Index: /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 9732) +++ /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 9733) @@ -163,8 +163,9 @@ MeshVertexonsurfaceEnum, MeshElements2dEnum, + MeshElementsEnum, + MeshEdgesEnum, /*}}}*/ /*Datasets {{{1*/ ConstraintsEnum, - ElementsEnum, LoadsEnum, MaterialsEnum, @@ -474,5 +475,4 @@ YEnum, ZEnum, - EdgesEnum, XEnum, OutputfilenameEnum, Index: /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp =================================================================== --- /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 9732) +++ /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 9733) @@ -167,6 +167,7 @@ case MeshVertexonsurfaceEnum : return "MeshVertexonsurface"; case MeshElements2dEnum : return "MeshElements2d"; + case MeshElementsEnum : return "MeshElements"; + case MeshEdgesEnum : return "MeshEdges"; case ConstraintsEnum : return "Constraints"; - case ElementsEnum : return "Elements"; case LoadsEnum : return "Loads"; case MaterialsEnum : return "Materials"; @@ -417,5 +418,4 @@ case YEnum : return "Y"; case ZEnum : return "Z"; - case EdgesEnum : return "Edges"; case XEnum : return "X"; case OutputfilenameEnum : return "Outputfilename"; Index: /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp (revision 9733) @@ -36,5 +36,5 @@ /*Get edges and elements*/ - iomodel->FetchData(3,EdgesEnum,ElementsEnum,ThicknessEnum); + iomodel->FetchData(3,MeshEdgesEnum,MeshElementsEnum,ThicknessEnum); /*First load data:*/ @@ -42,5 +42,5 @@ /*Get left and right elements*/ - element=(int)iomodel->Data(EdgesEnum)[4*i+2]-1; //edges are [node1 node2 elem1 elem2] + element=(int)iomodel->Data(MeshEdgesEnum)[4*i+2]-1; //edges are [node1 node2 elem1 elem2] /*Now, if this element is not in the partition, pass: */ @@ -52,5 +52,5 @@ /*Free data: */ - iomodel->DeleteData(3,EdgesEnum,ElementsEnum,ThicknessEnum); + iomodel->DeleteData(3,MeshEdgesEnum,MeshElementsEnum,ThicknessEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp (revision 9733) @@ -49,5 +49,5 @@ /*First fetch data: */ - iomodel->FetchData(7,ElementsEnum,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); + iomodel->FetchData(7,MeshElementsEnum,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); if(continuous_galerkin){ @@ -72,5 +72,5 @@ //Get index of the vertex on which the current node is located - vertex_id=(int)*(iomodel->Data(ElementsEnum)+3*i+j); //(Matlab indexing) + vertex_id=(int)*(iomodel->Data(MeshElementsEnum)+3*i+j); //(Matlab indexing) io_index=vertex_id-1; //(C indexing) _assert_(vertex_id>0 && vertex_id<=numberofvertices); @@ -88,5 +88,5 @@ /*Clean fetched data: */ - iomodel->DeleteData(7,ElementsEnum,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); + iomodel->DeleteData(7,MeshElementsEnum,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); /*Assign output pointer: */ Index: /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp (revision 9733) @@ -22,5 +22,5 @@ iomodel->Constant(&dim,MeshDimensionEnum); iomodel->Constant(&numberofelements,MeshNumberofelementsEnum); - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -52,4 +52,4 @@ } /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp (revision 9733) @@ -22,5 +22,5 @@ iomodel->Constant(&dim,MeshDimensionEnum); iomodel->Constant(&numberofelements,MeshNumberofelementsEnum); - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -44,4 +44,4 @@ /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 9733) @@ -35,5 +35,5 @@ /*Fetch data needed: */ - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); iomodel->FetchDataToInput(elements,InversionVxObsEnum); iomodel->FetchDataToInput(elements,InversionVyObsEnum); @@ -66,4 +66,4 @@ /*Free data: */ - iomodel->DeleteData(1+4+5,ElementsEnum,InversionControlParametersEnum,InversionCostFunctionsCoefficientsEnum,InversionMinParametersEnum,InversionMaxParametersEnum,BalancethicknessThickeningRateEnum,VxEnum,VyEnum,FrictionCoefficientEnum,MaterialsRheologyBEnum); + iomodel->DeleteData(1+4+5,MeshElementsEnum,InversionControlParametersEnum,InversionCostFunctionsCoefficientsEnum,InversionMinParametersEnum,InversionMaxParametersEnum,BalancethicknessThickeningRateEnum,VxEnum,VyEnum,FrictionCoefficientEnum,MaterialsRheologyBEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (revision 9733) @@ -37,5 +37,5 @@ /*First create the elements, vertices, nodes and material properties, if they don't already exist */ - elements = new Elements(ElementsEnum); + elements = new Elements(MeshElementsEnum); vertices = new Vertices(VerticesEnum); materials = new Materials(MaterialsEnum); @@ -45,5 +45,5 @@ /*Fetch data needed: */ - iomodel->FetchData(4,ElementsEnum,MeshElementconnectivityEnum,MaterialsRheologyBEnum,MaterialsRheologyNEnum); + iomodel->FetchData(4,MeshElementsEnum,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,MeshElementconnectivityEnum,MeshUpperelementsEnum,MeshLowerelementsEnum, + iomodel->DeleteData(9,MeshElementsEnum,MeshElementconnectivityEnum,MeshUpperelementsEnum,MeshLowerelementsEnum, MaterialsRheologyBEnum,MaterialsRheologyNEnum,InversionControlParametersEnum,InversionMinParametersEnum,InversionMaxParametersEnum); Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp (revision 9733) @@ -32,5 +32,5 @@ iomodel->Constant(&numberofelements,MeshNumberofelementsEnum); iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum); - elements=iomodel->Data(ElementsEnum); + elements=iomodel->Data(MeshElementsEnum); /*Some checks if debugging*/ Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp (revision 9733) @@ -35,5 +35,5 @@ iomodel->Constant(&numberofelements,MeshNumberofelementsEnum); iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum); - elements=iomodel->Data(ElementsEnum); + elements=iomodel->Data(MeshElementsEnum); /*Some checks if debugging*/ Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp (revision 9733) @@ -128,5 +128,5 @@ iomodel->FetchData(&nodeonstokes,NULL,NULL,FlowequationBorderstokesEnum); iomodel->FetchData(&vertices_type,NULL,NULL,FlowequationVertexEquationEnum); - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); CreateSingleNodeToElementConnectivity(iomodel); @@ -146,5 +146,5 @@ xfree((void**)&nodeonicesheet); xfree((void**)&vertices_type); - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); /*Create Penpair for penalties: */ Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp (revision 9733) @@ -35,5 +35,5 @@ /*Fetch data needed: */ - iomodel->FetchData(2,ElementsEnum,FlowequationElementEquationEnum); + iomodel->FetchData(2,MeshElementsEnum,FlowequationElementEquationEnum); /*Update elements: */ @@ -95,4 +95,4 @@ /*Free data: */ - iomodel->DeleteData(2,ElementsEnum,FlowequationElementEquationEnum); + iomodel->DeleteData(2,MeshElementsEnum,FlowequationElementEquationEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp (revision 9733) @@ -44,5 +44,5 @@ /*First fetch data: */ - iomodel->FetchData(7,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,ElementsEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); + iomodel->FetchData(7,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,MeshElementsEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); CreateNumberNodeToElementConnectivity(iomodel); @@ -57,5 +57,5 @@ /*Clean fetched data: */ - iomodel->DeleteData(7,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,ElementsEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); + iomodel->DeleteData(7,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,MeshElementsEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); /*Assign output pointer: */ Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp (revision 9733) @@ -27,5 +27,5 @@ if (!ishutter)return; - iomodel->FetchData(2,ElementsEnum,FlowequationElementEquationEnum); + iomodel->FetchData(2,MeshElementsEnum,FlowequationElementEquationEnum); /*Update elements: */ @@ -43,4 +43,4 @@ /*Free data: */ - iomodel->DeleteData(2,ElementsEnum,FlowequationElementEquationEnum); + iomodel->DeleteData(2,MeshElementsEnum,FlowequationElementEquationEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp (revision 9733) @@ -27,5 +27,5 @@ /*Fetch data needed: */ - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -55,5 +55,5 @@ /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (revision 9733) @@ -67,5 +67,5 @@ if(dim==2){ /*load elements: */ - iomodel->FetchData(&elements,NULL,NULL,ElementsEnum); + iomodel->FetchData(&elements,NULL,NULL,MeshElementsEnum); } else{ @@ -101,5 +101,5 @@ /*Start figuring out, out of the partition, which elements belong to this cpu: */ - iomodel->FetchData(&elements,NULL,NULL,ElementsEnum); + iomodel->FetchData(&elements,NULL,NULL,MeshElementsEnum); for (i=0;iFetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -61,4 +61,4 @@ /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp (revision 9733) @@ -20,5 +20,5 @@ /*Fetch data needed: */ iomodel->Constant(&numberofelements,MeshNumberofelementsEnum); - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -57,4 +57,4 @@ /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/Melting/CreateLoadsMelting.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Melting/CreateLoadsMelting.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Melting/CreateLoadsMelting.cpp (revision 9733) @@ -35,5 +35,5 @@ //create penalties for nodes: no node can have a temperature over the melting point - iomodel->FetchData(2,MeshVertexonbedEnum,ElementsEnum); + iomodel->FetchData(2,MeshVertexonbedEnum,MeshElementsEnum); CreateSingleNodeToElementConnectivity(iomodel); @@ -45,5 +45,5 @@ } } - iomodel->DeleteData(2,MeshVertexonbedEnum,ElementsEnum); + iomodel->DeleteData(2,MeshVertexonbedEnum,MeshElementsEnum); /*Assign output pointer: */ Index: /issm/trunk/src/c/modules/ModelProcessorx/Melting/UpdateElementsMelting.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Melting/UpdateElementsMelting.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Melting/UpdateElementsMelting.cpp (revision 9733) @@ -27,5 +27,5 @@ /*Fetch data needed: */ - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -60,4 +60,4 @@ /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/NodesPartitioning.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/NodesPartitioning.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/NodesPartitioning.cpp (revision 9733) @@ -109,6 +109,6 @@ /*Get edges and elements*/ - iomodel->FetchData(&edges,&numberofedges,&cols,EdgesEnum); - iomodel->FetchData(&elements,NULL,NULL,ElementsEnum); + iomodel->FetchData(&edges,&numberofedges,&cols,MeshEdgesEnum); + iomodel->FetchData(&elements,NULL,NULL,MeshElementsEnum); if (cols!=4) _error_("field edges should have 4 columns"); Index: /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp (revision 9733) @@ -41,5 +41,5 @@ /*Get edges and elements*/ - iomodel->FetchData(3,EdgesEnum,ElementsEnum,ThicknessEnum); + iomodel->FetchData(3,MeshEdgesEnum,MeshElementsEnum,ThicknessEnum); /*First load data:*/ @@ -47,5 +47,5 @@ /*Get left and right elements*/ - element=(int)(iomodel->Data(EdgesEnum)[4*i+2])-1; //edges are [node1 node2 elem1 elem2] + element=(int)(iomodel->Data(MeshEdgesEnum)[4*i+2])-1; //edges are [node1 node2 elem1 elem2] /*Now, if this element is not in the partition, pass: */ @@ -57,5 +57,5 @@ /*Free data: */ - iomodel->DeleteData(3,EdgesEnum,ElementsEnum,ThicknessEnum); + iomodel->DeleteData(3,MeshEdgesEnum,MeshElementsEnum,ThicknessEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp (revision 9733) @@ -49,5 +49,5 @@ /*First fetch data: */ - iomodel->FetchData(7,ElementsEnum,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); + iomodel->FetchData(7,MeshElementsEnum,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); if(continuous_galerkin){ @@ -72,5 +72,5 @@ //Get index of the vertex on which the current node is located - vertex_id=(int)*(iomodel->Data(ElementsEnum)+3*i+j); //(Matlab indexing) + vertex_id=(int)*(iomodel->Data(MeshElementsEnum)+3*i+j); //(Matlab indexing) io_index=vertex_id-1; //(C indexing) _assert_(vertex_id>0 && vertex_id<=numberofvertices); @@ -88,5 +88,5 @@ /*Clean fetched data: */ - iomodel->DeleteData(7,ElementsEnum,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); + iomodel->DeleteData(7,MeshElementsEnum,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,FlowequationVertexEquationEnum,MaskVertexonwaterEnum); /*Assign output pointer: */ Index: /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp (revision 9733) @@ -24,5 +24,5 @@ iomodel->Constant(&numberofelements,MeshNumberofelementsEnum); iomodel->Constant(&stabilization,PrognosticStabilizationEnum); - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -61,4 +61,4 @@ /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/UpdateElementsSurfaceSlope.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/UpdateElementsSurfaceSlope.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/UpdateElementsSurfaceSlope.cpp (revision 9733) @@ -22,5 +22,5 @@ iomodel->Constant(&dim,MeshDimensionEnum); iomodel->Constant(&numberofelements,MeshNumberofelementsEnum); - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -44,4 +44,4 @@ /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/ModelProcessorx/Thermal/CreateLoadsThermal.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Thermal/CreateLoadsThermal.