/[escript]/trunk/finley/src/CPPAdapter/MeshAdapter.cpp
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Diff of /trunk/finley/src/CPPAdapter/MeshAdapter.cpp

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revision 2856 by gross, Mon Jan 18 04:14:37 2010 UTC revision 3344 by caltinay, Thu Nov 11 23:26:52 2010 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*******************************************************
3  *  *
4  * Copyright (c) 2003-2009 by University of Queensland  * Copyright (c) 2003-2010 by University of Queensland
5  * Earth Systems Science Computational Center (ESSCC)  * Earth Systems Science Computational Center (ESSCC)
6  * http://www.uq.edu.au/esscc  * http://www.uq.edu.au/esscc
7  *  *
# Line 18  Line 18 
18  #ifdef USE_NETCDF  #ifdef USE_NETCDF
19  #include <netcdfcpp.h>  #include <netcdfcpp.h>
20  #endif  #endif
 #ifdef PASO_MPI  
 #include <mpi.h>  
 #include "paso/Paso_MPI.h"  
 #endif  
21  extern "C" {  extern "C" {
22  #include "esysUtils/blocktimer.h"  #include "esysUtils/blocktimer.h"
23  }  }
24    
25    #include <boost/python/import.hpp>
26    #include <boost/python/tuple.hpp>
27    
28  using namespace std;  using namespace std;
29  using namespace escript;  using namespace escript;
30    
# Line 85  int MeshAdapter::getMPIRank() const Line 84  int MeshAdapter::getMPIRank() const
84  }  }
85  void MeshAdapter::MPIBarrier() const  void MeshAdapter::MPIBarrier() const
86  {  {
87  #ifdef PASO_MPI  #ifdef ESYS_MPI
88     MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);     MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
89  #endif  #endif
90     return;     return;
# Line 96  bool MeshAdapter::onMasterProcessor() co Line 95  bool MeshAdapter::onMasterProcessor() co
95  }  }
96    
97    
98  #ifdef PASO_MPI  #ifdef ESYS_MPI
99    MPI_Comm    MPI_Comm
100  #else  #else
101    unsigned int    unsigned int
102  #endif  #endif
103  MeshAdapter::getMPIComm() const  MeshAdapter::getMPIComm() const
104  {  {
105  #ifdef PASO_MPI  #ifdef ESYS_MPI
106      return m_finleyMesh->MPIInfo->comm;      return m_finleyMesh->MPIInfo->comm;
107  #else  #else
108      return 0;      return 0;
# Line 149  void MeshAdapter::dump(const string& fil Line 148  void MeshAdapter::dump(const string& fil
148     int num_Elements_numNodes        = mesh->Elements->numNodes;     int num_Elements_numNodes        = mesh->Elements->numNodes;
149     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
150     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
151  #ifdef PASO_MPI  #ifdef ESYS_MPI
152     MPI_Status status;     MPI_Status status;
153  #endif  #endif
154    
155  /* Incoming token indicates it's my turn to write */  /* Incoming token indicates it's my turn to write */
156  #ifdef PASO_MPI  #ifdef ESYS_MPI
157     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
158  #endif  #endif
159    
160     char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),     char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
161                                                       mpi_size, mpi_rank);                                                       mpi_size, mpi_rank);
162    
163     /* Figure out how much storage is required for tags */     /* Figure out how much storage is required for tags */
# Line 529  void MeshAdapter::dump(const string& fil Line 528  void MeshAdapter::dump(const string& fil
528     }     }
529    
530  /* Send token to next MPI process so he can take his turn */  /* Send token to next MPI process so he can take his turn */
531  #ifdef PASO_MPI  #ifdef ESYS_MPI
532     if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);     if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
533  #endif  #endif
534    
# Line 770  pair<int,int> MeshAdapter::getDataShape( Line 769  pair<int,int> MeshAdapter::getDataShape(
769  // adds linear PDE of second order into a given stiffness matrix and right hand side:  // adds linear PDE of second order into a given stiffness matrix and right hand side:
770  //  //
771  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
772                                   SystemMatrixAdapter& mat, escript::Data& rhs,                                   AbstractSystemMatrix& mat, escript::Data& rhs,
773                                   const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,                                   const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
774                                   const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
775                                   const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
776  {  {
777       SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
778       if (smat==0)
779       {
780        throw FinleyAdapterException("finley only supports its own system matrices.");
781       }
782     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
783     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
784     escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
# Line 789  void MeshAdapter::addPDEToSystem( Line 793  void MeshAdapter::addPDEToSystem(
793    
794     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
795    
796     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,smat->getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
797     checkFinleyError();     checkFinleyError();
798    
799     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, smat->getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
800     checkFinleyError();     checkFinleyError();
801    
802     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
803     checkFinleyError();     checkFinleyError();
