/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 3736 by jfenwick, Mon Dec 12 01:26:51 2011 UTC revision 4441 by caltinay, Fri Jun 7 02:23:49 2013 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*****************************************************************************
3  *  *
4  * Copyright (c) 2003-2010 by University of Queensland  * Copyright (c) 2003-2013 by University of Queensland
5  * Earth Systems Science Computational Center (ESSCC)  * http://www.uq.edu.au
 * http://www.uq.edu.au/esscc  
6  *  *
7  * Primary Business: Queensland, Australia  * Primary Business: Queensland, Australia
8  * Licensed under the Open Software License version 3.0  * Licensed under the Open Software License version 3.0
9  * http://www.opensource.org/licenses/osl-3.0.php  * http://www.opensource.org/licenses/osl-3.0.php
10  *  *
11  *******************************************************/  * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12    * Development since 2012 by School of Earth Sciences
13    *
14    *****************************************************************************/
15    
16  #include <pasowrap/PasoException.h>  #include <pasowrap/PasoException.h>
17  #include <pasowrap/TransportProblemAdapter.h>  #include <pasowrap/TransportProblemAdapter.h>
18  #include "MeshAdapter.h"  #include "MeshAdapter.h"
19  #include "escript/Data.h"  #include "escript/Data.h"
20  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
 #ifdef USE_NETCDF  
 #include <netcdfcpp.h>  
 #endif  
 extern "C" {  
21  #include "esysUtils/blocktimer.h"  #include "esysUtils/blocktimer.h"
 }  
22    
23  #include <boost/python/import.hpp>  #include <boost/python/import.hpp>
24    #ifdef USE_NETCDF
25    #include <netcdfcpp.h>
26    #endif
27    
28  using namespace std;  using namespace std;
 using namespace escript;  
29  using namespace paso;  using namespace paso;
30    
31  namespace finley {  namespace finley {
32    
 //  
33  // define the static constants  // define the static constants
34  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
35  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
# Line 50  const int MeshAdapter::ReducedContactEle Line 48  const int MeshAdapter::ReducedContactEle
48    
49  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
50  {  {
51     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
52     //      // need to use a null_deleter as Finley_Mesh_free deletes the pointer
53     // need to use a null_deleter as Finley_Mesh_free deletes the pointer      // for us.
54     // for us.      m_finleyMesh.reset(finleyMesh, null_deleter());
    m_finleyMesh.reset(finleyMesh,null_deleter());  
55  }  }
56    
57  //  //
58  // The copy constructor should just increment the use count  // The copy constructor should just increment the use count
59  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in) :
60  m_finleyMesh(in.m_finleyMesh)      m_finleyMesh(in.m_finleyMesh)
61  {  {
62     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
63  }  }
64    
65  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
66  {  {
67     //      // I hope the case for the pointer being zero has been taken care of
68     // I hope the case for the pointer being zero has been taken care of.      if (m_finleyMesh.unique()) {
69     //  cout << "In MeshAdapter destructor." << endl;          Finley_Mesh_free(m_finleyMesh.get());
70     if (m_finleyMesh.unique()) {      }
       Finley_Mesh_free(m_finleyMesh.get());  
    }  
71  }  }
72    
73  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
74  {  {
75     return m_finleyMesh.get()->MPIInfo->size;      return m_finleyMesh.get()->MPIInfo->size;
76  }  }
77    
78  int MeshAdapter::getMPIRank() const  int MeshAdapter::getMPIRank() const
79  {  {
80     return m_finleyMesh.get()->MPIInfo->rank;      return m_finleyMesh.get()->MPIInfo->rank;
81  }  }
82    
83  void MeshAdapter::MPIBarrier() const  void MeshAdapter::MPIBarrier() const
84  {  {
85  #ifdef ESYS_MPI  #ifdef ESYS_MPI
86     MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);      MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
87  #endif  #endif
    return;  
88  }  }
89    
90  bool MeshAdapter::onMasterProcessor() const  bool MeshAdapter::onMasterProcessor() const
91  {  {
92     return m_finleyMesh.get()->MPIInfo->rank == 0;      return m_finleyMesh.get()->MPIInfo->rank == 0;
93  }  }
94    
   
95  #ifdef ESYS_MPI  #ifdef ESYS_MPI
96    MPI_Comm  MPI_Comm
97  #else  #else
98    unsigned int  unsigned int
99  #endif  #endif
100  MeshAdapter::getMPIComm() const  MeshAdapter::getMPIComm() const
101  {  {
102  #ifdef ESYS_MPI  #ifdef ESYS_MPI
103      return m_finleyMesh->MPIInfo->comm;      return m_finleyMesh->MPIInfo->comm;
104  #else  #else
105      return 0;      return 0;
106  #endif  #endif
107  }  }
108    
109    Finley_Mesh* MeshAdapter::getFinley_Mesh() const
110  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  {
111     return m_finleyMesh.get();      return m_finleyMesh.get();
112  }  }
113    
114  void MeshAdapter::write(const string& fileName) const  void MeshAdapter::write(const string& fileName) const
115  {  {
116     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;      Finley_Mesh_write(m_finleyMesh.get(), fileName.c_str());
117     strcpy(fName,fileName.c_str());      checkFinleyError();
    Finley_Mesh_write(m_finleyMesh.get(),fName);  
    checkFinleyError();  
    TMPMEMFREE(fName);  
118  }  }
119    
120  void MeshAdapter::Print_Mesh_Info(const bool full) const  void MeshAdapter::Print_Mesh_Info(const bool full) const
121  {  {
122     Finley_PrintMesh_Info(m_finleyMesh.get(), full);      Finley_PrintMesh_Info(m_finleyMesh.get(), full);
123  }  }
124    
125  void MeshAdapter::dump(const string& fileName) const  void MeshAdapter::dump(const string& fileName) const
126  {  {
127  #ifdef USE_NETCDF  #ifdef USE_NETCDF
128     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};      const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
129     NcVar *ids;      NcVar *ids;
130     int *int_ptr;      int *int_ptr;
131     Finley_Mesh *mesh = m_finleyMesh.get();      Finley_Mesh *mesh = m_finleyMesh.get();
132     Finley_TagMap* tag_map;      int num_Tags = 0;
133     int num_Tags = 0;      int mpi_size                         = mesh->MPIInfo->size;
134     int mpi_size             = mesh->MPIInfo->size;      int mpi_rank                         = mesh->MPIInfo->rank;
135     int mpi_rank             = mesh->MPIInfo->rank;      int numDim                           = mesh->Nodes->numDim;
136     int numDim               = mesh->Nodes->numDim;      int numNodes                         = mesh->Nodes->numNodes;
137     int numNodes             = mesh->Nodes->numNodes;      int num_Elements                     = mesh->Elements->numElements;
138     int num_Elements         = mesh->Elements->numElements;      int num_FaceElements                 = mesh->FaceElements->numElements;
139     int num_FaceElements         = mesh->FaceElements->numElements;      int num_ContactElements              = mesh->ContactElements->numElements;
140     int num_ContactElements      = mesh->ContactElements->numElements;      int num_Points                       = mesh->Points->numElements;
141     int num_Points           = mesh->Points->numElements;      int num_Elements_numNodes            = mesh->Elements->numNodes;
142     int num_Elements_numNodes        = mesh->Elements->numNodes;      int num_FaceElements_numNodes        = mesh->FaceElements->numNodes;
143     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;      int num_ContactElements_numNodes     = mesh->ContactElements->numNodes;
    int num_ContactElements_numNodes = mesh->ContactElements->numNodes;  
144  #ifdef ESYS_MPI  #ifdef ESYS_MPI
145     MPI_Status status;      MPI_Status status;
146  #endif  #endif
147    
148  /* Incoming token indicates it's my turn to write */  /* Incoming token indicates it's my turn to write */
149  #ifdef ESYS_MPI  #ifdef ESYS_MPI
150     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);      if (mpi_rank>0) {
151            MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
152        }
153  #endif  #endif
154    
155     char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),      char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
156                                                       mpi_size, mpi_rank);                                                       mpi_size, mpi_rank);
157    
158     /* Figure out how much storage is required for tags */      // Figure out how much storage is required for tags
159     tag_map = mesh->TagMap;      num_Tags = mesh->tagMap.size();
    num_Tags = 0;  
    while (tag_map) {  
       num_Tags++;  
       tag_map=tag_map->next;  
    }  
   