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Thermal/CreateLoadsThermal.cpp (revision 9733) @@ -36,5 +36,5 @@ //create penalties for nodes: no node can have a temperature over the melting point - iomodel->FetchData(2,ThermalSpctemperatureEnum,ElementsEnum); + iomodel->FetchData(2,ThermalSpctemperatureEnum,MeshElementsEnum); CreateSingleNodeToElementConnectivity(iomodel); @@ -48,5 +48,5 @@ } } - iomodel->DeleteData(2,ThermalSpctemperatureEnum,ElementsEnum); + iomodel->DeleteData(2,ThermalSpctemperatureEnum,MeshElementsEnum); /*Assign output pointer: */ Index: /issm/trunk/src/c/modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp (revision 9732) +++ /issm/trunk/src/c/modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp (revision 9733) @@ -29,5 +29,5 @@ /*Fetch data needed: */ - iomodel->FetchData(1,ElementsEnum); + iomodel->FetchData(1,MeshElementsEnum); /*Update elements: */ @@ -64,4 +64,4 @@ /*Free data: */ - iomodel->DeleteData(1,ElementsEnum); + iomodel->DeleteData(1,MeshElementsEnum); } Index: /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 9732) +++ /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 9733) @@ -165,6 +165,7 @@ else if (strcmp(name,"MeshVertexonsurface")==0) return MeshVertexonsurfaceEnum; else if (strcmp(name,"MeshElements2d")==0) return MeshElements2dEnum; + else if (strcmp(name,"MeshElements")==0) return MeshElementsEnum; + else if (strcmp(name,"MeshEdges")==0) return MeshEdgesEnum; else if (strcmp(name,"Constraints")==0) return ConstraintsEnum; - else if (strcmp(name,"Elements")==0) return ElementsEnum; else if (strcmp(name,"Loads")==0) return LoadsEnum; else if (strcmp(name,"Materials")==0) return MaterialsEnum; @@ -415,5 +416,4 @@ else if (strcmp(name,"Y")==0) return YEnum; else if (strcmp(name,"Z")==0) return ZEnum; - else if (strcmp(name,"Edges")==0) return EdgesEnum; else if (strcmp(name,"X")==0) return XEnum; else if (strcmp(name,"Outputfilename")==0) return OutputfilenameEnum; Index: /issm/trunk/src/c/objects/Elements/Penta.cpp =================================================================== --- /issm/trunk/src/c/objects/Elements/Penta.cpp (revision 9732) +++ /issm/trunk/src/c/objects/Elements/Penta.cpp (revision 9733) @@ -4853,5 +4853,5 @@ /*Recover vertices ids needed to initialize inputs*/ for(i=0;i<6;i++){ - penta_vertex_ids[i]=(int)iomodel->Data(ElementsEnum)[6*index+i]; //ids for vertices are in the elements array from Matlab + penta_vertex_ids[i]=(int)iomodel->Data(MeshElementsEnum)[6*index+i]; //ids for vertices are in the elements array from Matlab } @@ -4947,5 +4947,5 @@ /*Step1: Get original input (to be depth avegaged): */ - if (object_enum==ElementsEnum) + if (object_enum==MeshElementsEnum) original_input=(Input*)penta->inputs->GetInput(enum_type); else if (object_enum==MaterialsEnum) @@ -5007,5 +5007,5 @@ /*Finally, add to inputs*/ - if (object_enum==ElementsEnum) + if (object_enum==MeshElementsEnum) this->inputs->AddInput((Input*)depth_averaged_input); else if (object_enum==MaterialsEnum) @@ -5037,5 +5037,5 @@ /*Step1: Extrude the original input: */ - if (object_type==ElementsEnum) + if (object_type==MeshElementsEnum) original_input=(Input*)this->inputs->GetInput(enum_type); else if (object_type==MaterialsEnum) @@ -5060,5 +5060,5 @@ Input* copy=NULL; copy=(Input*)original_input->copy(); - if (object_type==ElementsEnum) + if (object_type==MeshElementsEnum) penta->inputs->AddInput((Input*)copy); else if (object_type==MaterialsEnum) @@ -5160,10 +5160,10 @@ /*Checks if debuging*/ /*{{{2*/ - _assert_(iomodel->Data(ElementsEnum)); + _assert_(iomodel->Data(MeshElementsEnum)); /*}}}*/ /*Recover vertices ids needed to initialize inputs*/ for(i=0;i<6;i++){ - penta_vertex_ids[i]=(int)iomodel->Data(ElementsEnum)[6*index+i]; //ids for vertices are in the elements array from Matlab + penta_vertex_ids[i]=(int)iomodel->Data(MeshElementsEnum)[6*index+i]; //ids for vertices are in the elements array from Matlab } @@ -7515,5 +7515,5 @@ /*Checks if debuging*/ /*{{{2*/ - _assert_(iomodel->Data(ElementsEnum)); + _assert_(iomodel->Data(MeshElementsEnum)); /*}}}*/ @@ -7530,5 +7530,5 @@ /*Recover vertices ids needed to initialize inputs*/ - for(i=0;i<6;i++) penta_vertex_ids[i]=(int)iomodel->Data(ElementsEnum)[6*index+i]; //ids for vertices are in the elements array from Matlab + for(i=0;i<6;i++) penta_vertex_ids[i]=(int)iomodel->Data(MeshElementsEnum)[6*index+i]; //ids for vertices are in the elements array from Matlab /*Recover nodes ids needed to initialize the node hook.*/ @@ -7536,5 +7536,5 @@ //go recover node ids, needed to initialize the node hook. //WARNING: We assume P1 elements here!!!!! - penta_node_ids[i]=iomodel->nodecounter+(int)iomodel->Data(ElementsEnum)[6*index+i]; //ids for vertices are in the elements array from Matlab + penta_node_ids[i]=iomodel->nodecounter+(int)iomodel->Data(MeshElementsEnum)[6*index+i]; //ids for vertices are in the elements array from Matlab } Index: /issm/trunk/src/c/objects/Elements/Penta.h =================================================================== --- /issm/trunk/src/c/objects/Elements/Penta.h (revision 9732) +++ /issm/trunk/src/c/objects/Elements/Penta.h (revision 9733) @@ -101,5 +101,5 @@ void InputCreate(double scalar,int name,int code); void InputCreate(double* vector, int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code); - void InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum=ElementsEnum); + void InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum=MeshElementsEnum); void InputDuplicate(int original_enum,int new_enum); void InputScale(int enum_type,double scale_factor); Index: /issm/trunk/src/c/objects/Elements/Tria.cpp =================================================================== --- /issm/trunk/src/c/objects/Elements/Tria.cpp (revision 9732) +++ /issm/trunk/src/c/objects/Elements/Tria.cpp (revision 9733) @@ -3170,5 +3170,5 @@ /*copy input of enum_type*/ - if (object_enum==ElementsEnum) + if (object_enum==MeshElementsEnum) oldinput=(Input*)this->inputs->GetInput(enum_type); else if (object_enum==MaterialsEnum) @@ -3183,5 +3183,5 @@ /*Add new input to current element*/ - if (object_enum==ElementsEnum) + if (object_enum==MeshElementsEnum) this->inputs->AddInput((Input*)newinput); else if (object_enum==MaterialsEnum) @@ -3278,5 +3278,5 @@ /*Recover vertices ids needed to initialize inputs*/ for(i=0;i<3;i++){ - tria_vertex_ids[i]=(int)iomodel->Data(ElementsEnum)[3*index+i]; //ids for vertices are in the elements array from Matlab + tria_vertex_ids[i]=(int)iomodel->Data(MeshElementsEnum)[3*index+i]; //ids for vertices are in the elements array from Matlab } @@ -3907,5 +3907,5 @@ /*Recover vertices ids needed to initialize inputs*/ for(i=0;i<3;i++){ - tria_vertex_ids[i]=(int)iomodel->Data(ElementsEnum)[3*index+i]; //ids for vertices are in the elements array from Matlab + tria_vertex_ids[i]=(int)iomodel->Data(MeshElementsEnum)[3*index+i]; //ids for vertices are in the elements array from Matlab } @@ -5214,5 +5214,5 @@ /*Checks if debuging*/ /*{{{2*/ - _assert_(iomodel->Data(ElementsEnum)); + _assert_(iomodel->Data(MeshElementsEnum)); /*}}}*/ @@ -5236,5 +5236,5 @@ /*Recover vertices ids needed to initialize inputs*/ for(i=0;i<3;i++){ - tria_vertex_ids[i]=(int)iomodel->Data(ElementsEnum)[3*index+i]; //ids for vertices are in the elements array from Matlab + tria_vertex_ids[i]=(int)iomodel->Data(MeshElementsEnum)[3*index+i]; //ids for vertices are in the elements array from Matlab } @@ -5249,5 +5249,5 @@ /*Continuous Galerkin*/ for(i=0;i<3;i++){ - tria_node_ids[i]=iomodel->nodecounter+(int)*(iomodel->Data(ElementsEnum)+3*index+i); //ids for vertices are in the elements array from Matlab + tria_node_ids[i]=iomodel->nodecounter+(int)*(iomodel->Data(MeshElementsEnum)+3*index+i); //ids for vertices are in the elements array from Matlab } } Index: /issm/trunk/src/c/objects/Elements/Tria.h =================================================================== --- /issm/trunk/src/c/objects/Elements/Tria.h (revision 9732) +++ /issm/trunk/src/c/objects/Elements/Tria.h (revision 9733) @@ -102,5 +102,5 @@ void InputCreate(double scalar,int name,int code); void InputCreate(double* vector, int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code); - void InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum=ElementsEnum); + void InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum=MeshElementsEnum); void InputDuplicate(int original_enum,int new_enum); void InputScale(int enum_type,double scale_factor); Index: /issm/trunk/src/c/objects/Loads/Numericalflux.cpp =================================================================== --- /issm/trunk/src/c/objects/Loads/Numericalflux.cpp (revision 9732) +++ /issm/trunk/src/c/objects/Loads/Numericalflux.cpp (revision 9733) @@ -60,7 +60,7 @@ /*First, see wether this is an internal or boundary edge (if e2=NaN)*/ - if (isnan((double)iomodel->Data(EdgesEnum)[4*i+3])){ //edges are [node1 node2 elem1 elem2] + if (isnan((double)iomodel->Data(MeshEdgesEnum)[4*i+3])){ //edges are [node1 node2 elem1 elem2] /* Boundary edge, only one element */ - e1=(int)iomodel->Data(EdgesEnum)[4*i+2]; + e1=(int)iomodel->Data(MeshEdgesEnum)[4*i+2]; e2=(int)UNDEF; num_elems=1; @@ -71,6 +71,6 @@ else{ /* internal edge: connected to 2 elements */ - e1=(int)iomodel->Data(EdgesEnum)[4*i+2]; - e2=(int)iomodel->Data(EdgesEnum)[4*i+3]; + e1=(int)iomodel->Data(MeshEdgesEnum)[4*i+2]; + e2=(int)iomodel->Data(MeshEdgesEnum)[4*i+3]; num_elems=2; num_nodes=4; @@ -81,6 +81,6 @@ /*1: Get vertices ids*/ - i1=(int)iomodel->Data(EdgesEnum)[4*i+0]; - i2=(int)iomodel->Data(EdgesEnum)[4*i+1]; + i1=(int)iomodel->Data(MeshEdgesEnum)[4*i+0]; + i2=(int)iomodel->Data(MeshEdgesEnum)[4*i+1]; if (numericalflux_type==InternalEnum){ @@ -91,8 +91,8 @@ pos1=pos2=pos3=pos4=UNDEF; for(j=0;j<3;j++){ - if (iomodel->Data(ElementsEnum)[3*(e1-1)+j]==i1) pos1=j+1; - if (iomodel->Data(ElementsEnum)[3*(e1-1)+j]==i2) pos2=j+1; - if (iomodel->Data(ElementsEnum)[3*(e2-1)+j]==i1) pos3=j+1; - if (iomodel->Data(ElementsEnum)[3*(e2-1)+j]==i2) pos4=j+1; + if (iomodel->Data(MeshElementsEnum)[3*(e1-1)+j]==i1) pos1=j+1; + if (iomodel->Data(MeshElementsEnum)[3*(e1-1)+j]==i2) pos2=j+1; + if (iomodel->Data(MeshElementsEnum)[3*(e2-1)+j]==i1) pos3=j+1; + if (iomodel->Data(MeshElementsEnum)[3*(e2-1)+j]==i2) pos4=j+1; } _assert_(pos1!=UNDEF && pos2!=UNDEF && pos3!=UNDEF && pos4!=UNDEF); @@ -110,6 +110,6 @@ pos1=pos2=UNDEF; for(j=0;j<3;j++){ - if (iomodel->Data(ElementsEnum)[3*(e1-1)+j]==i1) pos1=j+1; - if (iomodel->Data(ElementsEnum)[3*(e1-1)+j]==i2) pos2=j+1; + if (iomodel->Data(MeshElementsEnum)[3*(e1-1)+j]==i1) pos1=j+1; + if (iomodel->Data(MeshElementsEnum)[3*(e1-1)+j]==i2) pos2=j+1; } _assert_(pos1!=UNDEF && pos2!=UNDEF); Index: /issm/trunk/src/c/objects/Materials/Matice.cpp =================================================================== --- /issm/trunk/src/c/objects/Materials/Matice.cpp (revision 9732) +++ /issm/trunk/src/c/objects/Materials/Matice.cpp (revision 9733) @@ -675,5 +675,5 @@ /*Get B*/ if (iomodel->Data(MaterialsRheologyBEnum)) { - for(i=0;iData(MaterialsRheologyBEnum)[int(iomodel->Data(ElementsEnum)[num_vertices*index+i]-1)]; + for(i=0;iData(MaterialsRheologyBEnum)[int(iomodel->Data(MeshElementsEnum)[num_vertices*index+i]-1)]; this->inputs->AddInput(new TriaVertexInput(MaterialsRheologyBbarEnum,nodeinputs)); } @@ -692,7 +692,7 @@ if (iomodel->Data(MaterialsRheologyBEnum)){ _assert_(iomodel->Data(MaterialsRheologyBEnum));_assert_(iomodel->Data(InversionMinParametersEnum)); _assert_(iomodel->Data(InversionMaxParametersEnum)); - for(j=0;jData(MaterialsRheologyBEnum)[int(iomodel->Data(ElementsEnum)[num_vertices*index+j]-1)]; - for(j=0;jData(InversionMinParametersEnum)[int(iomodel->Data(ElementsEnum)[num_vertices*index+j]-1)*num_control_type+i]; - for(j=0;jData(InversionMaxParametersEnum)[int(iomodel->Data(ElementsEnum)[num_vertices*index+j]-1)*num_control_type+i]; + for(j=0;jData(MaterialsRheologyBEnum)[int(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)]; + for(j=0;jData(InversionMinParametersEnum)[int(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i]; + for(j=0;jData(InversionMaxParametersEnum)[int(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i]; this->inputs->AddInput(new ControlInput(MaterialsRheologyBbarEnum,TriaVertexInputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1)); } @@ -714,5 +714,5 @@ /*Get B*/ if (iomodel->Data(MaterialsRheologyBEnum)) { - for(i=0;iData(MaterialsRheologyBEnum)[int(iomodel->Data(ElementsEnum)[num_vertices*index+i]-1)]; + for(i=0;iData(MaterialsRheologyBEnum)[int(iomodel->Data(MeshElementsEnum)[num_vertices*index+i]-1)]; this->inputs->AddInput(new PentaVertexInput(MaterialsRheologyBEnum,nodeinputs)); } @@ -731,7 +731,7 @@ if (iomodel->Data(MaterialsRheologyBEnum)){ _assert_(iomodel->Data(MaterialsRheologyBEnum));_assert_(iomodel->Data(InversionMinParametersEnum)); _assert_(iomodel->Data(InversionMaxParametersEnum)); - for(j=0;jData(MaterialsRheologyBEnum)[int(iomodel->Data(ElementsEnum)[num_vertices*index+j]-1)]; - for(j=0;jData(InversionMinParametersEnum)[int(iomodel->Data(ElementsEnum)[num_vertices*index+j]-1)*num_control_type+i]; - for(j=0;jData(InversionMaxParametersEnum)[int(iomodel->Data(ElementsEnum)[num_vertices*index+j]-1)*num_control_type+i]; + for(j=0;jData(MaterialsRheologyBEnum)[int(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)]; + for(j=0;jData(InversionMinParametersEnum)[int(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i]; + for(j=0;jData(InversionMaxParametersEnum)[int(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i]; this->inputs->AddInput(new ControlInput(MaterialsRheologyBEnum,PentaVertexInputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1)); } Index: /issm/trunk/src/m/classes/mesh.m =================================================================== --- /issm/trunk/src/m/classes/mesh.m (revision 9732) +++ /issm/trunk/src/m/classes/mesh.m (revision 9733) @@ -35,4 +35,6 @@ x2d = modelfield('default',NaN,'marshall',false); y2d = modelfield('default',NaN,'marshall',false); + elements = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); + edges = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); end methods Index: /issm/trunk/src/m/classes/model/model.m =================================================================== --- /issm/trunk/src/m/classes/model/model.m (revision 9732) +++ /issm/trunk/src/m/classes/model/model.m (revision 9733) @@ -43,9 +43,7 @@ %FIXME: all other fields should belong to other classes - elements = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); x = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); y = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); z = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - edges = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); %}}} @@ -207,5 +205,5 @@ if isfield(structmd,'ishutter'), md.flowequation.ishutter=structmd.ishutter; end if isfield(structmd,'isstokes'), md.flowequation.isstokes=structmd.isstokes; end - if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end + if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.mesh.elements_type; end if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end @@ -262,7 +260,9 @@ if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end if isfield(structmd,'nodeonbed'), md.mesh.vertexonbed=structmd.nodeonbed; end - if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end + if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.mesh.elements2d; end if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end + if isfield(structmd,'elements'), md.mesh.elements=structmd.mesh.elements; end + if isfield(structmd,'edges'), md.mesh.edges=structmd.mesh.edges; end %Field changes @@ -295,13 +295,13 @@ pos=find(structmd.pressureload(:,end)==119); md.pressureload(pos,end)=2; end - if (structmd.elements_type(end,end)>100), - pos=find(structmd.elements_type==59); md.elements_type(pos,end)=0; - pos=find(structmd.elements_type==55); md.elements_type(pos,end)=1; - pos=find(structmd.elements_type==56); md.elements_type(pos,end)=2; - pos=find(structmd.elements_type==60); md.elements_type(pos,end)=3; - pos=find(structmd.elements_type==62); md.elements_type(pos,end)=4; - pos=find(structmd.elements_type==57); md.elements_type(pos,end)=5; - pos=find(structmd.elements_type==58); md.elements_type(pos,end)=6; - pos=find(structmd.elements_type==61); md.elements_type(pos,end)=7; + if (structmd.mesh.elements_type(end,end)>100), + pos=find(structmd.mesh.elements_type==59); md.mesh.elements_type(pos,end)=0; + pos=find(structmd.mesh.elements_type==55); md.mesh.elements_type(pos,end)=1; + pos=find(structmd.mesh.elements_type==56); md.mesh.elements_type(pos,end)=2; + pos=find(structmd.mesh.elements_type==60); md.mesh.elements_type(pos,end)=3; + pos=find(structmd.mesh.elements_type==62); md.mesh.elements_type(pos,end)=4; + pos=find(structmd.mesh.elements_type==57); md.mesh.elements_type(pos,end)=5; + pos=find(structmd.mesh.elements_type==58); md.mesh.elements_type(pos,end)=6; + pos=find(structmd.mesh.elements_type==61); md.mesh.elements_type(pos,end)=7; end if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law), Index: sm/trunk/src/m/enum/EdgesEnum.m =================================================================== --- /issm/trunk/src/m/enum/EdgesEnum.m (revision 9732) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=EdgesEnum() -%EDGESENUM - Enum of Edges -% -% 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=EdgesEnum() - -macro=StringToEnum('Edges'); Index: sm/trunk/src/m/enum/Elements2dEnum.m =================================================================== --- /issm/trunk/src/m/enum/Elements2dEnum.m (revision 9732) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=Elements2dEnum() -%ELEMENTS2DENUM - Enum of Elements2d -% -% 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=Elements2dEnum() - -macro=StringToEnum('Elements2d'); Index: sm/trunk/src/m/enum/ElementsEnum.m =================================================================== --- /issm/trunk/src/m/enum/ElementsEnum.m (revision 9732) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=ElementsEnum() -%ELEMENTSENUM - Enum of Elements -% -% 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=ElementsEnum() - -macro=StringToEnum('Elements'); Index: /issm/trunk/src/m/enum/MeshEdgesEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshEdgesEnum.m (revision 9733) +++ /issm/trunk/src/m/enum/MeshEdgesEnum.m (revision 9733) @@ -0,0 +1,11 @@ +function macro=MeshEdgesEnum() +%MESHEDGESENUM - Enum of MeshEdges +% +% 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=MeshEdgesEnum() + +macro=StringToEnum('MeshEdges'); Index: /issm/trunk/src/m/enum/MeshElements2dEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshElements2dEnum.m (revision 9733) +++ /issm/trunk/src/m/enum/MeshElements2dEnum.m (revision 9733) @@ -0,0 +1,11 @@ +function macro=MeshElements2dEnum() +%MESHELEMENTS2DENUM - Enum of MeshElements2d +% +% 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=MeshElements2dEnum() + +macro=StringToEnum('MeshElements2d'); Index: /issm/trunk/src/m/enum/MeshElementsEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshElementsEnum.m (revision 9733) +++ /issm/trunk/src/m/enum/MeshElementsEnum.m (revision 9733) @@ -0,0 +1,11 @@ +function macro=MeshElementsEnum() +%MESHELEMENTSENUM - Enum of MeshElements +% +% 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=MeshElementsEnum() + +macro=StringToEnum('MeshElements'); Index: /issm/trunk/src/m/kml/kml_mesh_elem.m =================================================================== --- /issm/trunk/src/m/kml/kml_mesh_elem.m (revision 9732) +++ /issm/trunk/src/m/kml/kml_mesh_elem.m (revision 9733) @@ -80,9 +80,9 @@ display('Averaging nodal data to element data.'); edata=zeros(1,md.mesh.numberofelements); - for i=1:size(md.elements,1) - for j=1:size(md.elements,2) - edata(i)=edata(i)+ndata(md.elements(i,j)); + for i=1:size(md.mesh.elements,1) + for j=1:size(md.mesh.elements,2) + edata(i)=edata(i)+ndata(md.mesh.elements(i,j)); end - edata(i)=edata(i)/size(md.elements,2); + edata(i)=edata(i)/size(md.mesh.elements,2); end else @@ -126,12 +126,12 @@ md.mesh.numberofelements,md.mesh.numberofvertices); % see matlab_oop, "initializing a handle object array" -%kfold.feature ={repmat(kml_placemark(),1,size(md.elements,1))}; -kfeat(size(md.elements,1))=kml_placemark(); +%kfold.feature ={repmat(kml_placemark(),1,size(md.mesh.elements,1))}; +kfeat(size(md.mesh.elements,1))=kml_placemark(); kfold.feature={kfeat}; % write each element as a polygon placemark -disp(['Writing ' num2str(size(md.elements,1)) ' tria elements as KML polygons.']); -for i=1:size(md.elements,1) +disp(['Writing ' num2str(size(md.mesh.elements,1)) ' tria elements as KML polygons.']); +for i=1:size(md.mesh.elements,1) kplace=kml_placemark(); kplace.name =sprintf('Element %d',i); @@ -157,8 +157,8 @@ kring=kml_linearring(); - kring.coords =zeros(size(md.elements,2)+1,3); + kring.coords =zeros(size(md.mesh.elements,2)+1,3); - for j=1:size(md.elements,2) - kring.coords(j,:)=[md.mesh.long(md.elements(i,j)) md.mesh.lat(md.elements(i,j)) alt]; + for j=1:size(md.mesh.elements,2) + kring.coords(j,:)=[md.mesh.long(md.mesh.elements(i,j)) md.mesh.lat(md.mesh.elements(i,j)) alt]; end kring.coords(end,:)=kring.coords(1,:); Index: /issm/trunk/src/m/kml/kml_mesh_write.m =================================================================== --- /issm/trunk/src/m/kml/kml_mesh_write.m (revision 9732) +++ /issm/trunk/src/m/kml/kml_mesh_write.m (revision 9733) @@ -86,9 +86,9 @@ display('Averaging nodal data to element data.'); edata=zeros(1,md.mesh.numberofelements); - for i=1:size(md.elements,1) - for j=1:size(md.elements,2) - edata(i)=edata(i)+ndata(md.elements(i,j)); + for i=1:size(md.mesh.elements,1) + for j=1:size(md.mesh.elements,2) + edata(i)=edata(i)+ndata(md.mesh.elements(i,j)); end - edata(i)=edata(i)/size(md.elements,2); + edata(i)=edata(i)/size(md.mesh.elements,2); end else Index: /issm/trunk/src/m/kml/kml_part_edges.m =================================================================== --- /issm/trunk/src/m/kml/kml_part_edges.m (revision 9732) +++ /issm/trunk/src/m/kml/kml_part_edges.m (revision 9733) @@ -81,9 +81,9 @@ display('Averaging nodal data to element data.'); edata=zeros(1,md.mesh.numberofelements); - for i=1:size(md.elements,1) - for j=1:size(md.elements,2) - edata(i)=edata(i)+ndata(md.elements(i,j)); + for i=1:size(md.mesh.elements,1) + for j=1:size(md.mesh.elements,2) + edata(i)=edata(i)+ndata(md.mesh.elements(i,j)); end - edata(i)=edata(i)/size(md.elements,2); + edata(i)=edata(i)/size(md.mesh.elements,2); end else @@ -129,5 +129,5 @@ disp(['Writing ' num2str(md.qmu.numberofpartitions) ' partitions as KML linestrings.']); - epart=md.qmu.partition(md.elements)+1; + epart=md.qmu.partition(md.mesh.elements)+1; if exist('ndata','var') || exist('edata','var') pdata=zeros(1,md.qmu.numberofpartitions); @@ -148,5 +148,5 @@ end irow=unique(irow); - elemp=md.elements(irow,:); + elemp=md.mesh.elements(irow,:); epartp=epart(irow,:); nodeconp=nodeconnectivity(elemp,md.mesh.numberofvertices); Index: /issm/trunk/src/m/kml/kml_part_elems.m =================================================================== --- /issm/trunk/src/m/kml/kml_part_elems.m (revision 9732) +++ /issm/trunk/src/m/kml/kml_part_elems.m (revision 9733) @@ -81,9 +81,9 @@ display('Averaging nodal data to element data.'); edata=zeros(1,md.mesh.numberofelements); - for i=1:size(md.elements,1) - for j=1:size(md.elements,2) - edata(i)=edata(i)+ndata(md.elements(i,j)); - end - edata(i)=edata(i)/size(md.elements,2); + for i=1:size(md.mesh.elements,1) + for j=1:size(md.mesh.elements,2) + edata(i)=edata(i)+ndata(md.mesh.elements(i,j)); + end + edata(i)=edata(i)/size(md.mesh.elements,2); end else @@ -129,5 +129,5 @@ disp(['Writing ' num2str(md.qmu.numberofpartitions) ' partitions as KML polygons.']); - epart=md.qmu.partition(md.elements)+1; + epart=md.qmu.partition(md.mesh.elements)+1; if exist('ndata','var') || exist('edata','var') pdata=zeros(1,md.qmu.numberofpartitions); @@ -146,5 +146,5 @@ end irow=unique(irow); - elem=md.elements(irow,:); + elem=md.mesh.elements(irow,:); % determine the data to be used for the colors (if any) Index: /issm/trunk/src/m/kml/kml_part_flagedges.m =================================================================== --- /issm/trunk/src/m/kml/kml_part_flagedges.m (revision 9732) +++ /issm/trunk/src/m/kml/kml_part_flagedges.m (revision 9733) @@ -74,5 +74,5 @@ if (~exist('prtplt','var') || strncmpi(prtplt,'on' ,2) || strncmpi(prtplt,'y',1)) && ... md.qmu.numberofpartitions - [latseg,lonseg]=flagedges(md.elements,md.mesh.lat,md.mesh.long,md.qmu.partition); + [latseg,lonseg]=flagedges(md.mesh.elements,md.mesh.lat,md.mesh.long,md.qmu.partition); kfold=kml_folder(); kfold.name ='Partition Segments'; Index: /issm/trunk/src/m/kml/kml_partitions.m =================================================================== --- /issm/trunk/src/m/kml/kml_partitions.m (revision 9732) +++ /issm/trunk/src/m/kml/kml_partitions.m (revision 9733) @@ -82,9 +82,9 @@ display('Averaging nodal data to element data.'); edata=zeros(1,md.mesh.numberofelements); - for i=1:size(md.elements,1) - for j=1:size(md.elements,2) - edata(i)=edata(i)+ndata(md.elements(i,j)); + for i=1:size(md.mesh.elements,1) + for j=1:size(md.mesh.elements,2) + edata(i)=edata(i)+ndata(md.mesh.elements(i,j)); end - edata(i)=edata(i)/size(md.elements,2); + edata(i)=edata(i)/size(md.mesh.elements,2); end else @@ -130,5 +130,5 @@ disp(['Writing ' num2str(md.qmu.numberofpartitions) ' partitions as KML polygons.']); - epart=md.qmu.partition(md.elements)+1; + epart=md.qmu.partition(md.mesh.elements)+1; if exist('ndata','var') || exist('edata','var') pdata=zeros(1,md.qmu.numberofpartitions); @@ -149,5 +149,5 @@ end irow=unique(irow); - elemp=md.elements(irow,:); + elemp=md.mesh.elements(irow,:); epartp=epart(irow,:); nodeconp=nodeconnectivity(elemp,md.mesh.numberofvertices); Index: /issm/trunk/src/m/kml/kml_unsh_edges.m =================================================================== --- /issm/trunk/src/m/kml/kml_unsh_edges.m (revision 9732) +++ /issm/trunk/src/m/kml/kml_unsh_edges.m (revision 9733) @@ -74,10 +74,10 @@ if (~exist('prtplt','var') || strncmpi(prtplt,'on' ,2) || strncmpi(prtplt,'y',1)) && ... md.qmu.numberofpartitions - [edgeadj]=edgeadjacency(md.elements,md.nodeconnectivity); + [edgeadj]=edgeadjacency(md.mesh.elements,md.nodeconnectivity); [icol,irow]=find(edgeadj'==0); edgeuns=zeros(length(irow),2); for i=1:length(irow) - edgeuns(i,1)=md.elements(irow(i),icol(i)); - edgeuns(i,2)=md.elements(irow(i),mod(icol(i),size(md.elements,2))+1); + edgeuns(i,1)=md.mesh.elements(irow(i),icol(i)); + edgeuns(i,2)=md.mesh.elements(irow(i),mod(icol(i),size(md.mesh.elements,2))+1); end kfold=kml_folder(); Index: /issm/trunk/src/m/model/BasinConstrain.m =================================================================== --- /issm/trunk/src/m/model/BasinConstrain.m (revision 9732) +++ /issm/trunk/src/m/model/BasinConstrain.m (revision 9733) @@ -33,5 +33,5 @@ end %ok, flag elements and nodes - [vertexondomain elementondomain]=ContourToMesh(md.elements(:,1:3),md.x,md.y,domain,'element and node',2); + [vertexondomain elementondomain]=ContourToMesh(md.mesh.elements(:,1:3),md.x,md.y,domain,'element and node',2); end if invert, @@ -54,5 +54,5 @@ %now, make sure all elements on water have nodes that are spc'd, otherwise, we'll get a singular problem. pos=find(~md.mask.elementonwater); -numpos=unique(md.elements(pos,:)); +numpos=unique(md.mesh.elements(pos,:)); nodes=setdiff(1:1:md.mesh.numberofvertices,numpos); md.diagnostic.spcvx(nodes)=md.inversion.vx_obs(nodes); Index: /issm/trunk/src/m/model/BasinConstrainShelf.m =================================================================== --- /issm/trunk/src/m/model/BasinConstrainShelf.m (revision 9732) +++ /issm/trunk/src/m/model/BasinConstrainShelf.m (revision 9733) @@ -33,5 +33,5 @@ end %ok, flag elements and nodes - [vertexondomain elementondomain]=ContourToMesh(md.elements(:,1:3),md.x,md.y,domain,'element and node',2); + [vertexondomain elementondomain]=ContourToMesh(md.mesh.elements(:,1:3),md.x,md.y,domain,'element and node',2); end if invert, @@ -54,5 +54,5 @@ %now, make sure all elements on water have nodes that are spc'd, otherwise, we'll get a singular problem. pos=find(~md.mask.elementonwater); -numpos=unique(md.elements(pos,:)); +numpos=unique(md.mesh.elements(pos,:)); nodes=setdiff(1:1:md.mesh.numberofvertices,numpos); md.diagnostic.spcvx(nodes)=md.inversion.vx_obs(nodes); Index: /issm/trunk/src/m/model/MeltingGroundingLines.m =================================================================== --- /issm/trunk/src/m/model/MeltingGroundingLines.m (revision 9732) +++ /issm/trunk/src/m/model/MeltingGroundingLines.m (revision 9733) @@ -8,5 +8,5 @@ %get nodes on ice sheet and on ice shelf pos_shelf=find(~md.mask.vertexongroundedice); -pos_GL=intersect(unique(md.elements(find(md.mask.elementongroundedice),:)),unique(md.elements(find(md.mask.elementonfloatingice),:))); +pos_GL=intersect(unique(md.mesh.elements(find(md.mask.elementongroundedice),:)),unique(md.mesh.elements(find(md.mask.elementonfloatingice),:))); for i=1:length(pos_shelf) Index: /issm/trunk/src/m/model/PropagateFlagsUntilDistance.m =================================================================== --- /issm/trunk/src/m/model/PropagateFlagsUntilDistance.m (revision 9732) +++ /issm/trunk/src/m/model/PropagateFlagsUntilDistance.m (revision 9733) @@ -15,5 +15,5 @@ md.x=md.mesh.x2d; md.y=md.mesh.y2d; - md.elements=md.mesh.elements2d; + md.mesh.elements=md.mesh.elements2d; end @@ -27,6 +27,6 @@ %average x and y over elements: -x_elem=md.x(md.elements)*[1;1;1]/3; -y_elem=md.y(md.elements)*[1;1;1]/3; +x_elem=md.x(md.mesh.elements)*[1;1;1]/3; +y_elem=md.y(md.mesh.elements)*[1;1;1]/3; while 1, Index: /issm/trunk/src/m/model/SectionValues.m =================================================================== --- /issm/trunk/src/m/model/SectionValues.m (revision 9732) +++ /issm/trunk/src/m/model/SectionValues.m (revision 9733) @@ -82,5 +82,5 @@ %Interpolation of data on specified points - data_interp=InterpFromMeshToMesh2d(md.elements,md.x,md.y,data,X,Y); + data_interp=InterpFromMeshToMesh2d(md.mesh.elements,md.x,md.y,data,X,Y); %data_interp=griddata(md.x,md.y,data,X,Y); @@ -120,5 +120,5 @@ %Interpolation of data on specified points - data_interp=InterpFromMeshToMesh3d(md.elements,md.x,md.y,md.z,data,X3,Y3,Z3,NaN); + data_interp=InterpFromMeshToMesh3d(md.mesh.elements,md.x,md.y,md.z,data,X3,Y3,Z3,NaN); %build