Index: /issm/trunk/src/c/Container/Inputs.cpp =================================================================== --- /issm/trunk/src/c/Container/Inputs.cpp (revision 9733) +++ /issm/trunk/src/c/Container/Inputs.cpp (revision 9734) @@ -412,5 +412,5 @@ /*}}}*/ /*FUNCTION Inputs::AXPY{{{1*/ -void Inputs::AXPY(int YEnum, double scalar, int XEnum){ +void Inputs::AXPY(int MeshYEnum, double scalar, int MeshXEnum){ Input* xinput=NULL; @@ -418,10 +418,10 @@ /*Find x and y inputs: */ - xinput=(Input*)this->GetInput(XEnum); - yinput=(Input*)this->GetInput(YEnum); + xinput=(Input*)this->GetInput(MeshXEnum); + yinput=(Input*)this->GetInput(MeshYEnum); /*some checks: */ - if(!xinput) _error_(" input %s could not be found!",EnumToStringx(XEnum)); - if(!yinput) _error_(" input %s could not be found!",EnumToStringx(YEnum)); + if(!xinput) _error_(" input %s could not be found!",EnumToStringx(MeshXEnum)); + if(!yinput) _error_(" input %s could not be found!",EnumToStringx(MeshYEnum)); /*Apply AXPY: */ Index: /issm/trunk/src/c/Container/Inputs.h =================================================================== --- /issm/trunk/src/c/Container/Inputs.h (revision 9733) +++ /issm/trunk/src/c/Container/Inputs.h (revision 9734) @@ -37,5 +37,5 @@ Input* GetInput(int enum_name); Inputs* SpawnTriaInputs(int* indices); - void AXPY(int YEnum, double scalar, int XEnum); + void AXPY(int MeshYEnum, double scalar, int MeshXEnum); double InfinityNorm(int enumtype); double Max(int enumtype); Index: /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 9733) +++ /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 9734) @@ -165,4 +165,7 @@ MeshElementsEnum, MeshEdgesEnum, + MeshYEnum, + MeshZEnum, + MeshXEnum, /*}}}*/ /*Datasets {{{1*/ @@ -473,7 +476,4 @@ TransientInputEnum, /*Temporary*/ - YEnum, - ZEnum, - XEnum, OutputfilenameEnum, WaterfractionEnum, Index: /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp =================================================================== --- /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 9733) +++ /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 9734) @@ -169,4 +169,7 @@ case MeshElementsEnum : return "MeshElements"; case MeshEdgesEnum : return "MeshEdges"; + case MeshYEnum : return "MeshY"; + case MeshZEnum : return "MeshZ"; + case MeshXEnum : return "MeshX"; case ConstraintsEnum : return "Constraints"; case LoadsEnum : return "Loads"; @@ -416,7 +419,4 @@ case DragCoefficientAbsGradientEnum : return "DragCoefficientAbsGradient"; case TransientInputEnum : return "TransientInput"; - case YEnum : return "Y"; - case ZEnum : return "Z"; - case XEnum : return "X"; case OutputfilenameEnum : return "Outputfilename"; case WaterfractionEnum : return "Waterfraction"; Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (revision 9733) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (revision 9734) @@ -72,5 +72,5 @@ /*Fetch data:*/ - iomodel->FetchData(5,XEnum,YEnum,ZEnum,BedEnum,ThicknessEnum); + iomodel->FetchData(5,MeshXEnum,MeshYEnum,MeshZEnum,BedEnum,ThicknessEnum); for (i=0;iDeleteData(5,XEnum,YEnum,ZEnum,BedEnum,ThicknessEnum); + iomodel->DeleteData(5,MeshXEnum,MeshYEnum,MeshZEnum,BedEnum,ThicknessEnum); /*Assign output pointer: */ Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp (revision 9733) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp (revision 9734) @@ -69,5 +69,5 @@ iomodel->FetchData(&vertices_type,NULL,NULL,FlowequationVertexEquationEnum); iomodel->FetchData(&surface,NULL,NULL,SurfaceEnum); - iomodel->FetchData(&z,NULL,NULL,ZEnum); + iomodel->FetchData(&z,NULL,NULL,MeshZEnum); /*Initialize counter: */ Index: /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 9733) +++ /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 9734) @@ -167,4 +167,7 @@ else if (strcmp(name,"MeshElements")==0) return MeshElementsEnum; else if (strcmp(name,"MeshEdges")==0) return MeshEdgesEnum; + else if (strcmp(name,"MeshY")==0) return MeshYEnum; + else if (strcmp(name,"MeshZ")==0) return MeshZEnum; + else if (strcmp(name,"MeshX")==0) return MeshXEnum; else if (strcmp(name,"Constraints")==0) return ConstraintsEnum; else if (strcmp(name,"Loads")==0) return LoadsEnum; @@ -414,7 +417,4 @@ else if (strcmp(name,"DragCoefficientAbsGradient")==0) return DragCoefficientAbsGradientEnum; else if (strcmp(name,"TransientInput")==0) return TransientInputEnum; - else if (strcmp(name,"Y")==0) return YEnum; - else if (strcmp(name,"Z")==0) return ZEnum; - else if (strcmp(name,"X")==0) return XEnum; else if (strcmp(name,"Outputfilename")==0) return OutputfilenameEnum; else if (strcmp(name,"Waterfraction")==0) return WaterfractionEnum; Index: /issm/trunk/src/c/objects/Vertex.cpp =================================================================== --- /issm/trunk/src/c/objects/Vertex.cpp (revision 9733) +++ /issm/trunk/src/c/objects/Vertex.cpp (revision 9734) @@ -31,5 +31,5 @@ Vertex::Vertex(int vertex_id, int vertex_sid,int i, IoModel* iomodel){ - this->Init(vertex_id, vertex_sid, iomodel->Data(XEnum)[i],iomodel->Data(YEnum)[i],iomodel->Data(ZEnum)[i],(iomodel->Data(ZEnum)[i]-iomodel->Data(BedEnum)[i])/(iomodel->Data(ThicknessEnum)[i])); + this->Init(vertex_id, vertex_sid, iomodel->Data(MeshXEnum)[i],iomodel->Data(MeshYEnum)[i],iomodel->Data(MeshZEnum)[i],(iomodel->Data(MeshZEnum)[i]-iomodel->Data(BedEnum)[i])/(iomodel->Data(ThicknessEnum)[i])); } Index: /issm/trunk/src/m/classes/mesh.m =================================================================== --- /issm/trunk/src/m/classes/mesh.m (revision 9733) +++ /issm/trunk/src/m/classes/mesh.m (revision 9734) @@ -37,4 +37,7 @@ elements = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); edges = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); + 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); end methods Index: /issm/trunk/src/m/classes/model/model.m =================================================================== --- /issm/trunk/src/m/classes/model/model.m (revision 9733) +++ /issm/trunk/src/m/classes/model/model.m (revision 9734) @@ -41,9 +41,4 @@ autodiff = modelfield('default',0,'marshall',true); mesh = modelfield('default',0,'marshall',true); - - %FIXME: all other fields should belong to other classes - 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); %}}} @@ -265,4 +260,7 @@ if isfield(structmd,'elements'), md.mesh.elements=structmd.mesh.elements; end if isfield(structmd,'edges'), md.mesh.edges=structmd.mesh.edges; end + if isfield(structmd,'y'), md.mesh.y=structmd.y; end + if isfield(structmd,'x'), md.mesh.x=structmd.x; end + if isfield(structmd,'z'), md.mesh.z=structmd.z; end %Field changes Index: /issm/trunk/src/m/enum/MeshXEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshXEnum.m (revision 9734) +++ /issm/trunk/src/m/enum/MeshXEnum.m (revision 9734) @@ -0,0 +1,11 @@ +function macro=MeshXEnum() +%MESHXENUM - Enum of MeshX +% +% 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=MeshXEnum() + +macro=StringToEnum('MeshX'); Index: /issm/trunk/src/m/enum/MeshYEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshYEnum.m (revision 9734) +++ /issm/trunk/src/m/enum/MeshYEnum.m (revision 9734) @@ -0,0 +1,11 @@ +function macro=MeshYEnum() +%MESHYENUM - Enum of MeshY +% +% 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=MeshYEnum() + +macro=StringToEnum('MeshY'); Index: /issm/trunk/src/m/enum/MeshZEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeshZEnum.m (revision 9734) +++ /issm/trunk/src/m/enum/MeshZEnum.m (revision 9734) @@ -0,0 +1,11 @@ +function macro=MeshZEnum() +%MESHZENUM - Enum of MeshZ +% +% 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=MeshZEnum() + +macro=StringToEnum('MeshZ'); Index: sm/trunk/src/m/enum/XEnum.m =================================================================== --- /issm/trunk/src/m/enum/XEnum.m (revision 9733) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=XEnum() -%XENUM - Enum of X -% -% 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=XEnum() - -macro=StringToEnum('X'); Index: sm/trunk/src/m/enum/YEnum.m =================================================================== --- /issm/trunk/src/m/enum/YEnum.m (revision 9733) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=YEnum() -%YENUM - Enum of Y -% -% 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=YEnum() - -macro=StringToEnum('Y'); Index: sm/trunk/src/m/enum/ZEnum.m =================================================================== --- /issm/trunk/src/m/enum/ZEnum.m (revision 9733) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=ZEnum() -%ZENUM - Enum of Z -% -% 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=ZEnum() - -macro=StringToEnum('Z'); Index: /issm/trunk/src/m/model/BasinConstrain.m =================================================================== --- /issm/trunk/src/m/model/BasinConstrain.m (revision 9733) +++ /issm/trunk/src/m/model/BasinConstrain.m (revision 9734) @@ -33,5 +33,5 @@ end %ok, flag elements and nodes - [vertexondomain elementondomain]=ContourToMesh(md.mesh.elements(:,1:3),md.x,md.y,domain,'element and node',2); + [vertexondomain elementondomain]=ContourToMesh(md.mesh.elements(:,1:3),md.mesh.x,md.mesh.y,domain,'element and node',2); end if invert, Index: /issm/trunk/src/m/model/BasinConstrainShelf.m =================================================================== --- /issm/trunk/src/m/model/BasinConstrainShelf.m (revision 9733) +++ /issm/trunk/src/m/model/BasinConstrainShelf.m (revision 9734) @@ -33,5 +33,5 @@ end %ok, flag elements and nodes - [vertexondomain elementondomain]=ContourToMesh(md.mesh.elements(:,1:3),md.x,md.y,domain,'element and node',2); + [vertexondomain elementondomain]=ContourToMesh(md.mesh.elements(:,1:3),md.mesh.x,md.mesh.y,domain,'element and node',2); end if invert, Index: /issm/trunk/src/m/model/DepthAverage.m =================================================================== --- /issm/trunk/src/m/model/DepthAverage.m (revision 9733) +++ /issm/trunk/src/m/model/DepthAverage.m (revision 9734) @@ -17,5 +17,5 @@ vector_average=zeros(md.mesh.numberofvertices2d,1); for i=1:md.mesh.numberoflayers-1, - vector_average=vector_average+(project2d(md,vector,i)+project2d(md,vector,i+1))/2.*(project2d(md,md.z,i+1)-project2d(md,md.z,i)); + vector_average=vector_average+(project2d(md,vector,i)+project2d(md,vector,i+1))/2.*(project2d(md,md.mesh.z,i+1)-project2d(md,md.mesh.z,i)); end vector_average=vector_average./project2d(md,md.geometry.thickness,1); @@ -25,5 +25,5 @@ vector_average=zeros(md.mesh.numberofelements2d,1); for i=1:md.mesh.numberoflayers-1, - vector_average=vector_average+project2d(md,vector,i).*(project2d(md,md.z,i+1)-project2d(md,md.z,i)); + vector_average=vector_average+project2d(md,vector,i).*(project2d(md,md.mesh.z,i+1)-project2d(md,md.mesh.z,i)); end vector_average=vector_average./project2d(md,md.geometry.thickness,1); Index: /issm/trunk/src/m/model/MeltingGroundingLines.m =================================================================== --- /issm/trunk/src/m/model/MeltingGroundingLines.m (revision 9733) +++ /issm/trunk/src/m/model/MeltingGroundingLines.m (revision 9734) @@ -17,5 +17,5 @@ %search the node on ice sheet the closest to i - [d posd]=min(sqrt((md.x(pos_shelf(i))-md.x(pos_GL)).^2+(md.y(pos_shelf(i))-md.y(pos_GL)).^2)); + [d posd]=min(sqrt((md.mesh.x(pos_shelf(i))-md.mesh.x(pos_GL)).^2+(md.mesh.y(pos_shelf(i))-md.mesh.y(pos_GL)).