Changeset 9728

Timestamp:

09/09/11 13:40:05 (14 years ago)

Author:

seroussi

Message:

working on mesh class

Location:

issm/trunk

Files:

• src/c/EnumDefinitions/EnumDefinitions.h (modified) (2 diffs)
• src/c/modules/EnumToStringx/EnumToStringx.cpp (modified) (2 diffs)
• src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (modified) (2 diffs)
• src/c/modules/StringToEnumx/StringToEnumx.cpp (modified) (2 diffs)
• src/c/objects/Elements/Penta.cpp (modified) (2 diffs)
• src/c/objects/Elements/Tria.cpp (modified) (1 diff)
• src/m/classes/mesh.m (modified) (1 diff)
• src/m/classes/model/model.m (modified) (2 diffs)
• src/m/enum/ElementconnectivityEnum.m (deleted)
• src/m/enum/LowerelementsEnum.m (deleted)
• src/m/enum/MeshElementconnectivityEnum.m (added)
• src/m/enum/MeshLowerelementsEnum.m (added)
• src/m/enum/MeshUpperelementsEnum.m (added)
• src/m/enum/UpperelementsEnum.m (deleted)
• src/m/model/PropagateFlagsUntilDistance.m (modified) (3 diffs)
• src/m/model/bamg.m (modified) (1 diff)
• src/m/model/collapse.m (modified) (1 diff)
• src/m/model/contourenvelope.m (modified) (5 diffs)
• src/m/model/extrude.m (modified) (2 diffs)
• src/m/model/mesh/findsegments.m (modified) (3 diffs)
• src/m/model/mesh/meshnodensity.m (modified) (1 diff)
• src/m/model/mesh/meshrefine.m (modified) (1 diff)
• src/m/model/mesh/meshyams.m (modified) (2 diffs)
• src/m/model/mesh/rifts/meshaddrifts.m (modified) (1 diff)
• src/m/model/mesh/rifts/meshprocessrifts.m (modified) (1 diff)
• src/m/model/mesh/setmesh.m (modified) (1 diff)
• src/m/model/modelextract.m (modified) (2 diffs)
• src/m/model/modelsextract.m (modified) (1 diff)
• src/m/model/partition/AreaAverageOntoPartition.m (modified) (1 diff)
• src/m/model/partition/adjacency.m (modified) (1 diff)
• src/m/model/partition/partitioner.m (modified) (1 diff)
• src/m/model/setmask2.m (modified) (4 diffs)
• src/m/utils/Mesh/ProfileProjectOntoMesh.m (modified) (1 diff)
• src/m/utils/Mesh/squaremesh.m (modified) (1 diff)
• template (modified) (2 diffs)

issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h

@@ -155 +155 @@
         MeshNumberoflayersEnum,
         MeshNumberofvertices2dEnum,
+        MeshElementconnectivityEnum,
+        MeshLowerelementsEnum,
+        MeshUpperelementsEnum,
         /*}}}*/
         /*Datasets {{{1*/
@@ -470 +473 @@
         YEnum,
         ZEnum,
-        UpperelementsEnum,
         EdgesEnum,
         Elements2dEnum,
         XEnum,
-        ElementconnectivityEnum,
-        LowerelementsEnum,
         OutputfilenameEnum,
         WaterfractionEnum,

issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp

@@ -159 +159 @@
                 case MeshNumberoflayersEnum : return "MeshNumberoflayers";
                 case MeshNumberofvertices2dEnum : return "MeshNumberofvertices2d";
+                case MeshElementconnectivityEnum : return "MeshElementconnectivity";
+                case MeshLowerelementsEnum : return "MeshLowerelements";
+                case MeshUpperelementsEnum : return "MeshUpperelements";
                 case ConstraintsEnum : return "Constraints";
                 case ElementsEnum : return "Elements";
@@ -413 +416 @@
                 case YEnum : return "Y";
                 case ZEnum : return "Z";
-                case UpperelementsEnum : return "Upperelements";
                 case EdgesEnum : return "Edges";
                 case Elements2dEnum : return "Elements2d";
                 case XEnum : return "X";
-                case ElementconnectivityEnum : return "Elementconnectivity";
-                case LowerelementsEnum : return "Lowerelements";
                 case OutputfilenameEnum : return "Outputfilename";
                 case WaterfractionEnum : return "Waterfraction";

issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp

@@ -45 +45 @@
         
         /*Fetch data needed: */
-        iomodel->FetchData(4,ElementsEnum,ElementconnectivityEnum,MaterialsRheologyBEnum,MaterialsRheologyNEnum);
-        if(dim==3)          iomodel->FetchData(2,UpperelementsEnum,LowerelementsEnum);
+        iomodel->FetchData(4,ElementsEnum,MeshElementconnectivityEnum,MaterialsRheologyBEnum,MaterialsRheologyNEnum);
+        if(dim==3)          iomodel->FetchData(2,MeshUpperelementsEnum,MeshLowerelementsEnum);
         if(control_analysis)iomodel->FetchData(3,InversionControlParametersEnum,InversionMinParametersEnum,InversionMaxParametersEnum);
         
@@ -63 +63 @@
         
         /*Free data: */
-        iomodel->DeleteData(9,ElementsEnum,ElementconnectivityEnum,UpperelementsEnum,LowerelementsEnum,
+        iomodel->DeleteData(9,ElementsEnum,MeshElementconnectivityEnum,MeshUpperelementsEnum,MeshLowerelementsEnum,
                                 MaterialsRheologyBEnum,MaterialsRheologyNEnum,InversionControlParametersEnum,InversionMinParametersEnum,InversionMaxParametersEnum);
 

issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp

@@ -157 +157 @@
         else if (strcmp(name,"MeshNumberoflayers")==0) return MeshNumberoflayersEnum;
         else if (strcmp(name,"MeshNumberofvertices2d")==0) return MeshNumberofvertices2dEnum;
+        else if (strcmp(name,"MeshElementconnectivity")==0) return MeshElementconnectivityEnum;
+        else if (strcmp(name,"MeshLowerelements")==0) return MeshLowerelementsEnum;
+        else if (strcmp(name,"MeshUpperelements")==0) return MeshUpperelementsEnum;
         else if (strcmp(name,"Constraints")==0) return ConstraintsEnum;
         else if (strcmp(name,"Elements")==0) return ElementsEnum;
@@ -411 +414 @@
         else if (strcmp(name,"Y")==0) return YEnum;
         else if (strcmp(name,"Z")==0) return ZEnum;
-        else if (strcmp(name,"Upperelements")==0) return UpperelementsEnum;
         else if (strcmp(name,"Edges")==0) return EdgesEnum;
         else if (strcmp(name,"Elements2d")==0) return Elements2dEnum;
         else if (strcmp(name,"X")==0) return XEnum;
-        else if (strcmp(name,"Elementconnectivity")==0) return ElementconnectivityEnum;
-        else if (strcmp(name,"Lowerelements")==0) return LowerelementsEnum;
         else if (strcmp(name,"Outputfilename")==0) return OutputfilenameEnum;
         else if (strcmp(name,"Waterfraction")==0) return WaterfractionEnum;

issm/trunk/src/c/objects/Elements/Penta.cpp

@@ -57 +57 @@
         /*Checks in debugging mode*/
         /*{{{2*/
-        _assert_(iomodel->Data(UpperelementsEnum));
-        _assert_(iomodel->Data(LowerelementsEnum));
+        _assert_(iomodel->Data(MeshUpperelementsEnum));
+        _assert_(iomodel->Data(MeshLowerelementsEnum));
         /*}}}*/
 