outputs Index: /issm/trunk/src/m/model/ThicknessCorrection.m =================================================================== --- /issm/trunk/src/m/model/ThicknessCorrection.m (revision 9732) +++ /issm/trunk/src/m/model/ThicknessCorrection.m (revision 9733) @@ -24,5 +24,5 @@ %get nodes on ice sheet and on ice shelf pos_shelf=find(~md.mask.vertexongroundedice); -pos_GL=intersect(unique(md.elements(find(md.mask.elementongroundedice),:)),unique(md.elements(find(md.mask.elementonfloatingice),:))); +pos_GL=intersect(unique(md.mesh.elements(find(md.mask.elementongroundedice),:)),unique(md.mesh.elements(find(md.mask.elementonfloatingice),:))); debug=(length(pos_shelf)>50000); Index: /issm/trunk/src/m/model/averageconnectivity.m =================================================================== --- /issm/trunk/src/m/model/averageconnectivity.m (revision 9732) +++ /issm/trunk/src/m/model/averageconnectivity.m (revision 9733) @@ -7,5 +7,5 @@ nnz=0; for i=1:md.mesh.numberofvertices, - nnz=nnz+length(find(md.elements==i)); + nnz=nnz+length(find(md.mesh.elements==i)); end conn=nnz/md.mesh.numberofvertices; Index: /issm/trunk/src/m/model/averaging.m =================================================================== --- /issm/trunk/src/m/model/averaging.m (revision 9732) +++ /issm/trunk/src/m/model/averaging.m (revision 9733) @@ -25,5 +25,5 @@ %load some variables (it is much faster if the variab;es are loaded from md once for all) -index=md.elements; +index=md.mesh.elements; numberofnodes=md.mesh.numberofvertices; numberofelements=md.mesh.numberofelements; Index: /issm/trunk/src/m/model/bamg.m =================================================================== --- /issm/trunk/src/m/model/bamg.m (revision 9732) +++ /issm/trunk/src/m/model/bamg.m (revision 9733) @@ -271,5 +271,5 @@ else bamg_mesh.Vertices=[md.x md.y ones(md.mesh.numberofvertices,1)]; - bamg_mesh.Triangles=[md.elements ones(md.mesh.numberofelements,1)]; + bamg_mesh.Triangles=[md.mesh.elements ones(md.mesh.numberofelements,1)]; end @@ -319,6 +319,6 @@ md.x=bamgmesh_out.Vertices(:,1); md.y=bamgmesh_out.Vertices(:,2); -md.elements=bamgmesh_out.Triangles(:,1:3); -md.edges=bamgmesh_out.IssmEdges; +md.mesh.elements=bamgmesh_out.Triangles(:,1:3); +md.mesh.edges=bamgmesh_out.IssmEdges; md.mesh.segments=bamgmesh_out.IssmSegments(:,1:3); md.mesh.segmentmarkers=bamgmesh_out.IssmSegments(:,4); @@ -326,7 +326,7 @@ %Fill in rest of fields: md.mesh.dimension=2; -md.mesh.numberofelements=size(md.elements,1); +md.mesh.numberofelements=size(md.mesh.elements,1); md.mesh.numberofvertices=length(md.x); -md.mesh.numberofedges=size(md.edges,1); +md.mesh.numberofedges=size(md.mesh.edges,1); md.z=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); @@ -340,5 +340,5 @@ %Check for orphan -if any(~ismember(1:md.mesh.numberofvertices,sort(unique(md.elements(:))))) +if any(~ismember(1:md.mesh.numberofvertices,sort(unique(md.mesh.elements(:))))) error('Output mesh has orphans. Decrease MaxCornerAngle to prevent outside points (ex: 0.01)'); end Index: /issm/trunk/src/m/model/basevert.m =================================================================== --- /issm/trunk/src/m/model/basevert.m (revision 9732) +++ /issm/trunk/src/m/model/basevert.m (revision 9733) @@ -14,5 +14,5 @@ for n=1:md.mesh.numberofelements - X=inv([md.x(md.elements(n,:)) md.y(md.elements(n,:)) ones(3,1)]); + X=inv([md.x(md.mesh.elements(n,:)) md.y(md.mesh.elements(n,:)) ones(3,1)]); alpha(n,:)=X(1,:); beta(n,:)=X(2,:); @@ -24,12 +24,12 @@ summation=[1;1;1]; -hux=(hu(md.elements).*alpha)*summation; -hvy=(hv(md.elements).*beta)*summation; +hux=(hu(md.mesh.elements).*alpha)*summation; +hvy=(hv(md.mesh.elements).*beta)*summation; -uelem=md.initialization.vx(md.elements)*summation/3; -velem=md.initialization.vy(md.elements)*summation/3; +uelem=md.initialization.vx(md.mesh.elements)*summation/3; +velem=md.initialization.vy(md.mesh.elements)*summation/3; -dbdx=(md.geometry.bed(md.elements).*alpha)*summation; -dbdy=(md.geometry.bed(md.elements).*beta)*summation; +dbdx=(md.geometry.bed(md.mesh.elements).*alpha)*summation; +dbdy=(md.geometry.bed(md.mesh.elements).*beta)*summation; wb=-md.materials.rho_ice/md.materials.rho_water*(hux+hvy)+uelem.*dbdx+velem.*dbdy; Index: /issm/trunk/src/m/model/bedslope.m =================================================================== --- /issm/trunk/src/m/model/bedslope.m (revision 9732) +++ /issm/trunk/src/m/model/bedslope.m (revision 9733) @@ -9,5 +9,5 @@ numberofelements=md.mesh.numberofelements; numberofnodes=md.mesh.numberofvertices; - index=md.elements; + index=md.mesh.elements; x=md.x; y=md.y; else Index: /issm/trunk/src/m/model/collapse.m =================================================================== --- /issm/trunk/src/m/model/collapse.m (revision 9732) +++ /issm/trunk/src/m/model/collapse.m (revision 9733) @@ -95,5 +95,5 @@ md.mesh.numberofvertices=md.mesh.numberofvertices2d; md.mesh.numberofelements=md.mesh.numberofelements2d; -md.elements=md.mesh.elements2d; +md.mesh.elements=md.mesh.elements2d; %Keep a trace of lower and upper nodes Index: /issm/trunk/src/m/model/contourenvelope.m =================================================================== --- /issm/trunk/src/m/model/contourenvelope.m (revision 9732) +++ /issm/trunk/src/m/model/contourenvelope.m (revision 9733) @@ -36,8 +36,8 @@ %Computing connectivity if size(md.mesh.vertexconnectivity,1)~=md.mesh.numberofvertices, - md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); + md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); end if size(md.mesh.elementconnectivity,1)~=md.mesh.numberofelements, - md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); + md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); end @@ -47,6 +47,6 @@ if isfile, %get flag list of elements and nodes inside the contour - nodein=ContourToMesh(md.elements,md.x,md.y,file,'node',1); - elemin=(sum(nodein(md.elements),2)==size(md.elements,2)); + nodein=ContourToMesh(md.mesh.elements,md.x,md.y,file,'node',1); + elemin=(sum(nodein(md.mesh.elements),2)==size(md.mesh.elements,2)); %modify element connectivity elemout=find(~elemin); @@ -60,5 +60,5 @@ pos=find(flags); elemin(pos)=1; - nodein(md.elements(pos,:))=1; + nodein(md.mesh.elements(pos,:))=1; %modify element connectivity @@ -87,11 +87,11 @@ els2=mesh.elementconnectivity(el1,find(mesh.elementconnectivity(el1,:))); if length(els2)>1, - flag=intersect(md.elements(els2(1),:),md.elements(els2(2),:)); - nods1=md.elements(el1,:); + flag=intersect(md.mesh.elements(els2(1),:),md.mesh.elements(els2(2),:)); + nods1=md.mesh.elements(el1,:); nods1(find(nods1==flag))=[]; segments(count,:)=[nods1 el1]; - ord1=find(nods1(1)==md.elements(el1,:)); - ord2=find(nods1(2)==md.elements(el1,:)); + ord1=find(nods1(1)==md.mesh.elements(el1,:)); + ord2=find(nods1(2)==md.mesh.elements(el1,:)); %swap segment nodes if necessary @@ -104,12 +104,12 @@ count=count+1; else - nods1=md.elements(el1,:); - flag=setdiff(nods1,md.elements(els2,:)); + nods1=md.mesh.elements(el1,:); + flag=setdiff(nods1,md.mesh.elements(els2,:)); for j=1:3, nods=nods1; nods(j)=[]; if any(ismember(flag,nods)), segments(count,:)=[nods el1]; - ord1=find(nods(1)==md.elements(el1,:)); - ord2=find(nods(2)==md.elements(el1,:)); + ord1=find(nods(1)==md.mesh.elements(el1,:)); + ord2=find(nods(2)==md.mesh.elements(el1,:)); if ( (ord1==1 & ord2==2) | (ord1==2 & ord2==3) | (ord1==3 & ord2==1) ), temp=segments(count,1); Index: /issm/trunk/src/m/model/contourmassbalance.m =================================================================== --- /issm/trunk/src/m/model/contourmassbalance.m (revision 9732) +++ /issm/trunk/src/m/model/contourmassbalance.m (revision 9733) @@ -22,6 +22,6 @@ %get flag list of elements and nodes inside the contour -nodein=ContourToMesh(md.elements,md.x,md.y,file,'node',1); -elemin=(sum(nodein(md.elements),2)==size(md.elements,2)); +nodein=ContourToMesh(md.mesh.elements,md.x,md.y,file,'node',1); +elemin=(sum(nodein(md.mesh.elements),2)==size(md.mesh.elements,2)); %conputing Mass flux @@ -36,5 +36,5 @@ flux = - md.materials.rho_ice*sum(L.*H.*(vx.*nx+vy.*ny)); %outflux is negative! disp(['mass outflux on ' file ' = ' num2str(-flux/10^9) ' Gt/yr']); -areas=GetAreas(md.elements,md.x,md.y); +areas=GetAreas(md.mesh.elements,md.x,md.y); dhdt=flux/(sum(areas(find(elemin)))*md.materials.rho_ice); disp(['dhdt on ' file ' (Flux method) = ' num2str(dhdt) ' m/yr']); Index: /issm/trunk/src/m/model/divergence.m =================================================================== --- /issm/trunk/src/m/model/divergence.m (revision 9732) +++ /issm/trunk/src/m/model/divergence.m (revision 9733) @@ -8,5 +8,5 @@ numberofelements=md.mesh.numberofelements; numberofnodes=md.mesh.numberofvertices; - index=md.elements; + index=md.mesh.elements; x=md.x; y=md.y; z=md.z; else Index: /issm/trunk/src/m/model/drivingstress.m =================================================================== --- /issm/trunk/src/m/model/drivingstress.m (revision 9732) +++ /issm/trunk/src/m/model/drivingstress.m (revision 9733) @@ -12,5 +12,5 @@ %Average thickness over elements -thickness_bar=(md.geometry.thickness(md.elements(:,1))+md.geometry.thickness(md.elements(:,2))+md.geometry.thickness(md.elements(:,3)))/3; +thickness_bar=(md.geometry.thickness(md.mesh.elements(:,1))+md.geometry.thickness(md.mesh.elements(:,2))+md.geometry.thickness(md.mesh.elements(:,3)))/3; px=md.materials.rho_ice*md.constants.g*thickness_bar.*sx; Index: /issm/trunk/src/m/model/extrude.m =================================================================== --- /issm/trunk/src/m/model/extrude.m (revision 9732) +++ /issm/trunk/src/m/model/extrude.m (revision 9733) @@ -82,5 +82,5 @@ elements3d=[]; for i=1:numlayers-1, - elements3d=[elements3d;[md.elements+(i-1)*md.mesh.numberofvertices md.elements+i*md.mesh.numberofvertices]]; %Create the elements of the 3d mesh for the non extruded part + elements3d=[elements3d;[md.mesh.elements+(i-1)*md.mesh.numberofvertices md.mesh.elements+i*md.mesh.numberofvertices]]; %Create the elements of the 3d mesh for the non extruded part end number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh @@ -105,5 +105,5 @@ md.mesh.x2d=md.x; md.mesh.y2d=md.y; -md.mesh.elements2d=md.elements; +md.mesh.elements2d=md.mesh.elements; md.mesh.numberofelements2d=md.mesh.numberofelements; md.mesh.numberofvertices2d=md.mesh.numberofvertices; @@ -113,5 +113,5 @@ %Build global 3d mesh -md.elements=elements3d; +md.mesh.elements=elements3d; md.x=x3d; md.y=y3d; Index: /issm/trunk/src/m/model/kmlimagesc.m =================================================================== --- /issm/trunk/src/m/model/kmlimagesc.m (revision 9732) +++ /issm/trunk/src/m/model/kmlimagesc.m (revision 9733) @@ -49,5 +49,5 @@ %regrid to lat,long grid -[x_m,y_m,field]=InterpFromMeshToGrid(md.elements,md.mesh.long,md.mesh.lat,field,minlong,maxlat,posting,posting,nlines,ncols,NaN); +[x_m,y_m,field]=InterpFromMeshToGrid(md.mesh.elements,md.mesh.long,md.mesh.lat,field,minlong,maxlat,posting,posting,nlines,ncols,NaN); field=flipud(field); Index: /issm/trunk/src/m/model/mechanicalproperties.m =================================================================== --- /issm/trunk/src/m/model/mechanicalproperties.m (revision 9732) +++ /issm/trunk/src/m/model/mechanicalproperties.m (revision 9733) @@ -26,5 +26,5 @@ %initialization numberofelements=md.mesh.numberofelements; -index=md.elements; +index=md.mesh.elements; summation=[1;1;1]; directionsstress=zeros(numberofelements,4); Index: /issm/trunk/src/m/model/mesh/findsegments.m =================================================================== --- /issm/trunk/src/m/model/mesh/findsegments.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/findsegments.m (revision 9733) @@ -19,5 +19,5 @@ error(' ''mesh.elementconnectivity'' option does not have thge right size.'); else - mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); + mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); end end @@ -43,8 +43,8 @@ %get nodes of el1 - nods1=md.elements(el1,:); + nods1=md.mesh.elements(el1,:); %find the common vertices to the two elements connected to el1 (1 or 2) - flag=intersect(md.elements(els2(1),:),md.elements(els2(2),:)); + flag=intersect(md.mesh.elements(els2(1),:),md.mesh.elements(els2(2),:)); %get the vertices on the boundary and build segment @@ -53,6 +53,6 @@ %swap segment nodes if necessary - ord1=find(nods1(1)==md.elements(el1,:)); - ord2=find(nods1(2)==md.elements(el1,:)); + ord1=find(nods1(1)==md.mesh.elements(el1,:)); + ord2=find(nods1(2)==md.mesh.elements(el1,:)); if ( (ord1==1 & ord2==2) | (ord1==2 & ord2==3) | (ord1==3 & ord2==1) ), temp=segments(count,1); @@ -66,8 +66,8 @@ else %get nodes of el1 - nods1=md.elements(el1,:); + nods1=md.mesh.elements(el1,:); %find the vertex the el1 to not share with els2 - flag=setdiff(nods1,md.elements(els2,:)); + flag=setdiff(nods1,md.mesh.elements(els2,:)); for j=1:3, @@ -78,6 +78,6 @@ %swap segment nodes if necessary - ord1=find(nods(1)==md.elements(el1,:)); - ord2=find(nods(2)==md.elements(el1,:)); + ord1=find(nods(1)==md.mesh.elements(el1,:)); + ord2=find(nods(2)==md.mesh.elements(el1,:)); if ( (ord1==1 & ord2==2) | (ord1==2 & ord2==3) | (ord1==3 & ord2==1) ), temp=segments(count,1); Index: /issm/trunk/src/m/model/mesh/meshadaptation.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshadaptation.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/meshadaptation.m (revision 9733) @@ -24,5 +24,5 @@ %initialization -index=md.elements; +index=md.mesh.elements; numberofnodes=md.mesh.numberofvertices; numberofelements=md.mesh.numberofelements; Index: /issm/trunk/src/m/model/mesh/meshbamg.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshbamg.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/meshbamg.m (revision 9733) @@ -97,5 +97,5 @@ %set nodeonwater field if ~strcmp(groundeddomain,'N/A'), - nodeground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); + nodeground=ContourToMesh(md.mesh.elements,md.x,md.y,groundeddomain,'node',2); md.nodeonwater=ones(md.mesh.numberofvertices,1); md.nodeonwater(find(nodeground))=0; Index: /issm/trunk/src/m/model/mesh/meshconvert.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshconvert.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/meshconvert.m (revision 9733) @@ -14,5 +14,5 @@ x=md.x; y=md.y; - index=md.elements; + index=md.mesh.elements; else x=varargin{1}; @@ -30,6 +30,6 @@ md.x=bamgmesh_out.Vertices(:,1); md.y=bamgmesh_out.Vertices(:,2); -md.elements=bamgmesh_out.Triangles(:,1:3); -md.edges=bamgmesh_out.IssmEdges; +md.mesh.elements=bamgmesh_out.Triangles(:,1:3); +md.mesh.edges=bamgmesh_out.IssmEdges; md.mesh.segments=bamgmesh_out.IssmSegments(:,1:3); md.mesh.segmentmarkers=bamgmesh_out.IssmSegments(:,4); @@ -37,7 +37,7 @@ %Fill in rest of fields: md.mesh.dimension=2; -md.mesh.numberofelements=size(md.elements,1); +md.mesh.numberofelements=size(md.mesh.elements,1); md.mesh.numberofvertices=length(md.x); -md.mesh.numberofedges=size(md.edges,1); +md.mesh.numberofedges=size(md.mesh.edges,1); md.z=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/model/mesh/meshexprefine.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshexprefine.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/meshexprefine.m (revision 9733) @@ -35,6 +35,6 @@ %Read domainame file into a matlab array (x,y): -refinearea=ContourToMesh(md.elements,md.x,md.y,domainname,'element',1); -aires=GetAreas(md.elements,md.x,md.y); +refinearea=ContourToMesh(md.mesh.elements,md.x,md.y,domainname,'element',1); +aires=GetAreas(md.mesh.elements,md.x,md.y); %flags areas within the domain Index: /issm/trunk/src/m/model/mesh/meshnodensity.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 9733) @@ -25,5 +25,5 @@ %Mesh using TriMeshNoDensity if strcmp(riftname,''), - [md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshNoDensity(domainname); + [md.mesh.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshNoDensity(domainname); else [elements,x,y,segments,segmentmarkers]=TriMeshNoDensity(domainname,riftname); @@ -49,5 +49,5 @@ md.x=x; md.y=y; - md.elements=elements; + md.mesh.elements=elements; md.mesh.segments=segments; md.mesh.segmentmarkers=segmentmarkers; @@ -55,5 +55,5 @@ %Fill in rest of fields: -md.mesh.numberofelements=length(md.elements); +md.mesh.numberofelements=length(md.mesh.elements); md.mesh.numberofvertices=length(md.x); md.z=zeros(md.mesh.numberofvertices,1); @@ -65,6 +65,6 @@ %Now, build the connectivity tables for this mesh. -md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); -md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); %type of model Index: /issm/trunk/src/m/model/mesh/meshrefine.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshrefine.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/meshrefine.m (revision 9733) @@ -16,8 +16,8 @@ %Refine using TriMeshRefine -[md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshRefine(md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers,areas,'yes'); +[md.mesh.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshRefine(md.mesh.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers,areas,'yes'); %Fill in rest of fields: -md.mesh.numberofelements=length(md.elements); +md.mesh.numberofelements=length(md.mesh.elements); md.mesh.numberofvertices=length(md.x); md.z=zeros(md.mesh.numberofvertices,1); @@ -29,6 +29,6 @@ %Now, build the connectivity tables for this mesh. -md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); -md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); %type of model Index: /issm/trunk/src/m/model/mesh/meshyams.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshyams.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/meshyams.m (revision 9733) @@ -81,5 +81,5 @@ %set nodeonwater field if ~strcmp(groundeddomain,'N/A'), - nodeground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); + nodeground=ContourToMesh(md.mesh.elements,md.x,md.y,groundeddomain,'node',2); md.nodeonwater=ones(md.mesh.numberofvertices,1); md.nodeonwater(find(nodeground))=0; @@ -95,6 +95,6 @@ %rifts, because the segments are used in YamsCall to freeze the rifts elements during refinement. if md.rifts.numrifts, - md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); - md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); + md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); + md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); md.mesh.segments=findsegments(md); md=meshyamsrecreateriftsegments(md); @@ -106,6 +106,6 @@ %Now, build the connectivity tables for this mesh. -md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); -md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); %recreate segments @@ -120,5 +120,5 @@ md.mesh.elementonsurface=ones(md.mesh.numberofelements,1); if ~strcmp(groundeddomain,'N/A'), - nodeground=ContourToMesh(md.elements,md.x,md.y,groundeddomain,'node',2); + nodeground=ContourToMesh(md.mesh.elements,md.x,md.y,groundeddomain,'node',2); md.nodeonwater=ones(md.mesh.numberofvertices,1); md.nodeonwater(find(nodeground))=0; Index: /issm/trunk/src/m/model/mesh/reorder.m =================================================================== --- /issm/trunk/src/m/model/mesh/reorder.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/reorder.m (revision 9733) @@ -20,5 +20,5 @@ %update all fields -md.elements=tnewnodes(md.elements(newelements,:)); +md.mesh.elements=tnewnodes(md.mesh.elements(newelements,:)); md.mesh.segments=[tnewnodes(md.mesh.segments(:,1)) tnewnodes(md.mesh.segments(:,2)) tnewelements(md.mesh.segments(:,3))]; md.x=md.x(newnodes); Index: /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m (revision 9733) @@ -56,6 +56,6 @@ %plug md2 mesh into md mesh: - [md.elements,md.x,md.y,md.z,md.mesh.numberofelements,md.mesh.numberofvertices,elconv,nodeconv,elconv2,nodeconv2]=meshplug(md.elements,md.x,md.y,md.z,... - md2.elements,md2.x,md2.y,md2.z,md2.extractednodes,md2.extractedelements,domain_index); + [md.mesh.elements,md.x,md.y,md.z,md.mesh.numberofelements,md.mesh.numberofvertices,elconv,nodeconv,elconv2,nodeconv2]=meshplug(md.mesh.elements,md.x,md.y,md.z,... + md2.mesh.elements,md2.x,md2.y,md2.z,md2.extractednodes,md2.extractedelements,domain_index); %update md2 rifts using elconv and nodeconv, and plug them into md: @@ -87,6 +87,6 @@ %Now, build the connectivity tables for this mesh. -md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); -md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); %type of model Index: /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m (revision 9733) @@ -12,5 +12,5 @@ %first, flag nodes that belong to the domain outline - flags=ContourToMesh(md.elements,md.x,md.y,domainoutline,'node',0); + flags=ContourToMesh(md.mesh.elements,md.x,md.y,domainoutline,'node',0); rift=md.rifts.riftstruct(i); @@ -43,5 +43,5 @@ while flags(B), %as long as B does not belong to the domain outline, keep looking. %detect elements on edge A,B: - edgeelements=ElementsFromEdge(md.elements,A,B); + edgeelements=ElementsFromEdge(md.mesh.elements,A,B); %rule out those we already detected already_detected=ismember(edgeelements,elements); @@ -50,5 +50,5 @@ elements=[elements;nextelement]; %new B: - B=md.elements(nextelement,find(~ismember(md.elements(nextelement,:),[A B]))); + B=md.mesh.elements(nextelement,find(~ismember(md.mesh.elements(nextelement,:),[A B]))); end @@ -61,8 +61,8 @@ %replace tip in elements - newelements=md.elements(elements,:); + newelements=md.mesh.elements(elements,:); pos=find(newelements==tip); newelements(pos)=num; - md.elements(elements,:)=newelements; + md.mesh.elements(elements,:)=newelements; md.rifts.riftstruct(i).tips=[md.rifts.riftstruct(i).tips num]; @@ -73,5 +73,5 @@ pos=find(md.mesh.segments(segment_index,1:2)~=tip); other_node=md.mesh.segments(segment_index,pos); - if ~isconnected(md.elements,other_node,tip), + if ~isconnected(md.mesh.elements,other_node,tip), pos=find(md.mesh.segments(segment_index,1:2)==tip); md.mesh.segments(segment_index,pos)=num; @@ -83,5 +83,5 @@ %Fill in rest of fields: -md.mesh.numberofelements=length(md.elements); +md.mesh.numberofelements=length(md.mesh.elements); md.mesh.numberofvertices=length(md.x); md.z=zeros(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m (revision 9733) @@ -25,5 +25,5 @@ %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.mesh.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers,md.rifts.riftstruct]=TriMeshProcessRifts(md.mesh.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers); md.rifts md.rifts.riftstruct @@ -33,5 +33,5 @@ %Fill in rest of fields: -md.mesh.numberofelements=length(md.elements); +md.mesh.numberofelements=length(md.mesh.elements); md.mesh.numberofvertices=length(md.x); md.z=zeros(md.mesh.numberofvertices,1); @@ -51,5 +51,5 @@ %In case we have rifts that open up the domain outline, we need to open them: -flags=ContourToMesh(md.elements,md.x,md.y,domainoutline,'node',0); +flags=ContourToMesh(md.mesh.elements,md.x,md.y,domainoutline,'node',0); found=0; for i=1:md.rifts.numrifts, @@ -68,5 +68,5 @@ %get elements that are not correctly oriented in the correct direction: -aires=GetAreas(md.elements,md.x,md.y); +aires=GetAreas(md.mesh.elements,md.x,md.y); pos=find(aires<0); -md.elements(pos,:)=[md.elements(pos,2) md.elements(pos,1) md.elements(pos,3)]; +md.mesh.elements(pos,:)=[md.mesh.elements(pos,2) md.mesh.elements(pos,1) md.mesh.elements(pos,3)]; Index: /issm/trunk/src/m/model/mesh/setmesh.m =================================================================== --- /issm/trunk/src/m/model/mesh/setmesh.m (revision 9732) +++ /issm/trunk/src/m/model/mesh/setmesh.m (revision 9733) @@ -39,5 +39,5 @@ %Mesh using TriMesh if strcmp(riftname,''), - [md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,area,'yes'); + [md.mesh.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,area,'yes'); else [elements,x,y,segments,segmentmarkers]=TriMesh(domainname,riftname,area,'yes'); @@ -63,5 +63,5 @@ md.x=x; md.y=y; - md.elements=elements; + md.mesh.elements=elements; md.mesh.segments=segments; md.mesh.segmentmarkers=segmentmarkers; @@ -69,5 +69,5 @@ %Fill in rest of fields: -md.mesh.numberofelements=length(md.elements); +md.mesh.numberofelements=length(md.mesh.elements); md.mesh.numberofvertices=length(md.x); md.z=zeros(md.mesh.numberofvertices,1); @@ -79,6 +79,6 @@ %Now, build the connectivity tables for this mesh. -md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); -md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); %type of model Index: /issm/trunk/src/m/model/misfit.m =================================================================== --- /issm/trunk/src/m/model/misfit.m (revision 9732) +++ /issm/trunk/src/m/model/misfit.m (revision 9733) @@ -10,5 +10,5 @@ if md.mesh.dimension==2, - elements=md.elements; + elements=md.mesh.elements; x=md.x; y=md.y; Index: /issm/trunk/src/m/model/modelextract.m =================================================================== --- /issm/trunk/src/m/model/modelextract.m (revision 9732) +++ /issm/trunk/src/m/model/modelextract.m (revision 9733) @@ -38,13 +38,13 @@ %kick out all elements with 3 dirichlets spc_elem=find(~flag_elem); -spc_node=sort(unique(md1.elements(spc_elem,:))); +spc_node=sort(unique(md1.mesh.elements(spc_elem,:))); flag=ones(md1.numberofnodes,1); flag(spc_node)=0; -pos=find(sum(flag(md1.elements),2)==0); +pos=find(sum(flag(md1.mesh.elements),2)==0); flag_elem(pos)=0; %extracted elements and nodes lists pos_elem=find(flag_elem); -pos_node=sort(unique(md1.elements(pos_elem,:))); +pos_node=sort(unique(md1.mesh.elements(pos_elem,:))); %keep track of some fields @@ -63,5 +63,5 @@ %renumber the elements (some node won't exist anymore) -elements_1=md1.elements; +elements_1=md1.mesh.elements; elements_2=elements_1(pos_elem,:); elements_2(:,1)=Pnode(elements_2(:,1)); @@ -121,5 +121,5 @@ md2.numberofelements=numberofelements2; md2.numberofnodes=numberofnodes2; - md2.elements=elements_2; + md2.mesh.elements=elements_2; %mesh.uppervertex mesh.lowervertex @@ -161,28 +161,28 @@ %Edges - if size(md2.edges,2)>1, %do not use ~isnan because there are some NaNs... + if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs... %renumber first two columns - pos=find(~isnan(md2.edges(:,4))); - md2.edges(: ,1)=Pnode(md2.edges(:,1)); - md2.edges(: ,2)=Pnode(md2.edges(:,2)); - md2.edges(: ,3)=Pelem(md2.edges(:,3)); - md2.edges(pos,4)=Pelem(md2.edges(pos,4)); + pos=find(~isnan(md2.mesh.edges(:,4))); + md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1)); + md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2)); + md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3)); + md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4)); %remove edges when the 2 vertices are not in the domain. - md2.edges=md2.edges(find(md2.edges(:,1) & md2.edges(:,2)),:); + md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:); %Replace all zeros by NaN in the last two columns; - pos=find(md2.edges(:,3)==0); - md2.edges(pos,3)=NaN; - pos=find(md2.edges(:,4)==0); - md2.edges(pos,4)=NaN; + pos=find(md2.mesh.edges(:,3)==0); + md2.mesh.edges(pos,3)=NaN; + pos=find(md2.mesh.edges(:,4)==0); + md2.mesh.edges(pos,4)=NaN; %Invert NaN of the third column with last column (Also invert first two columns!!) - pos=find(isnan(md2.edges(:,3))); - md2.edges(pos,3)=md2.edges(pos,4); - md2.edges(pos,4)=NaN; - values=md2.edges(pos,2); - md2.edges(pos,2)=md2.edges(pos,1); - md2.edges(pos,1)=values; + pos=find(isnan(md2.mesh.edges(:,3))); + md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4); + md2.mesh.edges(pos,4)=NaN; + values=md2.mesh.edges(pos,2); + md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1); + md2.mesh.edges(pos,1)=values; %Finally remove edges that do not belong to any element - pos=find(isnan(md2.edges(:,3)) & isnan(md2.edges(:,4))); - md2.edges(pos,:)=[]; + pos=find(isnan(md2.mesh.edges(:,3)) & isnan(md2.mesh.edges(:,4))); + md2.mesh.edges(pos,:)=[]; end @@ -203,6 +203,6 @@ %recreate segments if md1.dim==2 - md2.mesh.vertexconnectivity=NodeConnectivity(md2.elements,md2.numberofnodes); - md2.mesh.elementconnectivity=ElementConnectivity(md2.elements,md2.mesh.vertexconnectivity); + md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.numberofnodes); + md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity); md2.segments=contourenvelope(md2); md2.mesh.vertexonboundary=zeros(numberofnodes2,1); md2.nodeonboundary(md2.segments(:,1:2))=1; @@ -212,5 +212,5 @@ %Catch the elements that have not been extracted orphans_elem=find(~flag_elem); - orphans_node=unique(md1.elements(orphans_elem,:))'; + orphans_node=unique(md1.mesh.elements(orphans_elem,:))'; %Figure out which node are on the boundary between md2 and md1 nodestoflag1=intersect(orphans_node,pos_node); Index: /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m =================================================================== --- /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m (revision 9732) +++ /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m (revision 9733) @@ -16,5 +16,5 @@ md3d=md; - md.elements=md.mesh.elements2d; + md.mesh.elements=md.mesh.elements2d; md.x=md.mesh.x2d; md.y=md.mesh.y2d; Index: /issm/trunk/src/m/model/partition/adjacency.m =================================================================== --- /issm/trunk/src/m/model/partition/adjacency.m (revision 9732) +++ /issm/trunk/src/m/model/partition/adjacency.m (revision 9733) @@ -8,6 +8,6 @@ % md.qmu.vertex_weight (double [nv], vertex weights) -indi=[md.elements(:,1);md.elements(:,2);md.elements(:,3)]; -indj=[md.elements(:,2);md.elements(:,3);md.elements(:,1)]; +indi=[md.mesh.elements(:,1);md.mesh.elements(:,2);md.mesh.elements(:,3)]; +indj=[md.mesh.elements(:,2);md.mesh.elements(:,3);md.mesh.elements(:,1)]; values=1; @@ -16,8 +16,8 @@ %now, build vwgt: -areas=GetAreas(md.elements,md.x,md.y); +areas=GetAreas(md.mesh.elements,md.x,md.y); %get node connectivity -md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); connectivity=md.mesh.vertexconnectivity(:,1:end-1); Index: /issm/trunk/src/m/model/partition/partitioner.m =================================================================== --- /issm/trunk/src/m/model/partition/partitioner.m (revision 9732) +++ /issm/trunk/src/m/model/partition/partitioner.m (revision 9733) @@ -34,5 +34,5 @@ %extrude the partition vector vertically. md3d=md; %save for later - md.elements=md.mesh.elements2d; + md.mesh.elements=md.mesh.elements2d; md.x=md.mesh.x2d; md.y=md.mesh.y2d; Index: /issm/trunk/src/m/model/plot/applyoptions.m =================================================================== --- /issm/trunk/src/m/model/plot/applyoptions.m (revision 9732) +++ /issm/trunk/src/m/model/plot/applyoptions.m (revision 9733) @@ -437,5 +437,5 @@ %flag edges of a partition if exist(options,'partitionedges') -[xsegments ysegments]=flagedges(md.elements,md.x,md.y,md.qmu.partition); +[xsegments ysegments]=flagedges(md.mesh.elements,md.x,md.y,md.qmu.partition); xsegments=xsegments*getfieldvalue(options,'unit',1); ysegments=ysegments*getfieldvalue(options,'unit',1); Index: /issm/trunk/src/m/model/plot/plot_edges.