^2)); if ddistance, Index: /issm/trunk/src/m/model/averaging.m =================================================================== --- /issm/trunk/src/m/model/averaging.m (revision 9733) +++ /issm/trunk/src/m/model/averaging.m (revision 9734) @@ -33,8 +33,8 @@ if md.mesh.dimension==3 rep=6; - areas=GetAreas(index,md.x,md.y,md.z); + areas=GetAreas(index,md.mesh.x,md.mesh.y,md.mesh.z); else rep=3; - areas=GetAreas(index,md.x,md.y); + areas=GetAreas(index,md.mesh.x,md.mesh.y); end summation=1/rep*ones(rep,1); Index: /issm/trunk/src/m/model/bamg.m =================================================================== --- /issm/trunk/src/m/model/bamg.m (revision 9733) +++ /issm/trunk/src/m/model/bamg.m (revision 9734) @@ -270,5 +270,5 @@ bamg_mesh=bamgmesh(md.private.bamg.mesh); else - bamg_mesh.Vertices=[md.x md.y ones(md.mesh.numberofvertices,1)]; + bamg_mesh.Vertices=[md.mesh.x md.mesh.y ones(md.mesh.numberofvertices,1)]; bamg_mesh.Triangles=[md.mesh.elements ones(md.mesh.numberofelements,1)]; end @@ -317,6 +317,6 @@ md.private.bamg.mesh=bamgmesh(bamgmesh_out); md.private.bamg.geometry=bamggeom(bamggeom_out); -md.x=bamgmesh_out.Vertices(:,1); -md.y=bamgmesh_out.Vertices(:,2); +md.mesh.x=bamgmesh_out.Vertices(:,1); +md.mesh.y=bamgmesh_out.Vertices(:,2); md.mesh.elements=bamgmesh_out.Triangles(:,1:3); md.mesh.edges=bamgmesh_out.IssmEdges; @@ -327,7 +327,7 @@ md.mesh.dimension=2; md.mesh.numberofelements=size(md.mesh.elements,1); -md.mesh.numberofvertices=length(md.x); +md.mesh.numberofvertices=length(md.mesh.x); md.mesh.numberofedges=size(md.mesh.edges,1); -md.z=zeros(md.mesh.numberofvertices,1); +md.mesh.z=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); md.mask.vertexonwater=zeros(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/model/basevert.m =================================================================== --- /issm/trunk/src/m/model/basevert.m (revision 9733) +++ /issm/trunk/src/m/model/basevert.m (revision 9734) @@ -14,5 +14,5 @@ for n=1:md.mesh.numberofelements - X=inv([md.x(md.mesh.elements(n,:)) md.y(md.mesh.elements(n,:)) ones(3,1)]); + X=inv([md.mesh.x(md.mesh.elements(n,:)) md.mesh.y(md.mesh.elements(n,:)) ones(3,1)]); alpha(n,:)=X(1,:); beta(n,:)=X(2,:); Index: /issm/trunk/src/m/model/bedslope.m =================================================================== --- /issm/trunk/src/m/model/bedslope.m (revision 9733) +++ /issm/trunk/src/m/model/bedslope.m (revision 9734) @@ -10,5 +10,5 @@ numberofnodes=md.mesh.numberofvertices; index=md.mesh.elements; - x=md.x; y=md.y; + x=md.mesh.x; y=md.mesh.y; else numberofelements=md.mesh.numberofelements2d; Index: /issm/trunk/src/m/model/collapse.m =================================================================== --- /issm/trunk/src/m/model/collapse.m (revision 9733) +++ /issm/trunk/src/m/model/collapse.m (revision 9734) @@ -90,7 +90,7 @@ %Initialize with the 2d mesh -md.x=md.mesh.x2d; -md.y=md.mesh.y2d; -md.z=zeros(size(md.mesh.x2d)); +md.mesh.x=md.mesh.x2d; +md.mesh.y=md.mesh.y2d; +md.mesh.z=zeros(size(md.mesh.x2d)); md.mesh.numberofvertices=md.mesh.numberofvertices2d; md.mesh.numberofelements=md.mesh.numberofelements2d; Index: /issm/trunk/src/m/model/contourenvelope.m =================================================================== --- /issm/trunk/src/m/model/contourenvelope.m (revision 9733) +++ /issm/trunk/src/m/model/contourenvelope.m (revision 9734) @@ -47,5 +47,5 @@ if isfile, %get flag list of elements and nodes inside the contour - nodein=ContourToMesh(md.mesh.elements,md.x,md.y,file,'node',1); + nodein=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,file,'node',1); elemin=(sum(nodein(md.mesh.elements),2)==size(md.mesh.elements,2)); %modify element connectivity Index: /issm/trunk/src/m/model/contourmassbalance.m =================================================================== --- /issm/trunk/src/m/model/contourmassbalance.m (revision 9733) +++ /issm/trunk/src/m/model/contourmassbalance.m (revision 9734) @@ -22,10 +22,10 @@ %get flag list of elements and nodes inside the contour -nodein=ContourToMesh(md.mesh.elements,md.x,md.y,file,'node',1); +nodein=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,file,'node',1); elemin=(sum(nodein(md.mesh.elements),2)==size(md.mesh.elements,2)); %conputing Mass flux -x=md.x; -y=md.y; +x=md.mesh.x; +y=md.mesh.y; vx=mean(md.initialization.vx(segments(:,1:end-1)),2); vy=mean(md.initialization.vy(segments(:,1:end-1)),2); @@ -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.mesh.elements,md.x,md.y); +areas=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/model/divergence.m (revision 9734) @@ -9,5 +9,5 @@ numberofnodes=md.mesh.numberofvertices; index=md.mesh.elements; - x=md.x; y=md.y; z=md.z; + x=md.mesh.x; y=md.mesh.y; z=md.mesh.z; else numberofelements=md.mesh.numberofelements2d; Index: /issm/trunk/src/m/model/extrude.m =================================================================== --- /issm/trunk/src/m/model/extrude.m (revision 9733) +++ /issm/trunk/src/m/model/extrude.m (revision 9734) @@ -72,6 +72,6 @@ %Create the new layers for i=1:numlayers, - x3d=[x3d; md.x]; - y3d=[y3d; md.y]; + x3d=[x3d; md.mesh.x]; + y3d=[y3d; md.mesh.y]; %nodes are distributed between bed and surface accordingly to the given exponent z3d=[z3d; bed3d+thickness3d*extrusionlist(i)]; @@ -103,6 +103,6 @@ %Save old mesh -md.mesh.x2d=md.x; -md.mesh.y2d=md.y; +md.mesh.x2d=md.mesh.x; +md.mesh.y2d=md.mesh.y; md.mesh.elements2d=md.mesh.elements; md.mesh.numberofelements2d=md.mesh.numberofelements; @@ -114,7 +114,7 @@ %Build global 3d mesh md.mesh.elements=elements3d; -md.x=x3d; -md.y=y3d; -md.z=z3d; +md.mesh.x=x3d; +md.mesh.y=y3d; +md.mesh.z=z3d; md.mesh.numberofelements=number_el3d; md.mesh.numberofvertices=number_nodes3d; @@ -213,5 +213,5 @@ %Put lithostatic pressure is there is an existing pressure if ~isnan(md.initialization.pressure), - md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.z); + md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z); end Index: /issm/trunk/src/m/model/mechanicalproperties.m =================================================================== --- /issm/trunk/src/m/model/mechanicalproperties.m (revision 9733) +++ /issm/trunk/src/m/model/mechanicalproperties.m (revision 9734) @@ -34,5 +34,5 @@ %compute nodal functions coefficients N(x,y)=alpha x + beta y +gamma -[alpha beta]=GetNodalFunctionsCoeff(index,md.x,md.y); +[alpha beta]=GetNodalFunctionsCoeff(index,md.mesh.x,md.mesh.y); %compute shear Index: /issm/trunk/src/m/model/mesh/meshadaptation.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshadaptation.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/meshadaptation.m (revision 9734) @@ -41,6 +41,6 @@ %get areas and nodal functions coefficients N(x,y)=alpha x + beta y + gamma -[alpha beta]=GetNodalFunctionsCoeff(index,md.x,md.y); -areas=GetAreas(index,md.x,md.y); +[alpha beta]=GetNodalFunctionsCoeff(index,md.mesh.x,md.mesh.y); +areas=GetAreas(index,md.mesh.x,md.mesh.y); %Compute gradient for each element Index: /issm/trunk/src/m/model/mesh/meshbamg.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshbamg.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/meshbamg.m (revision 9734) @@ -77,9 +77,9 @@ disp(' interpolating velocities...'); if strcmpi(NamesV.interp,'node'), - vx_obs=InterpFromGridToMesh(Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vxname),md.x,md.y,0); - vy_obs=InterpFromGridToMesh(Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vyname),md.x,md.y,0); + vx_obs=InterpFromGridToMesh(Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vxname),md.mesh.x,md.mesh.y,0); + vy_obs=InterpFromGridToMesh(Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vyname),md.mesh.x,md.mesh.y,0); else - vx_obs=InterpFromMeshToMesh2d(Vel.(NamesV.indexname),Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vxname),md.x,md.y,0); - vy_obs=InterpFromMeshToMesh2d(Vel.(NamesV.indexname),Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vyname),md.x,md.y,0); + vx_obs=InterpFromMeshToMesh2d(Vel.(NamesV.indexname),Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vxname),md.mesh.x,md.mesh.y,0); + vy_obs=InterpFromMeshToMesh2d(Vel.(NamesV.indexname),Vel.(NamesV.xname),Vel.(NamesV.yname),Vel.(NamesV.vyname),md.mesh.x,md.mesh.y,0); end field=sqrt(vx_obs.^2+vy_obs.^2); @@ -88,7 +88,7 @@ disp(' interpolating thickness...'); if strcmpi(NamesH.interp,'node'), - h=InterpFromGridToMesh(Thi.(NamesH.xname),Thi.(NamesH.yname),Thi.(NamesH.dataname),md.x,md.y,0); + h=InterpFromGridToMesh(Thi.(NamesH.xname),Thi.(NamesH.yname),Thi.(NamesH.dataname),md.mesh.x,md.mesh.y,0); else - h=InterpFromMeshToMesh2d(Thi.(NamesH.indexname),Thi.(NamesH.xname),Thi.(NamesH.yname),Thi.(NamesH.dataname),md.x,md.y,0); + h=InterpFromMeshToMesh2d(Thi.(NamesH.indexname),Thi.(NamesH.xname),Thi.(NamesH.yname),Thi.(NamesH.dataname),md.mesh.x,md.mesh.y,0); end field=[field h]; @@ -97,5 +97,5 @@ %set nodeonwater field if ~strcmp(groundeddomain,'N/A'), - nodeground=ContourToMesh(md.mesh.elements,md.x,md.y,groundeddomain,'node',2); + nodeground=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/model/mesh/meshconvert.m (revision 9734) @@ -12,6 +12,6 @@ if nargin==1, - x=md.x; - y=md.y; + x=md.mesh.x; + y=md.mesh.y; index=md.mesh.elements; else @@ -28,6 +28,6 @@ md.private.bamg.mesh=bamgmesh(bamgmesh_out); md.private.bamg.geometry=bamggeom(bamggeom_out); -md.x=bamgmesh_out.Vertices(:,1); -md.y=bamgmesh_out.Vertices(:,2); +md.mesh.x=bamgmesh_out.Vertices(:,1); +md.mesh.y=bamgmesh_out.Vertices(:,2); md.mesh.elements=bamgmesh_out.Triangles(:,1:3); md.mesh.edges=bamgmesh_out.IssmEdges; @@ -38,7 +38,7 @@ md.mesh.dimension=2; md.mesh.numberofelements=size(md.mesh.elements,1); -md.mesh.numberofvertices=length(md.x); +md.mesh.numberofvertices=length(md.mesh.x); md.mesh.numberofedges=size(md.mesh.edges,1); -md.z=zeros(md.mesh.numberofvertices,1); +md.mesh.z=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); md.mask.vertexonwater=zeros(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/model/mesh/meshexprefine.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshexprefine.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/meshexprefine.m (revision 9734) @@ -35,6 +35,6 @@ %Read domainame file into a matlab array (x,y): -refinearea=ContourToMesh(md.mesh.elements,md.x,md.y,domainname,'element',1); -aires=GetAreas(md.mesh.elements,md.x,md.y); +refinearea=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,domainname,'element',1); +aires=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y); %flags areas within the domain Index: /issm/trunk/src/m/model/mesh/meshnodensity.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 9734) @@ -25,5 +25,5 @@ %Mesh using TriMeshNoDensity if strcmp(riftname,''), - [md.mesh.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshNoDensity(domainname); + [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshNoDensity(domainname); else [elements,x,y,segments,segmentmarkers]=TriMeshNoDensity(domainname,riftname); @@ -47,6 +47,6 @@ %plug into md - md.x=x; - md.y=y; + md.mesh.x=x; + md.mesh.y=y; md.mesh.elements=elements; md.mesh.segments=segments; @@ -56,6 +56,6 @@ %Fill in rest of fields: md.mesh.numberofelements=length(md.mesh.elements); -md.mesh.numberofvertices=length(md.x); -md.z=zeros(md.mesh.numberofvertices,1); +md.mesh.numberofvertices=length(md.mesh.x); +md.mesh.z=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/model/mesh/meshrefine.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshrefine.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/meshrefine.m (revision 9734) @@ -16,10 +16,10 @@ %Refine using TriMeshRefine -[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'); +[md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshRefine(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers,areas,'yes'); %Fill in rest of fields: md.mesh.numberofelements=length(md.mesh.elements); -md.mesh.numberofvertices=length(md.x); -md.z=zeros(md.mesh.numberofvertices,1); +md.mesh.numberofvertices=length(md.mesh.x); +md.mesh.z=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/model/mesh/meshyams.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshyams.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/meshyams.m (revision 9734) @@ -71,9 +71,9 @@ disp(' interpolating velocities...'); if strcmpi(Names.interp,'node'), - vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,0); - vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,0); + vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.mesh.x,md.mesh.y,0); + vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.mesh.x,md.mesh.y,0); else - vx_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,0); - vy_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,0); + vx_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.mesh.x,md.mesh.y,0); + vy_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.mesh.x,md.mesh.y,0); end field=sqrt(vx_obs.^2+vy_obs.^2); @@ -81,5 +81,5 @@ %set nodeonwater field if ~strcmp(groundeddomain,'N/A'), - nodeground=ContourToMesh(md.mesh.elements,md.x,md.y,groundeddomain,'node',2); + nodeground=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,groundeddomain,'node',2); md.nodeonwater=ones(md.mesh.numberofvertices,1); md.nodeonwater(find(nodeground))=0; @@ -114,5 +114,5 @@ %Fill in rest of fields: -md.z=zeros(md.mesh.numberofvertices,1); +md.mesh.z=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); md.mesh.vertexonsurface=ones(md.mesh.numberofvertices,1); @@ -120,5 +120,5 @@ md.mesh.elementonsurface=ones(md.mesh.numberofelements,1); if ~strcmp(groundeddomain,'N/A'), - nodeground=ContourToMesh(md.mesh.elements,md.x,md.y,groundeddomain,'node',2); + nodeground=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,groundeddomain,'node',2); md.nodeonwater=ones(md.mesh.numberofvertices,1); md.nodeonwater(find(nodeground))=0; @@ -127,9 +127,9 @@ end if strcmpi(Names.interp,'node'), - md.inversion.vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,0); - md.inversion.vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,0); + md.inversion.vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.mesh.x,md.mesh.y,0); + md.inversion.vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.mesh.x,md.mesh.y,0); else - md.inversion.vx_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,0); - md.inversion.vy_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,0); + md.inversion.vx_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.mesh.x,md.mesh.y,0); + md.inversion.vy_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.mesh.x,md.mesh.y,0); end md.inversion.vel_obs=sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); @@ -145,7 +145,7 @@ %build normals and lengths of segments: - lengths=sqrt((md.x(rift.segments(:,1))-md.x(rift.segments(:,2))).^2 + (md.y(rift.segments(:,1))-md.y(rift.segments(:,2))).^2 ); - normalsx=cos(atan2((md.x(rift.segments(:,1))-md.x(rift.segments(:,2))) , (md.y(rift.segments(:,2))-md.y(rift.segments(:,1))))); - normalsy=sin(atan2((md.x(rift.segments(:,1))-md.x(rift.segments(:,2))) , (md.y(rift.segments(:,2))-md.y(rift.segments(:,1))))); + lengths=sqrt((md.mesh.x(rift.segments(:,1))-md.mesh.x(rift.segments(:,2))).^2 + (md.mesh.y(rift.segments(:,1))-md.mesh.y(rift.segments(:,2))).