@@ -66 +66 @@
 
         /*Build neighbors list*/
-        if (isnan(iomodel->Data(UpperelementsEnum)[index])) penta_elements_ids[1]=this->id; //upper penta is the same penta
-        else                                    penta_elements_ids[1]=(int)(iomodel->Data(UpperelementsEnum)[index]);
-        if (isnan(iomodel->Data(LowerelementsEnum)[index])) penta_elements_ids[0]=this->id; //lower penta is the same penta
-        else                                    penta_elements_ids[0]=(int)(iomodel->Data(LowerelementsEnum)[index]);
+        if (isnan(iomodel->Data(MeshUpperelementsEnum)[index])) penta_elements_ids[1]=this->id; //upper penta is the same penta
+        else                                    penta_elements_ids[1]=(int)(iomodel->Data(MeshUpperelementsEnum)[index]);
+        if (isnan(iomodel->Data(MeshLowerelementsEnum)[index])) penta_elements_ids[0]=this->id; //lower penta is the same penta
+        else                                    penta_elements_ids[0]=(int)(iomodel->Data(MeshLowerelementsEnum)[index]);
         this->InitHookNeighbors(penta_elements_ids);
 
         /*Build horizontalneighborsids list: */
-        _assert_(iomodel->Data(ElementconnectivityEnum));
-        for(i=0;i<3;i++) this->horizontalneighborsids[i]=(int)iomodel->Data(ElementconnectivityEnum)[3*index+i]-1;
+        _assert_(iomodel->Data(MeshElementconnectivityEnum));
+        for(i=0;i<3;i++) this->horizontalneighborsids[i]=(int)iomodel->Data(MeshElementconnectivityEnum)[3*index+i]-1;
 
         //this->parameters: we still can't point to it, it may not even exist. Configure will handle this.

issm/trunk/src/c/objects/Elements/Tria.cpp

@@ -52 +52 @@
 
                 /*Build horizontalneighborsids list: */
-                _assert_(iomodel->Data(ElementconnectivityEnum));
+                _assert_(iomodel->Data(MeshElementconnectivityEnum));
                 //for (i=0;i<3;i++) this->horizontalneighborsids[i]=(int)iomodel->elementconnectivity[3*index+i]-1;
 

issm/trunk/src/m/classes/mesh.m

@@ -22 +22 @@
                 numberofvertices2d    = modelfield('default',0,'marshall',true,'format','Integer');
                 numberofelements2d = modelfield('default',0,'marshall',true,'format','Integer');
+                nodeconnectivity    = modelfield('default',NaN,'marshall',false);
+                elementconnectivity = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3);
+                uppernodes           = modelfield('default',NaN,'marshall',false);
+                upperelements        = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2);
+                lowerelements        = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2);
+                lowernodes           = modelfield('default',NaN,'marshall',false);
         end
         methods

issm/trunk/src/m/classes/model/model.m

@@ -47 +47 @@
                  y                   = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1);
                  z                   = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1);
-                 nodeconnectivity    = modelfield('default',NaN,'marshall',false);
-                 elementconnectivity = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3);
                  edges               = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3);
                  elements2d         = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3);
                  x2d                = modelfield('default',NaN,'marshall',false);
                  y2d                = modelfield('default',NaN,'marshall',false);
-
-                 uppernodes           = modelfield('default',NaN,'marshall',false);
-                 upperelements        = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2);
-                 lowerelements        = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2);
-                 lowernodes           = modelfield('default',NaN,'marshall',false);
 
                  elementonbed      = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',2);
@@ -318 +311 @@
                          if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
                          if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
+                         if isfield(structmd,'nodeconnectivity'), md.mesh.nodeconnectivityension=structmd.nodeconnectivity; end
+                         if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivityension=structmd.elementconnectivity; end
+                         if isfield(structmd,'uppernodes'), md.mesh.uppernodesension=structmd.uppernodes; end
+                         if isfield(structmd,'lowernodes'), md.mesh.lowernodesension=structmd.lowernodes; end
+                         if isfield(structmd,'upperelements'), md.mesh.upperelementsension=structmd.upperelements; end
+                         if isfield(structmd,'lowerelements'), md.mesh.lowerelementsension=structmd.lowerelements; end
 
                          %Field changes

issm/trunk/src/m/model/PropagateFlagsUntilDistance.m

@@ -20 +20 @@
 %find elements that are at the border of flags: 
 flag_elements=find(flags);
-conn=md.elementconnectivity(flag_elements,:);
+conn=md.mesh.elementconnectivity(flag_elements,:);
 pos=find(conn);conn(pos)=~flags(conn(pos));
 sum_conn=sum(conn,2);
@@ -38 +38 @@
         pos=find(new_flags);
 
