Index: /issm/trunk-jpl/src/c/Container/Elements.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Elements.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Elements.cpp (revision 14951) @@ -19,4 +19,8 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" +#include "../classes/objects/Elements/Element.h" +#include "../classes/objects/ExternalResults/GenericExternalResult.h" +#include "../classes/Patch.h" +#include "../classes/toolkits/Vector.h" using namespace std; Index: /issm/trunk-jpl/src/c/Container/Inputs.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Inputs.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Inputs.cpp (revision 14951) @@ -19,4 +19,5 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" +#include "../classes/objects/Inputs/Input.h" using namespace std; Index: /issm/trunk-jpl/src/c/Container/Inputs.h =================================================================== --- /issm/trunk-jpl/src/c/Container/Inputs.h (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Inputs.h (revision 14951) @@ -3,15 +3,7 @@ /*forward declarations */ -class Materials; class Parameters; -class Elements; -class Vertices; -class Loads; -class Nodes; class DataSet; class Input; -class Node; -class GaussTria; -class GaussPenta; #include "../shared/Numerics/types.h" Index: /issm/trunk-jpl/src/c/Container/Loads.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Loads.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Loads.cpp (revision 14951) @@ -19,4 +19,5 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" +#include "../classes/objects/Loads/Load.h" using namespace std; Index: /issm/trunk-jpl/src/c/Container/Materials.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Materials.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Materials.cpp (revision 14951) @@ -19,4 +19,5 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" +#include "../classes/objects/Materials/Material.h" using namespace std; Index: /issm/trunk-jpl/src/c/Container/Nodes.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Nodes.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Nodes.cpp (revision 14951) @@ -19,4 +19,5 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" +#include "../classes/objects/Node.h" using namespace std; Index: /issm/trunk-jpl/src/c/Container/Parameters.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Parameters.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Parameters.cpp (revision 14951) @@ -19,4 +19,5 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" +#include "../classes/objects/objects.h" using namespace std; Index: /issm/trunk-jpl/src/c/Container/Results.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Results.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Results.cpp (revision 14951) @@ -19,4 +19,6 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" +#include "../classes/objects/ExternalResults/ExternalResult.h" +#include "../classes/objects/ElementResults/ElementResult.h" using namespace std; Index: /issm/trunk-jpl/src/c/Container/Vertices.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Vertices.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/Container/Vertices.cpp (revision 14951) @@ -19,4 +19,5 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" +#include "../classes/objects/Vertex.h" using namespace std; Index: /issm/trunk-jpl/src/c/Makefile.am =================================================================== --- /issm/trunk-jpl/src/c/Makefile.am (revision 14950) +++ /issm/trunk-jpl/src/c/Makefile.am (revision 14951) @@ -216,8 +216,4 @@ ./shared/Elements/Paterson.cpp\ ./shared/Elements/Arrhenius.cpp\ - ./shared/Elements/GetVerticesCoordinates.cpp\ - ./shared/Elements/GetLocalDofList.cpp\ - ./shared/Elements/GetGlobalDofList.cpp\ - ./shared/Elements/GetNumberOfDofs.cpp\ ./shared/Elements/PrintArrays.cpp\ ./shared/Elements/PddSurfaceMassBalance.cpp\ @@ -487,9 +483,4 @@ ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \ - ./shared/Elements/CoordinateSystemTransform.cpp\ - ./shared/Elements/TransformLoadVectorCoord.cpp \ - ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ - ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ - ./shared/Elements/TransformSolutionCoord.cpp\ ./solutions/diagnostic_core.cpp\ ./solvers/solver_stokescoupling_nonlinear.cpp Index: /issm/trunk-jpl/src/c/classes/objects/Elements/Element.