Index: /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 9727) +++ /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 9728) @@ -155,4 +155,7 @@ MeshNumberoflayersEnum, MeshNumberofvertices2dEnum, + MeshElementconnectivityEnum, + MeshLowerelementsEnum, + MeshUpperelementsEnum, /*}}}*/ /*Datasets {{{1*/ @@ -470,10 +473,7 @@ YEnum, ZEnum, - UpperelementsEnum, EdgesEnum, Elements2dEnum, XEnum, - ElementconnectivityEnum, - LowerelementsEnum, OutputfilenameEnum, WaterfractionEnum, Index: /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp =================================================================== --- /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 9727) +++ /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 9728) @@ -159,4 +159,7 @@ 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"; @@ -413,10 +416,7 @@ 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"; Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (revision 9727) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (revision 9728) @@ -45,6 +45,6 @@ /*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); @@ -63,5 +63,5 @@ /*Free data: */ - iomodel->DeleteData(9,ElementsEnum,ElementconnectivityEnum,UpperelementsEnum,LowerelementsEnum, + iomodel->DeleteData(9,ElementsEnum,MeshElementconnectivityEnum,MeshUpperelementsEnum,MeshLowerelementsEnum, MaterialsRheologyBEnum,MaterialsRheologyNEnum,InversionControlParametersEnum,InversionMinParametersEnum,InversionMaxParametersEnum); Index: /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 9727) +++ /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 9728) @@ -157,4 +157,7 @@ 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; @@ -411,10 +414,7 @@ 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; Index: /issm/trunk/src/c/objects/Elements/Penta.cpp =================================================================== --- /issm/trunk/src/c/objects/Elements/Penta.cpp (revision 9727) +++ /issm/trunk/src/c/objects/Elements/Penta.cpp (revision 9728) @@ -57,6 +57,6 @@ /*Checks in debugging mode*/ /*{{{2*/ - _assert_(iomodel->Data(UpperelementsEnum)); - _assert_(iomodel->Data(LowerelementsEnum)); + _assert_(iomodel->Data(MeshUpperelementsEnum)); + _assert_(iomodel->Data(MeshLowerelementsEnum)); /*}}}*/ @@ -66,13 +66,13 @@ /*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. Index: /issm/trunk/src/c/objects/Elements/Tria.cpp =================================================================== --- /issm/trunk/src/c/objects/Elements/Tria.cpp (revision 9727) +++ /issm/trunk/src/c/objects/Elements/Tria.cpp (revision 9728) @@ -52,5 +52,5 @@ /*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; Index: /issm/trunk/src/m/classes/mesh.m =================================================================== --- /issm/trunk/src/m/classes/mesh.m (revision 9727) +++ /issm/trunk/src/m/classes/mesh.m (revision 9728) @@ -22,4 +22,10 @@ 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 Index: /issm/trunk/src/m/classes/model/model.m =================================================================== --- /issm/trunk/src/m/classes/model/model.m (revision 9727) +++ /issm/trunk/src/m/classes/model/model.m (revision 9728) @@ -47,15 +47,8 @@ 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); @@ -318,4 +311,10 @@ 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 Index: sm/trunk/src/m/enum/ElementconnectivityEnum.m =================================================================== --- /issm/trunk/src/m/enum/ElementconnectivityEnum.m (revision 9727) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=ElementconnectivityEnum() -%ELEMENTCONNECTIVITYENUM - Enum of Elementconnectivity -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=ElementconnectivityEnum() - -macro=StringToEnum('Elementconnectivity'); Index: sm/trunk/src/m/enum/LowerelementsEnum.m =================================================================== --- /issm/trunk/src/m/enum/LowerelementsEnum.m (revision 9727) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=LowerelementsEnum() -%LOWERELEMENTSENUM - Enum of Lowerelements -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=LowerelementsEnum() - -macro=StringToEnum('Lowerelements'); Index: /issm/trunk/src/m/enum/MeshElementconnectivityEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshElementconnectivityEnum.m (revision 9728) +++ /issm/trunk/src/m/enum/MeshElementconnectivityEnum.m (revision 9728) @@ -0,0 +1,11 @@ +function