-        connected_elements=md.elementconnectivity(pos,:);
+        connected_elements=md.mesh.elementconnectivity(pos,:);
         connected_elements=connected_elements(find(connected_elements));
         new_flags(connected_elements)=1;
@@ -56 +56 @@
                         %none of the border elements are within distance, this element is outside out area of interest.
                         %ensure this element never gets found again in the connectivity.
-                        pos=find(md.elementconnectivity==new_elements(i));
-                        md.elementconnectivity(pos)=0;
+                        pos=find(md.mesh.elementconnectivity==new_elements(i));
+                        md.mesh.elementconnectivity(pos)=0;
                         %exclude this new element from the new_flags!
                         new_flags(new_elements(i))=0;

issm/trunk/src/m/model/bamg.m

@@ -335 +335 @@
 md.elementonsurface=ones(md.mesh.numberofelements,1);
 md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
-md.elementconnectivity=md.private.bamg.mesh.ElementConnectivity;
-md.elementconnectivity(find(isnan(md.elementconnectivity)))=0;
+md.mesh.elementconnectivity=md.private.bamg.mesh.ElementConnectivity;
+md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
 
 %Check for orphan

issm/trunk/src/m/model/collapse.m

@@ -98 +98 @@
 
 %Keep a trace of lower and upper nodes
-md.lowernodes=NaN;
-md.uppernodes=NaN;
+md.mesh.lowernodes=NaN;
+md.mesh.uppernodes=NaN;
 
 %Remove old mesh 

issm/trunk/src/m/model/contourenvelope.m

@@ -35 +35 @@
 %Now, build the connectivity tables for this mesh.
 %Computing connectivity
-if size(md.nodeconnectivity,1)~=md.mesh.numberofvertices,
-        md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+if size(md.mesh.nodeconnectivity,1)~=md.mesh.numberofvertices,
+        md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
 end
-if size(md.elementconnectivity,1)~=md.mesh.numberofelements,
-        md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+if size(md.mesh.elementconnectivity,1)~=md.mesh.numberofelements,
+        md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
 end
 
 %get nodes inside profile
-elementconnectivity=md.elementconnectivity;
+mesh.elementconnectivity=md.mesh.elementconnectivity;
 if nargin==2,
         if isfile,
@@ -51 +51 @@
                 %modify element connectivity
                 elemout=find(~elemin);
-                elementconnectivity(elemout,:)=0;
-                elementconnectivity(find(ismember(elementconnectivity,elemout)))=0;
+                mesh.elementconnectivity(elemout,:)=0;
+                mesh.elementconnectivity(find(ismember(mesh.elementconnectivity,elemout)))=0;
         else
                 %get flag list of elements and nodes inside the contour
@@ -64 +64 @@
                 %modify element connectivity
                 elemout=find(~elemin);
-                elementconnectivity(elemout,:)=0;
-                elementconnectivity(find(ismember(elementconnectivity,elemout)))=0;
+                mesh.elementconnectivity(elemout,:)=0;
+                mesh.elementconnectivity(find(ismember(mesh.elementconnectivity,elemout)))=0;
         end
 end
@@ -71 +71 @@
 %Find element on boundary
 %First: find elements on the boundary of the domain
-flag=elementconnectivity;
+flag=mesh.elementconnectivity;
 if nargin==2,
         flag(find(flag))=elemin(flag(find(flag)));
@@ -85 +85 @@
 for i=1:num_segments,
         el1=pos(i);
-        els2=elementconnectivity(el1,find(elementconnectivity(el1,:)));
+        els2=mesh.elementconnectivity(el1,find(mesh.elementconnectivity(el1,:)));
         if length(els2)>1,
                 flag=intersect(md.elements(els2(1),:),md.elements(els2(2),:));

issm/trunk/src/m/model/extrude.m

@@ -87 +87 @@
 
 %Keep a trace of lower and upper nodes
-lowernodes=NaN*ones(number_nodes3d,1);
-uppernodes=NaN*ones(number_nodes3d,1);
-lowernodes(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
-uppernodes(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
-md.lowernodes=lowernodes;
-md.uppernodes=uppernodes;
+mesh.lowernodes=NaN*ones(number_nodes3d,1);
+mesh.uppernodes=NaN*ones(number_nodes3d,1);
+mesh.lowernodes(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
+mesh.uppernodes(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
+md.mesh.lowernodes=mesh.lowernodes;
+md.mesh.uppernodes=mesh.uppernodes;
 