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Elements/Element.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Elements/Element.h (revision 14951) @@ -11,4 +11,5 @@ /*{{{*/ #include "../Object.h" +#include "../../Update.h" class DataSet; Index: /issm/trunk-jpl/src/c/classes/objects/Elements/PentaRef.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Elements/PentaRef.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Elements/PentaRef.h (revision 14951) @@ -7,4 +7,5 @@ #define _PENTAREF_H_ +class GaussPenta; class PentaRef{ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/BoolInput.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/BoolInput.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/BoolInput.h (revision 14951) @@ -10,4 +10,5 @@ #include "./Input.h" class GaussTria; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/ControlInput.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/ControlInput.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/ControlInput.h (revision 14951) @@ -10,4 +10,5 @@ #include "./Input.h" class GaussTria; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.h (revision 14951) @@ -10,4 +10,5 @@ #include "./Input.h" class GaussTria; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.h (revision 14951) @@ -10,4 +10,5 @@ #include "./Input.h" class GaussTria; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/Input.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/Input.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/Input.h (revision 14951) @@ -13,4 +13,5 @@ class GaussTria; class Parameters; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/IntInput.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/IntInput.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/IntInput.h (revision 14951) @@ -10,4 +10,5 @@ #include "./Input.h" class GaussTria; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.h (revision 14951) @@ -11,4 +11,5 @@ #include "../Elements/PentaRef.h" class GaussTria; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/TransientInput.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/TransientInput.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/TransientInput.h (revision 14951) @@ -11,4 +11,5 @@ class GaussTria; class Parameters; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.h (revision 14951) @@ -11,4 +11,5 @@ #include "../Elements/TriaRef.h" class GaussTria; +class GaussPenta; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Loads/Friction.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Loads/Friction.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Loads/Friction.h (revision 14951) @@ -10,4 +10,6 @@ class Inputs; class Matpar; +class GaussPenta; +class GaussTria; /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Loads/Load.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Loads/Load.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Loads/Load.h (revision 14951) @@ -15,4 +15,5 @@ #include "../Object.h" +#include "../../Update.h" #include "../../../toolkits/toolkits.h" #include "../../../Container/Container.h" Index: /issm/trunk-jpl/src/c/classes/objects/Materials/Material.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Materials/Material.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Materials/Material.h (revision 14951) @@ -10,4 +10,5 @@ class Object; #include "../Object.h" +#include "../../Update.h" #include "../../../toolkits/toolkits.h" /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Node.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Node.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Node.cpp (revision 14951) @@ -955,2 +955,387 @@ } /*}}}*/ + + +/*Methods inherent to Node: */ +int* GetLocalDofList(Node** nodes,int numnodes,int setenum,int approximation){ /*{{{*/ + + int i,j,count,numdof,numgdof; + int* ndof_list=NULL; + int* ngdof_list_cumulative=NULL; + int *doflist = NULL; + + if(numnodes){ + /*allocate: */ + ndof_list=xNew(numnodes); + ngdof_list_cumulative=xNew(numnodes); + + /*Get number of dofs per node, and total for this given set*/ + numdof=0; + numgdof=0; + for(i=0;iGetNumberOfDofs(approximation,setenum); + numgdof +=nodes[i]->GetNumberOfDofs(approximation,GsetEnum); + numdof +=ndof_list[i]; + } + + if(numdof){ + /*Allocate: */ + doflist=xNew(numdof); + + /*Populate: */ + count=0; + for(i=0;iGetLocalDofList(&doflist[count],approximation,setenum); + count+=ndof_list[i]; + } + + /*We