    // NetCDF error handler  
    NcError err(NcError::verbose_nonfatal);  
    // Create the file.  
    NcFile dataFile(newFileName, NcFile::Replace);  
    string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");  
    // check if writing was successful  
    if (!dataFile.is_valid())  
       throw DataException(msgPrefix+"Open file for output");  
   
    // Define dimensions (num_Elements and dim_Elements are identical,  
    // dim_Elements only appears if > 0)  
    if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )  
       throw DataException(msgPrefix+"add_dim(numNodes)");  
    if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )  
       throw DataException(msgPrefix+"add_dim(numDim)");  
    if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )  
       throw DataException(msgPrefix+"add_dim(mpi_size)");  
    if (num_Elements>0)  
       if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )  
          throw DataException(msgPrefix+"add_dim(dim_Elements)");  
    if (num_FaceElements>0)  
       if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )  
          throw DataException(msgPrefix+"add_dim(dim_FaceElements)");  
    if (num_ContactElements>0)  
       if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )  
          throw DataException(msgPrefix+"add_dim(dim_ContactElements)");  
    if (num_Points>0)  
       if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )  
          throw DataException(msgPrefix+"add_dim(dim_Points)");  
    if (num_Elements>0)  
       if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )  
          throw DataException(msgPrefix+"add_dim(dim_Elements_Nodes)");  
    if (num_FaceElements>0)  
       if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )  
          throw DataException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");  
    if (num_ContactElements>0)  
       if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )  
          throw DataException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");  
    if (num_Tags>0)  
       if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )  
          throw DataException(msgPrefix+"add_dim(dim_Tags)");  
   
    // Attributes: MPI size, MPI rank, Name, order, reduced_order  
    if (!dataFile.add_att("mpi_size", mpi_size) )  
       throw DataException(msgPrefix+"add_att(mpi_size)");  
    if (!dataFile.add_att("mpi_rank", mpi_rank) )  
       throw DataException(msgPrefix+"add_att(mpi_rank)");  
    if (!dataFile.add_att("Name",mesh->Name) )  
       throw DataException(msgPrefix+"add_att(Name)");  
    if (!dataFile.add_att("numDim",numDim) )  
       throw DataException(msgPrefix+"add_att(order)");  
    if (!dataFile.add_att("order",mesh->integrationOrder) )  
       throw DataException(msgPrefix+"add_att(order)");  
    if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )  
       throw DataException(msgPrefix+"add_att(reduced_order)");  
    if (!dataFile.add_att("numNodes",numNodes) )  
       throw DataException(msgPrefix+"add_att(numNodes)");  
    if (!dataFile.add_att("num_Elements",num_Elements) )  
       throw DataException(msgPrefix+"add_att(num_Elements)");  
    if (!dataFile.add_att("num_FaceElements",num_FaceElements) )  
       throw DataException(msgPrefix+"add_att(num_FaceElements)");  
    if (!dataFile.add_att("num_ContactElements",num_ContactElements) )  
       throw DataException(msgPrefix+"add_att(num_ContactElements)");  
    if (!dataFile.add_att("num_Points",num_Points) )  
       throw DataException(msgPrefix+"add_att(num_Points)");  
    if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )  
       throw DataException(msgPrefix+"add_att(num_Elements_numNodes)");  
    if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )  
       throw DataException(msgPrefix+"add_att(num_FaceElements_numNodes)");  
    if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )  
       throw DataException(msgPrefix+"add_att(num_ContactElements_numNodes)");  
    if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )  
       throw DataException(msgPrefix+"add_att(Elements_TypeId)");  
    if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )  
       throw DataException(msgPrefix+"add_att(FaceElements_TypeId)");  
    if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )  
       throw DataException(msgPrefix+"add_att(ContactElements_TypeId)");  
    if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )  
       throw DataException(msgPrefix+"add_att(Points_TypeId)");  
    if (!dataFile.add_att("num_Tags", num_Tags) )  
       throw DataException(msgPrefix+"add_att(num_Tags)");  
   
    // // // // // Nodes // // // // //  
   
    // Nodes nodeDistribution  
    if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )  
       throw DataException(msgPrefix+"add_var(Nodes_NodeDistribution)");  
    int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];  
    if (! (ids->put(int_ptr, mpi_size+1)) )  
       throw DataException(msgPrefix+"put(Nodes_NodeDistribution)");  
   
    // Nodes degreesOfFreedomDistribution  
    if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )  
       throw DataException(msgPrefix+"add_var(Nodes_DofDistribution)");  
    int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];  
    if (! (ids->put(int_ptr, mpi_size+1)) )  
       throw DataException(msgPrefix+"put(Nodes_DofDistribution)");  
   
    // Only write nodes if non-empty because NetCDF doesn't like empty arrays  
    // (it treats them as NC_UNLIMITED)  
    if (numNodes>0) {  
   
       // Nodes Id  
       if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )  
          throw DataException(msgPrefix+"add_var(Nodes_Id)");  
       int_ptr = &mesh->Nodes->Id[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException(msgPrefix+"put(Nodes_Id)");  
   
       // Nodes Tag  
       if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )  
          throw DataException(msgPrefix+"add_var(Nodes_Tag)");  
       int_ptr = &mesh->Nodes->Tag[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException(msgPrefix+"put(Nodes_Tag)");  
   
       // Nodes gDOF  
       if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )  
          throw DataException(msgPrefix+"add_var(Nodes_gDOF)");  
       int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException(msgPrefix+"put(Nodes_gDOF)");  
   
       // Nodes global node index  
       if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )  
          throw DataException(msgPrefix+"add_var(Nodes_gNI)");  
       int_ptr = &mesh->Nodes->globalNodesIndex[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException(msgPrefix+"put(Nodes_gNI)");  
   
       // Nodes grDof  
       if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )  
          throw DataException(msgPrefix+"add_var(Nodes_grDfI)");  
       int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException(msgPrefix+"put(Nodes_grDfI)");  
   
       // Nodes grNI  
       if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )  
          throw DataException(msgPrefix+"add_var(Nodes_grNI)");  
       int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];  
       if (! (ids->put(int_ptr, numNodes)) )  
          throw DataException(msgPrefix+"put(Nodes_grNI)");  
   
       // Nodes Coordinates  
       if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )  
          throw DataException(msgPrefix+"add_var(Nodes_Coordinates)");  
       if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )  
          throw DataException(msgPrefix+"put(Nodes_Coordinates)");  
   
    }  
   
    // // // // // Elements // // // // //  
   
    if (num_Elements>0) {  
   
       // Elements_Id  
       if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )  
          throw DataException(msgPrefix+"add_var(Elements_Id)");  
       int_ptr = &mesh->Elements->Id[0];  
       if (! (ids->put(int_ptr, num_Elements)) )  
          throw DataException(msgPrefix+"put(Elements_Id)");  
   