macro=MeshElementconnectivityEnum() +%MESHELEMENTCONNECTIVITYENUM - Enum of MeshElementconnectivity +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=MeshElementconnectivityEnum() + +macro=StringToEnum('MeshElementconnectivity'); Index: /issm/trunk/src/m/enum/MeshLowerelementsEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshLowerelementsEnum.m (revision 9728) +++ /issm/trunk/src/m/enum/MeshLowerelementsEnum.m (revision 9728) @@ -0,0 +1,11 @@ +function macro=MeshLowerelementsEnum() +%MESHLOWERELEMENTSENUM - Enum of MeshLowerelements +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=MeshLowerelementsEnum() + +macro=StringToEnum('MeshLowerelements'); Index: /issm/trunk/src/m/enum/MeshUpperelementsEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshUpperelementsEnum.m (revision 9728) +++ /issm/trunk/src/m/enum/MeshUpperelementsEnum.m (revision 9728) @@ -0,0 +1,11 @@ +function macro=MeshUpperelementsEnum() +%MESHUPPERELEMENTSENUM - Enum of MeshUpperelements +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=MeshUpperelementsEnum() + +macro=StringToEnum('MeshUpperelements'); Index: sm/trunk/src/m/enum/UpperelementsEnum.m =================================================================== --- /issm/trunk/src/m/enum/UpperelementsEnum.m (revision 9727) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=UpperelementsEnum() -%UPPERELEMENTSENUM - Enum of Upperelements -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=UpperelementsEnum() - -macro=StringToEnum('Upperelements'); Index: /issm/trunk/src/m/model/PropagateFlagsUntilDistance.m =================================================================== --- /issm/trunk/src/m/model/PropagateFlagsUntilDistance.m (revision 9727) +++ /issm/trunk/src/m/model/PropagateFlagsUntilDistance.m (revision 9728) @@ -20,5 +20,5 @@ %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); @@ -38,5 +38,5 @@ 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; @@ -56,6 +56,6 @@ %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; Index: /issm/trunk/src/m/model/bamg.m =================================================================== --- /issm/trunk/src/m/model/bamg.m (revision 9727) +++ /issm/trunk/src/m/model/bamg.m (revision 9728) @@ -335,6 +335,6 @@ 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 Index: /issm/trunk/src/m/model/collapse.m =================================================================== --- /issm/trunk/src/m/model/collapse.m (revision 9727) +++ /issm/trunk/src/m/model/collapse.m (revision 9728) @@ -98,6 +98,6 @@ %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 Index: /issm/trunk/src/m/model/contourenvelope.m =================================================================== --- /issm/trunk/src/m/model/contourenvelope.m (revision 9727) +++ /issm/trunk/src/m/model/contourenvelope.m (revision 9728) @@ -35,13 +35,13 @@ %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, @@ -51,6 +51,6 @@ %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 @@ -64,6 +64,6 @@ %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 @@ -71,5 +71,5 @@ %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))); @@ -85,5 +85,5 @@ 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),:)); Index: /issm/trunk/src/m/model/extrude.m =================================================================== --- /issm/trunk/src/m/model/extrude.m (revision 9727) +++ /issm/trunk/src/m/model/extrude.m (revision 9728) @@ -87,18 +87,18 @@ %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 @@ -184,11 +184,11 @@ %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 Index: /issm/trunk/src/m/model/mesh/findsegments.m =================================================================== --- /issm/trunk/src/m/model/mesh/findsegments.m (revision 9727) +++ /issm/trunk/src/m/model/mesh/findsegments.m (revision 9728) @@ -3,5 +3,5 @@ % % Optional inputs: -% 'elementconnectivity' +% 'mesh.elementconnectivity' % % Usage: @@ -12,17 +12,17 @@ %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); @@ -37,5 +37,5 @@ %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 Index: /issm/trunk/src/m/model/mesh/meshnodensity.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 9727) +++ /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 9728) @@ -65,6 +65,6 @@ %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 Index: /issm/trunk/src/m/model/mesh/meshrefine.