now have something like: [0 1 0 2 1 2]. Offset by gsize, to get something like: [0 1 2 4 6 7]:*/ + count=0; + for(i=0;i(ndof_list); + xDelete(ngdof_list_cumulative); + + /*CLean-up and return*/ + return doflist; +} +/*}}}*/ +int* GetGlobalDofList(Node** nodes,int numnodes,int setenum,int approximation){/*{{{*/ + + + int i,numdof,count; + int* ndof_list=NULL; + int *doflist = NULL; + + if(numnodes){ + + /*Allocate:*/ + ndof_list=xNew(numnodes); + + /*First, figure out size of doflist: */ + numdof=0; + for(i=0;iGetNumberOfDofs(approximation,setenum); + numdof+=ndof_list[i]; + } + + if(numdof){ + /*Allocate: */ + doflist=xNew(numdof); + + /*Populate: */ + count=0; + for(i=0;iGetDofList(&doflist[count],approximation,setenum); + count+=ndof_list[i]; + } + } + else doflist=NULL; + } + /*Free ressources:*/ + xDelete(ndof_list); + + return doflist; +} +/*}}}*/ +int GetNumberOfDofs(Node** nodes,int numnodes,int setenum,int approximation){/*{{{*/ + + + /*output: */ + int numberofdofs=0; + + for(int i=0;iGetNumberOfDofs(approximation,setenum); + } + + return numberofdofs; +} +/*}}}*/ +#ifdef _HAVE_DIAGNOSTIC_ +void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum){/*{{{*/ + + + int* cs_array=NULL; + + /*All nodes have the same Coordinate System*/ + cs_array=xNew(numnodes); + for(int i=0;i(cs_array); +} +/*}}}*/ +void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array){/*{{{*/ + + + int i,j; + int numdofs = 0; + IssmDouble *transform = NULL; + IssmDouble *values = NULL; + + /*Get total number of dofs*/ + for(i=0;i(Ke->nrows*Ke->ncols); + for(i=0;inrows;i++) for(j=0;jncols;j++) values[i*Ke->ncols+j]=Ke->values[i*Ke->ncols+j]; + + /*Get Coordinate Systems transform matrix*/ + CoordinateSystemTransform(&transform,nodes,numnodes,cs_array); + + /*Transform matrix: R*Ke*R^T */ + TripleMultiply(transform,numdofs,numdofs,0, + values,Ke->nrows,Ke->ncols,0, + transform,numdofs,numdofs,1, + &Ke->values[0],0); + + /*Free Matrix*/ + xDelete(transform); + xDelete(values); +} +/*}}}*/ +void TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int cs_enum){/*{{{*/ + + int* cs_array=NULL; + + /*All nodes have the same Coordinate System*/ + cs_array=xNew(numnodes); + for(int i=0;i(cs_array); +} +/*}}}*/ +void TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int* cs_array){/*{{{*/ + + + int i; + int numdofs = 0; + IssmDouble *transform = NULL; + IssmDouble *values = NULL; + + /*Get total number of dofs*/ + for(i=0;i(pe->nrows); + for(i=0;inrows;i++) values[i]=pe->values[i]; + + /*Get Coordinate Systems transform matrix*/ + CoordinateSystemTransform(&transform,nodes,numnodes,cs_array); + + /*Transform matrix: R^T*pe */ + MatrixMultiply(transform,numdofs,numdofs,1, + values,pe->nrows,1,0, + &pe->values[0],0); + + /*Free Matrices*/ + xDelete(transform); + xDelete(values); +} +/*}}}*/ +void TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int cs_enum){/*{{{*/ + + + int* cs_array=NULL; + + /*All nodes have the same Coordinate System*/ + cs_array=xNew(numnodes); + for(int i=0;i(cs_array); +} +/*}}}*/ +void TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int* cs_array){/*{{{*/ + + + int i; + int numdofs = 0; + IssmDouble *transform = NULL; + IssmDouble *values = NULL; + + /*Get total number of dofs*/ + for(i=0;i(numdofs); + for(i=0;i(transform); + xDelete(values); +} +/*}}}*/ +void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum){/*{{{*/ + + + int* cs_array=NULL; + + /*All nodes have the same Coordinate System*/ + cs_array=xNew(numnodes); + for(int i=0;i(cs_array); +} +/*}}}*/ +void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array){/*{{{*/ + + + int i,j; + int numdofs = 0; + IssmDouble *transform = NULL; + IssmDouble *values = NULL; + + /*Get total number of dofs*/ + for(i=0;i(Ke->nrows*Ke->ncols); + for(i=0;inrows;i++) for(j=0;jncols;j++) values[i*Ke->ncols+j]=Ke->values[i*Ke->ncols+j]; + + /*Get Coordinate Systems transform matrix*/ + CoordinateSystemTransform(&transform,nodes,numnodes,cs_array); + + /*Transform matrix: R^T*Ke*R */ + TripleMultiply(transform,numdofs,numdofs,1, + values,Ke->nrows,Ke->ncols,0, + transform,numdofs,numdofs,0, + &Ke->values[0],0); + + /*Free Matrix*/ + xDelete(transform); + xDelete(values); +} +/*}}}*/ +void CoordinateSystemTransform(IssmDouble** ptransform,Node** nodes,int numnodes,int* cs_array){/*{{{*/ + + + int i,counter; + int numdofs = 0; + IssmDouble norm; + IssmDouble *transform = NULL; + IssmDouble *values = NULL; + IssmDouble coord_system[3][3]; + + /*Some checks in debugging mode*/ + _assert_(numnodes && nodes); + + /*Get total number of dofs*/ + for(i=0;i(numdofs*numdofs); + for(i=0;iGetCoordinateSystem(&coord_system[0][0]); + switch(cs_array[i]){ + case XYEnum: + /*We remove the z component, we need to renormalize x and y: x=[x1 x2 0] y=[-x2 x1 0]*/ + norm = sqrt( coord_system[0][0]*coord_system[0][0] + coord_system[1][0]*coord_system[1][0]); _assert_(norm>1.e-4); + transform[(numdofs)*(counter+0) + counter+0] = coord_system[0][0]/norm; + transform[(numdofs)*(counter+0) + counter+1] = - coord_system[1][0]/norm; + transform[(numdofs)*(counter+1) + counter+0] = coord_system[1][0]/norm; + transform[(numdofs)*(counter+1) + counter+1] = coord_system[0][0]/norm; + counter+=2; + break; + case XYZPEnum: + /*Only the first 3 coordinates are changed (x,y,z), leave the others (P) unchanged*/ + transform[(numdofs)*(counter+0) + counter+0] = coord_system[0][0]; + transform[(numdofs)*(counter+0) + counter+1] = coord_system[0][1]; + transform[(numdofs)*(counter+0) + counter+2] = coord_system[0][2]; + transform[(numdofs)*(counter+1) + counter+0] = coord_system[1][0]; + transform[(numdofs)*(counter+1) + counter+1] = coord_system[1][1]; + transform[(numdofs)*(counter+1) + counter+2] = coord_system[1][2]; + transform[(numdofs)*(counter+2) + counter+0] = coord_system[2][0]; + transform[(numdofs)*(counter+2) + counter+1] = coord_system[2][1]; + transform[(numdofs)*(counter+2) + counter+2] = coord_system[2][2]; + transform[(numdofs)*(counter+3) + counter+3] = 1.0; + counter+=4; + break; + default: + _error_("Coordinate system " << EnumToStringx(cs_array[i]) << " not supported yet"); + } + } + + /*Assign output pointer*/ + *ptransform=transform; +} +/*}}}*/ +#endif Index: /issm/trunk-jpl/src/c/classes/objects/Node.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Node.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Node.h (revision 14951) @@ -18,4 +18,6 @@ template class Vector; template class Matrix; +class ElementVector; +class ElementMatrix; #include "../Update.h" /*}}}*/ @@ -100,3 +102,19 @@ }; +/*Methods inherent to Node: */ +int* GetLocalDofList(Node** nodes,int numnodes,int setenum,int approximation); +int* GetGlobalDofList(Node** nodes,int numnodes,int setenum,int approximation); +int GetNumberOfDofs(Node** nodes,int numnodes,int setenum,int approximation); +#ifdef _HAVE_DIAGNOSTIC_ +void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); +void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array); +void TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int cs_enum); +void TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int* cs_array); +void TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int cs_enum); +void TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int* cs_array); +void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); +void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array); +void CoordinateSystemTransform(IssmDouble** ptransform,Node** nodes,int numnodes,int* cs_array); +#endif + #endif /* _NODE_H_ */ Index: /issm/trunk-jpl/src/c/classes/objects/Profiler.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Profiler.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Profiler.cpp (revision 14951) @@ -11,4 +11,5 @@ #include "./Profiler.h" +#include "./Params/DoubleParam.h" /*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Vertex.cpp =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Vertex.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Vertex.cpp (revision 14951) @@ -238,2 +238,15 @@ } /*}}}*/ + +/*Methods relating to Vertex, but not internal methods: */ +void GetVerticesCoordinates(IssmDouble* xyz,Vertex** vertices, int numvertices){ /*{{{*/ + + _assert_(vertices); + _assert_(xyz); + + for(int i=0;iGetX(); + xyz[i*3+1]=vertices[i]->GetY(); + xyz[i*3+2]=vertices[i]->GetZ(); + } +}/*}}}*/ Index: /issm/trunk-jpl/src/c/classes/objects/Vertex.h =================================================================== --- /issm/trunk-jpl/src/c/classes/objects/Vertex.h (revision 14950) +++ /issm/trunk-jpl/src/c/classes/objects/Vertex.h (revision 14951) @@ -59,3 +59,7 @@ void VertexCoordinates(Vector* vx,Vector* vy,Vector* vz); }; + +/*Methods relating to Vertex object: */ +void GetVerticesCoordinates(IssmDouble* xyz,Vertex** vertices, int numvertices); + #endif /* _VERTEX_H */ Index: /issm/trunk-jpl/src/c/modules/ConfigureObjectsx/ConfigureObjectsx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ConfigureObjectsx/ConfigureObjectsx.