^2 ); + normalsx=cos(atan2((md.mesh.x(rift.segments(:,1))-md.mesh.x(rift.segments(:,2))) , (md.mesh.y(rift.segments(:,2))-md.mesh.y(rift.segments(:,1))))); + normalsy=sin(atan2((md.mesh.x(rift.segments(:,1))-md.mesh.x(rift.segments(:,2))) , (md.mesh.y(rift.segments(:,2))-md.mesh.y(rift.segments(:,1))))); %ok, build penaltypairs: Index: /issm/trunk/src/m/model/mesh/reorder.m =================================================================== --- /issm/trunk/src/m/model/mesh/reorder.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/reorder.m (revision 9734) @@ -22,6 +22,6 @@ 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); -md.y=md.y(newnodes); -md.z=md.z(newnodes); +md.mesh.x=md.mesh.x(newnodes); +md.mesh.y=md.mesh.y(newnodes); +md.mesh.z=md.mesh.z(newnodes); md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; Index: /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m (revision 9734) @@ -56,5 +56,5 @@ %plug md2 mesh into md mesh: - [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,... + [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.z,md.mesh.numberofelements,md.mesh.numberofvertices,elconv,nodeconv,elconv2,nodeconv2]=meshplug(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.z,... md2.mesh.elements,md2.x,md2.y,md2.z,md2.extractednodes,md2.extractedelements,domain_index); Index: /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m (revision 9734) @@ -12,5 +12,5 @@ %first, flag nodes that belong to the domain outline - flags=ContourToMesh(md.mesh.elements,md.x,md.y,domainoutline,'node',0); + flags=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,domainoutline,'node',0); rift=md.rifts.riftstruct(i); @@ -55,7 +55,7 @@ %take the list of elements on one side of the rift that connect to the tip, %and duplicate the tip on them, so as to open the rift to the outside. - num=length(md.x)+1; - md.x=[md.x;md.x(tip)]; - md.y=[md.y;md.y(tip)]; + num=length(md.mesh.x)+1; + md.mesh.x=[md.mesh.x;md.mesh.x(tip)]; + md.mesh.y=[md.mesh.y;md.mesh.y(tip)]; md.mesh.numberofvertices=num; @@ -84,7 +84,7 @@ %Fill in rest of fields: md.mesh.numberofelements=length(md.mesh.elements); -md.mesh.numberofvertices=length(md.x); -md.z=zeros(md.mesh.numberofvertices,1); -md.mesh.vertexonboundary=zeros(length(md.x),1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; +md.mesh.numberofvertices=length(md.mesh.x); +md.mesh.z=zeros(md.mesh.numberofvertices,1); +md.mesh.vertexonboundary=zeros(length(md.mesh.x),1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; md.rifts.numrifts=length(md.rifts.riftstruct); md.flowequation.element_equation=3*ones(md.mesh.numberofelements,1); Index: /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m (revision 9734) @@ -25,5 +25,5 @@ %Call MEX file -[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.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers,md.rifts.riftstruct]=TriMeshProcessRifts(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers); md.rifts md.rifts.riftstruct @@ -34,7 +34,7 @@ %Fill in rest of fields: md.mesh.numberofelements=length(md.mesh.elements); -md.mesh.numberofvertices=length(md.x); -md.z=zeros(md.mesh.numberofvertices,1); -md.mesh.vertexonboundary=zeros(length(md.x),1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; +md.mesh.numberofvertices=length(md.mesh.x); +md.mesh.z=zeros(md.mesh.numberofvertices,1); +md.mesh.vertexonboundary=zeros(length(md.mesh.x),1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; md.rifts.numrifts=length(md.rifts.riftstruct); md.flowequation.element_equation=3*ones(md.mesh.numberofelements,1); @@ -46,10 +46,10 @@ %get coordinates of rift tips for i=1:md.rifts.numrifts, - md.rifts.riftstruct(i).tip1coordinates=[md.x(md.rifts.riftstruct(i).tips(1)) md.y(md.rifts.riftstruct(i).tips(1))]; - md.rifts.riftstruct(i).tip2coordinates=[md.x(md.rifts.riftstruct(i).tips(2)) md.y(md.rifts.riftstruct(i).tips(2))]; + md.rifts.riftstruct(i).tip1coordinates=[md.mesh.x(md.rifts.riftstruct(i).tips(1)) md.mesh.y(md.rifts.riftstruct(i).tips(1))]; + md.rifts.riftstruct(i).tip2coordinates=[md.mesh.x(md.rifts.riftstruct(i).tips(2)) md.mesh.y(md.rifts.riftstruct(i).tips(2))]; end %In case we have rifts that open up the domain outline, we need to open them: -flags=ContourToMesh(md.mesh.elements,md.x,md.y,domainoutline,'node',0); +flags=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.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.mesh.elements,md.x,md.y); +aires=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y); pos=find(aires<0); 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/rifts/meshyamsrecreateriftsegments.m =================================================================== --- /issm/trunk/src/m/model/mesh/rifts/meshyamsrecreateriftsegments.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/rifts/meshyamsrecreateriftsegments.m (revision 9734) @@ -11,11 +11,11 @@ %find tip1 and tip2 for this rift, in the new mesh created by yams. - pos=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2)); + pos=find_point(md.mesh.x(md.mesh.segments(:,1)),md.mesh.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2)); tip1=md.mesh.segments(pos,1); - pos=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip2coordinates(1),rift.tip2coordinates(2)); + pos=find_point(md.mesh.x(md.mesh.segments(:,1)),md.mesh.y(md.mesh.segments(:,1)),rift.tip2coordinates(1),rift.tip2coordinates(2)); tip2=md.mesh.segments(pos,1); %start from tip1, and build segments of this rift. - pos=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2)); + pos=find_point(md.mesh.x(md.mesh.segments(:,1)),md.mesh.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2)); pos_record=[pos_record; pos]; riftsegs=md.mesh.segments(pos,:); @@ -39,7 +39,7 @@ %find tip1 and tip2 for this rift, in the new mesh created by yams. - pos1=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2)); + pos1=find_point(md.mesh.x(md.mesh.segments(:,1)),md.mesh.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2)); tip1=md.mesh.segments(pos1,1); - pos2=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip2coordinates(1),rift.tip2coordinates(2)); + pos2=find_point(md.mesh.x(md.mesh.segments(:,1)),md.mesh.y(md.mesh.segments(:,1)),rift.tip2coordinates(1),rift.tip2coordinates(2)); tip2=md.mesh.segments(pos2,1); if length(tip1)==2, Index: /issm/trunk/src/m/model/mesh/setmesh.m =================================================================== --- /issm/trunk/src/m/model/mesh/setmesh.m (revision 9733) +++ /issm/trunk/src/m/model/mesh/setmesh.m (revision 9734) @@ -39,5 +39,5 @@ %Mesh using TriMesh if strcmp(riftname,''), - [md.mesh.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,area,'yes'); + [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,area,'yes'); else [elements,x,y,segments,segmentmarkers]=TriMesh(domainname,riftname,area,'yes'); @@ -61,6 +61,6 @@ %plug into md - md.x=x; - md.y=y; + md.mesh.x=x; + md.mesh.y=y; md.mesh.elements=elements; md.mesh.segments=segments; @@ -70,6 +70,6 @@ %Fill in rest of fields: md.mesh.numberofelements=length(md.mesh.elements); -md.mesh.numberofvertices=length(md.x); -md.z=zeros(md.mesh.numberofvertices,1); +md.mesh.numberofvertices=length(md.mesh.x); +md.mesh.z=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/model/misfit.m =================================================================== --- /issm/trunk/src/m/model/misfit.m (revision 9733) +++ /issm/trunk/src/m/model/misfit.m (revision 9734) @@ -11,6 +11,6 @@ if md.mesh.dimension==2, elements=md.mesh.elements; - x=md.x; - y=md.y; + x=md.mesh.x; + y=md.mesh.y; vx=md.initialization.vx; vy=md.initialization.vy; Index: /issm/trunk/src/m/model/outflow.m =================================================================== --- /issm/trunk/src/m/model/outflow.m (revision 9733) +++ /issm/trunk/src/m/model/outflow.m (revision 9734) @@ -7,6 +7,6 @@ A=md.mesh.segments(:,1); B=md.mesh.segments(:,2); -Nx=-(md.y(A)-md.y(B)); -Ny= md.x(A)-md.x(B); +Nx=-(md.mesh.y(A)-md.mesh.y(B)); +Ny= md.mesh.x(A)-md.mesh.x(B); Vx=(md.initialization.vx(A)+md.initialization.vx(B))/2; Vy=(md.initialization.vy(A)+md.initialization.vy(B))/2; Index: /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m =================================================================== --- /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m (revision 9733) +++ /issm/trunk/src/m/model/partition/AreaAverageOntoPartition.m (revision 9734) @@ -17,6 +17,6 @@ md.mesh.elements=md.mesh.elements2d; - md.x=md.mesh.x2d; - md.y=md.mesh.y2d; + md.mesh.x=md.mesh.x2d; + md.mesh.y=md.mesh.y2d; md.mesh.numberofvertices=md.mesh.numberofvertices2d; md.mesh.numberofelements=md.mesh.numberofelements2d; Index: /issm/trunk/src/m/model/partition/adjacency.m =================================================================== --- /issm/trunk/src/m/model/partition/adjacency.m (revision 9733) +++ /issm/trunk/src/m/model/partition/adjacency.m (revision 9734) @@ -16,5 +16,5 @@ %now, build vwgt: -areas=GetAreas(md.mesh.elements,md.x,md.y); +areas=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y); %get node connectivity Index: /issm/trunk/src/m/model/partition/partitioner.m =================================================================== --- /issm/trunk/src/m/model/partition/partitioner.m (revision 9733) +++ /issm/trunk/src/m/model/partition/partitioner.m (revision 9734) @@ -35,6 +35,6 @@ md3d=md; %save for later md.mesh.elements=md.mesh.elements2d; - md.x=md.mesh.x2d; - md.y=md.mesh.y2d; + md.mesh.x=md.mesh.x2d; + md.mesh.y=md.mesh.y2d; md.mesh.numberofvertices=md.mesh.numberofvertices2d; md.mesh.numberofelements=md.mesh.numberofelements2d; @@ -70,5 +70,5 @@ % partition into nparts - part=Chaco(md.qmu.adjacency,weights,[],md.x, md.y ,md.z,method,npart,[])'+1; %index partitions from 1 up. like metis. + part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y ,md.mesh.z,method,npart,[])'+1; %index partitions from 1 up. like metis. elseif strcmpi(package,'scotch'), Index: /issm/trunk/src/m/model/plot/applyoptions.m =================================================================== --- /issm/trunk/src/m/model/plot/applyoptions.m (revision 9733) +++ /issm/trunk/src/m/model/plot/applyoptions.m (revision 9734) @@ -424,6 +424,6 @@ [mdx mdy]=basinzoom(options); else - mdx=[min(md.x) max(md.x)]; - mdy=[min(md.y) max(md.y)]; + mdx=[min(md.mesh.x) max(md.mesh.x)]; + mdy=[min(md.mesh.y) max(md.mesh.y)]; end line(A.x,A.y,ones(size(A.x)),'color','b'); @@ -437,5 +437,5 @@ %flag edges of a partition if exist(options,'partitionedges') -[xsegments ysegments]=flagedges(md.mesh.elements,md.x,md.y,md.qmu.partition); +[xsegments ysegments]=flagedges(md.mesh.elements,md.mesh.x,md.mesh.y,md.qmu.partition); xsegments=xsegments*getfieldvalue(options,'unit',1); ysegments=ysegments*getfieldvalue(options,'unit',1); Index: /issm/trunk/src/m/model/plot/checkplotoptions.m =================================================================== --- /issm/trunk/src/m/model/plot/checkplotoptions.m (revision 9733) +++ /issm/trunk/src/m/model/plot/checkplotoptions.m (revision 9734) @@ -180,8 +180,8 @@ if strcmpi(getfieldvalue(options,'northarrow'),'on') %default values - Lx=max(md.y)-min(md.y); - Ly=max(md.y)-min(md.y); - %default values - options=changefieldvalue(options,'northarrow',[min(md.x)+1/6*Lx min(md.y)+5/6*Ly 1/15*Ly 0.25 1/250*Ly]); + Lx=max(md.mesh.y)-min(md.mesh.y); + Ly=max(md.mesh.y)-min(md.mesh.y); + %default values + options=changefieldvalue(options,'northarrow',[min(md.mesh.x)+1/6*Lx min(md.mesh.y)+5/6*Ly 1/15*Ly 0.25 1/250*Ly]); end end @@ -191,8 +191,8 @@ if strcmpi(getfieldvalue(options,'scaleruler'),'on') %default values - Lx=max(md.y)-min(md.y); - Ly=max(md.y)-min(md.y); - %default values - options=changefieldvalue(options,'scaleruler',[min(md.x)+6/8*Lx min(md.y)+1/10*Ly 10^(ceil(log10(Lx)))/5 floor(Lx/100) 5]); + Lx=max(md.mesh.y)-min(md.mesh.y); + Ly=max(md.mesh.y)-min(md.mesh.y); + %default values + options=changefieldvalue(options,'scaleruler',[min(md.mesh.x)+6/8*Lx min(md.mesh.y)+1/10*Ly 10^(ceil(log10(Lx)))/5 floor(Lx/100) 5]); end end Index: /issm/trunk/src/m/model/plot/plot_BC.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_BC.m (revision 9733) +++ /issm/trunk/src/m/model/plot/plot_BC.m (revision 9734) @@ -7,7 +7,7 @@ %plot dirichlets -h1=plot(md.x(find(~isnan(md.diagnostic.spcvx))),md.y(find(~isnan(md.diagnostic.spcvx))),'ro','MarkerSize',14,'MarkerFaceColor','r'); -h2=plot(md.x(find(~isnan(md.diagnostic.spcvy))),md.y(find(~isnan(md.diagnostic.spcvy))),'bo','MarkerSize',10,'MarkerFaceColor','b'); -h3=plot(md.x(find(~isnan(md.diagnostic.spcvz))),md.y(find(~isnan(md.diagnostic.spcvz))),'yo','MarkerSize',6 ,'MarkerFaceColor','y'); +h1=plot(md.mesh.x(find(~isnan(md.diagnostic.spcvx))),md.mesh.y(find(~isnan(md.diagnostic.spcvx))),'ro','MarkerSize',14,'MarkerFaceColor','r'); +h2=plot(md.mesh.x(find(~isnan(md.diagnostic.spcvy))),md.mesh.y(find(~isnan(md.diagnostic.spcvy))),'bo','MarkerSize',10,'MarkerFaceColor','b'); +h3=plot(md.mesh.x(find(~isnan(md.diagnostic.spcvz))),md.mesh.y(find(~isnan(md.diagnostic.spcvz))),'yo','MarkerSize',6 ,'MarkerFaceColor','y'); %update legend Index: /issm/trunk/src/m/model/plot/plot_quiver.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_quiver.m (revision 9733) +++ /issm/trunk/src/m/model/plot/plot_quiver.m (revision 9734) @@ -8,5 +8,5 @@ % % Example: -% plot_quiver(md.x,md.y,md.initialization.vx,md.initialization.vy,options); +% plot_quiver(md.mesh.x,md.mesh.y,md.initialization.vx,md.initialization.vy,options); %process fields Index: /issm/trunk/src/m/model/plot/plot_quiver3.