       // Elements_Tag  
       if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )  
          throw DataException(msgPrefix+"add_var(Elements_Tag)");  
       int_ptr = &mesh->Elements->Tag[0];  
       if (! (ids->put(int_ptr, num_Elements)) )  
          throw DataException(msgPrefix+"put(Elements_Tag)");  
   
       // Elements_Owner  
       if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )  
          throw DataException(msgPrefix+"add_var(Elements_Owner)");  
       int_ptr = &mesh->Elements->Owner[0];  
       if (! (ids->put(int_ptr, num_Elements)) )  
          throw DataException(msgPrefix+"put(Elements_Owner)");  
   
       // Elements_Color  
       if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )  
          throw DataException(msgPrefix+"add_var(Elements_Color)");  
       int_ptr = &mesh->Elements->Color[0];  
       if (! (ids->put(int_ptr, num_Elements)) )  
          throw DataException(msgPrefix+"put(Elements_Color)");  
   
       // Elements_Nodes  
       if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )  
          throw DataException(msgPrefix+"add_var(Elements_Nodes)");  
       if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )  
          throw DataException(msgPrefix+"put(Elements_Nodes)");  
   
    }  
   
    // // // // // Face_Elements // // // // //  
   
    if (num_FaceElements>0) {  
   
       // FaceElements_Id  
       if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )  
          throw DataException(msgPrefix+"add_var(FaceElements_Id)");  
       int_ptr = &mesh->FaceElements->Id[0];  
       if (! (ids->put(int_ptr, num_FaceElements)) )  
          throw DataException(msgPrefix+"put(FaceElements_Id)");  
   
       // FaceElements_Tag  
       if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )  
          throw DataException(msgPrefix+"add_var(FaceElements_Tag)");  
       int_ptr = &mesh->FaceElements->Tag[0];  
       if (! (ids->put(int_ptr, num_FaceElements)) )  
          throw DataException(msgPrefix+"put(FaceElements_Tag)");  
   
       // FaceElements_Owner  
       if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )  
          throw DataException(msgPrefix+"add_var(FaceElements_Owner)");  
       int_ptr = &mesh->FaceElements->Owner[0];  
       if (! (ids->put(int_ptr, num_FaceElements)) )  
          throw DataException(msgPrefix+"put(FaceElements_Owner)");  
   
       // FaceElements_Color  
       if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )  
          throw DataException(msgPrefix+"add_var(FaceElements_Color)");  
       int_ptr = &mesh->FaceElements->Color[0];  
       if (! (ids->put(int_ptr, num_FaceElements)) )  
          throw DataException(msgPrefix+"put(FaceElements_Color)");  
   
       // FaceElements_Nodes  
       if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )  
          throw DataException(msgPrefix+"add_var(FaceElements_Nodes)");  
       if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )  
          throw DataException(msgPrefix+"put(FaceElements_Nodes)");  
   
    }  
   
    // // // // // Contact_Elements // // // // //  
   
    if (num_ContactElements>0) {  
   
       // ContactElements_Id  
       if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )  
          throw DataException(msgPrefix+"add_var(ContactElements_Id)");  
       int_ptr = &mesh->ContactElements->Id[0];  
       if (! (ids->put(int_ptr, num_ContactElements)) )  
          throw DataException(msgPrefix+"put(ContactElements_Id)");  
   
       // ContactElements_Tag  
       if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )  
          throw DataException(msgPrefix+"add_var(ContactElements_Tag)");  
       int_ptr = &mesh->ContactElements->Tag[0];  
       if (! (ids->put(int_ptr, num_ContactElements)) )  
          throw DataException(msgPrefix+"put(ContactElements_Tag)");  
   
       // ContactElements_Owner  
       if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )  
          throw DataException(msgPrefix+"add_var(ContactElements_Owner)");  
       int_ptr = &mesh->ContactElements->Owner[0];  
       if (! (ids->put(int_ptr, num_ContactElements)) )  
          throw DataException(msgPrefix+"put(ContactElements_Owner)");  
   
       // ContactElements_Color  
       if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )  
          throw DataException(msgPrefix+"add_var(ContactElements_Color)");  
       int_ptr = &mesh->ContactElements->Color[0];  
       if (! (ids->put(int_ptr, num_ContactElements)) )  
          throw DataException(msgPrefix+"put(ContactElements_Color)");  
   
       // ContactElements_Nodes  
       if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )  
          throw DataException(msgPrefix+"add_var(ContactElements_Nodes)");  
       if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )  
          throw DataException(msgPrefix+"put(ContactElements_Nodes)");  
   
    }  
   
    // // // // // Points // // // // //  
   
    if (num_Points>0) {  
   
       fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");  
   
       // Points_Id  
       if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )  
          throw DataException(msgPrefix+"add_var(Points_Id)");  
       int_ptr = &mesh->Points->Id[0];  
       if (! (ids->put(int_ptr, num_Points)) )  
          throw DataException(msgPrefix+"put(Points_Id)");  
   
       // Points_Tag  
       if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )  
          throw DataException(msgPrefix+"add_var(Points_Tag)");  
       int_ptr = &mesh->Points->Tag[0];  
       if (! (ids->put(int_ptr, num_Points)) )  
          throw DataException(msgPrefix+"put(Points_Tag)");  
   
       // Points_Owner  
       if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )  
          throw DataException(msgPrefix+"add_var(Points_Owner)");  
       int_ptr = &mesh->Points->Owner[0];  
       if (! (ids->put(int_ptr, num_Points)) )  
          throw DataException(msgPrefix+"put(Points_Owner)");  
   
       // Points_Color  
       if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )  
          throw DataException(msgPrefix+"add_var(Points_Color)");  
       int_ptr = &mesh->Points->Color[0];  
       if (! (ids->put(int_ptr, num_Points)) )  
          throw DataException(msgPrefix+"put(Points_Color)");  
   
       // Points_Nodes  
       // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]  
       if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )  
          throw DataException(msgPrefix+"add_var(Points_Nodes)");  
       if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )  
          throw DataException(msgPrefix+"put(Points_Nodes)");  
   
    }  
   
    // // // // // TagMap // // // // //  
   
    if (num_Tags>0) {  
   
       // Temp storage to gather node IDs  
       int *Tags_keys = TMPMEMALLOC(num_Tags, int);  
       char name_temp[4096];  
   
       /* Copy tag data into temp arrays */  
       tag_map = mesh->TagMap;  
       if (tag_map) {  
          int i = 0;  
          while (tag_map) {  
             Tags_keys[i++] = tag_map->tag_key;  
             tag_map=tag_map->next;  
          }  
       }  
   
       // Tags_keys  
       if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )  
          throw DataException(msgPrefix+"add_var(Tags_keys)");  
       int_ptr = &Tags_keys[0];  
       if (! (ids->put(int_ptr, num_Tags)) )  
          throw DataException(msgPrefix+"put(Tags_keys)");  
   