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_edges.m (revision 9732) +++ /issm/trunk/src/m/model/plot/plot_edges.m (revision 9733) @@ -12,5 +12,5 @@ %process mesh and data [x y z elements is2d isplanet]=processmesh(md,[],options); -edges=md.edges; +edges=md.mesh.edges; if isnan(edges) error('edges in NaN') Index: /issm/trunk/src/m/model/plot/plot_rifts.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_rifts.m (revision 9732) +++ /issm/trunk/src/m/model/plot/plot_rifts.m (revision 9733) @@ -30,5 +30,5 @@ tip=md.rifts.riftstruct(i).tips(3); %who is tip connected to? - if isconnected(md.elements,penaltypairs(1,1),tip), + if isconnected(md.mesh.elements,penaltypairs(1,1),tip), normal(1)=penaltypairs(1,5); normal(2)=penaltypairs(1,6); @@ -37,5 +37,5 @@ end - if isconnected(md.elements,penaltypairs(1,2),tip), + if isconnected(md.mesh.elements,penaltypairs(1,2),tip), normal(1)=penaltypairs(1,5); normal(2)=penaltypairs(1,6); @@ -43,5 +43,5 @@ y(tip)=y(tip)+normal(2)*offset; end - if isconnected(md.elements,penaltypairs(end,1),tip), + if isconnected(md.mesh.elements,penaltypairs(end,1),tip), normal(1)=penaltypairs(end,5); normal(2)=penaltypairs(end,6); @@ -49,5 +49,5 @@ y(tip)=y(tip)-normal(2)*offset; end - if isconnected(md.elements,penaltypairs(end,2),tip), + if isconnected(md.mesh.elements,penaltypairs(end,2),tip), normal(1)=penaltypairs(end,5); normal(2)=penaltypairs(end,6); Index: /issm/trunk/src/m/model/plot/plot_section.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_section.m (revision 9732) +++ /issm/trunk/src/m/model/plot/plot_section.m (revision 9733) @@ -32,5 +32,5 @@ md3d=md; if exist(options,'layer') - md.x=md.mesh.x2d; md.y=md.mesh.y2d; md.elements=md.mesh.elements2d; md.mesh.dimension=2; + md.x=md.mesh.x2d; md.y=md.mesh.y2d; md.mesh.elements=md.mesh.elements2d; md.mesh.dimension=2; end Index: /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m (revision 9732) +++ /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m (revision 9733) @@ -29,5 +29,5 @@ %take the center of each element if ~isonnode if datatype==1, - x=mean(md.x(md.elements'))'; y=mean(md.y(md.elements'))'; z=mean(md.z(md.elements'))'; + x=mean(md.x(md.mesh.elements'))'; y=mean(md.y(md.mesh.elements'))'; z=mean(md.z(md.mesh.elements'))'; end Index: /issm/trunk/src/m/model/plot/processdata.m =================================================================== --- /issm/trunk/src/m/model/plot/processdata.m (revision 9732) +++ /issm/trunk/src/m/model/plot/processdata.m (revision 9733) @@ -123,5 +123,5 @@ pos=find(~flags); if length(flags)==md.mesh.numberofvertices, - [pos2 dummy]=find(ismember(md.elements,pos)); + [pos2 dummy]=find(ismember(md.mesh.elements,pos)); data(pos2,:)=NaN; elseif length(flags)==md.mesh.numberofelements @@ -155,5 +155,5 @@ data(pos,:)=NaN; elseif length(flags)==md.mesh.numberofelements - data(md.elements(pos,:),:)=NaN; + data(md.mesh.elements(pos,:),:)=NaN; else disp('plotmodel warning: mask length not supported yet (supported length are md.mesh.numberofvertices and md.mesh.numberofelements'); Index: /issm/trunk/src/m/model/plot/processmesh.m =================================================================== --- /issm/trunk/src/m/model/plot/processmesh.m (revision 9732) +++ /issm/trunk/src/m/model/plot/processmesh.m (revision 9733) @@ -38,5 +38,5 @@ elements2d=md.mesh.elements2d; - elements=md.elements; + elements=md.mesh.elements; %is it a 2d plot? Index: /issm/trunk/src/m/model/setflowequation.m =================================================================== --- /issm/trunk/src/m/model/setflowequation.m (revision 9732) +++ /issm/trunk/src/m/model/setflowequation.m (revision 9733) @@ -72,10 +72,10 @@ %1: Hutter elements nodeonhutter=zeros(md.mesh.numberofvertices,1); -nodeonhutter(md.elements(find(hutterflag),:))=1; +nodeonhutter(md.mesh.elements(find(hutterflag),:))=1; md.flowequation.element_equation(find(hutterflag))=1; %2: MacAyeal elements nodeonmacayeal=zeros(md.mesh.numberofvertices,1); -nodeonmacayeal(md.elements(find(macayealflag),:))=1; +nodeonmacayeal(md.mesh.elements(find(macayealflag),:))=1; md.flowequation.bordermacayeal=nodeonmacayeal; md.flowequation.element_equation(find(macayealflag))=2; @@ -83,5 +83,5 @@ %3: Pattyn elements nodeonpattyn=zeros(md.mesh.numberofvertices,1); -nodeonpattyn(md.elements(find(pattynflag),:))=1; +nodeonpattyn(md.mesh.elements(find(pattynflag),:))=1; md.flowequation.borderpattyn=nodeonpattyn; md.flowequation.element_equation(find(pattynflag))=3; @@ -91,11 +91,11 @@ if any(stokesflag), nodeonstokes=zeros(md.mesh.numberofvertices,1); - nodeonstokes(md.elements(find(stokesflag),:))=1; + nodeonstokes(md.mesh.elements(find(stokesflag),:))=1; fullspcnodes=double((~isnan(md.diagnostic.spcvx)+~isnan(md.diagnostic.spcvy)+~isnan(md.diagnostic.spcvz))==3 | (nodeonpattyn & nodeonstokes)); %find all the nodes on the boundary of the domain without icefront - fullspcelems=double(sum(fullspcnodes(md.elements),2)==6); %find all the nodes on the boundary of the domain without icefront + fullspcelems=double(sum(fullspcnodes(md.mesh.elements),2)==6); %find all the nodes on the boundary of the domain without icefront stokesflag(find(fullspcelems))=0; end nodeonstokes=zeros(md.mesh.numberofvertices,1); -nodeonstokes(md.elements(find(stokesflag),:))=1; +nodeonstokes(md.mesh.elements(find(stokesflag),:))=1; md.flowequation.borderstokes=nodeonstokes; md.flowequation.element_equation(find(stokesflag))=4; @@ -105,10 +105,10 @@ if any(pattynflag), %fill with pattyn pattynflag(~stokesflag)=1; - nodeonpattyn(md.elements(find(pattynflag),:))=1; + nodeonpattyn(md.mesh.elements(find(pattynflag),:))=1; md.flowequation.borderpattyn=nodeonpattyn; md.flowequation.element_equation(find(~stokesflag))=3; elseif any(macayealflag), %fill with macayeal macayealflag(~stokesflag)=1; - nodeonmacayeal(md.elements(find(macayealflag),:))=1; + nodeonmacayeal(md.mesh.elements(find(macayealflag),:))=1; md.flowequation.bordermacayeal=nodeonmacayeal; md.flowequation.element_equation(find(~stokesflag))=2; @@ -143,5 +143,5 @@ nodeonmacayealpattyn(find(nodeonmacayeal & nodeonpattyn))=1; %Macayeal elements in contact with this layer become MacAyealPattyn elements - matrixelements=ismember(md.elements,find(nodeonmacayealpattyn)); + matrixelements=ismember(md.mesh.elements,find(nodeonmacayealpattyn)); commonelements=sum(matrixelements,2)~=0; commonelements(find(pattynflag))=0; %only one layer: the elements previously in macayeal @@ -150,5 +150,5 @@ macayealpattynflag(find(commonelements))=1; nodeonmacayeal=zeros(md.mesh.numberofvertices,1); - nodeonmacayeal(md.elements(find(macayealflag),:))=1; + nodeonmacayeal(md.mesh.elements(find(macayealflag),:))=1; md.flowequation.bordermacayeal=nodeonmacayeal; @@ -157,10 +157,10 @@ %Now recreate nodeonmacayeal and nodeonmacayealpattyn - nodeonmacayealpattyn(md.elements(find(macayealpattynflag),:))=1; + nodeonmacayealpattyn(md.mesh.elements(find(macayealpattynflag),:))=1; elseif any(pattynflag) & any(stokesflag), %coupling pattyn stokes %Find node at the border nodeonpattynstokes(find(nodeonpattyn & nodeonstokes))=1; %Stokes elements in contact with this layer become PattynStokes elements - matrixelements=ismember(md.elements,find(nodeonpattynstokes)); + matrixelements=ismember(md.mesh.elements,find(nodeonpattynstokes)); commonelements=sum(matrixelements,2)~=0; commonelements(find(pattynflag))=0; %only one layer: the elements previously in macayeal @@ -169,5 +169,5 @@ pattynstokesflag(find(commonelements))=1; nodeonstokes=zeros(md.mesh.numberofvertices,1); - nodeonstokes(md.elements(find(stokesflag),:))=1; + nodeonstokes(md.mesh.elements(find(stokesflag),:))=1; md.flowequation.borderstokes=nodeonstokes; @@ -177,10 +177,10 @@ %Now recreate nodeonpattynstokes nodeonpattynstokes=zeros(md.mesh.numberofvertices,1); - nodeonpattynstokes(md.elements(find(pattynstokesflag),:))=1; + nodeonpattynstokes(md.mesh.elements(find(pattynstokesflag),:))=1; elseif any(stokesflag) & any(macayealflag), %Find node at the border nodeonmacayealstokes(find(nodeonmacayeal & nodeonstokes))=1; %Stokes elements in contact with this layer become MacAyealStokes elements - matrixelements=ismember(md.elements,find(nodeonmacayealstokes)); + matrixelements=ismember(md.mesh.elements,find(nodeonmacayealstokes)); commonelements=sum(matrixelements,2)~=0; commonelements(find(macayealflag))=0; %only one layer: the elements previously in macayeal @@ -189,5 +189,5 @@ macayealstokesflag(find(commonelements))=1; nodeonstokes=zeros(md.mesh.numberofvertices,1); - nodeonstokes(md.elements(find(stokesflag),:))=1; + nodeonstokes(md.mesh.elements(find(stokesflag),:))=1; md.flowequation.borderstokes=nodeonstokes; @@ -197,5 +197,5 @@ %Now recreate nodeonmacayealstokes nodeonmacayealstokes=zeros(md.mesh.numberofvertices,1); - nodeonmacayealstokes(md.elements(find(macayealstokesflag),:))=1; + nodeonmacayealstokes(md.mesh.elements(find(macayealstokesflag),:))=1; elseif any(stokesflag) & any(hutterflag), error('type of coupling not supported yet'); Index: /issm/trunk/src/m/model/setmask.m =================================================================== --- /issm/trunk/src/m/model/setmask.m (revision 9732) +++ /issm/trunk/src/m/model/setmask.m (revision 9733) @@ -23,5 +23,5 @@ x=md.x; y=md.y; -elements=md.elements; +elements=md.mesh.elements; %Assign elementonfloatingice, elementongroundedice, vertexongroundedice and vertexonfloatingice. Only change at your own peril! This is synchronized heavily with the GroundingLineMigration module. {{{1 @@ -37,5 +37,5 @@ vertexonfloatingice=zeros(md.mesh.numberofvertices,1); vertexongroundedice=zeros(md.mesh.numberofvertices,1); -vertexongroundedice(md.elements(find(elementongroundedice),:))=1; +vertexongroundedice(md.mesh.elements(find(elementongroundedice),:))=1; vertexonfloatingice(find(~vertexongroundedice))=1; %}}} Index: /issm/trunk/src/m/model/setmask2.m =================================================================== --- /issm/trunk/src/m/model/setmask2.m (revision 9732) +++ /issm/trunk/src/m/model/setmask2.m (revision 9733) @@ -11,5 +11,5 @@ x=md.x; y=md.y; -elements=md.elements; +elements=md.mesh.elements; %recover elements and nodes on land. @@ -22,5 +22,5 @@ elementonland=landname; vertexonland=zeros(md.mesh.numberofvertices,1); - vertexonland(md.elements(find(elementonland),:))=1; + vertexonland(md.mesh.elements(find(elementonland),:))=1; else error('Invalid area option option'); @@ -29,13 +29,13 @@ %Now, build the connectivity tables for this mesh. if size(md.mesh.vertexconnectivity,1)~=md.mesh.numberofvertices, - md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); + md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); end if size(md.mesh.elementconnectivity,1)~=md.mesh.numberofelements, - md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); + md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); 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)) ... +wrongelements=elementsonwater(find(( vertexonland(md.mesh.elements(elementsonwater,1)) + vertexonland(md.mesh.elements(elementsonwater,2)) + vertexonland(md.mesh.elements(elementsonwater,3)) ... )==3)); elementonland(wrongelements)=1; @@ -45,6 +45,6 @@ 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}); + xelem=x(md.mesh.elements)*weights{i}/sum(weights{i}); + yelem=y(md.mesh.elements)*weights{i}/sum(weights{i}); end baryonland=ContourToNodes(xelem,yelem,landname,1); @@ -79,6 +79,6 @@ elementonfloatingice=double((elementonfloatingice & ~elementongroundedice)); elementongroundedice=double(~elementonfloatingice); -vertexonfloatingice(md.elements(find(elementonfloatingice),:))=1; -vertexongroundedice(md.elements(find(elementongroundedice),:))=1; +vertexonfloatingice(md.mesh.elements(find(elementonfloatingice),:))=1; +vertexongroundedice(md.mesh.elements(find(elementongroundedice),:))=1; %now correct, so that none of the floatingice and groundedice elements and nodes are in the water. Index: /issm/trunk/src/m/model/shear2d.m =================================================================== --- /issm/trunk/src/m/model/shear2d.m (revision 9732) +++ /issm/trunk/src/m/model/shear2d.m (revision 9733) @@ -8,11 +8,11 @@ % s=shear2d(md); -[alpha beta]=GetNodalFunctionsCoeff(md.elements,md.x,md.y); +[alpha beta]=GetNodalFunctionsCoeff(md.mesh.elements,md.x,md.y); summation=[1;1;1]; -sx=(md.initialization.vx(md.elements).*alpha)*summation; -uy=(md.initialization.vx(md.elements).*beta)*summation; -vx=(md.initialization.vy(md.elements).*alpha)*summation; -sy=(md.initialization.vy(md.elements).*beta)*summation; +sx=(md.initialization.vx(md.mesh.elements).*alpha)*summation; +uy=(md.initialization.vx(md.mesh.elements).*beta)*summation; +vx=(md.initialization.vy(md.mesh.elements).*alpha)*summation; +sy=(md.initialization.vy(md.mesh.elements).