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_quiver3.m (revision 9733) +++ /issm/trunk/src/m/model/plot/plot_quiver3.m (revision 9734) @@ -8,5 +8,5 @@ % % Example: -% plot_quiver(md.x,md.y,md.z,md.initialization.vx,md.initialization.vy,md.initialization.vz,options); +% plot_quiver(md.mesh.x,md.mesh.y,md.mesh.z,md.initialization.vx,md.initialization.vy,md.initialization.vz,options); %keep only non NaN elements Index: /issm/trunk/src/m/model/plot/plot_sarpwr.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_sarpwr.m (revision 9733) +++ /issm/trunk/src/m/model/plot/plot_sarpwr.m (revision 9734) @@ -13,7 +13,7 @@ if exist(options,'unit'), unit=getfieldvalue(options,'unit'); - md.x=md.x*unit; - md.y=md.y*unit; - md.z=md.z*unit; + md.mesh.x=md.mesh.x*unit; + md.mesh.y=md.mesh.y*unit; + md.mesh.z=md.mesh.z*unit; end Index: /issm/trunk/src/m/model/plot/plot_section.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_section.m (revision 9733) +++ /issm/trunk/src/m/model/plot/plot_section.m (revision 9734) @@ -32,5 +32,5 @@ md3d=md; if exist(options,'layer') - md.x=md.mesh.x2d; md.y=md.mesh.y2d; md.mesh.elements=md.mesh.elements2d; md.mesh.dimension=2; + md.mesh.x=md.mesh.x2d; md.mesh.y=md.mesh.y2d; md.mesh.elements=md.mesh.elements2d; md.mesh.dimension=2; end @@ -96,5 +96,5 @@ text(x(end),y(end),'end','backgroundcolor',[0.8 0.9 0.8]) plot(x,y,'-r') - axis([min(md.x)-1 max(md.x)+1 min(md.y)-1 max(md.y)+1]) + axis([min(md.mesh.x)-1 max(md.mesh.x)+1 min(md.mesh.y)-1 max(md.mesh.y)+1]) view(2) end @@ -138,5 +138,5 @@ text(x(end),y(end),'end','backgroundcolor',[0.8 0.9 0.8]) plot(x,y,'-r') - axis([min(md.x)-1 max(md.x)+1 min(md.y)-1 max(md.y)+1]) + axis([min(md.mesh.x)-1 max(md.mesh.x)+1 min(md.mesh.y)-1 max(md.mesh.y)+1]) view(2) end @@ -173,5 +173,5 @@ text(x(end),y(end),'end','backgroundcolor',[0.8 0.9 0.8]) plot(x,y,'-r') - axis([min(md.x)-1 max(md.x)+1 min(md.y)-1 max(md.y)+1]) + axis([min(md.mesh.x)-1 max(md.mesh.x)+1 min(md.mesh.y)-1 max(md.mesh.y)+1]) view(2) end Index: /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m (revision 9733) +++ /issm/trunk/src/m/model/plot/plot_tensor_principalaxis.m (revision 9734) @@ -29,5 +29,5 @@ %take the center of each element if ~isonnode if datatype==1, - x=mean(md.x(md.mesh.elements'))'; y=mean(md.y(md.mesh.elements'))'; z=mean(md.z(md.mesh.elements'))'; + x=mean(md.mesh.x(md.mesh.elements'))'; y=mean(md.mesh.y(md.mesh.elements'))'; z=mean(md.mesh.z(md.mesh.elements'))'; end Index: /issm/trunk/src/m/model/plot/processmesh.m =================================================================== --- /issm/trunk/src/m/model/plot/processmesh.m (revision 9733) +++ /issm/trunk/src/m/model/plot/processmesh.m (revision 9734) @@ -16,7 +16,7 @@ if ~strcmpi(getfieldvalue(options,'coord','xy'),'latlon'), - x=md.x; + x=md.mesh.x; x2d=md.mesh.x2d; - y=md.y; + y=md.mesh.y; y2d=md.mesh.y2d; else @@ -27,5 +27,5 @@ end - z_field=getfieldvalue(options,'z',md.z); + z_field=getfieldvalue(options,'z',md.mesh.z); if ischar(z_field), z=md.(z_field); @@ -33,5 +33,5 @@ z=z_field; else - z=md.z; + z=md.mesh.z; end @@ -68,13 +68,13 @@ if (md.mesh.dimension==2), elements=transpose(reshape(1:3*md.mesh.numberofelements,3,md.mesh.numberofelements)); - x=transpose(reshape(md.x(data.index)',1,3*md.mesh.numberofelements)); - y=transpose(reshape(md.y(data.index)',1,3*md.mesh.numberofelements)); + x=transpose(reshape(md.mesh.x(data.index)',1,3*md.mesh.numberofelements)); + y=transpose(reshape(md.mesh.y(data.index)',1,3*md.mesh.numberofelements)); z=zeros(3*md.mesh.numberofelements,1); is2d=1; else elements=transpose(reshape(1:6*md.mesh.numberofelements,6,md.mesh.numberofelements)); - x=transpose(reshape(md.x(data.index)',1,6*md.mesh.numberofelements)); - y=transpose(reshape(md.y(data.index)',1,6*md.mesh.numberofelements)); - z=transpose(reshape(md.z(data.index)',1,6*md.mesh.numberofelements)); + x=transpose(reshape(md.mesh.x(data.index)',1,6*md.mesh.numberofelements)); + y=transpose(reshape(md.mesh.y(data.index)',1,6*md.mesh.numberofelements)); + z=transpose(reshape(md.mesh.z(data.index)',1,6*md.mesh.numberofelements)); is2d=0; end Index: /issm/trunk/src/m/model/plot/showregion.m =================================================================== --- /issm/trunk/src/m/model/plot/showregion.m (revision 9733) +++ /issm/trunk/src/m/model/plot/showregion.m (revision 9734) @@ -26,6 +26,6 @@ Ay=[min(A.y) max(A.y)]; -mdx=[min(md.x) max(md.x)]; -mdy=[min(md.y) max(md.y)]; +mdx=[min(md.mesh.x) max(md.mesh.x)]; +mdy=[min(md.mesh.y) max(md.mesh.y)]; line(A.x,A.y,'color','b'); Index: /issm/trunk/src/m/model/radarpower.m =================================================================== --- /issm/trunk/src/m/model/radarpower.m (revision 9733) +++ /issm/trunk/src/m/model/radarpower.m (revision 9734) @@ -19,6 +19,6 @@ highres=getfieldvalue(options,'highres',0); -xlim=getfieldvalue(options,'xlim',[min(md.x) max(md.x)]); -ylim=getfieldvalue(options,'ylim',[min(md.y) max(md.y)]); +xlim=getfieldvalue(options,'xlim',[min(md.mesh.x) max(md.mesh.x)]); +ylim=getfieldvalue(options,'ylim',[min(md.mesh.y) max(md.mesh.y)]); posting=getfieldvalue(options,'posting',0); % 0 -> image posting default Index: /issm/trunk/src/m/model/setmask.m =================================================================== --- /issm/trunk/src/m/model/setmask.m (revision 9733) +++ /issm/trunk/src/m/model/setmask.m (revision 9734) @@ -21,6 +21,6 @@ %Get assigned fields -x=md.x; -y=md.y; +x=md.mesh.x; +y=md.mesh.y; elements=md.mesh.elements; Index: /issm/trunk/src/m/model/setmask2.m =================================================================== --- /issm/trunk/src/m/model/setmask2.m (revision 9733) +++ /issm/trunk/src/m/model/setmask2.m (revision 9734) @@ -9,6 +9,6 @@ %Get assigned fields -x=md.x; -y=md.y; +x=md.mesh.x; +y=md.mesh.y; elements=md.mesh.elements; Index: /issm/trunk/src/m/model/shear2d.m =================================================================== --- /issm/trunk/src/m/model/shear2d.m (revision 9733) +++ /issm/trunk/src/m/model/shear2d.m (revision 9734) @@ -8,5 +8,5 @@ % s=shear2d(md); -[alpha beta]=GetNodalFunctionsCoeff(md.mesh.elements,md.x,md.y); +[alpha beta]=GetNodalFunctionsCoeff(md.mesh.elements,md.mesh.x,md.mesh.y); summation=[1;1;1]; Index: /issm/trunk/src/m/model/slope.m =================================================================== --- /issm/trunk/src/m/model/slope.m (revision 9733) +++ /issm/trunk/src/m/model/slope.m (revision 9734) @@ -10,5 +10,5 @@ numberofnodes=md.mesh.numberofvertices; index=md.mesh.elements; - x=md.x; y=md.y; + x=md.mesh.x; y=md.mesh.y; else numberofelements=md.mesh.numberofelements2d; Index: /issm/trunk/src/m/model/thicknessevolution.m =================================================================== --- /issm/trunk/src/m/model/thicknessevolution.m (revision 9733) +++ /issm/trunk/src/m/model/thicknessevolution.m (revision 9734) @@ -20,5 +20,5 @@ %compute nodal functions coefficients N(x,y)=alpha x + beta y + gamma -[alpha beta]=GetNodalFunctionsCoeff(md.mesh.elements,md.x,md.y); +[alpha beta]=GetNodalFunctionsCoeff(md.mesh.elements,md.mesh.x,md.mesh.y); %compute dhdt=div(Hu) Index: /issm/trunk/src/m/utils/BC/SetIceShelfBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetIceShelfBC.m (revision 9733) +++ /issm/trunk/src/m/utils/BC/SetIceShelfBC.m (revision 9734) @@ -19,5 +19,5 @@ icefrontfile=varargin{1}; if ~exist(icefrontfile), error(['SetIceShelfBC error message: ice front file ' icefrontfile ' not found']); end - nodeinsideicefront=ContourToMesh(md.mesh.elements,md.x,md.y,icefrontfile,'node',2); + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m (revision 9734) @@ -23,5 +23,5 @@ error(['SetMarineIceSheetBC error message: ice front file ' icefrontfile ' not found']); end - nodeinsideicefront=ContourToMesh(md.mesh.elements,md.x,md.y,icefrontfile,'node',2); + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2); vertexonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront); else Index: /issm/trunk/src/m/utils/Exp/clicktoflowline.m =================================================================== --- /issm/trunk/src/m/utils/Exp/clicktoflowline.m (revision 9733) +++ /issm/trunk/src/m/utils/Exp/clicktoflowline.m (revision 9734) @@ -4,5 +4,5 @@ % Usage: clicktoflowline(index,x,y,u,v,x0,y0,filename) % -% Ex: clicktoflowline(md.mesh.elements,md.x,md.y,md.inversion.vx_obs,md.inversion.vy_obs,'flowline1.exp') +% Ex: clicktoflowline(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/utils/Exp/downstreamflowlines.m (revision 9734) @@ -10,5 +10,5 @@ % % Example: -% flowpath=downstreamflowlines(md.mesh.elements,md.x,md.y,md.vx,md.initialization.vy,x0,y0) +% flowpath=downstreamflowlines(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/utils/Exp/flowlines.m (revision 9734) @@ -10,5 +10,5 @@ % % Example: -% flowpath=flowlines(md.mesh.elements,md.x,md.y,md.vx,md.initialization.vy,x0,y0) +% flowpath=flowlines(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/utils/Geometry/FlagElements.m (revision 9734) @@ -33,9 +33,9 @@ if ~exist(region,'file'), [xlim,ylim]=basinzoom('basin',region); - flag_nodes=double(md.xxlim(1) & md.yylim(1)); + flag_nodes=double(md.mesh.xxlim(1) & md.mesh.yylim(1)); flag=prod(flag_nodes(md.mesh.elements),2); else %ok, flag elements - flag=ContourToMesh(md.mesh.elements(:,1:3),md.x,md.y,region,'element',1); + flag=ContourToMesh(md.mesh.elements(:,1:3),md.mesh.x,md.mesh.y,region,'element',1); end end Index: /issm/trunk/src/m/utils/Interp/FillHole.m =================================================================== --- /issm/trunk/src/m/utils/Interp/FillHole.m (revision 9733) +++ /issm/trunk/src/m/utils/Interp/FillHole.m (revision 9734) @@ -6,5 +6,5 @@ % % Example: -% md.geometry.surface=FillHole(md.mesh.elements,x,md.y,md.geometry.surface) +% md.geometry.surface=FillHole(md.mesh.elements,x,md.mesh.y,md.geometry.surface) % Index: /issm/trunk/src/m/utils/Interp/InterpFromFile.m =================================================================== --- /issm/trunk/src/m/utils/Interp/InterpFromFile.m (revision 9733) +++ /issm/trunk/src/m/utils/Interp/InterpFromFile.m (revision 9734) @@ -19,5 +19,5 @@ % % Example: -% md.geometry.surface=InterpFromFile(md.x,md.y,'surfacefile.mat',0); +% md.geometry.surface=InterpFromFile(md.mesh.x,md.mesh.y,'surfacefile.mat',0); % % See also: PLUGVELOCITIES, INTERPFROMGRID, INTERPFROMMESH2D, INTERPFROMMESH3D Index: /issm/trunk/src/m/utils/Interp/plugvelocities.m =================================================================== --- /issm/trunk/src/m/utils/Interp/plugvelocities.m (revision 9733) +++ /issm/trunk/src/m/utils/Interp/plugvelocities.m (revision 9734) @@ -29,9 +29,9 @@ %Interpolation if strcmpi(Names.interp,'node'), - md.inversion.vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,default_value); - md.inversion.vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,default_value); + md.inversion.vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.mesh.x,md.mesh.y,default_value); + md.inversion.vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.mesh.x,md.mesh.y,default_value); else - md.inversion.vx_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.x,md.y,default_value); - md.inversion.vy_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.x,md.y,default_value); + md.inversion.vx_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.mesh.x,md.mesh.y,default_value); + md.inversion.vy_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.mesh.x,md.mesh.y,default_value); end Index: /issm/trunk/src/m/utils/Mesh/BamgCall.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/BamgCall.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/BamgCall.m (revision 9734) @@ -20,5 +20,5 @@ %Compute Hessian t1=clock; fprintf('%s',' computing Hessian...'); -hessian=ComputeHessian(md.mesh.elements,md.x,md.y,field,'node'); +hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,field,'node'); t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); @@ -50,5 +50,5 @@ %Vertices fprintf(fid,'\n%s\n%i\n\n','Vertices',md.mesh.numberofvertices); -fprintf(fid,'%8g %8g %i\n',[md.x md.y ones(md.mesh.numberofvertices,1)]'); +fprintf(fid,'%8g %8g %i\n',[md.mesh.x md.mesh.y ones(md.mesh.numberofvertices,1)]'); %Triangles @@ -68,6 +68,6 @@ t1=clock; fprintf('\n%s',' reading final mesh files...'); A=meshread('carre1.mesh'); -md.x=A.x; -md.y=A.y; +md.mesh.x=A.x; +md.mesh.y=A.y; md.z=zeros(A.nods,1); md.mesh.elements=A.index; Index: /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/BamgCallFromMetric.m (revision 9734) @@ -31,5 +31,5 @@ %Vertices fprintf(fid,'\n%s\n%i\n\n','Vertices',md.mesh.numberofvertices); -fprintf(fid,'%8g %8g %i\n',[md.x md.y ones(md.mesh.numberofvertices,1)]'); +fprintf(fid,'%8g %8g %i\n',[md.mesh.x md.mesh.y ones(md.mesh.numberofvertices,1)]'); %Triangles @@ -49,6 +49,6 @@ t1=clock; fprintf('\n%s',' reading final mesh files...'); A=meshread('carre1.mesh'); -md.x=A.x; -md.y=A.y; +md.mesh.x=A.x; +md.mesh.y=A.y; md.z=zeros(A.nods,1); md.mesh.elements=A.index; Index: /issm/trunk/src/m/utils/Mesh/ComputeHessian.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/ComputeHessian.