       // Tags_names_*  
       // This is an array of strings, it should be stored as an array but  
       // instead I have hacked in one attribute per string because the NetCDF  
       // manual doesn't tell how to do an array of strings  
       tag_map = mesh->TagMap;  
       if (tag_map) {  
          int i = 0;  
          while (tag_map) {  
             sprintf(name_temp, "Tags_name_%d", i);  
             if (!dataFile.add_att(name_temp, tag_map->name) )  
                throw DataException(msgPrefix+"add_att(Tags_names_XX)");  
             tag_map=tag_map->next;  
             i++;  
          }  
       }  
160    
161        TMPMEMFREE(Tags_keys);      // NetCDF error handler
162     }      NcError err(NcError::verbose_nonfatal);
163        // Create the file.
164        NcFile dataFile(newFileName, NcFile::Replace);
165        string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
166        // check if writing was successful
167        if (!dataFile.is_valid())
168            throw FinleyAdapterException(msgPrefix+"Open file for output");
169    
170        // Define dimensions (num_Elements and dim_Elements are identical,
171        // dim_Elements only appears if > 0)
172        if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
173            throw FinleyAdapterException(msgPrefix+"add_dim(numNodes)");
174        if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
175            throw FinleyAdapterException(msgPrefix+"add_dim(numDim)");
176        if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
177            throw FinleyAdapterException(msgPrefix+"add_dim(mpi_size)");
178        if (num_Elements>0)
179            if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
180                throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements)");
181        if (num_FaceElements>0)
182            if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
183                throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements)");
184        if (num_ContactElements>0)
185            if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
186                throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements)");
187        if (num_Points>0)
188            if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
189                throw FinleyAdapterException(msgPrefix+"add_dim(dim_Points)");
190        if (num_Elements>0)
191            if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
192                throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements_Nodes)");
193        if (num_FaceElements>0)
194            if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
195                throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
196        if (num_ContactElements>0)
197            if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
198                throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
199        if (num_Tags>0)
200            if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
201                throw FinleyAdapterException(msgPrefix+"add_dim(dim_Tags)");
202    
203        // Attributes: MPI size, MPI rank, Name, order, reduced_order
204        if (!dataFile.add_att("mpi_size", mpi_size) )
205            throw FinleyAdapterException(msgPrefix+"add_att(mpi_size)");
206        if (!dataFile.add_att("mpi_rank", mpi_rank) )
207            throw FinleyAdapterException(msgPrefix+"add_att(mpi_rank)");
208        if (!dataFile.add_att("Name",mesh->Name) )
209            throw FinleyAdapterException(msgPrefix+"add_att(Name)");
210        if (!dataFile.add_att("numDim",numDim) )
211            throw FinleyAdapterException(msgPrefix+"add_att(order)");
212        if (!dataFile.add_att("order",mesh->integrationOrder) )
213            throw FinleyAdapterException(msgPrefix+"add_att(order)");
214        if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
215            throw FinleyAdapterException(msgPrefix+"add_att(reduced_order)");
216        if (!dataFile.add_att("numNodes",numNodes) )
217            throw FinleyAdapterException(msgPrefix+"add_att(numNodes)");
218        if (!dataFile.add_att("num_Elements",num_Elements) )
219            throw FinleyAdapterException(msgPrefix+"add_att(num_Elements)");
220        if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
221            throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements)");
222        if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
223            throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements)");
224        if (!dataFile.add_att("num_Points",num_Points) )
225            throw FinleyAdapterException(msgPrefix+"add_att(num_Points)");
226        if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
227            throw FinleyAdapterException(msgPrefix+"add_att(num_Elements_numNodes)");
228        if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
229            throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements_numNodes)");
230        if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
231            throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements_numNodes)");
232        if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
233            throw FinleyAdapterException(msgPrefix+"add_att(Elements_TypeId)");
234        if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
235            throw FinleyAdapterException(msgPrefix+"add_att(FaceElements_TypeId)");
236        if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
237            throw FinleyAdapterException(msgPrefix+"add_att(ContactElements_TypeId)");
238        if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
239            throw FinleyAdapterException(msgPrefix+"add_att(Points_TypeId)");
240        if (!dataFile.add_att("num_Tags", num_Tags) )
241            throw FinleyAdapterException(msgPrefix+"add_att(num_Tags)");
242    
243        // // // // // Nodes // // // // //
244    
245        // Nodes nodeDistribution
246        if (! (ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
247            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_NodeDistribution)");
248        int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
249        if (! (ids->put(int_ptr, mpi_size+1)) )
250            throw FinleyAdapterException(msgPrefix+"put(Nodes_NodeDistribution)");
251    
252        // Nodes degreesOfFreedomDistribution
253        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
254            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_DofDistribution)");
255        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
256        if (! (ids->put(int_ptr, mpi_size+1)) )
257            throw FinleyAdapterException(msgPrefix+"put(Nodes_DofDistribution)");
258    
259        // Only write nodes if non-empty because NetCDF doesn't like empty arrays
260        // (it treats them as NC_UNLIMITED)
261        if (numNodes>0) {
262            // Nodes Id
263            if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
264                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Id)");
265            int_ptr = &mesh->Nodes->Id[0];
266            if (! (ids->put(int_ptr, numNodes)) )
267                throw FinleyAdapterException(msgPrefix+"put(Nodes_Id)");
268    
269            // Nodes Tag
270            if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
271                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Tag)");
272            int_ptr = &mesh->Nodes->Tag[0];
273            if (! (ids->put(int_ptr, numNodes)) )
274                throw FinleyAdapterException(msgPrefix+"put(Nodes_Tag)");
275    
276            // Nodes gDOF
277            if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
278                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gDOF)");
279            int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
280            if (! (ids->put(int_ptr, numNodes)) )
281                throw FinleyAdapterException(msgPrefix+"put(Nodes_gDOF)");
282    
283            // Nodes global node index
284            if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
285                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gNI)");
286            int_ptr = &mesh->Nodes->globalNodesIndex[0];
287            if (! (ids->put(int_ptr, numNodes)) )
288                throw FinleyAdapterException(msgPrefix+"put(Nodes_gNI)");
289    
290            // Nodes grDof
291            if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
292                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grDfI)");
293            int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
294            if (! (ids->put(int_ptr, numNodes)) )
295                throw FinleyAdapterException(msgPrefix+"put(Nodes_grDfI)");
296    
297            // Nodes grNI
298            if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
299                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grNI)");
300            int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
301            if (! (ids->put(int_ptr, numNodes)) )
302                throw FinleyAdapterException(msgPrefix+"put(Nodes_grNI)");
303    
304            // Nodes Coordinates
305            if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
306                throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Coordinates)");
307            if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
308                throw FinleyAdapterException(msgPrefix+"put(Nodes_Coordinates)");
309        }
310    
311  /* Send token to next MPI process so he can take his turn */      // // // // // Elements // // // // //
312        if (num_Elements>0) {
313            // Elements_Id
314            if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
315                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Id)");
316            int_ptr = &mesh->Elements->Id[0];
317            if (! (ids->put(int_ptr, num_Elements)) )
318                throw FinleyAdapterException(msgPrefix+"put(Elements_Id)");
319    
320            // Elements_Tag
321            if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
322                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Tag)");
323            int_ptr = &mesh->Elements->Tag[0];
324            if (! (ids->put(int_ptr, num_Elements)) )
325                throw FinleyAdapterException(msgPrefix+"put(Elements_Tag)");
326    
327            // Elements_Owner
328            if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
329                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Owner)");
330            int_ptr = &mesh->Elements->Owner[0];
331            if (! (ids->put(int_ptr, num_Elements)) )
332                throw FinleyAdapterException(msgPrefix+"put(Elements_Owner)");
333    
334            // Elements_Color
335            if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
336                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Color)");
337            int_ptr = &mesh->Elements->Color[0];
338            if (! (ids->put(int_ptr, num_Elements)) )
339                throw FinleyAdapterException(msgPrefix+"put(Elements_Color)");
340    
341            // Elements_Nodes
342            if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
343                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Nodes)");
344            if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
345                throw FinleyAdapterException(msgPrefix+"put(Elements_Nodes)");