804  }  }
805    
# Line 811  void  MeshAdapter::addPDEToLumpedSystem( Line 815  void  MeshAdapter::addPDEToLumpedSystem(
815     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
816    
817     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
818       checkFinleyError();
819      
820     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
   
821     checkFinleyError();     checkFinleyError();
822    
823  }  }
824    
825    
# Line 843  void MeshAdapter::addPDEToRHS( escript:: Line 849  void MeshAdapter::addPDEToRHS( escript::
849  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
850  //  //
851  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
852                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,                                             AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,
853                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,
854                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
855                                             const escript::Data& d, const escript::Data& y,                                             const escript::Data& d, const escript::Data& y,
856                                             const escript::Data& d_contact,const escript::Data& y_contact) const                                             const escript::Data& d_contact,const escript::Data& y_contact) const
857  {  {
858       TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
859       if (tpa==0)
860       {
861        throw FinleyAdapterException("finley only supports its own transport problems.");
862       }
863    
864    
865     DataTypes::ShapeType shape;     DataTypes::ShapeType shape;
866     source.expand();     source.expand();
867     escriptDataC _source=source.getDataC();     escriptDataC _source=source.getDataC();
# Line 865  void MeshAdapter::addPDEToTransportProbl Line 878  void MeshAdapter::addPDEToTransportProbl
878     escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
879    
880     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
881     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();     Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
882    
883     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
884     checkFinleyError();     checkFinleyError();
# Line 1042  void MeshAdapter::interpolateOnDomain(es Line 1055  void MeshAdapter::interpolateOnDomain(es
1055        case(Elements):        case(Elements):
1056        case(ReducedElements):        case(ReducedElements):
1057        if (getMPISize()>1) {        if (getMPISize()>1) {
1058           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1059           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1060           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1061        } else {        } else {
# Line 1052  void MeshAdapter::interpolateOnDomain(es Line 1065  void MeshAdapter::interpolateOnDomain(es
1065        case(FaceElements):        case(FaceElements):
1066        case(ReducedFaceElements):        case(ReducedFaceElements):
1067        if (getMPISize()>1) {        if (getMPISize()>1) {
1068           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1069           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1070           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1071        
# Line 1062  void MeshAdapter::interpolateOnDomain(es Line 1075  void MeshAdapter::interpolateOnDomain(es
1075        break;        break;
1076        case(Points):        case(Points):
1077        if (getMPISize()>1) {        if (getMPISize()>1) {
1078           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1079           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1080        } else {        } else {
1081           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
# Line 1073  void MeshAdapter::interpolateOnDomain(es Line 1086  void MeshAdapter::interpolateOnDomain(es
1086        case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
1087        case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
1088        if (getMPISize()>1) {        if (getMPISize()>1) {
1089           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1090           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1091           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1092        } else {        } else {
# Line 1111  void MeshAdapter::interpolateOnDomain(es Line 1124  void MeshAdapter::interpolateOnDomain(es
1124        case(Elements):        case(Elements):
1125        case(ReducedElements):        case(ReducedElements):
1126        if (getMPISize()>1) {        if (getMPISize()>1) {
1127           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1128           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1129           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1130        } else {        } else {
# Line 1121  void MeshAdapter::interpolateOnDomain(es Line 1134  void MeshAdapter::interpolateOnDomain(es
1134        case(FaceElements):        case(FaceElements):
1135        case(ReducedFaceElements):        case(ReducedFaceElements):
1136        if (getMPISize()>1) {        if (getMPISize()>1) {
1137           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1138           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1139           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1140        } else {        } else {
# Line 1130  void MeshAdapter::interpolateOnDomain(es Line 1143  void MeshAdapter::interpolateOnDomain(es
1143        break;        break;
1144        case(Points):        case(Points):
1145        if (getMPISize()>1) {        if (getMPISize()>1) {
