalues_prog(:)=NaN; %free radiation
-	
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_prog2=md.segments(pos,:);
-	md.neumannvalues_prog2=zeros(size(md.segmentonneumann_prog2,1),1);
-	md.neumannvalues_prog2(:)=NaN; %free radiation
-	
-	disp('      boundary conditions for thermal model: ');
-	md.gridondirichlet_thermal=ones(md.numberofgrids,1); %surface temperature
-	md.dirichletvalues_thermal=md.observed_temperature;
-	md.geothermalflux=zeros(md.numberofgrids,1); 
-	pos=find(md.elementonicesheet);md.geothermalflux(md.elements(pos,:))=50*10^-3; %50 mW/m^2
-
-
-	
-
-% Some Cielo code, ignore.
-if strcmp(md.cluster,'yes')
-	ServerDisconnect;
-end   
+%Parallel options
+md.np=3;
+md.time=50;
+md.waitonlock=1;
Index: /issm/trunk/test/Validation/MacAyealVsPattyn/test1_iceshelf/runme.m
===================================================================
--- /issm/trunk/test/Validation/MacAyealVsPattyn/test1_iceshelf/runme.m	(revision 908)
+++ /issm/trunk/test/Validation/MacAyealVsPattyn/test1_iceshelf/runme.m	(revision 909)
@@ -24,5 +24,5 @@
 for i=1:md.numberofgrids2d
 	for j=1:(md.numlayers-1)
-		grid_vel=grid_vel+1/(2*(md.numlayers-1))*(md.results.diagnostic.veli+j*md.numberofgrids2d,1)+md.results.diagnostic.vel(i+(j-1)*md.numberofgrids2d,1));
+		grid_vel=grid_vel+1/(2*(md.numlayers-1))*(md.results.diagnostic.vel(i+j*md.numberofgrids2d,1)+md.results.diagnostic.vel(i+(j-1)*md.numberofgrids2d,1));
 	end
 	vel_3d(i,1)=grid_vel;
Index: /issm/trunk/test/Validation/MacAyealVsPattyn/test2_icesheet/Square.par
===================================================================
--- /issm/trunk/test/Validation/MacAyealVsPattyn/test2_icesheet/Square.par	(revision 908)
+++ /issm/trunk/test/Validation/MacAyealVsPattyn/test2_icesheet/Square.par	(revision 909)
@@ -1,122 +1,36 @@
-
 %Ok, start defining model parameters here
 
-%material parameters
-	md.g=9.8;
-	md.rho_ice=917;
-	md.rho_water=1023;
-	di=md.rho_ice/md.rho_water;
-	md.yts=365*24*3600;
-	md.heatcapacity=2009;
-	md.thermalconductivity=2.2; %W/mK
-	md.beta=9.8*10^-8;
+disp('      creating thickness');
+hmin=300;
+hmax=1000;
+ymin=min(md.y);
+ymax=max(md.y);
+md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin);
+md.firn_layer=10*ones(md.numberofgrids,1);
+md.bed=-md.rho_ice/md.rho_water*md.thickness+10;
+md.surface=md.bed+md.thickness;
 
-%Solution parameters
-	%parallelization 
-	md.cluster='none';
-	md.np=2;
-	md.time=1;
-	md.exclusive=0;
+disp('      creating temperature');
+md.observed_temperature=(273-20)*ones(md.numberofgrids,1);
 
-	%statics
-	md.eps_rel=0.01;
-	md.eps_abs=10;
-	md.lowmem=1;
-	if md.numberofgrids<1000000,
-	md.sparsity=.001;
-	else
-	md.sparsity=.0001;
-	end
+disp('      creating drag');
+md.drag_type=2; %0 none 1 plastic 2 viscous
+md.drag=10*ones(md.numberofgrids,1); %q=1.
+%Take care of iceshelves: no basal drag
+pos=find(md.elementoniceshelf);
+md.drag(md.elements(pos,:))=0;
+md.p=ones(md.numberofelements,1);
+md.q=ones(md.numberofelements,1);
 
-	%dynamics
-	md.dt=1*md.yts; %1 year
-	md.ndt=md.dt*10; 
-	md.artificial_diffusivity=1;
+disp('      creating flow law paramter');
+md.B=paterson(md.observed_temperature);
+md.n=3*ones(md.numberofelements,1);
 
-	%control
-	md.control_type={'drag'}; %'drag', 'B'
-	md.nsteps=5;
-	md.tolx=10^-4;
-	md.maxiter=20;
-	md.optscal=10;
-	md.fit='logarithmic'; %'absolute','relative','logarithmic'
-	md.meanvel=1000/md.yts; %1000 meters/year
-	md.epsvel=eps;
+%Deal with boundary conditions:
+disp('      boundary conditions for diagnostic model: ');
+md=SetMarineIceSheetBC(md,'Front.exp');
 