 %same for lower and upper elements
-lowerelements=NaN*ones(number_el3d,1);
-upperelements=NaN*ones(number_el3d,1);
-lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
-upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
-md.lowerelements=lowerelements;
-md.upperelements=upperelements;
+mesh.lowerelements=NaN*ones(number_el3d,1);
+mesh.upperelements=NaN*ones(number_el3d,1);
+mesh.lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
+mesh.upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
+md.mesh.lowerelements=mesh.lowerelements;
+md.mesh.upperelements=mesh.upperelements;
 
 %Save old mesh 
@@ -184 +184 @@
 
 %connectivity
-md.elementconnectivity=repmat(md.elementconnectivity,numlayers-1,1);
-md.elementconnectivity(find(md.elementconnectivity==0))=NaN;
+md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
+md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
 for i=2:numlayers-1,
-        md.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
-        =md.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
-end
-md.elementconnectivity(find(isnan(md.elementconnectivity)))=0;
+        md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
+        =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
+end
+md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
 
 %materials

issm/trunk/src/m/model/mesh/findsegments.m

@@ -3 +3 @@
 %
 %   Optional inputs:
-%      'elementconnectivity'
+%      'mesh.elementconnectivity'
 %
 %   Usage:
@@ -12 +12 @@
 
 %Get connectivity
-elementconnectivity=getfieldvalue(options,'elementconnectivity',md.elementconnectivity);
+mesh.elementconnectivity=getfieldvalue(options,'mesh.elementconnectivity',md.mesh.elementconnectivity);
 
 %Now, build the connectivity tables for this mesh if not correclty done
-if size(md.elementconnectivity,1)~=md.mesh.numberofelements,
-        if exist(options,'elementconnectivity'),
-                error(' ''elementconnectivity'' option does not have thge right size.');
+if size(md.mesh.elementconnectivity,1)~=md.mesh.numberofelements,
+        if exist(options,'mesh.elementconnectivity'),
+                error(' ''mesh.elementconnectivity'' option does not have thge right size.');
         else
-                elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+                mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
         end
 end
 
 %Recreate the segments
-elementonboundary=double(elementconnectivity(:,3)==0);
+elementonboundary=double(mesh.elementconnectivity(:,3)==0);
 pos=find(elementonboundary);
 num_segments=length(pos);
@@ -37 +37 @@
 
         %get elements connected to el1
-        els2=elementconnectivity(el1,find(elementconnectivity(el1,:)));
+        els2=mesh.elementconnectivity(el1,find(mesh.elementconnectivity(el1,:)));
 
         %el1 is connected to 2 other elements

issm/trunk/src/m/model/mesh/meshnodensity.m

@@ -65 +65 @@
 
 %Now, build the connectivity tables for this mesh.
-md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
-md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
 
 %type of model

issm/trunk/src/m/model/mesh/meshrefine.m

@@ -29 +29 @@
 
 %Now, build the connectivity tables for this mesh.
-md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
-md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
 
 %type of model

issm/trunk/src/m/model/mesh/meshyams.m

@@ -95 +95 @@
         %rifts, because the segments are used in YamsCall to freeze the rifts elements during refinement.
         if md.rifts.numrifts, 
-                md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
-                md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+                md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+                md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
                 md.mesh.segments=findsegments(md);
                 md=meshyamsrecreateriftsegments(md);
@@ -106 +106 @@
 
 %Now, build the connectivity tables for this mesh.
-md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
-md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
 