346        }
347    
348        // // // // // Face_Elements // // // // //
349        if (num_FaceElements>0) {
350            // FaceElements_Id
351            if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
352                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Id)");
353            int_ptr = &mesh->FaceElements->Id[0];
354            if (! (ids->put(int_ptr, num_FaceElements)) )
355                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Id)");
356    
357            // FaceElements_Tag
358            if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
359                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Tag)");
360            int_ptr = &mesh->FaceElements->Tag[0];
361            if (! (ids->put(int_ptr, num_FaceElements)) )
362                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Tag)");
363    
364            // FaceElements_Owner
365            if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
366                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Owner)");
367            int_ptr = &mesh->FaceElements->Owner[0];
368            if (! (ids->put(int_ptr, num_FaceElements)) )
369                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Owner)");
370    
371            // FaceElements_Color
372            if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
373                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Color)");
374            int_ptr = &mesh->FaceElements->Color[0];
375            if (! (ids->put(int_ptr, num_FaceElements)) )
376                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Color)");
377    
378            // FaceElements_Nodes
379            if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
380                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Nodes)");
381            if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
382                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Nodes)");
383        }
384    
385        // // // // // Contact_Elements // // // // //
386        if (num_ContactElements>0) {
387    
388            // ContactElements_Id
389            if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
390                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Id)");
391            int_ptr = &mesh->ContactElements->Id[0];
392            if (! (ids->put(int_ptr, num_ContactElements)) )
393                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Id)");
394    
395            // ContactElements_Tag
396            if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
397                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Tag)");
398            int_ptr = &mesh->ContactElements->Tag[0];
399            if (! (ids->put(int_ptr, num_ContactElements)) )
400                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Tag)");
401    
402            // ContactElements_Owner
403            if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
404                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Owner)");
405            int_ptr = &mesh->ContactElements->Owner[0];
406            if (! (ids->put(int_ptr, num_ContactElements)) )
407                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Owner)");
408    
409            // ContactElements_Color
410            if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
411                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Color)");
412            int_ptr = &mesh->ContactElements->Color[0];
413            if (! (ids->put(int_ptr, num_ContactElements)) )
414                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Color)");
415    
416            // ContactElements_Nodes
417            if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
418                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Nodes)");
419            if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
420                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Nodes)");
421        }
422    
423        // // // // // Points // // // // //
424        if (num_Points>0) {
425            // Points_Id
426            if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
427                throw FinleyAdapterException(msgPrefix+"add_var(Points_Id)");
428            int_ptr = &mesh->Points->Id[0];
429            if (! (ids->put(int_ptr, num_Points)) )
430                throw FinleyAdapterException(msgPrefix+"put(Points_Id)");
431    
432            // Points_Tag
433            if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
434                throw FinleyAdapterException(msgPrefix+"add_var(Points_Tag)");
435            int_ptr = &mesh->Points->Tag[0];
436            if (! (ids->put(int_ptr, num_Points)) )
437                throw FinleyAdapterException(msgPrefix+"put(Points_Tag)");
438    
439            // Points_Owner
440            if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
441                throw FinleyAdapterException(msgPrefix+"add_var(Points_Owner)");
442            int_ptr = &mesh->Points->Owner[0];
443            if (! (ids->put(int_ptr, num_Points)) )
444                throw FinleyAdapterException(msgPrefix+"put(Points_Owner)");
445    
446            // Points_Color
447            if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
448                throw FinleyAdapterException(msgPrefix+"add_var(Points_Color)");
449            int_ptr = &mesh->Points->Color[0];
450            if (! (ids->put(int_ptr, num_Points)) )
451                throw FinleyAdapterException(msgPrefix+"put(Points_Color)");
452    
453            // Points_Nodes
454            // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
455            if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
456                throw FinleyAdapterException(msgPrefix+"add_var(Points_Nodes)");
457            if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
458                throw FinleyAdapterException(msgPrefix+"put(Points_Nodes)");
459        }
460    
461        // // // // // TagMap // // // // //
462        if (num_Tags>0) {
463            // Temp storage to gather node IDs
464            vector<int> Tags_keys;
465    
466            // Copy tag data into temp arrays
467            TagMap::const_iterator it;
468            for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++) {
469                Tags_keys.push_back(it->second);
470            }
471    
472            // Tags_keys
473            if (! (ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
474                throw FinleyAdapterException(msgPrefix+"add_var(Tags_keys)");
475            int_ptr = &Tags_keys[0];
476            if (! (ids->put(int_ptr, num_Tags)) )
477                throw FinleyAdapterException(msgPrefix+"put(Tags_keys)");
478    
479            // Tags_names_*
480            // This is an array of strings, it should be stored as an array but
481            // instead I have hacked in one attribute per string because the NetCDF
482            // manual doesn't tell how to do an array of strings
483            int i = 0;
484            for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++, i++) {
485                stringstream tagnamestream;
486                tagnamestream << "Tags_name_" << i;
487                const string tagname = tagnamestream.str();
488                if (!dataFile.add_att(tagname.c_str(), it->first.c_str()))
489                    throw FinleyAdapterException(msgPrefix+"add_att(Tags_names_X)");
490            }
491        }
492    
493        // Send token to next MPI process so he can take his turn
494  #ifdef ESYS_MPI  #ifdef ESYS_MPI
495     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) {
496            MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
497        }
498  #endif  #endif
499    
500     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
501    
502  #else  #else // USE_NETCDF
503     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");      Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with netCDF. Please contact your installation manager.");
504  #endif  /* USE_NETCDF */  #endif // USE_NETCDF
505     checkFinleyError();      checkFinleyError();
506  }  }
507    
508  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
509  {  {
510     return "FinleyMesh";      return "FinleyMesh";
511  }  }
512    
513  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
514  {  {
515     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
516     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
517     if (loc==m_functionSpaceTypeNames.end()) {      if (loc==m_functionSpaceTypeNames.end()) {
518        return "Invalid function space type code.";          return "Invalid function space type code.";
519     } else {      } else {
520        return loc->second;          return loc->second;
521     }      }
522  }  }
523    
524  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
525  {  {
526     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
527     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
528     return (loc!=m_functionSpaceTypeNames.end());      return (loc!=m_functionSpaceTypeNames.end());
529  }  }
530    
531  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
532  {  {
533     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
534     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));                  DegreesOfFreedom,"Finley_DegreesOfFreedom"));
535     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
536     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));                  ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
537     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
538     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));                  Nodes,"Finley_Nodes"));
539     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
540     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));                  ReducedNodes,"Finley_Reduced_Nodes"));
541     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
542     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));                  Elements,"Finley_Elements"));
543     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
544     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));                  ReducedElements,"Finley_Reduced_Elements"));
545     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
546     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));                  FaceElements,"Finley_Face_Elements"));
547     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
548     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));                  ReducedFaceElements,"Finley_Reduced_Face_Elements"));
549     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
550     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));                  Points,"Finley_Points"));
551     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
552     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));                  ContactElementsZero,"Finley_Contact_Elements_0"));
553     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
554     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));                  ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
555     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
556     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));                  ContactElementsOne,"Finley_Contact_Elements_1"));