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/ComputeHessian.m (revision 9734) @@ -10,5 +10,5 @@ % % Example: -% hessian=ComputeHessian(md.mesh.elements,md.x,md.y,md.inversion.vel_obs,'node') +% hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vel_obs,'node') %some variables Index: /issm/trunk/src/m/utils/Mesh/GetAreas.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/GetAreas.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/GetAreas.m (revision 9734) @@ -10,6 +10,6 @@ % % Examples: -% areas =GetAreas(md.mesh.elements,md.x,md.y); -% volumes=GetAreas(md.mesh.elements,md.x,md.y,md.z); +% areas =GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y); +% volumes=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/utils/Mesh/GetCharacteristicLength.m (revision 9734) @@ -9,6 +9,6 @@ % % Examples: -% length =GetCharacteristicLength(md.mesh.elements,md.x,md.y); -% length =GetCharacteristicLength(md.mesh.elements,md.x,md.y,md.z); +% length =GetCharacteristicLength(md.mesh.elements,md.mesh.x,md.mesh.y); +% length =GetCharacteristicLength(md.mesh.elements,md.mesh.x,md.mesh.y,md.z); Index: /issm/trunk/src/m/utils/Mesh/GetNodalFunctionsCoeff.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/GetNodalFunctionsCoeff.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/GetNodalFunctionsCoeff.m (revision 9734) @@ -12,5 +12,5 @@ % % Example: -% [alpha beta gamma]=GetNodalFunctionsCoeff(md.mesh.elements,md.x,md.y); +% [alpha beta gamma]=GetNodalFunctionsCoeff(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/utils/Mesh/MeshQuality.m (revision 9734) @@ -7,6 +7,6 @@ %Get some variables from the model index=md.mesh.elements; -x=md.x; -y=md.y; +x=md.mesh.x; +y=md.mesh.y; %2d geometric parameter (do not change) Index: /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/ProfileProjectOntoMesh.m (revision 9734) @@ -9,6 +9,6 @@ %make a curve out of the mesh, to use the intersections routine. rows=[md.mesh.elements md.mesh.elements(:,1)]'; rows=rows(:); -x=md.x(rows); -y=md.y(rows); +x=md.mesh.x(rows); +y=md.mesh.y(rows); %[x0,y0] = intersections(profile.x,profile.y,x,y,1); @@ -48,5 +48,5 @@ %now, for each node, figure out which element it belongs to. -node_in_element=NodeInElement(newx,newy,md.mesh.elements,md.x,md.y,md.mesh.vertexconnectivity); +node_in_element=NodeInElement(newx,newy,md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/src/m/utils/Mesh/YamsCall.m (revision 9734) @@ -20,5 +20,5 @@ %Compute Hessian t1=clock; fprintf('%s',' computing Hessian...'); -hessian=ComputeHessian(md.mesh.elements,md.x,md.y,field,'node'); +hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,field,'node'); t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); @@ -47,5 +47,5 @@ %Vertices fprintf(fid,'\n%s\n%i\n\n','Vertices',md.mesh.numberofvertices); -fprintf(fid,'%8g %8g %i\n',[md.x md.y zeros(md.mesh.numberofvertices,1)]'); +fprintf(fid,'%8g %8g %i\n',[md.mesh.x md.mesh.y zeros(md.mesh.numberofvertices,1)]'); %Triangles @@ -88,6 +88,6 @@ Tria=load('carre1.tria'); Coor=load('carre1.coor'); -md.x=Coor(:,1); -md.y=Coor(:,2); +md.mesh.x=Coor(:,1); +md.mesh.y=Coor(:,2); md.z=zeros(size(Coor,1),1); md.mesh.elements=Tria; Index: /issm/trunk/src/m/utils/Mesh/argusmesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/argusmesh.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/argusmesh.m (revision 9734) @@ -78,8 +78,8 @@ %Finally, use model constructor to build a complete model: md.mesh.elements=elements; -md.x=x; -md.y=y; +md.mesh.x=x; +md.mesh.y=y; md.z=z; -md.mesh.numberofvertices=size(md.x,1); +md.mesh.numberofvertices=size(md.mesh.x,1); md.mesh.numberofelements=size(md.mesh.elements,1); md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); Index: /issm/trunk/src/m/utils/Mesh/rifttipsonmesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/rifttipsonmesh.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/rifttipsonmesh.m (revision 9734) @@ -14,5 +14,5 @@ y_tip=rift.y(1); - index=find_point(md.x,md.y,x_tip,y_tip); + index=find_point(md.mesh.x,md.mesh.y,x_tip,y_tip); tips(end+1)=index; @@ -20,5 +20,5 @@ y_tip=rift.y(end); - index=find_point(md.x,md.y,x_tip,y_tip); + index=find_point(md.mesh.x,md.mesh.y,x_tip,y_tip); tips(end+1)=index; Index: /issm/trunk/src/m/utils/Mesh/roundmesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/roundmesh.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/roundmesh.m (revision 9734) @@ -27,7 +27,7 @@ %move the closest node to the center -[mini pos]=min(md.x.^2+md.y.^2); -md.x(pos)=0; -md.y(pos)=0; +[mini pos]=min(md.mesh.x.^2+md.mesh.y.^2); +md.mesh.x(pos)=0; +md.mesh.y(pos)=0; %delete domain Index: /issm/trunk/src/m/utils/Mesh/squaremesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 9733) +++ /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 9734) @@ -56,6 +56,6 @@ %plug coordinates and nodes -md.x=x; -md.y=y; +md.mesh.x=x; +md.mesh.y=y; md.z=zeros(nods,1); md.mesh.numberofvertices=nods; Index: /issm/trunk/src/m/utils/Numerics/cfl_step.m =================================================================== --- /issm/trunk/src/m/utils/Numerics/cfl_step.m (revision 9733) +++ /issm/trunk/src/m/utils/Numerics/cfl_step.m (revision 9734) @@ -16,6 +16,6 @@ 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); +edgex=max(md.mesh.x(index),[],2)-min(md.mesh.x(index),[],2); +edgey=max(md.mesh.y(index),[],2)-min(md.mesh.y(index),[],2); vx=max(abs(vx(index)),[],2); vy=max(abs(vy(index)),[],2); Index: /issm/trunk/template =================================================================== --- /issm/trunk/template (revision 9733) +++ /issm/trunk/template (revision 9734) @@ -1,16 +1,2 @@ -mesh {{{ - - projection - x - y - z - elements - edges - - elements2d - x2d - y2d -}}} - %To be completed cluster{{{ Index: /issm/trunk/test/Miscellaneous/Bump/Bump.par =================================================================== --- /issm/trunk/test/Miscellaneous/Bump/Bump.par (revision 9733) +++ /issm/trunk/test/Miscellaneous/Bump/Bump.par (revision 9734) @@ -5,10 +5,10 @@ hmin=1000; hmax=1000; -ymin=min(md.y); -ymax=max(md.y); -md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+10; md.geometry.surface=md.geometry.bed+md.geometry.thickness; -md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+height*exp(-((md.x-50000).^2+(md.y-50000).^2)/(4000)^2)+10; +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+height*exp(-((md.mesh.x-50000).^2+(md.mesh.y-50000).^2)/(4000)^2)+10; md.geometry.thickness=md.geometry.surface-md.geometry.bed; Index: /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par =================================================================== --- /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par (revision 9733) +++ /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par (revision 9734) @@ -4,7 +4,7 @@ hmin=300; hmax=1000; -ymin=min(md.y); -ymax=max(md.y); -md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; md.geometry.surface=md.geometry.bed+md.geometry.thickness; Index: /issm/trunk/test/Miscellaneous/connectivity/Square.par =================================================================== --- /issm/trunk/test/Miscellaneous/connectivity/Square.par (revision 9733) +++ /issm/trunk/test/Miscellaneous/connectivity/Square.par (revision 9734) @@ -9,7 +9,7 @@ hmin=300; hmax=1000; -ymin=min(md.y); -ymax=max(md.y); -md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; md.geometry.surface=md.geometry.bed+md.geometry.thickness; Index: /issm/trunk/test/NightlyRun/test1101.m =================================================================== --- /issm/trunk/test/NightlyRun/test1101.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1101.m (revision 9734) @@ -30,9 +30,9 @@ %Create MPCs to have periodic boundary conditions - posx=find(md.x==0); - posx2=find(md.x==max(md.x)); + posx=find(md.mesh.x==0); + posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.y==0 & md.x~=0 & md.x~=max(md.x)); %Don't take the same nodes two times - posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x)); + posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; Index: /issm/trunk/test/NightlyRun/test1102.m =================================================================== --- /issm/trunk/test/NightlyRun/test1102.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1102.m (revision 9734) @@ -17,5 +17,5 @@ % %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))); +% posnodes=find((md.mesh.x==0 | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0 | md.mesh.y==max(md.mesh.y))); % [a,b]=find(ismember(md.mesh.elements,posnodes)); % elements=ones(md.mesh.numberofelements,1); @@ -34,11 +34,11 @@ %Create MPCs to have periodic boundary conditions - %posx=find(md.x==0); - %posx2=find(md.x==max(md.x)); - %posx=find(md.x==0 & md.y~=0 & md.y~=max(md.y) & ~md.mesh.vertexonbed); - %posx2=find(md.x==max(md.x) & md.y~=0 & md.y~=max(md.y) & ~md.mesh.vertexonbed); + %posx=find(md.mesh.x==0); + %posx2=find(md.mesh.x==max(md.mesh.x)); + %posx=find(md.mesh.x==0 & md.mesh.y~=0 & md.mesh.y~=max(md.mesh.y) & ~md.mesh.vertexonbed); + %posx2=find(md.mesh.x==max(md.mesh.x) & md.mesh.y~=0 & md.mesh.y~=max(md.mesh.y) & ~md.mesh.vertexonbed); - %posy=find(md.y==0 & md.x~=0 & md.x~=max(md.x) & ~md.mesh.vertexonbed); %Don't take the same nodes two times - %posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x) & ~md.mesh.vertexonbed); + %posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x) & ~md.mesh.vertexonbed); %Don't take the same nodes two times + %posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x) & ~md.mesh.vertexonbed); %md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; Index: /issm/trunk/test/NightlyRun/test1103.m =================================================================== --- /issm/trunk/test/NightlyRun/test1103.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1103.m (revision 9734) @@ -27,9 +27,9 @@ %Create MPCs to have periodic boundary conditions - posx=find(md.x==0); - posx2=find(md.x==max(md.x)); + posx=find(md.mesh.x==0); + posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.y==0 & md.x~=0 & md.x~=max(md.x)); %Don't take the same nodes two times - posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x)); + posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; Index: /issm/trunk/test/NightlyRun/test1104.m =================================================================== --- /issm/trunk/test/NightlyRun/test1104.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1104.m (revision 9734) @@ -27,9 +27,9 @@ %Create MPCs to have periodic boundary conditions - posx=find(md.x==0); - posx2=find(md.x==max(md.x)); + posx=find(md.mesh.x==0); + posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.y==0 & md.x~=0 & md.x~=max(md.x)); %Don't take the same nodes two times - posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x)); + posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; Index: /issm/trunk/test/NightlyRun/test1105.m =================================================================== --- /issm/trunk/test/NightlyRun/test1105.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1105.m (revision 9734) @@ -25,14 +25,14 @@ md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - posx=find(md.x==0 & md.y~=0 & md.y~=L); - posx2=find(md.x==L & md.y~=0 & md.y~=L); + posx=find(md.mesh.x==0 & md.mesh.y~=0 & md.mesh.y~=L); + posx2=find(md.mesh.x==L & md.mesh.y~=0 & md.mesh.y~=L); - posy=find(md.y==0 & md.x~=0 & md.x~=L); %Don't take the same nodes two times - posy2=find(md.y==L & md.x~=0 & md.x~=L); + posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=L); %Don't take the same nodes two times + posy2=find(md.mesh.y==L & md.mesh.x~=0 & md.mesh.x~=L); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; %Add spc on the corners - pos=find((md.x==0 | md.x==L) & (md.y==0 | md.y==L) & md.mesh.vertexonbed); + pos=find((md.mesh.x==0 | md.mesh.x==L) & (md.mesh.y==0 | md.mesh.y==L) & md.mesh.vertexonbed); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvy(pos)=0; Index: /issm/trunk/test/NightlyRun/test1106.m =================================================================== --- /issm/trunk/test/NightlyRun/test1106.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1106.m (revision 9734) @@ -19,9 +19,9 @@ %Create MPCs to have periodic boundary conditions - %posx=find(md.x==0); - %posx2=find(md.x==L); + %posx=find(md.mesh.x==0); + %posx2=find(md.mesh.x==L); - %posy=find(md.y==0 & md.x~=0 & md.x~=L); %Don't take the same nodes two times - %posy2=find(md.y==L & md.x~=0 & md.x~=L); + %posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=L); %Don't take the same nodes two times + %posy2=find(md.mesh.y==L & md.mesh.x~=0 & md.mesh.x~=L); %md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; Index: /issm/trunk/test/NightlyRun/test1107.m =================================================================== --- /issm/trunk/test/NightlyRun/test1107.