Index: /issm/trunk/src/m/model/mask.m
===================================================================
--- /issm/trunk/src/m/model/mask.m	(revision 9640)
+++ /issm/trunk/src/m/model/mask.m	(revision 9640)
@@ -0,0 +1,49 @@
+function md=setmask(md,floatingicename,groundedicename)
+%GEOGRAPHY - establish boundaries between grounded and floating ice.
+%
+%   By default, ice is considered grounded. The contour floatingicename defines nodes 
+%   for which ice is floating. The contour groundedicename defines nodes inside an floatingice, 
+%   that are grounded (ie: ice rises, islands, etc ...)
+%   All input files are in the Argus format (extension .exp).
+%
+%   Usage:
+%      md=setmask(md,floatingicename,groundedicename)
+%
+%   Examples:
+%      md=setmask(md,'all','');
+%      md=setmask(md,'Iceshelves.exp','Islands.exp');
+
+%some checks on list of arguments
+if ((nargin~=3) | (nargout~=1)),
+	help mask
+	error('mask error message');
+end
+
+%Get assigned fields
+x=md.x;
+y=md.y;
+elements=md.elements;
+
+%Assign elementonfloatingice, elementongroundedice, vertexongroundedice and vertexonfloatingice. Only change at your own peril! This is synchronized heavily with the GroundingLineMigration module. {{{1
+elementonfloatingice=FlagElements(md,floatingicename);
+elementongroundedice=FlagElements(md,groundedicename);
+
+%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=double((elementonfloatingice & ~elementongroundedice));
+elementongroundedice=double(~elementonfloatingice);
+
+%the order here is important. we choose vertexongroundedice as default on the grounding line.
+vertexonfloatingice=zeros(md.numberofnodes,1);
+vertexongroundedice=zeros(md.numberofnodes,1);
+vertexongroundedice(md.elements(find(elementongroundedice),:))=1;
+vertexonfloatingice(find(~vertexongroundedice))=1;
+%}}}
+
+%Return: 
+md.mask.elementonfloatingice=elementonfloatingice;
+md.mask.vertexonfloatingice=vertexonfloatingice;
+md.mask.elementongroundedice=elementongroundedice;
+md.mask.vertexongroundedice=vertexongroundedice;
+md.mask.vertexonwater=zeros(md.numberofnodes,1);
+md.mask.elementonwater=zeros(md.numberofelements,1);
Index: /issm/trunk/src/m/model/mask2.m
===================================================================
--- /issm/trunk/src/m/model/mask2.m	(revision 9640)
+++ /issm/trunk/src/m/model/mask2.m	(revision 9640)
@@ -0,0 +1,148 @@
+function md=setmask2(md,landname,floatingicename,groundedicename)
+%GEOGRAPHY2 - establish land, ice sheet and ice shelf areas in a domains.
+%
+%   Usage:
+%      md=setmask2(md,landname,floatingicename,groundedicename)
+%
+%   Examples:
+%      md=setmask2(md,'LandName.exp','Iceshelves.exp','Islands.exp');
+
+%Get assigned fields
+x=md.x;
+y=md.y;
+elements=md.elements;
+
+%recover elements and nodes on land.
+if ischar(landname),
+	[vertexonland,elementonland]=ContourToMesh(elements,x,y,landname,'element and node',2);
+elseif isfloat(landname),
+	if size(landname,1)~=md.numberofelements,
+		error('Landname for area must be of same size as number of elements in model');
+	end
+	elementonland=landname;
+	vertexonland=zeros(md.numberofnodes,1);
+	vertexonland(md.elements(find(elementonland),:))=1;
+else
+	error('Invalid area option option');
+end
+
+%Now, build the connectivity tables for this mesh.
+if size(md.nodeconnectivity,1)~=md.numberofnodes,
+	md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes);
+end
+if size(md.elementconnectivity,1)~=md.numberofelements,
+	md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+end
+
+%any element with 3 nodes on land should be on land:
+elementsonwater=find(~elementonland);
+wrongelements=elementsonwater(find(( vertexonland(md.elements(elementsonwater,1)) + vertexonland(md.elements(elementsonwater,2)) + vertexonland(md.elements(elementsonwater,3)) ...
+                  )==3));
+elementonland(wrongelements)=1;
+
+%any element with its barycentre on land should be on land: (only if landname is an expfile)
+if ischar(landname),
+weights={[1;1;1],[2;1;1],[1;2;1],[1;1;2]};
+	for i=1:length(weights),
+		xelem=x(md.elements)*weights{i}/sum(weights{i});
+		yelem=y(md.elements)*weights{i}/sum(weights{i});
+	end
+	baryonland=ContourToNodes(xelem,yelem,landname,1);
+	pos=find(~baryonland); elementonland(pos)=0;
+	pos=find(baryonland); elementonland(pos)=1;
+end
+
+%figure out which elements on land are actually in the middle of the ocean!