*beta)*summation; sxy=(uy+vx)/2; s=sqrt(sx.^2+sy.^2+sxy.^2+sx.*sy); Index: /issm/trunk/src/m/model/sia.m =================================================================== --- /issm/trunk/src/m/model/sia.m (revision 9732) +++ /issm/trunk/src/m/model/sia.m (revision 9733) @@ -17,6 +17,6 @@ %Average thickness and B over all elements. summer=[1;1;1]; -hel=md.geometry.thickness(md.elements)*summer/3; -Bel=md.B(md.elements)*summer/3; +hel=md.geometry.thickness(md.mesh.elements)*summer/3; +Bel=md.B(md.mesh.elements)*summer/3; Ael=Bel.^(-3); Index: /issm/trunk/src/m/model/slope.m =================================================================== --- /issm/trunk/src/m/model/slope.m (revision 9732) +++ /issm/trunk/src/m/model/slope.m (revision 9733) @@ -9,5 +9,5 @@ numberofelements=md.mesh.numberofelements; numberofnodes=md.mesh.numberofvertices; - index=md.elements; + index=md.mesh.elements; x=md.x; y=md.y; else Index: /issm/trunk/src/m/model/thicknessevolution.m =================================================================== --- /issm/trunk/src/m/model/thicknessevolution.m (revision 9732) +++ /issm/trunk/src/m/model/thicknessevolution.m (revision 9733) @@ -17,8 +17,8 @@ vx=md.initialization.vx; vy=md.initialization.vy; -index=md.elements; +index=md.mesh.elements; %compute nodal functions coefficients N(x,y)=alpha x + beta y + gamma -[alpha beta]=GetNodalFunctionsCoeff(md.elements,md.x,md.y); +[alpha beta]=GetNodalFunctionsCoeff(md.mesh.elements,md.x,md.y); %compute dhdt=div(Hu) Index: /issm/trunk/src/m/planet/planetmixedmesh.m =================================================================== --- /issm/trunk/src/m/planet/planetmixedmesh.m (revision 9732) +++ /issm/trunk/src/m/planet/planetmixedmesh.m (revision 9733) @@ -86,5 +86,5 @@ -md.elements=quads; +md.mesh.elements=quads; md.x=x; md.y=y; @@ -95,5 +95,5 @@ md.mesh.numberofvertices=length(md.x); -md.mesh.numberofelements=size(md.elements,1); +md.mesh.numberofelements=size(md.mesh.elements,1); md.mesh.dimension=3; Index: /issm/trunk/src/m/planet/planettrimesh.m =================================================================== --- /issm/trunk/src/m/planet/planettrimesh.m (revision 9732) +++ /issm/trunk/src/m/planet/planettrimesh.m (revision 9733) @@ -9,5 +9,5 @@ md.y=results.vertices(:,2); md.z=results.vertices(:,3); -md.elements=results.faces; +md.mesh.elements=results.faces; md.r=sqrt(md.x.^2+md.y.^2+md.z.^2); @@ -16,5 +16,5 @@ md.mesh.numberofvertices=length(md.x); -md.mesh.numberofelements=size(md.elements,1); +md.mesh.numberofelements=size(md.mesh.elements,1); md.mesh.dimension=3; Index: /issm/trunk/src/m/qmu/importancefactors.m =================================================================== --- /issm/trunk/src/m/qmu/importancefactors.m (revision 9732) +++ /issm/trunk/src/m/qmu/importancefactors.m (revision 9733) @@ -53,5 +53,5 @@ %if numel(factors)==md.mesh.numberofvertices, % %get areas for each vertex. -% aire=GetAreas(md.elements,md.x,md.y); +% aire=GetAreas(md.mesh.elements,md.x,md.y); % num_elements_by_node=md.nodeconnectivity(:,end); % grid_aire=zeros(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/qmu/process_qmu_response_data.m =================================================================== --- /issm/trunk/src/m/qmu/process_qmu_response_data.m (revision 9732) +++ /issm/trunk/src/m/qmu/process_qmu_response_data.m (revision 9733) @@ -47,5 +47,5 @@ for i=1:num_mass_flux, - md.qmu.mass_flux_segments{i}=MeshProfileIntersection(md.elements,md.x,md.y,[md.qmu.mass_flux_profile_directory '/' md.qmu.mass_flux_profiles{i}]); + md.qmu.mass_flux_segments{i}=MeshProfileIntersection(md.mesh.elements,md.x,md.y,[md.qmu.mass_flux_profile_directory '/' md.qmu.mass_flux_profiles{i}]); end Index: /issm/trunk/src/m/solutions/flaim.m =================================================================== --- /issm/trunk/src/m/solutions/flaim.m (revision 9732) +++ /issm/trunk/src/m/solutions/flaim.m (revision 9733) @@ -80,5 +80,5 @@ display('Calling KMLMeshWrite.'); -KMLMeshWrite(md.miscellaneous.name,md.miscellaneous.notes,md.elements,md.nodeconnectivity,md.mesh.lat,md.mesh.long,md.qmu.partition,md.flaim.criterion,options.cmap,filekml); +KMLMeshWrite(md.miscellaneous.name,md.miscellaneous.notes,md.mesh.elements,md.nodeconnectivity,md.mesh.lat,md.mesh.long,md.qmu.partition,md.flaim.criterion,options.cmap,filekml); % for testing %filekml='issm-split-geikie1-targets.kml'; Index: /issm/trunk/src/m/utils/BC/SetIceShelfBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetIceShelfBC.m (revision 9732) +++ /issm/trunk/src/m/utils/BC/SetIceShelfBC.m (revision 9733) @@ -19,5 +19,5 @@ icefrontfile=varargin{1}; if ~exist(icefrontfile), error(['SetIceShelfBC error message: ice front file ' icefrontfile ' not found']); end - nodeinsideicefront=ContourToMesh(md.elements,md.x,md.y,icefrontfile,'node',2); + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.x,md.y,icefrontfile,'node',2); nodeonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront); elseif nargin==1, Index: /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m (revision 9732) +++ /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m (revision 9733) @@ -23,10 +23,10 @@ error(['SetMarineIceSheetBC error message: ice front file ' icefrontfile ' not found']); end - nodeinsideicefront=ContourToMesh(md.elements,md.x,md.y,icefrontfile,'node',2); + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.x,md.y,icefrontfile,'node',2); vertexonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront); else %Guess where the ice front is vertexonfloatingice=zeros(md.mesh.numberofvertices,1); - vertexonfloatingice(md.elements(find(md.mask.elementonfloatingice),:))=1; + vertexonfloatingice(md.mesh.elements(find(md.mask.elementonfloatingice),:))=1; vertexonicefront=double(md.mesh.vertexonboundary & vertexonfloatingice); end Index: /issm/trunk/src/m/utils/Exp/clicktoflowline.m =================================================================== --- /issm/trunk/src/m/utils/Exp/clicktoflowline.m (revision 9732) +++ /issm/trunk/src/m/utils/Exp/clicktoflowline.m (revision 9733) @@ -4,5 +4,5 @@ % Usage: clicktoflowline(index,x,y,u,v,x0,y0,filename) % -% Ex: clicktoflowline(md.elements,md.x,md.y,md.inversion.vx_obs,md.inversion.vy_obs,'flowline1.exp') +% Ex: clicktoflowline(md.mesh.elements,md.x,md.y,md.inversion.vx_obs,md.inversion.vy_obs,'flowline1.exp') Index: /issm/trunk/src/m/utils/Exp/downstreamflowlines.m =================================================================== --- /issm/trunk/src/m/utils/Exp/downstreamflowlines.m (revision 9732) +++ /issm/trunk/src/m/utils/Exp/downstreamflowlines.m (revision 9733) @@ -10,5 +10,5 @@ % % Example: -% flowpath=downstreamflowlines(md.elements,md.x,md.y,md.vx,md.initialization.vy,x0,y0) +% flowpath=downstreamflowlines(md.mesh.elements,md.x,md.y,md.vx,md.initialization.vy,x0,y0) %check input size Index: /issm/trunk/src/m/utils/Exp/flowlines.m =================================================================== --- /issm/trunk/src/m/utils/Exp/flowlines.m (revision 9732) +++ /issm/trunk/src/m/utils/Exp/flowlines.m (revision 9733) @@ -10,5 +10,5 @@ % % Example: -% flowpath=flowlines(md.elements,md.x,md.y,md.vx,md.initialization.vy,x0,y0) +% flowpath=flowlines(md.mesh.elements,md.x,md.y,md.vx,md.initialization.vy,x0,y0) %check input size Index: /issm/trunk/src/m/utils/Geometry/FlagElements.m =================================================================== --- /issm/trunk/src/m/utils/Geometry/FlagElements.m (revision 9732) +++ /issm/trunk/src/m/utils/Geometry/FlagElements.m (revision 9733) @@ -34,8 +34,8 @@ [xlim,ylim]=basinzoom('basin',region); flag_nodes=double(md.xxlim(1) & md.yylim(1)); - flag=prod(flag_nodes(md.elements),2); + flag=prod(flag_nodes(md.mesh.elements),2); else %ok, flag elements - flag=ContourToMesh(md.elements(:,1:3),md.x,md.y,region,'element',1); + flag=ContourToMesh(md.mesh.elements(:,1:3),md.x,md.y,region,'element',1); end end Index: /issm/trunk/src/m/utils/Interp/FillHole.m =================================================================== --- /issm/trunk/src/m/utils/Interp/FillHole.m (revision 9732) +++ /issm/trunk/src/m/utils/Interp/FillHole.m (revision 9733) @@ -6,5 +6,5 @@ % % Example: -% md.geometry.surface=FillHole(md.elements,x,md.y,md.geometry.surface) +% md.geometry.surface=FillHole(md.mesh.elements,x,md.y,md.geometry.surface) % Index: /issm/trunk/src/m/utils/Mesh/BamgCall.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/BamgCall.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/BamgCall.m (revision 9733) @@ -20,5 +20,5 @@ %Compute Hessian t1=clock; fprintf('%s',' computing Hessian...'); -hessian=ComputeHessian(md.elements,md.x,md.y,field,'node'); +hessian=ComputeHessian(md.mesh.elements,md.x,md.y,field,'node'); t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); @@ -54,5 +54,5 @@ %Triangles fprintf(fid,'\n\n%s\n%i\n\n','Triangles',md.mesh.numberofelements); -fprintf(fid,'%i %i %i %i\n',[md.elements ones(md.mesh.numberofelements,1)]'); +fprintf(fid,'%i %i %i %i\n',[md.mesh.elements ones(md.mesh.numberofelements,1)]'); numberofelements1=md.mesh.numberofelements; @@ -71,5 +71,5 @@ md.y=A.y; md.z=zeros(A.nods,1); -md.elements=A.index; +md.mesh.elements=A.index; md.mesh.numberofvertices=A.nods; md.mesh.numberofelements=A.nels; Index: /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m (revision 9733) @@ -35,5 +35,5 @@ %Triangles fprintf(fid,'\n\n%s\n%i\n\n','Triangles',md.mesh.numberofelements); -fprintf(fid,'%i %i %i %i\n',[md.elements ones(md.mesh.numberofelements,1)]'); +fprintf(fid,'%i %i %i %i\n',[md.mesh.elements ones(md.mesh.numberofelements,1)]'); numberofelements1=md.mesh.numberofelements; @@ -52,5 +52,5 @@ md.y=A.y; md.z=zeros(A.nods,1); -md.elements=A.index; +md.mesh.elements=A.index; md.mesh.numberofvertices=A.nods; md.mesh.numberofelements=A.nels; Index: /issm/trunk/src/m/utils/Mesh/ComputeHessian.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/ComputeHessian.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/ComputeHessian.m (revision 9733) @@ -10,5 +10,5 @@ % % Example: -% hessian=ComputeHessian(md.elements,md.x,md.y,md.inversion.vel_obs,'node') +% hessian=ComputeHessian(md.mesh.elements,md.x,md.y,md.inversion.vel_obs,'node') %some variables Index: /issm/trunk/src/m/utils/Mesh/ElementsFromEdge.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/ElementsFromEdge.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/ElementsFromEdge.m (revision 9733) @@ -4,5 +4,5 @@ % Usage: edgeelements=ElementsFromEdge(elements,A,B) % -% Eg: edgeelements=ElementsFromEdge(md.elements,tip1,tip2) +% Eg: edgeelements=ElementsFromEdge(md.mesh.elements,tip1,tip2) % % Index: /issm/trunk/src/m/utils/Mesh/GetAreas.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/GetAreas.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/GetAreas.m (revision 9733) @@ -10,6 +10,6 @@ % % Examples: -% areas =GetAreas(md.elements,md.x,md.y); -% volumes=GetAreas(md.elements,md.x,md.y,md.z); +% areas =GetAreas(md.mesh.elements,md.x,md.y); +% volumes=GetAreas(md.mesh.elements,md.x,md.y,md.z); %get number of elements and number of nodes Index: /issm/trunk/src/m/utils/Mesh/GetCharacteristicLength.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/GetCharacteristicLength.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/GetCharacteristicLength.m (revision 9733) @@ -9,6 +9,6 @@ % % Examples: -% length =GetCharacteristicLength(md.elements,md.x,md.y); -% length =GetCharacteristicLength(md.elements,md.x,md.y,md.z); +% length =GetCharacteristicLength(md.mesh.elements,md.x,md.y); +% length =GetCharacteristicLength(md.mesh.elements,md.x,md.y,md.z); Index: /issm/trunk/src/m/utils/Mesh/GetNodalFunctionsCoeff.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/GetNodalFunctionsCoeff.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/GetNodalFunctionsCoeff.m (revision 9733) @@ -12,5 +12,5 @@ % % Example: -% [alpha beta gamma]=GetNodalFunctionsCoeff(md.elements,md.x,md.y); +% [alpha beta gamma]=GetNodalFunctionsCoeff(md.mesh.elements,md.x,md.y); %make columns out of x and y Index: /issm/trunk/src/m/utils/Mesh/MeshQuality.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/MeshQuality.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/MeshQuality.m (revision 9733) @@ -6,5 +6,5 @@ %Get some variables from the model -index=md.elements; +index=md.mesh.elements; x=md.x; y=md.y; Index: /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m (revision 9733) @@ -8,5 +8,5 @@ %make a curve out of the mesh, to use the intersections routine. -rows=[md.elements md.elements(:,1)]'; rows=rows(:); +rows=[md.mesh.elements md.mesh.elements(:,1)]'; rows=rows(:); x=md.x(rows); y=md.y(rows); @@ -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.mesh.vertexconnectivity); +node_in_element=NodeInElement(newx,newy,md.mesh.elements,md.x,md.y,md.mesh.vertexconnectivity); % eliminate nodes that don't fall in any element Index: /issm/trunk/src/m/utils/Mesh/YamsCall.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/YamsCall.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/YamsCall.m (revision 9733) @@ -20,5 +20,5 @@ %Compute Hessian t1=clock; fprintf('%s',' computing Hessian...'); -hessian=ComputeHessian(md.elements,md.x,md.y,field,'node'); +hessian=ComputeHessian(md.mesh.elements,md.x,md.y,field,'node'); t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); @@ -51,5 +51,5 @@ %Triangles fprintf(fid,'\n\n%s\n%i\n\n','Triangles',md.mesh.numberofelements); -fprintf(fid,'%i %i %i %i\n',[md.elements zeros(md.mesh.numberofelements,1)]'); +fprintf(fid,'%i %i %i %i\n',[md.mesh.elements zeros(md.mesh.numberofelements,1)]'); numberofelements1=md.mesh.numberofelements; @@ -91,5 +91,5 @@ md.y=Coor(:,2); md.z=zeros(size(Coor,1),1); -md.elements=Tria; +md.mesh.elements=Tria; md.mesh.numberofvertices=size(Coor,1); md.mesh.numberofelements=size(Tria,1); Index: /issm/trunk/src/m/utils/Mesh/argusmesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/argusmesh.