557     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
558     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));                  ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
559  }  }
560    
561  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
562  {  {
563     return Nodes;      return Nodes;
564  }  }
565    
566  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
567  {  {
568     return ReducedNodes;      return ReducedNodes;
569  }  }
570    
571  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
572  {  {
573     return Elements;      return Elements;
574  }  }
575    
576  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
577  {  {
578     return ReducedElements;      return ReducedElements;
579  }  }
580    
581  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
582  {  {
583     return FaceElements;      return FaceElements;
584  }  }
585    
586  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
587  {  {
588     return ReducedFaceElements;      return ReducedFaceElements;
589  }  }
590    
591  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
592  {  {
593     return ContactElementsZero;      return ContactElementsZero;
594  }  }
595    
596  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
597  {  {
598     return ReducedContactElementsZero;      return ReducedContactElementsZero;
599  }  }
600    
601  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
602  {  {
603     return ContactElementsOne;      return ContactElementsOne;
604  }  }
605    
606  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
607  {  {
608     return ReducedContactElementsOne;      return ReducedContactElementsOne;
609  }  }
610    
611  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
612  {  {
613     return DegreesOfFreedom;      return DegreesOfFreedom;
614  }  }
615    
616  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
617  {  {
618     return ReducedDegreesOfFreedom;      return ReducedDegreesOfFreedom;
619  }  }
620    
621  int MeshAdapter::getDiracDeltaFunctionsCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
622  {  {
623     return Points;      return Points;
624  }  }
625    
626  //  //
# Line 659  int MeshAdapter::getDiracDeltaFunctionsC Line 628  int MeshAdapter::getDiracDeltaFunctionsC
628  //  //
629  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
630  {  {
631     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
632     int numDim=Finley_Mesh_getDim(mesh);      int numDim=Finley_Mesh_getDim(mesh);
633     checkFinleyError();      checkFinleyError();
634     return numDim;      return numDim;
635  }  }
636    
637  //  //
# Line 670  int MeshAdapter::getDim() const Line 639  int MeshAdapter::getDim() const
639  //  //
640  int MeshAdapter::getNumDataPointsGlobal() const  int MeshAdapter::getNumDataPointsGlobal() const
641  {  {
642     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);      return m_finleyMesh.get()->Nodes->getGlobalNumNodes();
643  }  }
644    
645  //  //
# Line 679  int MeshAdapter::getNumDataPointsGlobal( Line 648  int MeshAdapter::getNumDataPointsGlobal(
648  //  //
649  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const
650  {  {
651     int numDataPointsPerSample=0;      int numDataPointsPerSample=0;
652     int numSamples=0;      int numSamples=0;
653     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
654     switch (functionSpaceCode) {      switch (functionSpaceCode) {
655     case(Nodes):          case Nodes:
656     numDataPointsPerSample=1;              numDataPointsPerSample=1;
657     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumNodes();
658     break;              break;
659     case(ReducedNodes):          case ReducedNodes:
660     numDataPointsPerSample=1;              numDataPointsPerSample=1;
661     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumReducedNodes();
662     break;              break;
663     case(Elements):          case Elements:
664     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
665        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
666        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
667     }              }
668     break;              break;
669     case(ReducedElements):          case ReducedElements:
670     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
671        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
672        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
673     }              }
674     break;              break;
675     case(FaceElements):          case FaceElements:
676     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
677        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
678        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
679     }              }
680     break;              break;
681     case(ReducedFaceElements):          case ReducedFaceElements:
682     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
683        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
684        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
685     }              }
686     break;              break;
687     case(Points):          case Points:
688     if (mesh->Points!=NULL) {              if (mesh->Points!=NULL) {
689        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
690        numSamples=mesh->Points->numElements;                  numSamples=mesh->Points->numElements;
691     }              }
692     break;              break;
693     case(ContactElementsZero):          case ContactElementsZero:
694     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
695        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
696        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
697     }              }
698     break;              break;
699     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
700     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
701        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
702        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
703     }              }
704     break;              break;
705     case(ContactElementsOne):          case ContactElementsOne:
706     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
707        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
708        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
709     }              }
710     break;              break;
711     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
712     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
713        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
714        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
715     }              }
716     break;              break;
717     case(DegreesOfFreedom):          case DegreesOfFreedom:
718     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
719        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
720        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumDegreesOfFreedom();
721     }              }
722     break;              break;
723     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
724     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
725        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
726        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumReducedDegreesOfFreedom();
727     }              }
728     break;              break;
729     default:          default:
730        stringstream temp;              stringstream temp;
731        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();              temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
732        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
733        break;              break;
734     }      }
735     return pair<int,int>(numDataPointsPerSample,numSamples);      return pair<int,int>(numDataPointsPerSample,numSamples);
736  }  }
737    
738  //  //
739  // 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
740    // hand side:
741  //  //
742  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
743                                   AbstractSystemMatrix& mat, escript::Data& rhs,          escript::AbstractSystemMatrix& mat, escript::Data& rhs,
744                                   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,
745                                   const escript::Data& d, const escript::Data& y,          const escript::Data& D, const escript::Data& X, const escript::Data& Y,
746                                   const escript::Data& d_contact,const escript::Data& y_contact,          const escript::Data& d, const escript::Data& y,
747                                   const escript::Data& d_dirac,const escript::Data& y_dirac) const          const escript::Data& d_contact, const escript::Data& y_contact,
748  {          const escript::Data& d_dirac, const escript::Data& y_dirac) const
749     SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);  {
750     if (smat==0)      SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
751     {      if (!smat)
752      throw FinleyAdapterException("finley only supports Paso system matrices.");          throw FinleyAdapterException("finley only supports Paso system matrices.");
753     }  
754     escriptDataC _rhs=rhs.getDataC();      Finley_Mesh* mesh=m_finleyMesh.get();
755     escriptDataC _A  =A.getDataC();      Paso_SystemMatrix* S = smat->getPaso_SystemMatrix();
756     escriptDataC _B=B.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, S, rhs, A, B, C, D, X, Y);
757     escriptDataC _C=C.getDataC();      checkFinleyError();
758     escriptDataC _D=D.getDataC();  
759     escriptDataC _X=X.getDataC();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, S, rhs,
760     escriptDataC _Y=Y.getDataC();              escript::Data(), escript::Data(), escript::Data(), d,
761     escriptDataC _d=d.getDataC();              escript::Data(), y);
762     escriptDataC _y=y.getDataC();      checkFinleyError();
763     escriptDataC _d_contact=d_contact.getDataC();  
764     escriptDataC _y_contact=y_contact.getDataC();      Assemble_PDE(mesh->Nodes, mesh->ContactElements, S, rhs,
765     escriptDataC _d_dirac=d_dirac.getDataC();              escript::Data(), escript::Data(), escript::Data(), d_contact,
766     escriptDataC _y_dirac=y_dirac.getDataC();              escript::Data(), y_contact);
767        checkFinleyError();
768     Finley_Mesh* mesh=m_finleyMesh.get();  
769        Assemble_PDE(mesh->Nodes, mesh->Points, S, rhs, escript::Data(),
770     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,smat->getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );              escript::Data(), escript::Data(), d_dirac, escript::Data(), y_dirac);
771     checkFinleyError();      checkFinleyError();
772    }
773     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, smat->getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );  
774     checkFinleyError();  void MeshAdapter::addPDEToLumpedSystem(escript::Data& mat,
775            const escript::Data& D, const escript::Data& d,
776     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );          const escript::Data& d_dirac, const bool useHRZ) const
777     checkFinleyError();  {
778        Finley_Mesh* mesh=m_finleyMesh.get();
779      Finley_Assemble_PDE(mesh->Nodes,mesh->Points, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_dirac, 0, &_y_dirac );      Assemble_LumpedSystem(mesh->Nodes, mesh->Elements, mat, D, useHRZ);
780     checkFinleyError();      checkFinleyError();
 }  
   