 %recreate segments

issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m

@@ -87 +87 @@
 
 %Now, build the connectivity tables for this mesh.
-md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
-md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
 
 %type of model

issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m

@@ -26 +26 @@
 %Call MEX file
 [md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers,md.rifts.riftstruct]=TriMeshProcessRifts(md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers);
+md.rifts
+md.rifts.riftstruct
 if ~isstruct(md.rifts.riftstruct),
         error('TriMeshProcessRifts did not find any rift');

issm/trunk/src/m/model/mesh/setmesh.m

@@ -79 +79 @@
 
 %Now, build the connectivity tables for this mesh.
-md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
-md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
 
 %type of model

issm/trunk/src/m/model/modelextract.m

@@ -123 +123 @@
         md2.elements=elements_2;
 
-        %uppernodes lowernodes
+        %mesh.uppernodes mesh.lowernodes
         if md1.dim==3
-                md2.uppernodes=md1.uppernodes(pos_node);
-                pos=find(~isnan(md2.uppernodes));
-                md2.uppernodes(pos)=Pnode(md2.uppernodes(pos));
-
-                md2.lowernodes=md1.lowernodes(pos_node);
-                pos=find(~isnan(md2.lowernodes));
-                md2.lowernodes(pos)=Pnode(md2.lowernodes(pos));
-
-                md2.upperelements=md1.upperelements(pos_elem);
-                pos=find(~isnan(md2.upperelements));
-                md2.upperelements(pos)=Pelem(md2.upperelements(pos));
-
-                md2.lowerelements=md1.lowerelements(pos_elem);
-                pos=find(~isnan(md2.lowerelements));
-                md2.lowerelements(pos)=Pelem(md2.lowerelements(pos));
+                md2.mesh.uppernodes=md1.mesh.uppernodes(pos_node);
+                pos=find(~isnan(md2.mesh.uppernodes));
+                md2.mesh.uppernodes(pos)=Pnode(md2.mesh.uppernodes(pos));
+
+                md2.mesh.lowernodes=md1.mesh.lowernodes(pos_node);
+                pos=find(~isnan(md2.mesh.lowernodes));
+                md2.mesh.lowernodes(pos)=Pnode(md2.mesh.lowernodes(pos));
+
+                md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
+                pos=find(~isnan(md2.mesh.upperelements));
+                md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
+
+                md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
+                pos=find(~isnan(md2.mesh.lowerelements));
+                md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
         end
 
@@ -203 +203 @@
         %recreate segments
         if md1.dim==2
-                md2.nodeconnectivity=NodeConnectivity(md2.elements,md2.numberofnodes);
-                md2.elementconnectivity=ElementConnectivity(md2.elements,md2.nodeconnectivity);
+                md2.mesh.nodeconnectivity=NodeConnectivity(md2.elements,md2.numberofnodes);
+                md2.mesh.elementconnectivity=ElementConnectivity(md2.elements,md2.mesh.nodeconnectivity);
                 md2.segments=contourenvelope(md2);
                 md2.mesh.vertexonboundary=zeros(numberofnodes2,1); md2.nodeonboundary(md2.segments(:,1:2))=1;

issm/trunk/src/m/model/modelsextract.m

@@ -42 +42 @@
                 %ok, we are sure element i is part of a new pool.
                 pool=zeros(numberofelements,1);
-                pool=PropagateFlagsFromConnectivity(md.elementconnectivity,pool,i,flags);
+                pool=PropagateFlagsFromConnectivity(md.mesh.elementconnectivity,pool,i,flags);
                 flag_list{end+1,1}=pool;
                 

issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m

@@ -22 +22 @@
         md.mesh.numberofelements=md.mesh.numberofelements2d;
         md.vertex_weight=[];
-        md.nodeconnectivity=[];
+        md.mesh.nodeconnectivity=[];
 