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/ConfigureObjectsx/ConfigureObjectsx.cpp (revision 14951) @@ -8,4 +8,5 @@ #include "../../shared/io/io.h" #include "../../toolkits/toolkits.h" +#include "../../classes/classes.h" #include "../../EnumDefinitions/EnumDefinitions.h" Index: /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 14951) @@ -8,4 +8,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" #include "../../Container/Container.h" +#include "../../classes/classes.h" #include "./GroundinglineMigrationx.h" Index: /issm/trunk-jpl/src/c/modules/InputControlUpdatex/InputControlUpdatex.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/InputControlUpdatex/InputControlUpdatex.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/InputControlUpdatex/InputControlUpdatex.cpp (revision 14951) @@ -5,4 +5,5 @@ #include "./InputControlUpdatex.h" #include "../../shared/shared.h" +#include "../../classes/classes.h" #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" Index: /issm/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 14951) @@ -5,4 +5,5 @@ #include "../../shared/shared.h" #include "../../shared/io/io.h" +#include "../../classes/classes.h" #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" Index: /issm/trunk-jpl/src/c/modules/InputDuplicatex/InputDuplicatex.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/InputDuplicatex/InputDuplicatex.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/InputDuplicatex/InputDuplicatex.cpp (revision 14951) @@ -5,4 +5,5 @@ #include "./InputDuplicatex.h" #include "../../shared/shared.h" +#include "../../classes/classes.h" #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" Index: /issm/trunk-jpl/src/c/modules/InputScalex/InputScalex.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/InputScalex/InputScalex.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/InputScalex/InputScalex.cpp (revision 14951) @@ -6,4 +6,5 @@ #include "../../shared/shared.h" #include "../../toolkits/toolkits.h" +#include "../../classes/classes.h" #include "../../EnumDefinitions/EnumDefinitions.h" Index: /issm/trunk-jpl/src/c/modules/InputToResultx/InputToResultx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/InputToResultx/InputToResultx.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/InputToResultx/InputToResultx.cpp (revision 14951) @@ -5,4 +5,5 @@ #include "./InputToResultx.h" #include "../../shared/shared.h" +#include "../../classes/classes.h" #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" Index: /issm/trunk-jpl/src/c/modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp (revision 14951) @@ -10,4 +10,5 @@ #include "../../shared/shared.h" +#include "../../classes/classes.h" #include "../../shared/io/io.h" #include "./ModelProcessorx.h" Index: /issm/trunk-jpl/src/c/modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp (revision 14951) @@ -11,4 +11,5 @@ #include "../../shared/shared.h" #include "../../shared/io/io.h" +#include "../../classes/classes.h" #include "./ModelProcessorx.h" Index: /issm/trunk-jpl/src/c/modules/ModelProcessorx/DistributeNumDofs.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ModelProcessorx/DistributeNumDofs.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/modules/ModelProcessorx/DistributeNumDofs.cpp (revision 14951) @@ -4,4 +4,5 @@ #include "../../shared/shared.h" +#include "../../classes/classes.h" #include "../../EnumDefinitions/EnumDefinitions.h" Index: /issm/trunk-jpl/src/c/shared/Elements/Arrhenius.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/Arrhenius.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/shared/Elements/Arrhenius.cpp (revision 14951) @@ -3,6 +3,7 @@ */ +#include #include "./elements.h" -#include +#include "../Exceptions/exceptions.h" IssmDouble Arrhenius(IssmDouble temperature,IssmDouble depth,IssmDouble n){ Index: /issm/trunk-jpl/src/c/shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp (revision 14951) @@ -5,4 +5,5 @@ #include "./elements.h" +#include "../Numerics/numerics.h" void ComputeDelta18oTemperaturePrecipitation(IssmDouble Delta18oSurfacePresent, IssmDouble Delta18oSurfaceLgm, IssmDouble Delta18oSurfaceTime, Index: sm/trunk-jpl/src/c/shared/Elements/CoordinateSystemTransform.