+pos1=find(elementonland); 
+connectedtoland=md.elementconnectivity(pos1,:);
+pos=find(connectedtoland); connectedtoland(pos)=1-elementonland(connectedtoland(pos));
+connectedtolandsum=sum(connectedtoland,2);
+waterelements=pos1(find(connectedtolandsum==3));
+elementonland(waterelements)=0;
+
+%figure out which elements on water  are actually in the middle of the land!
+pos1=find(~elementonland); 
+connectedtowater=md.elementconnectivity(pos1,:);
+pos=find(connectedtowater); connectedtowater(pos)=elementonland(connectedtowater(pos));
+connectedtowatersum=sum(connectedtowater,2);
+landelements=pos1(find(connectedtowatersum==3));
+elementonland(landelements)=1;
+
+%recover arrays of ice shelf nodes and elements, and ice sheet nodes and elements.
+elementonfloatingice=FlagElements(md,floatingicename);
+elementongroundedice=FlagElements(md,groundedicename);
+
+%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: 
+vertexonfloatingice=zeros(md.numberofnodes,1);
+vertexongroundedice=zeros(md.numberofnodes,1);
+elementonfloatingice=double((elementonfloatingice & ~elementongroundedice));
+elementongroundedice=double(~elementonfloatingice);
+vertexonfloatingice(md.elements(find(elementonfloatingice),:))=1;
+vertexongroundedice(md.elements(find(elementongroundedice),:))=1;
+
+%now correct, so that none of the floatingice and groundedice elements and nodes are in the water.
+pos=find(~elementonland);
+elementonfloatingice(pos)=0; 
+elementongroundedice(pos)=0;
+
+pos=find(~vertexonland);
+vertexonfloatingice(pos)=0; 
+vertexongroundedice(pos)=0;
+
+%create vertexonwater and elementonwater: 
+vertexonwater=double(~vertexonland);
+elementonwater=double(~elementonland);
+
+%correct for islands:
+vertexonfloatingice=double(vertexonfloatingice & ~vertexongroundedice);
+elementonfloatingice=double(elementonfloatingice & ~elementongroundedice);
+
+%now, groundedices are everything except iceshelves and water
+vertexongroundedice=double(~vertexonfloatingice & ~vertexonwater);
+elementongroundedice=double(~elementonfloatingice & ~elementonwater);
+
+%Deal with segments on neumann:
+
+%Get current connectivity
+elementconnectivity=md.elementconnectivity;
+
+%put 0 for elements on water
+pos=find(elementconnectivity);
+elementconnectivity(pos)=elementconnectivity(pos).*(~elementonwater(elementconnectivity(pos)));
+
+%put line of ones for elements on water
+pos=find(elementonwater);
+elementconnectivity(pos,:)=1;% line of ones for elements on water so they won't be considered
+
+%resort lines (zeros must be at the last column for findsegments)
+elementconnectivity=sort(elementconnectivity,2,'descend');
+
+%call findsegments to build segment using THIS conectivity
+md.segments=findsegments(md,'elementconnectivity',elementconnectivity);
+
+%some final checks: 
+%check that no node thinks it's on an ice shelf or ice sheet, and lies actually in the middle of the water.
+nodesgrounded=find(~vertexonwater);
+lengthconnectivity=size(md.nodeconnectivity,2);
+groundedcounters=md.nodeconnectivity(nodesgrounded,lengthconnectivity);
+groundedconnectivity=md.nodeconnectivity(nodesgrounded,1:lengthconnectivity-1);
+pos=find(groundedconnectivity);
+groundedconnectivity(pos)=elementonwater(groundedconnectivity(pos));
+groundedsum=sum(groundedconnectivity,2);
+errorflags=find(groundedsum==groundedcounters);
+errornodes=nodesgrounded(errorflags);
+
+vertexonwater(errornodes)=1;
+vertexongroundedice(errornodes)=0;
+vertexonfloatingice(errornodes)=0;
+
+%Return: 
+md.mask.vertexonfloatingice=vertexonfloatingice;
+md.mask.elementonfloatingice=elementonfloatingice;
+md.mask.vertexonwater=vertexonwater;
+md.mask.elementonwater=elementonwater;
+md.mask.vertexongroundedice=vertexongroundedice;
+md.mask.elementongroundedice=elementongroundedice;
+
+md.segmentmarkers(:)=1;