 void  MeshAdapter::addPDEToLumpedSystem(  
                                         escript::Data& mat,  
                                         const escript::Data& D,  
                                         const escript::Data& d,  
                                         const escript::Data& d_dirac,  
                                         const bool useHRZ) const  
 {  
    escriptDataC _mat=mat.getDataC();  
    escriptDataC _D=D.getDataC();  
    escriptDataC _d=d.getDataC();  
    escriptDataC _d_dirac=d_dirac.getDataC();  
   
    Finley_Mesh* mesh=m_finleyMesh.get();  
   
    Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D, useHRZ);  
    checkFinleyError();  
     
    Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d, useHRZ);  
    checkFinleyError();  
781    
782     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Points,&_mat, &_d_dirac, useHRZ);      Assemble_LumpedSystem(mesh->Nodes, mesh->FaceElements, mat, d, useHRZ);
783     checkFinleyError();      checkFinleyError();
784    
785        Assemble_LumpedSystem(mesh->Nodes, mesh->Points, mat, d_dirac, useHRZ);
786        checkFinleyError();
787  }  }
788    
   
789  //  //
790  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
791  //  //
792  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact,  const escript::Data& y_dirac) const  void MeshAdapter::addPDEToRHS(escript::Data& rhs, const escript::Data& X,
793  {          const escript::Data& Y, const escript::Data& y,
794     Finley_Mesh* mesh=m_finleyMesh.get();          const escript::Data& y_contact, const escript::Data& y_dirac) const
795    {
796     escriptDataC _rhs=rhs.getDataC();      Finley_Mesh* mesh=m_finleyMesh.get();
797     escriptDataC _X=X.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, 0, rhs,
798     escriptDataC _Y=Y.getDataC();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
799     escriptDataC _y=y.getDataC();              X, Y);
800     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
801     escriptDataC _y_dirac=y_dirac.getDataC();  
802        Assemble_PDE(mesh->Nodes, mesh->FaceElements, 0, rhs,
803     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
804     checkFinleyError();              escript::Data(), y);
805        checkFinleyError();
806     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );  
807     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->ContactElements, 0, rhs,
808                escript::Data(), escript::Data(), escript::Data(),
809     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );              escript::Data(), escript::Data(), y_contact);
810     checkFinleyError();      checkFinleyError();
811    
812     Finley_Assemble_PDE(mesh->Nodes,mesh->Points, 0, &_rhs , 0, 0, 0, 0, 0, &_y_dirac );      Assemble_PDE(mesh->Nodes, mesh->Points, 0, rhs,
813     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
814                escript::Data(), y_dirac);
815        checkFinleyError();
816  }  }
817    
818  //  //
819  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
820  //  //
821  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
822                                             AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,          escript::AbstractTransportProblem& tp, escript::Data& source,
823                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,          const escript::Data& M, const escript::Data& A, const escript::Data& B,
824                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& C, const escript::Data& D, const escript::Data& X,
825                                             const escript::Data& d, const escript::Data& y,          const escript::Data& Y, const escript::Data& d, const escript::Data& y,
826                                             const escript::Data& d_contact,const escript::Data& y_contact,          const escript::Data& d_contact, const escript::Data& y_contact,
827                                             const escript::Data& d_dirac, const escript::Data& y_dirac) const          const escript::Data& d_dirac, const escript::Data& y_dirac) const
828  {  {
829     TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);      TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
830     if (tpa==0)      if (!tpa)
831     {          throw FinleyAdapterException("finley only supports Paso transport problems.");
832      throw FinleyAdapterException("finley only supports Paso transport problems.");  
833     }      source.expand();
834    
835        Finley_Mesh* mesh=m_finleyMesh.get();
836     DataTypes::ShapeType shape;      Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
837     source.expand();  
838     escriptDataC _source=source.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->mass_matrix, source,
839     escriptDataC _M=M.getDataC();                          escript::Data(), escript::Data(), escript::Data(),
840     escriptDataC _A=A.getDataC();                          M, escript::Data(), escript::Data());
841     escriptDataC _B=B.getDataC();      checkFinleyError();
842     escriptDataC _C=C.getDataC();  
843     escriptDataC _D=D.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->transport_matrix,
844     escriptDataC _X=X.getDataC();                          source, A, B, C, D, X, Y);
845     escriptDataC _Y=Y.getDataC();      checkFinleyError();
846     escriptDataC _d=d.getDataC();  
847     escriptDataC _y=y.getDataC();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, _tp->transport_matrix,
848     escriptDataC _d_contact=d_contact.getDataC();                          source, escript::Data(), escript::Data(),
849     escriptDataC _y_contact=y_contact.getDataC();                          escript::Data(), d, escript::Data(), y);
850     escriptDataC _d_dirac=d_dirac.getDataC();      checkFinleyError();
851     escriptDataC _y_dirac=y_dirac.getDataC();  
852        Assemble_PDE(mesh->Nodes, mesh->ContactElements,
853                            _tp->transport_matrix, source, escript::Data(),
854     Finley_Mesh* mesh=m_finleyMesh.get();                          escript::Data(), escript::Data(), d_contact,
855     Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();                          escript::Data(), y_contact);
856        checkFinleyError();
857     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );  
858     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->Points, _tp->transport_matrix,
859                            source, escript::Data(), escript::Data(),
860     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );                          escript::Data(), d_dirac, escript::Data(), y_dirac);
861     checkFinleyError();      checkFinleyError();
862    }
863     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );  
864     checkFinleyError();  //
865    // interpolates data between different function spaces
866     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );  //
867     checkFinleyError();  void MeshAdapter::interpolateOnDomain(escript::Data& target, const escript::Data& in) const
868    {
869     Finley_Assemble_PDE(mesh->Nodes,mesh->Points, _tp->transport_matrix, &_source , 0, 0, 0, &_d_dirac, 0, &_y_dirac );      const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
870     checkFinleyError();      const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
871        if (inDomain!=*this)
872  }          throw FinleyAdapterException("Error - Illegal domain of interpolant.");
873        if (targetDomain!=*this)
874  //          throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
875  // interpolates data between different function spaces:  
876  //      Finley_Mesh* mesh=m_finleyMesh.get();
877  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const      switch(in.getFunctionSpace().getTypeCode()) {
878  {          case Nodes:
879     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));              switch(target.getFunctionSpace().getTypeCode()) {
880     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));                  case Nodes:
881     if (inDomain!=*this)                    case ReducedNodes:
882        throw FinleyAdapterException("Error - Illegal domain of interpolant.");                  case DegreesOfFreedom:
883     if (targetDomain!=*this)                  case ReducedDegreesOfFreedom:
884        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");                      Assemble_CopyNodalData(mesh->Nodes, target, in);
885                        break;
886     Finley_Mesh* mesh=m_finleyMesh.get();                  case Elements:
887     escriptDataC _target=target.getDataC();                  case ReducedElements:
888     escriptDataC _in=in.getDataC();                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in,target);
889     switch(in.getFunctionSpace().getTypeCode()) {                      break;
890     case(Nodes):                  case FaceElements:
891        switch(target.getFunctionSpace().getTypeCode()) {                  case ReducedFaceElements:
892        case(Nodes):                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
893        case(ReducedNodes):                      break;
894        case(DegreesOfFreedom):                  case Points:
895        case(ReducedDegreesOfFreedom):                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
896        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
897        break;                  case ContactElementsZero:
898        case(Elements):                  case ReducedContactElementsZero:
899        case(ReducedElements):                  case ContactElementsOne:
900        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case ReducedContactElementsOne:
901        break;                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
902        case(FaceElements):                      break;
903        case(ReducedFaceElements):                  default:
904        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      stringstream temp;
905        break;                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
906        case(Points):                      throw FinleyAdapterException(temp.str());
907        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      break;
908        break;              }
909        case(ContactElementsZero):              break;
910        case(ReducedContactElementsZero):          case ReducedNodes:
911        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              switch(target.getFunctionSpace().getTypeCode()) {
912        break;                  case Nodes:
913        case(ContactElementsOne):                  case ReducedNodes:
914        case(ReducedContactElementsOne):                  case DegreesOfFreedom:
915        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedDegreesOfFreedom:
916        break;                      Assemble_CopyNodalData(mesh->Nodes, target, in);
917        default:                      break;
918           stringstream temp;                  case Elements:
919           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                  case ReducedElements:
920           throw FinleyAdapterException(temp.str());                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
921           break;                      break;
922        }                  case FaceElements:
923        break;                  case ReducedFaceElements:
924     case(ReducedNodes):                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
925        switch(target.getFunctionSpace().getTypeCode()) {                      break;
926        case(Nodes):                  case Points:
927        case(ReducedNodes):                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
928        case(DegreesOfFreedom):                      break;
929        case(ReducedDegreesOfFreedom):                  case ContactElementsZero:
930        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedContactElementsZero:
931        break;                  case ContactElementsOne:
932        case(Elements):                  case ReducedContactElementsOne:
933        case(ReducedElements):                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
934        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
935        break;                  default:
936        case(FaceElements):                      stringstream temp;