-
-	disp('      creating thickness');
-	hmin=300;
-	hmax=1000;
-	ymin=min(md.y);
-	ymax=max(md.y);
-	md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin);
-	md.firn_layer=10*ones(md.numberofgrids,1);
-	md.bed=-di*md.thickness+10;
-	md.surface=md.bed+md.thickness;
-
-	disp('      creating velocities');
-	md.vx_obs=zeros(md.numberofgrids,1);
-	md.vy_obs=zeros(md.numberofgrids,1);
-	md.vel_obs=sqrt(md.vx_obs.^2+md.vy_obs.^2);
-	
-	disp('      creating drag');
-	md.drag_type=2; %0 none 1 plastic 2 viscous
-	md.drag=10*ones(md.numberofgrids,1); %q=1.
-	%Take care of iceshelves: no basal drag
-	pos=find(md.elementoniceshelf);
-	md.drag(md.elements(pos,:))=0;
-	md.p=ones(md.numberofelements,1);
-	md.q=ones(md.numberofelements,1);
-
-	disp('      creating temperature');
-	md.observed_temperature=(273-20)*ones(md.numberofgrids,1);
-
-	disp('      creating flow law paramter');
-	md.B=paterson(md.observed_temperature);
-	md.n=3*ones(md.numberofelements,1);
-
-	disp('      creating accumulation rates');
-	md.accumulation=ones(md.numberofgrids,1)/md.yts; %1m/a
-	md.melting=0*ones(md.numberofgrids,1)/md.yts; %1m/a
-
-	%Deal with boundary conditions:
-	
-	disp('      boundary conditions for diagnostic model: ');
-	%Build gridonicefront, array of boundary grids belonging to the icefront:
-	gridinsideicefront=ArgusContourToMesh(md.elements,md.x,md.y,expread('Front.exp',1),'node',2);
-	gridonicefront=double(md.gridonboundary & gridinsideicefront);
-
-	md.gridondirichlet_diag=zeros(md.numberofgrids,1);
-	pos=find(md.gridonboundary & ~gridonicefront);md.gridondirichlet_diag(pos)=1;
-	md.dirichletvalues_diag=zeros(md.numberofgrids,2);
-
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_diag=md.segments(pos,:);
-	md.neumannvalues_diag=NaN*ones(length(md.segmentonneumann_diag),1); %dynamic boundary conditions (water pressure)
-
-	disp('      boundary conditions for prognostic model: ');
-	md.gridondirichlet_prog=zeros(md.numberofgrids,1);
-	md.dirichletvalues_prog=zeros(md.numberofgrids,1);
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_prog=md.segments(pos,:);
-	md.neumannvalues_prog=zeros(size(md.segmentonneumann_prog,1),1);
-	md.neumannvalues_prog(:)=NaN; %free radiation
-	
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_prog2=md.segments(pos,:);
-	md.neumannvalues_prog2=zeros(size(md.segmentonneumann_prog2,1),1);
-	md.neumannvalues_prog2(:)=NaN; %free radiation
-	
-	disp('      boundary conditions for thermal model: ');
-	md.gridondirichlet_thermal=ones(md.numberofgrids,1); %surface temperature
-	md.dirichletvalues_thermal=md.observed_temperature;
-	md.geothermalflux=zeros(md.numberofgrids,1); 
-	pos=find(md.elementonicesheet);md.geothermalflux(md.elements(pos,:))=50*10^-3; %50 mW/m^2
-
-
-	
-
-% Some Cielo code, ignore.
-if strcmp(md.cluster,'yes')
-	ServerDisconnect;
-end   
+%Parallel options
+md.np=3;
+md.time=50;
+md.waitonlock=1;
Index: /issm/trunk/test/Validation/MacAyealVsPattyn/test3_icesheet_iceshelf/Square.par
===================================================================
--- /issm/trunk/test/Validation/MacAyealVsPattyn/test3_icesheet_iceshelf/Square.par	(revision 908)
+++ /issm/trunk/test/Validation/MacAyealVsPattyn/test3_icesheet_iceshelf/Square.par	(revision 909)
@@ -1,122 +1,35 @@
-
 %Ok, start defining model parameters here
 
-%material parameters
-	md.g=9.8;
-	md.rho_ice=917;
-	md.rho_water=1023;
-	di=md.rho_ice/md.rho_water;
-	md.yts=365*24*3600;
-	md.heatcapacity=2009;
-	md.thermalconductivity=2.2; %W/mK
-	md.beta=9.8*10^-8;
+disp('      creating thickness'); hmin=300;
+hmax=1000;
+ymin=min(md.y);
+ymax=max(md.y);
+md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin);
+md.firn_layer=10*ones(md.numberofgrids,1);
+md.bed=-md.rho_ice/md.rho_water*md.thickness+10;
+md.surface=md.bed+md.thickness;
 
-%Solution parameters
-	%parallelization 
-	md.cluster='none';
-	md.np=2;
-	md.time=1;
-	md.exclusive=0;
+disp('      creating drag');
+md.drag_type=2; %0 none 1 plastic 2 viscous
+md.drag=200*ones(md.numberofgrids,1); %q=1.
+%Take care of iceshelves: no basal drag
+pos=find(md.elementoniceshelf);
+md.drag(md.elements(pos,:))=0;
+md.p=ones(md.numberofelements,1);
+md.q=ones(md.numberofelements,1);
 