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshrefine.m (revision 9727) +++ /issm/trunk/src/m/model/mesh/meshrefine.m (revision 9728) @@ -29,6 +29,6 @@ %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 Index: /issm/trunk/src/m/model/mesh/meshyams.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshyams.m (revision 9727) +++ /issm/trunk/src/m/model/mesh/meshyams.m (revision 9728) @@ -95,6 +95,6 @@ %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); @@ -106,6 +106,6 @@ %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 Index: /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m (revision 9727) +++ /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m (revision 9728) @@ -87,6 +87,6 @@ %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 Index: /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m (revision 9727) +++ /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m (revision 9728) @@ -26,4 +26,6 @@ %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'); Index: /issm/trunk/src/m/model/mesh/setmesh.m =================================================================== --- /issm/trunk/src/m/model/mesh/setmesh.m (revision 9727) +++ /issm/trunk/src/m/model/mesh/setmesh.m (revision 9728) @@ -79,6 +79,6 @@ %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 Index: /issm/trunk/src/m/model/modelextract.m =================================================================== --- /issm/trunk/src/m/model/modelextract.m (revision 9727) +++ /issm/trunk/src/m/model/modelextract.m (revision 9728) @@ -123,21 +123,21 @@ 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 @@ -203,6 +203,6 @@ %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; Index: /issm/trunk/src/m/model/modelsextract.m =================================================================== --- /issm/trunk/src/m/model/modelsextract.m (revision 9727) +++ /issm/trunk/src/m/model/modelsextract.m (revision 9728) @@ -42,5 +42,5 @@ %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; Index: /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m =================================================================== --- /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m (revision 9727) +++ /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m (revision 9728) @@ -22,5 +22,5 @@ md.mesh.numberofelements=md.mesh.numberofelements2d; md.vertex_weight=[]; - md.nodeconnectivity=[]; + md.mesh.nodeconnectivity=[]; %run connectivity routine Index: /issm/trunk/src/m/model/partition/adjacency.m =================================================================== --- /issm/trunk/src/m/model/partition/adjacency.m (revision 9727) +++ /issm/trunk/src/m/model/partition/adjacency.m (revision 9728) @@ -19,7 +19,7 @@ %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; Index: /issm/trunk/src/m/model/partition/partitioner.m =================================================================== --- /issm/trunk/src/m/model/partition/partitioner.m (revision 9727) +++ /issm/trunk/src/m/model/partition/partitioner.m (revision 9728) @@ -40,5 +40,5 @@ md.mesh.numberofelements=md.mesh.numberofelements2d; md.qmu.vertex_weight=[]; - md.nodeconnectivity=[]; + md.mesh.nodeconnectivity=[]; end Index: /issm/trunk/src/m/model/setmask2.m =================================================================== --- /issm/trunk/src/m/model/setmask2.m (revision 9727) +++ /issm/trunk/src/m/model/setmask2.m (revision 9728) @@ -28,9 +28,9 @@ %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 @@ -55,5 +55,5 @@ %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); @@ -63,5 +63,5 @@ %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); @@ -106,26 +106,26 @@ %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)); Index: /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m (revision 9727) +++ /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m (revision 9728) @@ -48,5 +48,5 @@ %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 Index: /issm/trunk/src/m/utils/Mesh/squaremesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 9727) +++ /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 9728) @@ -72,6 +72,6 @@ %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 Index: /issm/trunk/template =================================================================== --- /issm/trunk/template (revision 9727) +++ /issm/trunk/template (revision 9728) @@ -8,9 +8,4 @@ edges - uppernodes - upperelements - lowerelements - lowernodes - elements2d x2d @@ -21,7 +16,4 @@ nodeonbed nodeonsurface - - nodeconnectivity - elementconnectivity }}}