         %run connectivity routine

issm/trunk/src/m/model/partition/adjacency.m

@@ -19 +19 @@
 
 %get node connectivity
-md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
 
-connectivity=md.nodeconnectivity(:,1:end-1);
+connectivity=md.mesh.nodeconnectivity(:,1:end-1);
 pos=find(connectivity);
 connectivity(pos)=areas(connectivity(pos))/3;

issm/trunk/src/m/model/partition/partitioner.m

@@ -40 +40 @@
         md.mesh.numberofelements=md.mesh.numberofelements2d;
         md.qmu.vertex_weight=[];
-        md.nodeconnectivity=[];
+        md.mesh.nodeconnectivity=[];
 end
 

issm/trunk/src/m/model/setmask2.m

@@ -28 +28 @@
 
 %Now, build the connectivity tables for this mesh.
-if size(md.nodeconnectivity,1)~=md.mesh.numberofvertices,
-        md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+if size(md.mesh.nodeconnectivity,1)~=md.mesh.numberofvertices,
+        md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
 end
-if size(md.elementconnectivity,1)~=md.mesh.numberofelements,
-        md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+if size(md.mesh.elementconnectivity,1)~=md.mesh.numberofelements,
+        md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
 end
 
@@ -55 +55 @@
 %figure out which elements on land are actually in the middle of the ocean!
 pos1=find(elementonland); 
-connectedtoland=md.elementconnectivity(pos1,:);
+connectedtoland=md.mesh.elementconnectivity(pos1,:);
 pos=find(connectedtoland); connectedtoland(pos)=1-elementonland(connectedtoland(pos));
 connectedtolandsum=sum(connectedtoland,2);
@@ -63 +63 @@
 %figure out which elements on water  are actually in the middle of the land!
 pos1=find(~elementonland); 
-connectedtowater=md.elementconnectivity(pos1,:);
+connectedtowater=md.mesh.elementconnectivity(pos1,:);
 pos=find(connectedtowater); connectedtowater(pos)=elementonland(connectedtowater(pos));
 connectedtowatersum=sum(connectedtowater,2);
@@ -106 +106 @@
 
 %Get current connectivity
-elementconnectivity=md.elementconnectivity;
+mesh.elementconnectivity=md.mesh.elementconnectivity;
 
 %put 0 for elements on water
-pos=find(elementconnectivity);
-elementconnectivity(pos)=elementconnectivity(pos).*(~elementonwater(elementconnectivity(pos)));
+pos=find(mesh.elementconnectivity);
+mesh.elementconnectivity(pos)=mesh.elementconnectivity(pos).*(~elementonwater(mesh.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
+mesh.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');
+mesh.elementconnectivity=sort(mesh.elementconnectivity,2,'descend');
 
 %call findsegments to build segment using THIS conectivity
-md.mesh.segments=findsegments(md,'elementconnectivity',elementconnectivity);
+md.mesh.segments=findsegments(md,'mesh.elementconnectivity',mesh.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);
+lengthconnectivity=size(md.mesh.nodeconnectivity,2);
+groundedcounters=md.mesh.nodeconnectivity(nodesgrounded,lengthconnectivity);
+groundedconnectivity=md.mesh.nodeconnectivity(nodesgrounded,1:lengthconnectivity-1);
 pos=find(groundedconnectivity);
 groundedconnectivity(pos)=elementonwater(groundedconnectivity(pos));

issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m

@@ -48 +48 @@
 
 %now, for each node, figure out which element it belongs to.
-node_in_element=NodeInElement(newx,newy,md.elements,md.x,md.y,md.nodeconnectivity);
+node_in_element=NodeInElement(newx,newy,md.elements,md.x,md.y,md.mesh.nodeconnectivity);
 
 % eliminate nodes that don't fall in any element

issm/trunk/src/m/utils/Mesh/squaremesh.m

@@ -72 +72 @@
 
 %Now, build the connectivity tables for this mesh.
-md.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
-md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+md.mesh.nodeconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices);
+md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.nodeconnectivity);
 
 %plug other field

issm/trunk/template

@@ -8 +8 @@
           edges
 
-          uppernodes
-          upperelements
-          lowerelements
-          lowernodes
-
           elements2d
           x2d
@@ -21 +16 @@
           nodeonbed
           nodeonsurface
-
-          nodeconnectivity
-          elementconnectivity
 }}}