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/CoordinateSystemTransform.cpp (revision 14950) +++ (revision ) @@ -1,75 +1,0 @@ -/*!\file: GetGlobalDofList.cpp - * \brief create transform matrix for different coordinate systems - */ -#include "./elements.h" -#include - -void CoordinateSystemTransform(IssmDouble** ptransform,Node** nodes,int numnodes,int* cs_array){ - - int i,counter; - int numdofs = 0; - IssmDouble norm; - IssmDouble *transform = NULL; - IssmDouble *values = NULL; - IssmDouble coord_system[3][3]; - - /*Some checks in debugging mode*/ - _assert_(numnodes && nodes); - - /*Get total number of dofs*/ - for(i=0;i(numdofs*numdofs); - for(i=0;iGetCoordinateSystem(&coord_system[0][0]); - switch(cs_array[i]){ - case XYEnum: - /*We remove the z component, we need to renormalize x and y: x=[x1 x2 0] y=[-x2 x1 0]*/ - norm = sqrt( coord_system[0][0]*coord_system[0][0] + coord_system[1][0]*coord_system[1][0]); _assert_(norm>1.e-4); - transform[(numdofs)*(counter+0) + counter+0] = coord_system[0][0]/norm; - transform[(numdofs)*(counter+0) + counter+1] = - coord_system[1][0]/norm; - transform[(numdofs)*(counter+1) + counter+0] = coord_system[1][0]/norm; - transform[(numdofs)*(counter+1) + counter+1] = coord_system[0][0]/norm; - counter+=2; - break; - case XYZPEnum: - /*Only the first 3 coordinates are changed (x,y,z), leave the others (P) unchanged*/ - transform[(numdofs)*(counter+0) + counter+0] = coord_system[0][0]; - transform[(numdofs)*(counter+0) + counter+1] = coord_system[0][1]; - transform[(numdofs)*(counter+0) + counter+2] = coord_system[0][2]; - transform[(numdofs)*(counter+1) + counter+0] = coord_system[1][0]; - transform[(numdofs)*(counter+1) + counter+1] = coord_system[1][1]; - transform[(numdofs)*(counter+1) + counter+2] = coord_system[1][2]; - transform[(numdofs)*(counter+2) + counter+0] = coord_system[2][0]; - transform[(numdofs)*(counter+2) + counter+1] = coord_system[2][1]; - transform[(numdofs)*(counter+2) + counter+2] = coord_system[2][2]; - transform[(numdofs)*(counter+3) + counter+3] = 1.0; - counter+=4; - break; - default: - _error_("Coordinate system " << EnumToStringx(cs_array[i]) << " not supported yet"); - } - } - - /*Assign output pointer*/ - *ptransform=transform; -} Index: sm/trunk-jpl/src/c/shared/Elements/GetGlobalDofList.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/GetGlobalDofList.cpp (revision 14950) +++ (revision ) @@ -1,41 +1,0 @@ -/*!\file: GetGlobalDofList.cpp - * \brief create new element matrix - */ -#include "./elements.h" - -int* GetGlobalDofList(Node** nodes,int numnodes,int setenum,int approximation){ - - int i,numdof,count; - int* ndof_list=NULL; - int *doflist = NULL; - - if(numnodes){ - - /*Allocate:*/ - ndof_list=xNew(numnodes); - - /*First, figure out size of doflist: */ - numdof=0; - for(i=0;iGetNumberOfDofs(approximation,setenum); - numdof+=ndof_list[i]; - } - - if(numdof){ - /*Allocate: */ - doflist=xNew(numdof); - - /*Populate: */ - count=0; - for(i=0;iGetDofList(&doflist[count],approximation,setenum); - count+=ndof_list[i]; - } - } - else doflist=NULL; - } - /*Free ressources:*/ - xDelete(ndof_list); - - return doflist; -} Index: sm/trunk-jpl/src/c/shared/Elements/GetLocalDofList.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/GetLocalDofList.cpp (revision 14950) +++ (revision ) @@ -1,61 +1,0 @@ -/*!\file: GetLocalDofList.cpp - * \brief create new element matrix - */ -#include "./elements.h" - -int* GetLocalDofList(Node** nodes,int numnodes,int setenum,int approximation){ - - int i,j,count,numdof,numgdof; - int* ndof_list=NULL; - int* ngdof_list_cumulative=NULL; - int *doflist = NULL; - - if(numnodes){ - /*allocate: */ - ndof_list=xNew(numnodes); - ngdof_list_cumulative=xNew(numnodes); - - /*Get number of dofs per node, and total for this given set*/ - numdof=0; - numgdof=0; - for(i=0;iGetNumberOfDofs(approximation,setenum); - numgdof +=nodes[i]->GetNumberOfDofs(approximation,GsetEnum); - numdof +=ndof_list[i]; - } - - if(numdof){ - /*Allocate: */ - doflist=xNew(numdof); - - /*Populate: */ - count=0; - for(i=0;iGetLocalDofList(&doflist[count],approximation,setenum); - count+=ndof_list[i]; - } - - /*We now have something like: [0 1 0 2 1 2]. Offset by gsize, to get something like: [0 1 2 4 6 7]:*/ - count=0; - for(i=0;i(ndof_list); - xDelete(ngdof_list_cumulative); - - /*CLean-up and return*/ - return doflist; -} Index: sm/trunk-jpl/src/c/shared/Elements/GetNumberOfDofs.