-	%statics
-	md.eps_rel=0.01;
-	md.eps_abs=10;
-	md.lowmem=1;
-	if md.numberofgrids<1000000,
-	md.sparsity=.001;
-	else
-	md.sparsity=.0001;
-	end
+disp('      creating temperature');
+md.observed_temperature=(273-20)*ones(md.numberofgrids,1);
 
-	%dynamics
-	md.dt=1*md.yts; %1 year
-	md.ndt=md.dt*10; 
-	md.artificial_diffusivity=1;
+disp('      creating flow law paramter');
+md.B=paterson(md.observed_temperature);
+md.n=3*ones(md.numberofelements,1);
 
-	%control
-	md.control_type={'drag'}; %'drag', 'B'
-	md.nsteps=5;
-	md.tolx=10^-4;
-	md.maxiter=20;
-	md.optscal=10;
-	md.fit='logarithmic'; %'absolute','relative','logarithmic'
-	md.meanvel=1000/md.yts; %1000 meters/year
-	md.epsvel=eps;
+%Deal with boundary conditions:
+disp('      boundary conditions for diagnostic model: ');
+md=SetIceShelfBC(md,'Front.exp');
 
-
-	disp('      creating thickness');
-	hmin=300;
-	hmax=1000;
-	ymin=min(md.y);
-	ymax=max(md.y);
-	md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin);
-	md.firn_layer=10*ones(md.numberofgrids,1);
-	md.bed=-di*md.thickness+10;
-	md.surface=md.bed+md.thickness;
-
-	disp('      creating velocities');
-	md.vx_obs=zeros(md.numberofgrids,1);
-	md.vy_obs=zeros(md.numberofgrids,1);
-	md.vel_obs=sqrt(md.vx_obs.^2+md.vy_obs.^2);
-	
-	disp('      creating drag');
-	md.drag_type=2; %0 none 1 plastic 2 viscous
-	md.drag=200*ones(md.numberofgrids,1); %q=1.
-	%Take care of iceshelves: no basal drag
-	pos=find(md.elementoniceshelf);
-	md.drag(md.elements(pos,:))=0;
-	md.p=ones(md.numberofelements,1);
-	md.q=ones(md.numberofelements,1);
-
-	disp('      creating temperature');
-	md.observed_temperature=(273-20)*ones(md.numberofgrids,1);
-
-	disp('      creating flow law paramter');
-	md.B=paterson(md.observed_temperature);
-	md.n=3*ones(md.numberofelements,1);
-
-	disp('      creating accumulation rates');
-	md.accumulation=ones(md.numberofgrids,1)/md.yts; %1m/a
-	md.melting=0*ones(md.numberofgrids,1)/md.yts; %1m/a
-
-	%Deal with boundary conditions:
-	
-	disp('      boundary conditions for diagnostic model: ');
-	%Build gridonicefront, array of boundary grids belonging to the icefront:
-	gridinsideicefront=ArgusContourToMesh(md.elements,md.x,md.y,expread('Front.exp',1),'node',2);
-	gridonicefront=double(md.gridonboundary & gridinsideicefront);
-
-	md.gridondirichlet_diag=zeros(md.numberofgrids,1);
-	pos=find(md.gridonboundary & ~gridonicefront);md.gridondirichlet_diag(pos)=1;
-	md.dirichletvalues_diag=zeros(md.numberofgrids,2);
-
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_diag=md.segments(pos,:);
-	md.neumannvalues_diag=NaN*ones(length(md.segmentonneumann_diag),1); %dynamic boundary conditions (water pressure)
-
-	disp('      boundary conditions for prognostic model: ');
-	md.gridondirichlet_prog=zeros(md.numberofgrids,1);
-	md.dirichletvalues_prog=zeros(md.numberofgrids,1);
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_prog=md.segments(pos,:);
-	md.neumannvalues_prog=zeros(size(md.segmentonneumann_prog,1),1);
-	md.neumannvalues_prog(:)=NaN; %free radiation
-	
-	pos=find(gridonicefront(md.segments(:,1)) | gridonicefront(md.segments(:,2)));
-	md.segmentonneumann_prog2=md.segments(pos,:);
-	md.neumannvalues_prog2=zeros(size(md.segmentonneumann_prog2,1),1);
-	md.neumannvalues_prog2(:)=NaN; %free radiation
-	
-	disp('      boundary conditions for thermal model: ');
-	md.gridondirichlet_thermal=ones(md.numberofgrids,1); %surface temperature
-	md.dirichletvalues_thermal=md.observed_temperature;
-	md.geothermalflux=zeros(md.numberofgrids,1); 
-	pos=find(md.elementonicesheet);md.geothermalflux(md.elements(pos,:))=50*10^-3; %50 mW/m^2
-
-
-	
-
-% Some Cielo code, ignore.
-if strcmp(md.cluster,'yes')
-	ServerDisconnect;
-end   
+%Parallel options
+md.np=3;
+md.time=50;
+md.waitonlock=1;