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1107.m (revision 9734) @@ -26,14 +26,14 @@ %Create MPCs to have periodic boundary conditions - posx=find(md.x==0 & ~(md.y==0 & md.mesh.vertexonbed) & ~(md.y==L & md.mesh.vertexonbed)); - posx2=find(md.x==max(md.x) & ~(md.y==0 & md.mesh.vertexonbed) & ~(md.y==L & md.mesh.vertexonbed)); + posx=find(md.mesh.x==0 & ~(md.mesh.y==0 & md.mesh.vertexonbed) & ~(md.mesh.y==L & md.mesh.vertexonbed)); + posx2=find(md.mesh.x==max(md.mesh.x) & ~(md.mesh.y==0 & md.mesh.vertexonbed) & ~(md.mesh.y==L & md.mesh.vertexonbed)); - posy=find(md.y==0 & md.x~=0 & md.x~=max(md.x)); %Don't take the same nodes two times - posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x)); + posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; %Add spc on the corners - pos=find((md.x==0 | md.x==L) & (md.y==0 | md.y==L) & md.mesh.vertexonbed); + pos=find((md.mesh.x==0 | md.mesh.x==L) & (md.mesh.y==0 | md.mesh.y==L) & md.mesh.vertexonbed); md.diagnostic.spcvy(:)=0; md.diagnostic.spcvx(pos)=0; Index: /issm/trunk/test/NightlyRun/test1108.m =================================================================== --- /issm/trunk/test/NightlyRun/test1108.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1108.m (revision 9734) @@ -22,5 +22,5 @@ %md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - %pos=find((md.x==0 | md.x==max(md.x)) & (md.y==0 | md.y==max(md.y))); + %pos=find((md.mesh.x==0 | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0 | md.mesh.y==max(md.mesh.y))); %md.diagnostic.spcvx(pos)=0; %md.diagnostic.spcvy(pos)=0; @@ -28,9 +28,9 @@ %%Create MPCs to have periodic boundary conditions - %posx=find(md.x==0); - %posx2=find(md.x==max(md.x)); + %posx=find(md.mesh.x==0); + %posx2=find(md.mesh.x==max(md.mesh.x)); - %posy=find(md.y==0 & md.x~=0 & md.x~=max(md.x)); %Don't take the same nodes two times - %posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x)); + %posy=find(md.mesh.y==0 & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %Don't take the same nodes two times + %posy2=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=0 & md.mesh.x~=max(md.mesh.x)); %md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; Index: /issm/trunk/test/NightlyRun/test1109.m =================================================================== --- /issm/trunk/test/NightlyRun/test1109.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1109.m (revision 9734) @@ -26,6 +26,6 @@ %Create MPCs to have periodic boundary conditions - posx=find(md.x==0); - posx2=find(md.x==max(md.x)); + posx=find(md.mesh.x==0); + posx2=find(md.mesh.x==max(md.mesh.x)); md.diagnostic.vertex_pairing=[posx,posx2]; @@ -41,5 +41,5 @@ %Remove the spc where there is some sliding (case 3 and 4): if i==3 | i==4, - pos=find(md.y/max(md.y)>=0.44 & md.y/max(md.y)<=0.5); + pos=find(md.mesh.y/max(md.mesh.y)>=0.44 & md.mesh.y/max(md.mesh.y)<=0.5); md.diagnostic.spcvx(pos)=NaN; md.diagnostic.spcvy(pos)=NaN; Index: /issm/trunk/test/NightlyRun/test1110.m =================================================================== --- /issm/trunk/test/NightlyRun/test1110.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1110.m (revision 9734) @@ -30,5 +30,5 @@ md.diagnostic.spcvz(pos)=0; else - pos=find(md.mesh.vertexonbed & (md.x==0 | md.x==max(md.x)) & (md.y==0 | md.y==max(md.y))); + pos=find(md.mesh.vertexonbed & (md.mesh.x==0 | md.mesh.x==max(md.mesh.x)) & (md.mesh.y==0 | md.mesh.y==max(md.mesh.y))); md.diagnostic.spcvx(pos)=100; %because we need a dirichlet somewhere md.diagnostic.spcvy(pos)=0; @@ -39,9 +39,9 @@ %Create MPCs to have periodic boundary conditions - posx=find(md.x==0); - posx2=find(md.x==max(md.x)); + posx=find(md.mesh.x==0); + posx2=find(md.mesh.x==max(md.mesh.x)); - posy=find(md.y==0); - posy2=find(md.y==max(md.y)); + posy=find(md.mesh.y==0); + posy2=find(md.mesh.y==max(md.mesh.y)); md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2]; Index: /issm/trunk/test/NightlyRun/test1201.m =================================================================== --- /issm/trunk/test/NightlyRun/test1201.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1201.m (revision 9734) @@ -27,5 +27,5 @@ %spc thickness - pos=find(md.y>199999.9); + pos=find(md.mesh.y>199999.9); times=0:1:500; md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices+1,length(times)); @@ -48,5 +48,5 @@ [elements,x,y,z,s,h2]=SectionValues(md,results{2},'../Exp/CrossLineEISMINT.exp',100); [elements,x,y,z,s,h3]=SectionValues(md,results{3},'../Exp/CrossLineEISMINT.exp',100); -[elements,x,y,z,s,hth]=SectionValues(md, 500+100*sin(2*pi/200*(500-md.y/400)),'../Exp/CrossLineEISMINT.exp',100); +[elements,x,y,z,s,hth]=SectionValues(md, 500+100*sin(2*pi/200*(500-md.mesh.y/400)),'../Exp/CrossLineEISMINT.exp',100); plot(s,h1,'r',s,h2,'b',s,h3,'g',s,hth,'k') legend('Art. diff.','No Art. diff.','D.G.','Theoretical') Index: /issm/trunk/test/NightlyRun/test1203.m =================================================================== --- /issm/trunk/test/NightlyRun/test1203.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1203.m (revision 9734) @@ -10,6 +10,6 @@ %Impose a non zero velocity on the upper boundary condition (y=max(y)) -pos=find(md.y==max(md.y)); -md.diagnostic.spcvy(pos)=400*(((md.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.x(pos)-100000)/25000).^2); +pos=find(md.mesh.y==max(md.mesh.y)); +md.diagnostic.spcvy(pos)=400*(((md.mesh.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.mesh.x(pos)-100000)/25000).^2); %Compute solution for MacAyeal's model Index: /issm/trunk/test/NightlyRun/test1204.m =================================================================== --- /issm/trunk/test/NightlyRun/test1204.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1204.m (revision 9734) @@ -10,6 +10,6 @@ %Impose a non zero velocity on the upper boundary condition (y=max(y)) -pos=find(md.y==max(md.y)); -md.diagnostic.spcvy(pos)=400*(((md.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.x(pos)-100000)/25000).^2); +pos=find(md.mesh.y==max(md.mesh.y)); +md.diagnostic.spcvy(pos)=400*(((md.mesh.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.mesh.x(pos)-100000)/25000).^2); %Compute solution for MacAyeal's model Index: /issm/trunk/test/NightlyRun/test1205.m =================================================================== --- /issm/trunk/test/NightlyRun/test1205.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1205.m (revision 9734) @@ -13,6 +13,6 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; -vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; +vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); @@ -51,5 +51,5 @@ set(gcf,'Position',[1 1 1580 1150]) subplot(2,2,1) -p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.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.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... vel_obs,'FaceColor','interp','EdgeColor','none'); title('Analytical velocity','FontSize',14,'FontWeight','bold') @@ -66,6 +66,6 @@ subplot(2,2,3) hold on; -plot(sqrt((md.x(1:md.mesh.numberofvertices2d)).^2+(md.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); -plot(sqrt((md.x2d).^2+(md.y2d).^2),vel_obs,'b.'); +plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); +plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); @@ -76,5 +76,5 @@ subplot(2,2,4) -p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.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 9733) +++ /issm/trunk/test/NightlyRun/test1206.m (revision 9734) @@ -13,6 +13,6 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; -vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; +vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); @@ -50,5 +50,5 @@ figure(1) subplot(2,2,1) -p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.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.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... vel_obs,'FaceColor','interp','EdgeColor','none'); title('Analytical velocity','FontSize',14,'FontWeight','bold') @@ -65,6 +65,6 @@ subplot(2,2,3) hold on; -plot(sqrt((md.x(1:md.mesh.numberofvertices2d)).^2+(md.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); -plot(sqrt((md.x2d).^2+(md.y2d).^2),vel_obs,'b.'); +plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); +plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); @@ -75,5 +75,5 @@ subplot(2,2,4) -p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.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 9733) +++ /issm/trunk/test/NightlyRun/test1207.m (revision 9734) @@ -13,6 +13,6 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; -vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; +vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); @@ -50,5 +50,5 @@ figure(1) subplot(2,2,1) -p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.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.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... vel_obs,'FaceColor','interp','EdgeColor','none'); title('Analytical velocity','FontSize',14,'FontWeight','bold') @@ -65,6 +65,6 @@ subplot(2,2,3) hold on; -plot(sqrt((md.x(1:md.mesh.numberofvertices2d)).^2+(md.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); -plot(sqrt((md.x2d).^2+(md.y2d).^2),vel_obs,'b.'); +plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); +plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); @@ -75,5 +75,5 @@ subplot(2,2,4) -p=patch('Faces',md.mesh.elements2d,'Vertices',[md.x2d md.y2d],'FaceVertexCData',... +p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.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 9733) +++ /issm/trunk/test/NightlyRun/test1302.m (revision 9734) @@ -23,5 +23,5 @@ A=10/(exp(alpha*(-1000))-1); %A=T(bed)/(exp(alpha*bed)-1) with bed=-1000 T(bed)=10 B=-A; -md.initialization.temperature=A*exp(alpha*md.z)+B; +md.initialization.temperature=A*exp(alpha*md.mesh.z)+B; %modeled results Index: /issm/trunk/test/NightlyRun/test1303.m =================================================================== --- /issm/trunk/test/NightlyRun/test1303.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1303.m (revision 9734) @@ -18,5 +18,5 @@ %d2T/dz2=0 T(bed)=10 T(surface)=0 => T=0*(z-bed)/thickness+10*(surface-z)/thickness %each layer of the 3d mesh must have a constant value -md.initialization.temperature=10*(md.geometry.surface-md.z)./md.geometry.thickness; +md.initialization.temperature=10*(md.geometry.surface-md.mesh.z)./md.geometry.thickness; %modeled results Index: /issm/trunk/test/NightlyRun/test1304.m =================================================================== --- /issm/trunk/test/NightlyRun/test1304.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1304.m (revision 9734) @@ -19,5 +19,5 @@ %the result is linear with depth and is equal to 0 on the upper surface (See BC) %d2T/dz2=0 -k*dT/dz(bed)=G T(surface)=0 => T=-G/k*(z-surface) -md.initialization.temperature=-0.1/md.thermalconductivity*(md.z-md.geometry.surface); %G=0.1 W/m2 +md.initialization.temperature=-0.1/md.thermalconductivity*(md.mesh.z-md.geometry.surface); %G=0.1 W/m2 %modeled results Index: /issm/trunk/test/NightlyRun/test137.m =================================================================== --- /issm/trunk/test/NightlyRun/test137.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test137.m (revision 9734) @@ -2,11 +2,11 @@ %Simple mesh md=bamg(model,'domain','../Exp/Square.exp','hmax',100000); -x1=md.x; -y1=md.y; +x1=md.mesh.x; +y1=md.mesh.y; %hVertices md=bamg(model,'domain','../Exp/Square.exp','hmax',300000,'hvertices',[10000 100000 400000 100000]'); -x2=md.x; -y2=md.y; +x2=md.mesh.x; +y2=md.mesh.y; %big mesh Index: /issm/trunk/test/NightlyRun/test1401.m =================================================================== --- /issm/trunk/test/NightlyRun/test1401.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1401.m (revision 9734) @@ -1,4 +1,4 @@ %test the anisotropic mesh adaptation -%function to capture = exp(-(sqrt((md.x+0.1).^2+(md.y+0.1).^2)-0.75).^2*10^6)+((md.x+0.1).^2+(md.y+0.1).^2)/2; +%function to capture = exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; printingflag=false; @@ -11,5 +11,5 @@ %mesh adaptation loop YAMS md=squaremesh(md,L,L,nx,ny); -md.inversion.vel_obs=exp(-(sqrt((md.x+0.1).^2+(md.y+0.1).^2)-0.75).^2*10^6)+((md.x+0.1).^2+(md.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; plotmodel(md,'data','vel_obs','data','vel_obs','nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); if printingflag, @@ -20,5 +20,5 @@ md=YamsCall(md,md.inversion.vel_obs,0.001,0.3,1.3,10^-4); -md.inversion.vel_obs=exp(-(sqrt((md.x+0.1).^2+(md.y+0.1).^2)-0.75).^2*10^6)+((md.x+0.1).^2+(md.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; plotmodel(md,'data','vel_obs','data','vel_obs','nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); if printingflag, @@ -29,5 +29,5 @@ md=YamsCall(md,md.inversion.vel_obs,0.001,0.3,2.5,0.008); -md.inversion.vel_obs=exp(-(sqrt((md.x+0.1).^2+(md.y+0.1).^2)-0.75).^2*10^6)+((md.x+0.1).^2+(md.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; plotmodel(md,'data','vel_obs','data','vel_obs','nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); if printingflag, @@ -36,10 +36,10 @@ system(['mv mesh1_yams3.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Mesh/ ']); end -x1=md.x; -y1=md.y; +x1=md.mesh.x; +y1=md.mesh.y; %mesh adaptation loop BAMG md=squaremesh(md,L,L,nx,ny); -md.inversion.vel_obs=exp(-(sqrt((md.x+0.1).^2+(md.y+0.1).^2)-0.75).^2*10^6)+((md.x+0.1).^2+(md.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; plotmodel(md,'data','vel_obs','data','vel_obs','nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); if printingflag, @@ -51,5 +51,5 @@ md.bamg=NaN; md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.001,'hmax',0.3,'gradation',1.3,'err',10^-4); -md.inversion.vel_obs=exp(-(sqrt((md.x+0.1).