1146           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1147           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1148           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1149        } else {        } else {
# Line 1142  void MeshAdapter::interpolateOnDomain(es Line 1155  void MeshAdapter::interpolateOnDomain(es
1155        case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
1156        case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
1157        if (getMPISize()>1) {        if (getMPISize()>1) {
1158           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1159           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1160           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1161        } else {        } else {
# Line 1179  void MeshAdapter::setToX(escript::Data& Line 1192  void MeshAdapter::setToX(escript::Data&
1192        escriptDataC _arg=arg.getDataC();        escriptDataC _arg=arg.getDataC();
1193        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1194     } else {     } else {
1195        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);        escript::Data tmp_data=Vector(0.0,continuousFunction(*this),true);
1196        escriptDataC _tmp_data=tmp_data.getDataC();        escriptDataC _tmp_data=tmp_data.getDataC();
1197        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1198        // this is then interpolated onto arg:        // this is then interpolated onto arg:
# Line 1273  void MeshAdapter::setToIntegrals(vector< Line 1286  void MeshAdapter::setToIntegrals(vector<
1286     escriptDataC _arg=arg.getDataC();     escriptDataC _arg=arg.getDataC();
1287     switch(arg.getFunctionSpace().getTypeCode()) {     switch(arg.getFunctionSpace().getTypeCode()) {
1288     case(Nodes):     case(Nodes):
1289     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1290     _temp=temp.getDataC();     _temp=temp.getDataC();
1291     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1292     break;     break;
1293     case(ReducedNodes):     case(ReducedNodes):
1294     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1295     _temp=temp.getDataC();     _temp=temp.getDataC();
1296     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1297     break;     break;
# Line 1310  void MeshAdapter::setToIntegrals(vector< Line 1323  void MeshAdapter::setToIntegrals(vector<
1323     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1324     break;     break;
1325     case(DegreesOfFreedom):     case(DegreesOfFreedom):
1326     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1327     _temp=temp.getDataC();     _temp=temp.getDataC();
1328     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1329     break;     break;
1330     case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1331     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1332     _temp=temp.getDataC();     _temp=temp.getDataC();
1333     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1334     break;     break;
# Line 1347  void MeshAdapter::setToGradient(escript: Line 1360  void MeshAdapter::setToGradient(escript:
1360     escript::Data temp;     escript::Data temp;
1361     if (getMPISize()>1) {     if (getMPISize()>1) {
1362        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1363           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  continuousFunction(*this) );
1364           nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1365        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1366           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  reducedContinuousFunction(*this) );
1367           nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1368        } else {        } else {
1369           nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
# Line 1469  void MeshAdapter::setNewX(const escript: Line 1482  void MeshAdapter::setNewX(const escript:
1482     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1483     if (newDomain!=*this)     if (newDomain!=*this)
1484        throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1485     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {     if ( new_x.getFunctionSpace() == continuousFunction(*this) ) {
1486         tmp = new_x.getDataC();         tmp = new_x.getDataC();
1487         Finley_Mesh_setCoordinates(mesh,&tmp);         Finley_Mesh_setCoordinates(mesh,&tmp);
1488     } else {     } else {
1489         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(*this) );
1490         tmp = new_x_inter.getDataC();         tmp = new_x_inter.getDataC();
1491         Finley_Mesh_setCoordinates(mesh,&tmp);         Finley_Mesh_setCoordinates(mesh,&tmp);
1492     }     }
# Line 1536  void MeshAdapter::saveDX(const string& f Line 1549  void MeshAdapter::saveDX(const string& f
1549  //  //
1550  void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const  void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1551  {  {
1552     int num_data;      boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("saveVTK");
1553     char **names;      pySaveVTK(*boost::python::make_tuple(filename,
1554     escriptDataC *data;                 const_cast<MeshAdapter*>(this)->getPtr(),
1555     escriptDataC **ptr_data;                 metadata, metadata_schema), **arg);
   
    extractArgsFromDict(arg, num_data, names, data, ptr_data);  
    Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data, metadata.c_str(), metadata_schema.c_str());  
    checkFinleyError();  
   
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0; i<num_data; i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
1556  }  }
1557    