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/argusmesh.m (revision 9733) @@ -77,10 +77,10 @@ %Finally, use model constructor to build a complete model: -md.elements=elements; +md.mesh.elements=elements; md.x=x; md.y=y; md.z=z; md.mesh.numberofvertices=size(md.x,1); -md.mesh.numberofelements=size(md.elements,1); +md.mesh.numberofelements=size(md.mesh.elements,1); md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); md.mesh.vertexonsurface=ones(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/utils/Mesh/squaremesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 9732) +++ /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 9733) @@ -65,5 +65,5 @@ %plug elements -md.elements=index; +md.mesh.elements=index; md.mesh.segments=segments; md.mesh.numberofelements=nel; @@ -72,6 +72,6 @@ %Now, build the connectivity tables for this mesh. -md.mesh.vertexconnectivity=NodeConnectivity(md.elements,md.mesh.numberofvertices); -md.mesh.elementconnectivity=ElementConnectivity(md.elements,md.mesh.vertexconnectivity); +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); %plug other field Index: /issm/trunk/src/m/utils/Numerics/cfl_step.m =================================================================== --- /issm/trunk/src/m/utils/Numerics/cfl_step.m (revision 9732) +++ /issm/trunk/src/m/utils/Numerics/cfl_step.m (revision 9733) @@ -15,5 +15,5 @@ end -index=md.elements; +index=md.mesh.elements; edgex=max(md.x(index),[],2)-min(md.x(index),[],2); edgey=max(md.y(index),[],2)-min(md.y(index),[],2); Index: /issm/trunk/test/Miscellaneous/Bump/Bump.par =================================================================== --- /issm/trunk/test/Miscellaneous/Bump/Bump.par (revision 9732) +++ /issm/trunk/test/Miscellaneous/Bump/Bump.par (revision 9733) @@ -17,5 +17,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.drag_coefficient(md.elements(pos,:))=0; +md.drag_coefficient(md.mesh.elements(pos,:))=0; md.drag_p=ones(md.mesh.numberofelements,1); md.drag_q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par =================================================================== --- /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par (revision 9732) +++ /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par (revision 9733) @@ -20,5 +20,5 @@ md.drag_type=2; md.drag_coefficient=20*ones(md.mesh.numberofvertices,1); -md.drag_coefficient(md.elements(pos,:))=0; +md.drag_coefficient(md.mesh.elements(pos,:))=0; md.drag_p=ones(md.mesh.numberofelements,1); md.drag_q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Miscellaneous/connectivity/Square.par =================================================================== --- /issm/trunk/test/Miscellaneous/connectivity/Square.par (revision 9732) +++ /issm/trunk/test/Miscellaneous/connectivity/Square.par (revision 9733) @@ -19,5 +19,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.drag_coefficient(md.elements(pos,:))=0; +md.drag_coefficient(md.mesh.elements(pos,:))=0; md.drag_p=ones(md.mesh.numberofelements,1); md.drag_q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/NightlyRun/test1102.m =================================================================== --- /issm/trunk/test/NightlyRun/test1102.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1102.m (revision 9733) @@ -18,5 +18,5 @@ % %Find elements at the corner and extract model % posnodes=find((md.x==0 | md.x==max(md.x)) & (md.y==0 | md.y==max(md.y))); -% [a,b]=find(ismember(md.elements,posnodes)); +% [a,b]=find(ismember(md.mesh.elements,posnodes)); % elements=ones(md.mesh.numberofelements,1); % elements(a)=0; Index: /issm/trunk/test/NightlyRun/test1205.m =================================================================== --- /issm/trunk/test/NightlyRun/test1205.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1205.m (revision 9733) @@ -51,5 +51,5 @@ set(gcf,'Position',[1 1 1580 1150]) subplot(2,2,1) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... vel,'FaceColor','interp','EdgeColor','none'); title('Modelled velocity','FontSize',14,'FontWeight','bold') @@ -58,5 +58,5 @@ subplot(2,2,2) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... vel_obs,'FaceColor','interp','EdgeColor','none'); title('Analytical velocity','FontSize',14,'FontWeight','bold') @@ -76,5 +76,5 @@ subplot(2,2,4) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); title('Relative misfit [%]','FontSize',14,'FontWeight','bold') Index: /issm/trunk/test/NightlyRun/test1206.m =================================================================== --- /issm/trunk/test/NightlyRun/test1206.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1206.m (revision 9733) @@ -50,5 +50,5 @@ figure(1) subplot(2,2,1) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... vel,'FaceColor','interp','EdgeColor','none'); title('Modelled velocity','FontSize',14,'FontWeight','bold') @@ -57,5 +57,5 @@ subplot(2,2,2) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... vel_obs,'FaceColor','interp','EdgeColor','none'); title('Analytical velocity','FontSize',14,'FontWeight','bold') @@ -75,5 +75,5 @@ subplot(2,2,4) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); title('Relative misfit [%]','FontSize',14,'FontWeight','bold') Index: /issm/trunk/test/NightlyRun/test1207.m =================================================================== --- /issm/trunk/test/NightlyRun/test1207.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1207.m (revision 9733) @@ -50,5 +50,5 @@ figure(1) subplot(2,2,1) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... vel,'FaceColor','interp','EdgeColor','none'); title('Modelled velocity','FontSize',14,'FontWeight','bold') @@ -57,5 +57,5 @@ subplot(2,2,2) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... vel_obs,'FaceColor','interp','EdgeColor','none'); title('Analytical velocity','FontSize',14,'FontWeight','bold') @@ -75,5 +75,5 @@ subplot(2,2,4) -p=patch('Faces',md.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); title('Relative misfit [%]','FontSize',14,'FontWeight','bold') Index: /issm/trunk/test/NightlyRun/test1302.m =================================================================== --- /issm/trunk/test/NightlyRun/test1302.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1302.m (revision 9733) @@ -12,6 +12,6 @@ %Thermal boundary conditions -pos1=find(md.mesh.elementonbed); md.thermal.spctemperature(md.elements(pos1,1:3))=10; -pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.elements(pos2,4:6))=0; +pos1=find(md.mesh.elementonbed); md.thermal.spctemperature(md.mesh.elements(pos1,1:3))=10; +pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0; md.initialization.vz=0.1*ones(md.mesh.numberofvertices,1); md.initialization.vel=sqrt( md.initialization.vx.^2+ md.initialization.vy.^2+ md.initialization.vz.^2); Index: /issm/trunk/test/NightlyRun/test1303.m =================================================================== --- /issm/trunk/test/NightlyRun/test1303.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1303.m (revision 9733) @@ -11,6 +11,6 @@ md=extrude(md,11,2); md=setflowequation(md,'Pattyn','all'); -pos1=find(md.mesh.elementonbed); md.thermal.spctemperature(md.elements(pos1,1:3))=10; -pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.elements(pos2,4:6))=0; +pos1=find(md.mesh.elementonbed); md.thermal.spctemperature(md.mesh.elements(pos1,1:3))=10; +pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0; md.initialization.pressure=zeros(md.mesh.numberofvertices,1); Index: /issm/trunk/test/NightlyRun/test1304.m =================================================================== --- /issm/trunk/test/NightlyRun/test1304.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1304.m (revision 9733) @@ -12,5 +12,5 @@ md=setflowequation(md,'Pattyn','all'); -pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.elements(pos2,4:6))=0; +pos2=find(md.mesh.elementonsurface); md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0; md.initialization.pressure=zeros(md.mesh.numberofvertices,1); md.basalforcings.geothermalflux(:)=0.1; %100mW/m^2 Index: /issm/trunk/test/NightlyRun/test1501.m =================================================================== --- /issm/trunk/test/NightlyRun/test1501.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1501.m (revision 9733) @@ -96,5 +96,5 @@ ts = [starttime:res:endtime]; - index = md.elements; + index = md.mesh.elements; x1=md.x(index(:,1)); x2=md.x(index(:,2)); x3=md.x(index(:,3)); y1=md.y(index(:,1)); y2=md.y(index(:,2)); y3=md.y(index(:,3)); Index: /issm/trunk/test/NightlyRun/test1502.m =================================================================== --- /issm/trunk/test/NightlyRun/test1502.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test1502.m (revision 9733) @@ -102,5 +102,5 @@ ts = [starttime:res:endtime]; - index = md.elements; + index = md.mesh.elements; x1=md.x(index(:,1)); x2=md.x(index(:,2)); x3=md.x(index(:,3)); y1=md.y(index(:,1)); y2=md.y(index(:,2)); y3=md.y(index(:,3)); Index: /issm/trunk/test/NightlyRun/test446.m =================================================================== --- /issm/trunk/test/NightlyRun/test446.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test446.m (revision 9733) @@ -10,6 +10,6 @@ %}}} %put our grounding line 'shelfextent' meters from the icefront {{{1 -xelem=md.x(md.elements)*[1;1;1]/3; -yelem=md.y(md.elements)*[1;1;1]/3; +xelem=md.x(md.mesh.elements)*[1;1;1]/3; +yelem=md.y(md.mesh.elements)*[1;1;1]/3; rad=sqrt((xelem).*xelem+(yelem).*yelem); flags=zeros(md.mesh.numberofelements,1); Index: /issm/trunk/test/NightlyRun/test527.m =================================================================== --- /issm/trunk/test/NightlyRun/test527.m (revision 9732) +++ /issm/trunk/test/NightlyRun/test527.m (revision 9733) @@ -14,5 +14,5 @@ %refine existing mesh 1 -hessian=ComputeHessian(md.elements,md.x,md.y,md.inversion.vy_obs,'node'); +hessian=ComputeHessian(md.mesh.elements,md.x,md.y,md.inversion.vy_obs,'node'); metric=ComputeMetric(hessian,2/9,1,1000,25*10^3,[]); md.miscellaneous.dummy=metric; Index: /issm/trunk/test/Par/79North.par =================================================================== --- /issm/trunk/test/Par/79North.par (revision 9732) +++ /issm/trunk/test/Par/79North.par (revision 9733) @@ -18,5 +18,5 @@ pos=find(md.mask.elementonfloatingice); md.friction.coefficient=50*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); @@ -25,5 +25,5 @@ md.basalforcings.melting_rate=zeros(md.mesh.numberofvertices,1); pos=zeros(md.mesh.numberofvertices,1); -pos(md.elements(find(md.mask.elementonfloatingice),:))=1; +pos(md.mesh.elements(find(md.mask.elementonfloatingice),:))=1; md.basalforcings.melting_rate(find(pos))=10; md.surfaceforcings.mass_balance=15*ones(md.mesh.numberofvertices,1); Index: /issm/trunk/test/Par/ISMIPA.par =================================================================== --- /issm/trunk/test/Par/ISMIPA.par (revision 9732) +++ /issm/trunk/test/Par/ISMIPA.par (revision 9733) @@ -10,5 +10,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/ISMIPB.par =================================================================== --- /issm/trunk/test/Par/ISMIPB.par (revision 9732) +++ /issm/trunk/test/Par/ISMIPB.par (revision 9733) @@ -10,5 +10,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/ISMIPC.par =================================================================== --- /issm/trunk/test/Par/ISMIPC.par (revision 9732) +++ /issm/trunk/test/Par/ISMIPC.par (revision 9733) @@ -11,5 +11,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=zeros(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/ISMIPD.par =================================================================== --- /issm/trunk/test/Par/ISMIPD.par (revision 9732) +++ /issm/trunk/test/Par/ISMIPD.par (revision 9733) @@ -10,5 +10,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=zeros(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/Pig.par =================================================================== --- /issm/trunk/test/Par/Pig.par (revision 9732) +++ /issm/trunk/test/Par/Pig.par (revision 9733) @@ -23,5 +23,5 @@ pos=find(md.mask.elementonfloatingice); md.friction.coefficient=50*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/RoundSheetShelf.par =================================================================== --- /issm/trunk/test/Par/RoundSheetShelf.par (revision 9732) +++ /issm/trunk/test/Par/RoundSheetShelf.par (revision 9733) @@ -52,5 +52,5 @@ pos=find(md.mask.elementonfloatingice); md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/RoundSheetStaticEISMINT.par =================================================================== --- /issm/trunk/test/Par/RoundSheetStaticEISMINT.par (revision 9732) +++ /issm/trunk/test/Par/RoundSheetStaticEISMINT.par (revision 9733) @@ -12,5 +12,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/SquareEISMINT.par =================================================================== --- /issm/trunk/test/Par/SquareEISMINT.par (revision 9732) +++ /issm/trunk/test/Par/SquareEISMINT.par (revision 9733) @@ -12,5 +12,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/SquareSheetConstrained.par =================================================================== --- /issm/trunk/test/Par/SquareSheetConstrained.par (revision 9732) +++ /issm/trunk/test/Par/SquareSheetConstrained.par (revision 9733) @@ -26,5 +26,5 @@ pos=find(md.mask.elementonfloatingice); md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/SquareSheetShelf.par =================================================================== --- /issm/trunk/test/Par/SquareSheetShelf.par (revision 9732) +++ /issm/trunk/test/Par/SquareSheetShelf.par (revision 9733) @@ -33,5 +33,5 @@ pos=find(md.mask.elementonfloatingice); md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/SquareShelf.par =================================================================== --- /issm/trunk/test/Par/SquareShelf.par (revision 9732) +++ /issm/trunk/test/Par/SquareShelf.par (revision 9733) @@ -26,5 +26,5 @@ pos=find(md.mask.elementonfloatingice); md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/SquareShelfConstrained.par =================================================================== --- /issm/trunk/test/Par/SquareShelfConstrained.par (revision 9732) +++ /issm/trunk/test/Par/SquareShelfConstrained.par (revision 9733) @@ -30,5 +30,5 @@ pos=find(md.mask.elementonfloatingice); md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); Index: /issm/trunk/test/Par/SquareThermal.par =================================================================== --- /issm/trunk/test/Par/SquareThermal.par (revision 9732) +++ /issm/trunk/test/Par/SquareThermal.par (revision 9733) @@ -18,5 +18,5 @@ %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); -md.friction.coefficient(md.elements(pos,:))=0; +md.friction.coefficient(md.mesh.elements(pos,:))=0; md.friction.p=ones(md.mesh.numberofelements,1); md.friction.q=ones(md.mesh.numberofelements,1); @@ -41,3 +41,3 @@ md.thermal.spctemperature(:)=md.initialization.temperature; md.basalforcings.geothermalflux=zeros(md.mesh.numberofvertices,1); -pos=find(md.mask.elementongroundedice);md.basalforcings.geothermalflux(md.elements(pos,:))=1*10^-3; %1 mW/m^2 +pos=find(md.mask.elementongroundedice);md.basalforcings.geothermalflux(md.mesh.elements(pos,:))=1*10^-3; %1 mW/m^2