^2+(md.y+0.1).^2)-0.75).^2*10^6)+((md.x+0.1).^2+(md.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; plotmodel(md,'data','vel_obs','data','vel_obs','nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); if printingflag, @@ -61,5 +61,5 @@ md.bamg=NaN; md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.001,'hmax',0.3,'gradation',2.5,'err',0.008); -md.inversion.vel_obs=exp(-(sqrt((md.x+0.1).^2+(md.y+0.1).^2)-0.75).^2*10^6)+((md.x+0.1).^2+(md.y+0.1).^2)/2; +md.inversion.vel_obs=exp(-(sqrt((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)-0.75).^2*10^6)+((md.mesh.x+0.1).^2+(md.mesh.y+0.1).^2)/2; plotmodel(md,'data','vel_obs','data','vel_obs','nlines',1,'ncols',2,'title','','figposition',[500 500 1000 500],'axis#all','equal','xlim#all',[0 1],'ylim#all',[0 1],'edgecolor#1','w'); pause(0.5); if printingflag, @@ -68,6 +68,6 @@ system(['mv mesh1_bamg3.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Mesh/ ']); end -x2=md.x; -y2=md.y; +x2=md.mesh.x; +y2=md.mesh.y; %Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test1402.m =================================================================== --- /issm/trunk/test/NightlyRun/test1402.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1402.m (revision 9734) @@ -10,5 +10,5 @@ %mesh adaptation loop YAMS md=squaremesh(md,L,L,nx,ny); -u=4*md.x-2; v=4*md.y-2; +u=4*md.mesh.x-2; v=4*md.mesh.y-2; md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... @@ -22,5 +22,5 @@ md=YamsCall(md,md.inversion.vel_obs,0.005,0.3,2.3,10^-2); -u=4*md.x-2; v=4*md.y-2; +u=4*md.mesh.x-2; v=4*md.mesh.y-2; md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... @@ -34,5 +34,5 @@ md=YamsCall(md,md.inversion.vel_obs,0.005,0.3,3,0.005); -u=4*md.x-2; v=4*md.y-2; +u=4*md.mesh.x-2; v=4*md.mesh.y-2; md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... @@ -44,10 +44,10 @@ system(['mv mesh2_yams3.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Mesh/ ']); end -x1=md.x; -y1=md.y; +x1=md.mesh.x; +y1=md.mesh.y; %mesh adaptation loop BAMG md=squaremesh(md,L,L,nx,ny); -u=4*md.x-2; v=4*md.y-2; +u=4*md.mesh.x-2; v=4*md.mesh.y-2; md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... @@ -62,5 +62,5 @@ md.bamg=NaN; md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.005,'hmax',0.3,'gradation',2.3,'err',10^-2); -u=4*md.x-2; v=4*md.y-2; +u=4*md.mesh.x-2; v=4*md.mesh.y-2; md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... @@ -75,5 +75,5 @@ md.bamg=NaN; md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.005,'hmax',0.3,'gradation',3,'err',0.005); -u=4*md.x-2; v=4*md.y-2; +u=4*md.mesh.x-2; v=4*md.mesh.y-2; md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... @@ -88,5 +88,5 @@ md.bamg=NaN; md=bamg(md,'field',md.inversion.vel_obs,'hmin',0.005,'hmax',0.3,'gradation',1.5,'err',0.003,'anisomax',1); -u=4*md.x-2; v=4*md.y-2; +u=4*md.mesh.x-2; v=4*md.mesh.y-2; md.inversion.vel_obs=tanh(30*(u.^2+v.^2-0.25)) ... +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... @@ -98,6 +98,6 @@ system(['mv mesh2_bamgiso.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Mesh/ ']); end -x2=md.x; -y2=md.y; +x2=md.mesh.x; +y2=md.mesh.y; %Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test1501.m =================================================================== --- /issm/trunk/test/NightlyRun/test1501.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1501.m (revision 9734) @@ -97,6 +97,6 @@ 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)); + x1=md.mesh.x(index(:,1)); x2=md.mesh.x(index(:,2)); x3=md.mesh.x(index(:,3)); + y1=md.mesh.y(index(:,1)); y2=md.mesh.y(index(:,2)); y3=md.mesh.y(index(:,3)); areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))); Index: /issm/trunk/test/NightlyRun/test1502.m =================================================================== --- /issm/trunk/test/NightlyRun/test1502.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test1502.m (revision 9734) @@ -103,6 +103,6 @@ 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)); + x1=md.mesh.x(index(:,1)); x2=md.mesh.x(index(:,2)); x3=md.mesh.x(index(:,3)); + y1=md.mesh.y(index(:,1)); y2=md.mesh.y(index(:,2)); y3=md.mesh.y(index(:,3)); areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))); Index: /issm/trunk/test/NightlyRun/test233.m =================================================================== --- /issm/trunk/test/NightlyRun/test233.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test233.m (revision 9734) @@ -13,8 +13,8 @@ %needed later -ymin=min(md.y); -ymax=max(md.y); -xmin=min(md.x); -xmax=max(md.x); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +xmin=min(md.mesh.x); +xmax=max(md.mesh.x); di=md.materials.rho_ice/md.materials.rho_water; @@ -42,10 +42,10 @@ %constrain flanks to 0 normal velocity -pos=find(md.x==xmin | md.x==xmax); +pos=find(md.mesh.x==xmin | md.mesh.x==xmax); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvz(pos)=NaN; %constrain grounding line to 0 velocity -pos=find(md.y==ymin); +pos=find(md.mesh.y==ymin); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvy(pos)=0; @@ -53,5 +53,5 @@ %icefront nodeonicefront=zeros(md.mesh.numberofvertices,1); -pos=find(md.y==ymax); nodeonicefront(pos)=1; +pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1; pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:); diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))]; @@ -62,5 +62,5 @@ %create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. %ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; -%vy_c=ey_c.*md.y*md.constants.yts; +%vy_c=ey_c.*md.mesh.y*md.constants.yts; %Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test234.m =================================================================== --- /issm/trunk/test/NightlyRun/test234.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test234.m (revision 9734) @@ -13,8 +13,8 @@ %needed later -ymin=min(md.y); -ymax=max(md.y); -xmin=min(md.x); -xmax=max(md.x); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +xmin=min(md.mesh.x); +xmax=max(md.mesh.x); di=md.materials.rho_ice/md.materials.rho_water; @@ -42,10 +42,10 @@ %constrain flanks to 0 normal velocity -pos=find(md.x==xmin | md.x==xmax); +pos=find(md.mesh.x==xmin | md.mesh.x==xmax); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvz(pos)=NaN; %constrain grounding line to 0 velocity -pos=find(md.y==ymin); +pos=find(md.mesh.y==ymin); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvy(pos)=0; @@ -53,5 +53,5 @@ %icefront nodeonicefront=zeros(md.mesh.numberofvertices,1); -pos=find(md.y==ymax); nodeonicefront(pos)=1; +pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1; pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:); diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))]; @@ -62,5 +62,5 @@ %create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. %ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; -%vy_c=ey_c.*md.y*md.constants.yts; +%vy_c=ey_c.*md.mesh.y*md.constants.yts; %Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test235.m =================================================================== --- /issm/trunk/test/NightlyRun/test235.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test235.m (revision 9734) @@ -10,8 +10,8 @@ %needed later -ymin=min(md.y); -ymax=max(md.y); -xmin=min(md.x); -xmax=max(md.x); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +xmin=min(md.mesh.x); +xmax=max(md.mesh.x); di=md.materials.rho_ice/md.materials.rho_water; @@ -39,10 +39,10 @@ %constrain flanks to 0 normal velocity -pos=find(md.x==xmin | md.x==xmax); +pos=find(md.mesh.x==xmin | md.mesh.x==xmax); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvz(pos)=NaN; %constrain grounding line to 0 velocity -pos=find(md.y==ymin); +pos=find(md.mesh.y==ymin); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvy(pos)=0; @@ -50,5 +50,5 @@ %icefront nodeonicefront=zeros(md.mesh.numberofvertices,1); -pos=find(md.y==ymax); nodeonicefront(pos)=1; +pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1; pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:); diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))]; Index: /issm/trunk/test/NightlyRun/test236.m =================================================================== --- /issm/trunk/test/NightlyRun/test236.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test236.m (revision 9734) @@ -10,8 +10,8 @@ %needed later -ymin=min(md.y); -ymax=max(md.y); -xmin=min(md.x); -xmax=max(md.x); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +xmin=min(md.mesh.x); +xmax=max(md.mesh.x); di=md.materials.rho_ice/md.materials.rho_water; @@ -39,10 +39,10 @@ %constrain flanks to 0 normal velocity -pos=find(md.x==xmin | md.x==xmax); +pos=find(md.mesh.x==xmin | md.mesh.x==xmax); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvz(pos)=NaN; %constrain grounding line to 0 velocity -pos=find(md.y==ymin); +pos=find(md.mesh.y==ymin); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvy(pos)=0; @@ -50,5 +50,5 @@ %icefront nodeonicefront=zeros(md.mesh.numberofvertices,1); -pos=find(md.y==ymax); nodeonicefront(pos)=1; +pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1; pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:); diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))]; Index: /issm/trunk/test/NightlyRun/test446.m =================================================================== --- /issm/trunk/test/NightlyRun/test446.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test446.m (revision 9734) @@ -5,11 +5,11 @@ md=roundmesh(model,radius,resolution); %fix center node to 0,0 -rad=sqrt((md.x).*md.x+(md.y).*md.y); +rad=sqrt((md.mesh.x).*md.mesh.x+(md.mesh.y).*md.mesh.y); pos=find(rad==min(rad)); -md.x(pos)=0; md.y(pos)=0; %the closest node to the center is changed to be exactly at the center +md.mesh.x(pos)=0; md.mesh.y(pos)=0; %the closest node to the center is changed to be exactly at the center %}}} %put our grounding line 'shelfextent' meters from the icefront {{{1 -xelem=md.x(md.mesh.elements)*[1;1;1]/3; -yelem=md.y(md.mesh.elements)*[1;1;1]/3; +xelem=md.mesh.x(md.mesh.elements)*[1;1;1]/3; +yelem=md.mesh.y(md.mesh.elements)*[1;1;1]/3; rad=sqrt((xelem).*xelem+(yelem).*yelem); flags=zeros(md.mesh.numberofelements,1); @@ -24,5 +24,5 @@ %plug holes into the ice sheet, to test for grounding line migration. {{{1 di=md.materials.rho_ice/md.materials.rho_water; -rad=sqrt((md.x).*md.x+(md.y).*md.y); +rad=sqrt((md.mesh.x).*md.mesh.x+(md.mesh.y).*md.mesh.y); pos=find(rad<200000); md.geometry.thickness(pos)=100; @@ -30,10 +30,10 @@ md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); -pos=find(md.x<.2*1e6 & md.x>-.2*1e6 & md.y>0); +pos=find(md.mesh.x<.2*1e6 & md.mesh.x>-.2*1e6 & md.mesh.y>0); md.geometry.thickness(pos)=100; md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); -pos=find(md.x<.1*1e6 & md.x>-.1*1e6 & md.y<-.5*1e6 & md.y>-.6*1e6); +pos=find(md.mesh.x<.1*1e6 & md.mesh.x>-.1*1e6 & md.mesh.y<-.5*1e6 & md.mesh.y>-.6*1e6); md.geometry.thickness(pos)=100; md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; Index: /issm/trunk/test/NightlyRun/test527.m =================================================================== --- /issm/trunk/test/NightlyRun/test527.m (revision 9733) +++ /issm/trunk/test/NightlyRun/test527.m (revision 9734) @@ -3,6 +3,6 @@ hVertices(1:5)=1000; md=bamg(model,'domain','../Exp/Pig.exp','hmax',20000,'hVertices',hVertices,'gradation',3,'geometricalmetric',1); -x1=md.x; -y1=md.y; +x1=md.mesh.x; +y1=md.mesh.y; %Simple mesh 2 @@ -10,9 +10,9 @@ md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); md=parameterize(md,'../Par/Pig.par'); -x2=md.x; -y2=md.y; +x2=md.mesh.x; +y2=md.mesh.y; %refine existing mesh 1 -hessian=ComputeHessian(md.mesh.elements,md.x,md.y,md.inversion.vy_obs,'node'); +hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.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 9733) +++ /issm/trunk/test/Par/79North.par (revision 9734) @@ -3,8 +3,8 @@ %Geometry and observation load('../Data/79North.data','-mat'); -md.initialization.vx =InterpFromMeshToMesh2d(index,x,y,vx,md.x,md.y); -md.initialization.vy =InterpFromMeshToMesh2d(index,x,y,vy,md.x,md.y); -md.geometry.surface =InterpFromMeshToMesh2d(index,x,y,surface,md.x,md.y); -md.geometry.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.x,md.y); +md.initialization.vx =InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy =InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); +md.geometry.surface =InterpFromMeshToMesh2d(index,x,y,surface,md.mesh.x,md.mesh.y); +md.geometry.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.mesh.x,md.mesh.y); md.geometry.bed=md.geometry.surface-md.geometry.thickness; clear surface thickness vx vy x y index; Index: /issm/trunk/test/Par/ISMIPA.par =================================================================== --- /issm/trunk/test/Par/ISMIPA.par (revision 9733) +++ /issm/trunk/test/Par/ISMIPA.par (revision 9734) @@ -2,6 +2,6 @@ disp(' creating thickness'); -md.geometry.surface=-md.x*tan(0.5*pi/180); -md.geometry.bed=md.geometry.surface-1000+500*sin(md.x*2*pi/max(md.x)).*sin(md.y*2*pi/max(md.x)); +md.geometry.surface=-md.mesh.x*tan(0.5*pi/180); +md.geometry.bed=md.geometry.surface-1000+500*sin(md.mesh.x*2*pi/max(md.mesh.x)).