1558  bool MeshAdapter::ownSample(int fs_code, index_t id) const  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1559  {  {
1560  #ifdef PASO_MPI  #ifdef ESYS_MPI
1561      index_t myFirstNode=0, myLastNode=0, k=0;      index_t myFirstNode=0, myLastNode=0, k=0;
1562      index_t* globalNodeIndex=0;      index_t* globalNodeIndex=0;
1563      Finley_Mesh* mesh_p=m_finleyMesh.get();      Finley_Mesh* mesh_p=m_finleyMesh.get();
# Line 1584  bool MeshAdapter::ownSample(int fs_code, Line 1584  bool MeshAdapter::ownSample(int fs_code,
1584  //  //
1585  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1586  //  //
1587  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  ASM_ptr MeshAdapter::newSystemMatrix(
1588                                                   const int row_blocksize,                                                   const int row_blocksize,
1589                                                   const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1590                                                   const int column_blocksize,                                                   const int column_blocksize,
# Line 1631  SystemMatrixAdapter MeshAdapter::newSyst Line 1631  SystemMatrixAdapter MeshAdapter::newSyst
1631     }     }
1632     checkPasoError();     checkPasoError();
1633     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1634     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1635       return ASM_ptr(sma);
1636    //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1637  }  }
1638    
1639  //  //
1640  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1641  //  //
1642  TransportProblemAdapter MeshAdapter::newTransportProblem(  ATP_ptr MeshAdapter::newTransportProblem(
1643                                                           const double theta,                                                           const bool useBackwardEuler,
1644                                                           const int blocksize,                                                           const int blocksize,
1645                                                           const escript::FunctionSpace& functionspace,                                                           const escript::FunctionSpace& functionspace,
1646                                                           const int type) const                                                           const int type) const
# Line 1660  TransportProblemAdapter MeshAdapter::new Line 1662  TransportProblemAdapter MeshAdapter::new
1662    
1663     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1664     checkFinleyError();     checkFinleyError();
1665     Paso_FCTransportProblem* transportProblem;     Paso_TransportProblem* transportProblem;
1666     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);     transportProblem=Paso_TransportProblem_alloc(useBackwardEuler,fsystemMatrixPattern,blocksize);
1667     checkPasoError();     checkPasoError();
1668     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1669     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);     TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1670       return ATP_ptr(tpa);
1671    //   return TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1672  }  }
1673    
1674  //  //
# Line 1727  MeshAdapter::commonFunctionSpace(const v Line 1731  MeshAdapter::commonFunctionSpace(const v
1731     For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.     For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1732     eg hasnodes is true if we have at least one instance of Nodes.     eg hasnodes is true if we have at least one instance of Nodes.
1733     */     */
1734      if (fs.size()==0)      if (fs.empty())
1735      {      {
1736          return false;          return false;
1737      }      }
# Line 2030  int MeshAdapter::getSystemMatrixTypeId(c Line 2034  int MeshAdapter::getSystemMatrixTypeId(c
2034  int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const  int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2035  {  {
2036     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2037     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);     int out=Paso_TransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2038     checkPasoError();     checkPasoError();
2039     return out;     return out;
2040  }  }
2041    
2042  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2043  {  {
2044     return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(*this).getX();
2045  }  }
2046    
2047  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2048  {  {
2049     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(*this).getNormal();
2050  }  }
2051    
2052  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2053  {  {
2054     return escript::function(asAbstractContinuousDomain()).getSize();     return escript::function(*this).getSize();
2055  }  }
2056    
2057  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
# Line 2395  int MeshAdapter::getApproximationOrder(c Line 2399  int MeshAdapter::getApproximationOrder(c
2399    return order;    return order;
2400  }  }
2401    
2402    bool MeshAdapter::supportsContactElements() const
2403    {
2404      return true;
2405    }
2406    
2407    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2408    {
2409      m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2410    }
2411    
2412    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2413    {
2414      Finley_ReferenceElementSet_dealloc(m_refSet);
2415    }
2416    
2417  }  // end of namespace  }  // end of namespace

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