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/GetNumberOfDofs.cpp (revision 14950) +++ (revision ) @@ -1,16 +1,0 @@ -/*!\file: GetNumberOfDofs.cpp - * \brief create new element matrix - */ -#include "./elements.h" - -int GetNumberOfDofs(Node** nodes,int numnodes,int setenum,int approximation){ - - /*output: */ - int numberofdofs=0; - - for(int i=0;iGetNumberOfDofs(approximation,setenum); - } - - return numberofdofs; -} Index: sm/trunk-jpl/src/c/shared/Elements/GetVerticesCoordinates.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/GetVerticesCoordinates.cpp (revision 14950) +++ (revision ) @@ -1,17 +1,0 @@ -/*!\file: GetVerticesCoordinates.cpp - * \brief get node coordinates - */ - -#include "./elements.h" - -void GetVerticesCoordinates(IssmDouble* xyz,Vertex** vertices, int numvertices){ - - _assert_(vertices); - _assert_(xyz); - - for(int i=0;iGetX(); - xyz[i*3+1]=vertices[i]->GetY(); - xyz[i*3+2]=vertices[i]->GetZ(); - } -} Index: /issm/trunk-jpl/src/c/shared/Elements/Paterson.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/Paterson.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/shared/Elements/Paterson.cpp (revision 14951) @@ -7,5 +7,5 @@ #include -#include "../../shared/Numerics/types.h" +#include "../Numerics/types.h" IssmDouble Paterson(IssmDouble temperature){ Index: /issm/trunk-jpl/src/c/shared/Elements/PddSurfaceMassBalance.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/PddSurfaceMassBalance.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/shared/Elements/PddSurfaceMassBalance.cpp (revision 14951) @@ -4,4 +4,5 @@ #include "./elements.h" +#include "../Numerics/numerics.h" IssmDouble PddSurfaceMassBlance(IssmDouble* monthlytemperatures, IssmDouble* monthlyprec, IssmDouble* pdds, IssmDouble* pds, IssmDouble signorm, IssmDouble yts, IssmDouble h, IssmDouble s, IssmDouble rho_ice, IssmDouble rho_water, IssmDouble desfac, IssmDouble s0p){ Index: /issm/trunk-jpl/src/c/shared/Elements/PrintArrays.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/PrintArrays.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/shared/Elements/PrintArrays.cpp (revision 14951) @@ -1,4 +1,5 @@ #include "./elements.h" +#include "../io/Print/Print.h" using namespace std; Index: sm/trunk-jpl/src/c/shared/Elements/TransformInvStiffnessMatrixCoord.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/TransformInvStiffnessMatrixCoord.cpp (revision 14950) +++ (revision ) @@ -1,53 +1,0 @@ -/*!\file: TransformInvStiffnessMatrixCoord.cpp - * \brief transform stiffness matrix inverse coordinate system - */ -#include "./elements.h" - -void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum){ - - int* cs_array=NULL; - - /*All nodes have the same Coordinate System*/ - cs_array=xNew(numnodes); - for(int i=0;i(cs_array); -} - -void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array){ - - int i,j; - int numdofs = 0; - IssmDouble *transform = NULL; - IssmDouble *values = NULL; - - /*Get total number of dofs*/ - for(i=0;i(Ke->nrows*Ke->ncols); - for(i=0;inrows;i++) for(j=0;jncols;j++) values[i*Ke->ncols+j]=Ke->values[i*Ke->ncols+j]; - - /*Get Coordinate Systems transform matrix*/ - CoordinateSystemTransform(&transform,nodes,numnodes,cs_array); - - /*Transform matrix: R*Ke*R^T */ - TripleMultiply(transform,numdofs,numdofs,0, - values,Ke->nrows,Ke->ncols,0, - transform,numdofs,numdofs,1, - &Ke->values[0],0); - - /*Free Matrix*/ - xDelete(transform); - xDelete(values); -} Index: sm/trunk-jpl/src/c/shared/Elements/TransformLoadVectorCoord.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/TransformLoadVectorCoord.cpp (revision 14950) +++ (revision ) @@ -1,51 +1,0 @@ -/*!\file: TransformLoadVectorCoord.cpp - * \brief transform load vector coordinate system - */ -#include "./elements.h" - -void TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int cs_enum){ - int* cs_array=NULL; - - /*All nodes have the same Coordinate System*/ - cs_array=xNew(numnodes); - for(int i=0;i(cs_array); -} - -void TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int* cs_array){ - - int i; - int numdofs = 0; - IssmDouble *transform = NULL; - IssmDouble *values = NULL; - - /*Get total number of dofs*/ - for(i=0;i(pe->nrows); - for(i=0;inrows;i++) values[i]=pe->values[i]; - - /*Get Coordinate Systems transform matrix*/ - CoordinateSystemTransform(&transform,nodes,numnodes,cs_array); - - /*Transform matrix: R^T*pe */ - MatrixMultiply(transform,numdofs,numdofs,1, - values,pe->nrows,1,0, - &pe->values[0],0); - - /*Free Matrices*/ - xDelete(transform); - xDelete(values); -} Index: sm/trunk-jpl/src/c/shared/Elements/TransformSolutionCoord.