*sin(md.mesh.y*2*pi/max(md.mesh.x)); md.geometry.thickness=md.geometry.surface-md.geometry.bed; Index: /issm/trunk/test/Par/ISMIPB.par =================================================================== --- /issm/trunk/test/Par/ISMIPB.par (revision 9733) +++ /issm/trunk/test/Par/ISMIPB.par (revision 9734) @@ -2,6 +2,6 @@ disp(' creating thickness'); -md.geometry.surface=-md.x*tan(0.5*pi/180); -md.geometry.bed=md.geometry.surface-1000+500*sin(md.x*2*pi/max(md.x)); +md.geometry.surface=-md.mesh.x*tan(0.5*pi/180); +md.geometry.bed=md.geometry.surface-1000+500*sin(md.mesh.x*2*pi/max(md.mesh.x)); md.geometry.thickness=md.geometry.surface-md.geometry.bed; Index: /issm/trunk/test/Par/ISMIPC.par =================================================================== --- /issm/trunk/test/Par/ISMIPC.par (revision 9733) +++ /issm/trunk/test/Par/ISMIPC.par (revision 9734) @@ -2,11 +2,11 @@ disp(' creating thickness'); -md.geometry.surface=2000-md.x*tan(0.1*pi/180); %to have z>0 +md.geometry.surface=2000-md.mesh.x*tan(0.1*pi/180); %to have z>0 md.geometry.bed=md.geometry.surface-1000; md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); -%md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.x*2*pi/max(md.x/2)).*sin(md.y*2*pi/max(md.x/2)))./(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed))); -md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.x*2*pi/max(md.x)).*sin(md.y*2*pi/max(md.x)))); +%md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.mesh.x*2*pi/max(md.mesh.x/2)).*sin(md.mesh.y*2*pi/max(md.mesh.x/2)))./(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed))); +md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.mesh.x*2*pi/max(md.mesh.x)).*sin(md.mesh.y*2*pi/max(md.mesh.x)))); %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); Index: /issm/trunk/test/Par/ISMIPD.par =================================================================== --- /issm/trunk/test/Par/ISMIPD.par (revision 9733) +++ /issm/trunk/test/Par/ISMIPD.par (revision 9734) @@ -2,10 +2,10 @@ disp(' creating thickness'); -md.geometry.surface=2000-md.x*tan(0.1*pi/180); %to have z>0 +md.geometry.surface=2000-md.mesh.x*tan(0.1*pi/180); %to have z>0 md.geometry.bed=md.geometry.surface-1000; md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); -md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.x*2*pi/max(md.x)))); +md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.mesh.x*2*pi/max(md.mesh.x)))); %Take care of iceshelves: no basal drag pos=find(md.mask.elementonfloatingice); Index: /issm/trunk/test/Par/ISMIPE.par =================================================================== --- /issm/trunk/test/Par/ISMIPE.par (revision 9733) +++ /issm/trunk/test/Par/ISMIPE.par (revision 9734) @@ -7,5 +7,5 @@ md.geometry.bed=zeros(md.mesh.numberofvertices,1); for i=1:md.mesh.numberofvertices - y=md.y(i); + y=md.mesh.y(i); point1=floor(y/100)+1; point2=min(point1+1,51); Index: /issm/trunk/test/Par/ISMIPF.par =================================================================== --- /issm/trunk/test/Par/ISMIPF.par (revision 9733) +++ /issm/trunk/test/Par/ISMIPF.par (revision 9734) @@ -3,7 +3,7 @@ disp(' creating thickness'); -md.geometry.surface=-md.x*tan(3*pi/180); +md.geometry.surface=-md.mesh.x*tan(3*pi/180); %md.geometry.bed=md.geometry.surface-1000; -md.geometry.bed=md.geometry.surface-1000+100*exp(-((md.x-max(md.x)/2).^2+(md.y-max(md.y)/2).^2)/(10000^2)); +md.geometry.bed=md.geometry.surface-1000+100*exp(-((md.mesh.x-max(md.mesh.x)/2).^2+(md.mesh.y-max(md.mesh.y)/2).^2)/(10000^2)); md.geometry.thickness=md.geometry.surface-md.geometry.bed; @@ -28,5 +28,5 @@ md.initialization.pressure=zeros(md.mesh.numberofvertices,1); md.initialization.temperature=255*ones(md.mesh.numberofvertices,1); -pos=find(md.x==min(md.x) | md.x==max(md.x) | md.y==min(md.y) | md.y==max(md.y)); +pos=find(md.mesh.x==min(md.mesh.x) | md.mesh.x==max(md.mesh.x) | md.mesh.y==min(md.mesh.y) | md.mesh.y==max(md.mesh.y)); md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); Index: /issm/trunk/test/Par/Pig.par =================================================================== --- /issm/trunk/test/Par/Pig.par (revision 9733) +++ /issm/trunk/test/Par/Pig.par (revision 9734) @@ -3,8 +3,8 @@ %Geometry and observation load('../Data/Pig.data','-mat'); -md.inversion.vx_obs =InterpFromMeshToMesh2d(index,x,y,vx_obs,md.x,md.y); -md.inversion.vy_obs =InterpFromMeshToMesh2d(index,x,y,vy_obs,md.x,md.y); -md.geometry.surface =InterpFromMeshToMesh2d(index,x,y,surface,md.x,md.y); -md.geometry.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.x,md.y); +md.inversion.vx_obs =InterpFromMeshToMesh2d(index,x,y,vx_obs,md.mesh.x,md.mesh.y); +md.inversion.vy_obs =InterpFromMeshToMesh2d(index,x,y,vy_obs,md.mesh.x,md.mesh.y); +md.geometry.surface =InterpFromMeshToMesh2d(index,x,y,surface,md.mesh.x,md.mesh.y); +md.geometry.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.mesh.x,md.mesh.y); md.geometry.bed=md.geometry.surface-md.geometry.thickness; clear surface thickness vx_obs vy_obs x y index; Index: /issm/trunk/test/Par/RoundSheetEISMINT.par =================================================================== --- /issm/trunk/test/Par/RoundSheetEISMINT.par (revision 9733) +++ /issm/trunk/test/Par/RoundSheetEISMINT.par (revision 9734) @@ -13,5 +13,5 @@ tmin=238.15; %K st=1.67*10^-2/1000; %k/m; -radius=sqrt((md.x).^2+(md.y).^2); +radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); md.initialization.temperature=(tmin+st*radius); md.basalforcings.geothermalflux=4.2*10^-2*ones(md.mesh.numberofvertices,1); @@ -29,6 +29,6 @@ disp(' creating velocities'); constant=0.3; -md.inversion.vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; -md.inversion.vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; +md.inversion.vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; +md.inversion.vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; md.inversion.vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); md.initialization.vx=zeros(md.mesh.numberofvertices,1); @@ -41,7 +41,7 @@ md=SetMarineIceSheetBC(md,'../Exp/RoundFrontEISMINT.exp'); -radius=sqrt((md.x).*md.x+(md.y).*md.y); +radius=sqrt((md.mesh.x).*md.mesh.x+(md.mesh.y).*md.mesh.y); pos=find(radius==min(radius)); -md.x(pos)=0; md.y(pos)=0; %the closest node to the center is changed to be exactly at the center +md.mesh.x(pos)=0; md.mesh.y(pos)=0; %the closest node to the center is changed to be exactly at the center md.diagnostic.spcvx(pos)=0; Index: /issm/trunk/test/Par/RoundSheetShelf.par =================================================================== --- /issm/trunk/test/Par/RoundSheetShelf.par (revision 9733) +++ /issm/trunk/test/Par/RoundSheetShelf.par (revision 9734) @@ -7,5 +7,5 @@ hmin=300; hmax=1000; -radius=sqrt((md.x).*md.x+(md.y).*md.y); +radius=sqrt((md.mesh.x).*md.mesh.x+(md.mesh.y).*md.mesh.y); ymin=min(radius); ymax=max(radius); @@ -23,10 +23,10 @@ -pos=find(md.x<.2*1e6 & md.x>-.2*1e6 & md.y>0); +pos=find(md.mesh.x<.2*1e6 & md.mesh.x>-.2*1e6 & md.mesh.y>0); md.geometry.thickness(pos)=100; md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); -pos=find(md.x<.1*1e6 & md.x>-.1*1e6 & md.y<-.5*1e6 & md.y>-.6*1e6); +pos=find(md.mesh.x<.1*1e6 & md.mesh.x>-.1*1e6 & md.mesh.y<-.5*1e6 & md.mesh.y>-.6*1e6); md.geometry.thickness(pos)=100; md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; @@ -79,5 +79,5 @@ md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); -pos=find(md.x==0 & md.y==0); +pos=find(md.mesh.x==0 & md.mesh.y==0); md.diagnostic.spcvx(pos)=0; md.diagnostic.spcvy(pos)=0; Index: /issm/trunk/test/Par/RoundSheetStaticEISMINT.par =================================================================== --- /issm/trunk/test/Par/RoundSheetStaticEISMINT.par (revision 9733) +++ /issm/trunk/test/Par/RoundSheetStaticEISMINT.par (revision 9734) @@ -2,7 +2,7 @@ hmin=0.01; hmax=2756.7; -radius=(sqrt((md.x).^2+(md.y).^2)); +radius=(sqrt((md.mesh.x).^2+(md.mesh.y).^2)); radiusmax=max(radius); -md.geometry.thickness=hmin*ones(size(md.x,1),1)+hmax*(4*((1/2)^(4/3)*ones(size(md.x,1),1)-((radius)./(2*radiusmax)).^(4/3))).^(3/8); +md.geometry.thickness=hmin*ones(size(md.mesh.x,1),1)+hmax*(4*((1/2)^(4/3)*ones(size(md.mesh.x,1),1)-((radius)./(2*radiusmax)).^(4/3))).^(3/8); md.geometry.bed=0*md.geometry.thickness; md.geometry.surface=md.geometry.bed+md.geometry.thickness; @@ -34,6 +34,6 @@ disp(' creating velocities'); constant=0.3; -md.inversion.vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; -md.inversion.vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; +md.inversion.vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; +md.inversion.vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; md.inversion.vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); md.initialization.vx=zeros(md.mesh.numberofvertices,1); @@ -46,7 +46,7 @@ md=SetMarineIceSheetBC(md,'../Exp/RoundFrontEISMINT.exp'); -radius=sqrt((md.x).*md.x+(md.y).*md.y); +radius=sqrt((md.mesh.x).*md.mesh.x+(md.mesh.y).*md.mesh.y); pos=find(radius==min(radius)); -md.x(pos)=0; md.y(pos)=0; %the closest node to the center is changed to be exactly at the center +md.mesh.x(pos)=0; md.mesh.y(pos)=0; %the closest node to the center is changed to be exactly at the center md.diagnostic.spcvx(pos)=0; Index: /issm/trunk/test/Par/SquareEISMINT.par =================================================================== --- /issm/trunk/test/Par/SquareEISMINT.par (revision 9733) +++ /issm/trunk/test/Par/SquareEISMINT.par (revision 9734) @@ -2,6 +2,6 @@ disp(' creating thickness'); -ymin=min(md.y); -ymax=max(md.y); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); md.geometry.thickness=500*ones(md.mesh.numberofvertices,1); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; @@ -31,5 +31,5 @@ %Evolution of the ice shelf -pos=find(md.y==200000); %nodes on the upper boundary condition +pos=find(md.mesh.y==200000); %nodes on the upper boundary condition md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); md.balancethickness.spcthickness(pos)=500; Index: /issm/trunk/test/Par/SquareSheetConstrained.par =================================================================== --- /issm/trunk/test/Par/SquareSheetConstrained.par (revision 9733) +++ /issm/trunk/test/Par/SquareSheetConstrained.par (revision 9734) @@ -4,7 +4,7 @@ hmin=300; hmax=1000; -ymin=min(md.y); -ymax=max(md.y); -md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+20; md.geometry.surface=md.geometry.bed+md.geometry.thickness; @@ -12,6 +12,6 @@ %Initial velocity load('../Data/SquareSheetConstrained.data','-mat'); -md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.x,md.y); -md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.x,md.y); +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); clear vx vy x y index; md.initialization.vz=zeros(md.mesh.numberofvertices,1); Index: /issm/trunk/test/Par/SquareSheetShelf.par =================================================================== --- /issm/trunk/test/Par/SquareSheetShelf.par (revision 9733) +++ /issm/trunk/test/Par/SquareSheetShelf.par (revision 9734) @@ -4,10 +4,10 @@ hmin=300; hmax=1000; -ymin=min(md.y); -ymax=max(md.y); -md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; bed_sheet=-md.materials.rho_ice/md.materials.rho_water*(hmax+(hmin-hmax)*(ymax/2-ymin)/(ymax-ymin)); -pos=find(md.y<=ymax/2); +pos=find(md.mesh.y<=ymax/2); md.geometry.bed(pos)=bed_sheet; md.geometry.surface=md.geometry.bed+md.geometry.thickness; @@ -15,6 +15,6 @@ %Initial velocity load('../Data/SquareSheetShelf.data','-mat'); -md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.x,md.y); -md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.x,md.y); +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); clear vx vy x y index; md.initialization.vz=zeros(md.mesh.numberofvertices,1); Index: /issm/trunk/test/Par/SquareShelf.par =================================================================== --- /issm/trunk/test/Par/SquareShelf.par (revision 9733) +++ /issm/trunk/test/Par/SquareShelf.par (revision 9734) @@ -4,7 +4,7 @@ hmin=300; hmax=1000; -ymin=min(md.y); -ymax=max(md.y); -md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; md.geometry.surface=md.geometry.bed+md.geometry.thickness; @@ -12,6 +12,6 @@ %Initial velocity and pressure load('../Data/SquareShelf.data','-mat'); -md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.x,md.y); -md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.x,md.y); +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); clear vx vy x y index; md.initialization.vz=zeros(md.mesh.numberofvertices,1); Index: /issm/trunk/test/Par/SquareShelfConstrained.par =================================================================== --- /issm/trunk/test/Par/SquareShelfConstrained.par (revision 9733) +++ /issm/trunk/test/Par/SquareShelfConstrained.par (revision 9734) @@ -4,7 +4,7 @@ hmin=300; hmax=1000; -ymin=min(md.y); -ymax=max(md.y); -md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; md.geometry.surface=md.geometry.bed+md.geometry.thickness; @@ -12,6 +12,6 @@ %Initial velocity load('../Data/SquareShelfConstrained.data','-mat'); -md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.x,md.y); -md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.x,md.y); +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); clear vx vy x y index; md.initialization.vz=zeros(md.mesh.numberofvertices,1);