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/TransformSolutionCoord.cpp (revision 14950) +++ (revision ) @@ -1,52 +1,0 @@ -/*!\file: TransformSolutionCoord.cpp - * \brief transform solution vector coordinate system - */ -#include "./elements.h" - -void TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int cs_enum){ - - int* cs_array=NULL; - - /*All nodes have the same Coordinate System*/ - cs_array=xNew(numnodes); - for(int i=0;i(cs_array); -} - -void TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int* cs_array){ - - int i; - int numdofs = 0; - IssmDouble *transform = NULL; - IssmDouble *values = NULL; - - /*Get total number of dofs*/ - for(i=0;i(numdofs); - for(i=0;i(transform); - xDelete(values); -} Index: sm/trunk-jpl/src/c/shared/Elements/TransformStiffnessMatrixCoord.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/TransformStiffnessMatrixCoord.cpp (revision 14950) +++ (revision ) @@ -1,53 +1,0 @@ -/*!\file: TransformStiffnessMatrixCoord.cpp - * \brief transform stiffness matrix coordinate system - */ -#include "./elements.h" - -void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum){ - - int* cs_array=NULL; - - /*All nodes have the same Coordinate System*/ - cs_array=xNew(numnodes); - for(int i=0;i(cs_array); -} - -void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array){ - - int i,j; - int numdofs = 0; - IssmDouble *transform = NULL; - IssmDouble *values = NULL; - - /*Get total number of dofs*/ - for(i=0;i(Ke->nrows*Ke->ncols); - for(i=0;inrows;i++) for(j=0;jncols;j++) values[i*Ke->ncols+j]=Ke->values[i*Ke->ncols+j]; - - /*Get Coordinate Systems transform matrix*/ - CoordinateSystemTransform(&transform,nodes,numnodes,cs_array); - - /*Transform matrix: R^T*Ke*R */ - TripleMultiply(transform,numdofs,numdofs,1, - values,Ke->nrows,Ke->ncols,0, - transform,numdofs,numdofs,0, - &Ke->values[0],0); - - /*Free Matrix*/ - xDelete(transform); - xDelete(values); -} Index: /issm/trunk-jpl/src/c/shared/Elements/elements.h =================================================================== --- /issm/trunk-jpl/src/c/shared/Elements/elements.h (revision 14950) +++ /issm/trunk-jpl/src/c/shared/Elements/elements.h (revision 14951) @@ -6,9 +6,9 @@ #define _SHARED_ELEMENTS_H_ -#include "../../classes/objects/objects.h" -#include "../../Container/Container.h" +#include "../Numerics/types.h" class ElementMatrix; class ElementVector; class Vertex; +class Node; IssmDouble Paterson(IssmDouble temperature); @@ -22,20 +22,4 @@ IssmDouble* TemperaturesLgm, IssmDouble* TemperaturesPresentday, IssmDouble* monthlytemperaturesout, IssmDouble* monthlyprecout); -void GetVerticesCoordinates(IssmDouble* xyz,Vertex** vertices,int numvertices); -int GetNumberOfDofs( Node** nodes,int numnodes,int setenum,int approximation_enum); -int* GetLocalDofList( Node** nodes,int numnodes,int setenum,int approximation_enum); -int* GetGlobalDofList(Node** nodes,int numnodes,int setenum,int approximation_enum); - -#ifdef _HAVE_DIAGNOSTIC_ -void CoordinateSystemTransform(IssmDouble** ptransform,Node** nodes,int numnodes,int* cs_array); -void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); -void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array); -void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); -void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array); -void TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int cs_enum); -void TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int* cs_array); -void TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int cs_enum); -void TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int* cs_array); -#endif /*Print arrays*/ Index: /issm/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp =================================================================== --- /issm/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp (revision 14950) +++ /issm/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp (revision 14951) @@ -9,5 +9,7 @@ #endif -#include "../shared.h" +#include "./exceptions.h" +#include "../io/Print/Print.h" +#include "../io/Comm/Comm.h" ErrorException::ErrorException(const string &what_arg){/*{{{*/