937        case(ReducedFaceElements):                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
938        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      throw FinleyAdapterException(temp.str());
939        break;                      break;
940        case(Points):              }
941        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);              break;
942        break;          case Elements:
943        case(ContactElementsZero):              if (target.getFunctionSpace().getTypeCode()==Elements) {
944        case(ReducedContactElementsZero):                  Assemble_CopyElementData(mesh->Elements, target, in);
945        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
946        break;                  Assemble_AverageElementData(mesh->Elements, target, in);
947        case(ContactElementsOne):              } else {
948        case(ReducedContactElementsOne):                  throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
949        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              }
950        break;              break;
951        default:          case ReducedElements:
952           stringstream temp;              if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
953           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                  Assemble_CopyElementData(mesh->Elements, target, in);
954           throw FinleyAdapterException(temp.str());              } else {
955           break;                  throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
956        }              }
957        break;              break;
958     case(Elements):          case FaceElements:
959        if (target.getFunctionSpace().getTypeCode()==Elements) {              if (target.getFunctionSpace().getTypeCode()==FaceElements) {
960           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);                  Assemble_CopyElementData(mesh->FaceElements, target, in);
961        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {              } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
962           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);                  Assemble_AverageElementData(mesh->FaceElements, target, in);
963        } else {              } else {
964           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");                  throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
965        }              }
966        break;              break;
967     case(ReducedElements):          case ReducedFaceElements:
968        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {              if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
969           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);                  Assemble_CopyElementData(mesh->FaceElements, target, in);
970        } else {              } else {
971           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");                  throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
972        }              }
973        break;              break;
974     case(FaceElements):          case Points:
975        if (target.getFunctionSpace().getTypeCode()==FaceElements) {              if (target.getFunctionSpace().getTypeCode()==Points) {
976           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);                  Assemble_CopyElementData(mesh->Points, target, in);
977        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {              } else {
978           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);                  throw FinleyAdapterException("Error - No interpolation with data on points possible.");
979        } else {              }
980           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");              break;
981        }          case ContactElementsZero:
982        break;          case ContactElementsOne:
983     case(ReducedFaceElements):              if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
984        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
985           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
986        } else {                  Assemble_AverageElementData(mesh->ContactElements, target, in);
987           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");              } else {
988        }                  throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
989        break;              }
990     case(Points):              break;
991        if (target.getFunctionSpace().getTypeCode()==Points) {          case ReducedContactElementsZero:
992           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);          case ReducedContactElementsOne:
993        } else {              if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
994           throw FinleyAdapterException("Error - No interpolation with data on points possible.");                  Assemble_CopyElementData(mesh->ContactElements, target, in);
995        }              } else {
996        break;                  throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
997     case(ContactElementsZero):              }
998     case(ContactElementsOne):              break;
999        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {          case DegreesOfFreedom:
1000           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              switch(target.getFunctionSpace().getTypeCode()) {
1001        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  case ReducedDegreesOfFreedom:
1002           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);                  case DegreesOfFreedom:
1003        } else {                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1004           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");                      break;
1005        }  
1006        break;                  case Nodes:
1007     case(ReducedContactElementsZero):                  case ReducedNodes:
1008     case(ReducedContactElementsOne):                      if (getMPISize()>1) {
1009        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                          escript::Data in2=escript::Data(in);
1010           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);                          in2.expand();
1011        } else {                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1012           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");                      } else {
1013        }                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1014        break;                      }
1015     case(DegreesOfFreedom):                            break;
1016        switch(target.getFunctionSpace().getTypeCode()) {                  case Elements:
1017        case(ReducedDegreesOfFreedom):                  case ReducedElements:
1018        case(DegreesOfFreedom):                      if (getMPISize()>1) {
1019        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1020        break;                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1021                          } else {
1022        case(Nodes):                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1023        case(ReducedNodes):                      }
1024        if (getMPISize()>1) {                      break;
1025           escript::Data temp=escript::Data(in);                  case FaceElements:
1026           temp.expand();                  case ReducedFaceElements:
1027           escriptDataC _in2 = temp.getDataC();                      if (getMPISize()>1) {
1028           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1029        } else {                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1030           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      } else {
1031        }                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1032        break;                      }
1033        case(Elements):                      break;
1034        case(ReducedElements):                  case Points:
1035        if (getMPISize()>1) {                      if (getMPISize()>1) {
1036           escript::Data temp=escript::Data( in,  continuousFunction(*this) );                          //escript::Data in2=escript::Data(in, continuousFunction(*this) );
1037           escriptDataC _in2 = temp.getDataC();                      } else {
1038           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1039        } else {                      }
1040           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
1041        }                  case ContactElementsZero:
1042        break;                  case ContactElementsOne:
1043        case(FaceElements):                  case ReducedContactElementsZero:
1044        case(ReducedFaceElements):                  case ReducedContactElementsOne:
1045        if (getMPISize()>1) {                      if (getMPISize()>1) {
1046           escript::Data temp=escript::Data( in,  continuousFunction(*this) );                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1047           escriptDataC _in2 = temp.getDataC();                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1048           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      } else {
1049                              Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1050        } else {                      }
1051           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      break;
1052        }                  default:
1053        break;                      stringstream temp;
1054        case(Points):                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1055        if (getMPISize()>1) {                      throw FinleyAdapterException(temp.str());
1056           //escript::Data temp=escript::Data( in,  continuousFunction(*this) );              }
1057           //escriptDataC _in2 = temp.getDataC();              break;
1058        } else {          case ReducedDegreesOfFreedom:
1059           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);              switch(target.getFunctionSpace().getTypeCode()) {
1060        }                  case Nodes:
1061        break;                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1062        case(ContactElementsZero):                  case ReducedNodes:
1063        case(ContactElementsOne):                      if (getMPISize()>1) {
1064        case(ReducedContactElementsZero):                          escript::Data in2=escript::Data(in);
1065        case(ReducedContactElementsOne):                          in2.expand();
1066        if (getMPISize()>1) {                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1067           escript::Data temp=escript::Data( in,  continuousFunction(*this) );                      } else {
1068           escriptDataC _in2 = temp.getDataC();                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1069           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);                      }
1070        } else {                      break;
1071           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case DegreesOfFreedom:
1072        }                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1073        break;                      break;
1074        default:                  case ReducedDegreesOfFreedom:
1075           stringstream temp;                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1076           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      break;
1077           throw FinleyAdapterException(temp.str());                  case Elements:
1078           break;                  case ReducedElements:
1079        }                      if (getMPISize()>1) {
1080        break;                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1081     case(ReducedDegreesOfFreedom):                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1082        switch(target.getFunctionSpace().getTypeCode()) {                      } else {
1083        case(Nodes):                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1084        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                      }
1085        break;                      break;
1086        case(ReducedNodes):                  case FaceElements:
1087        if (getMPISize()>1) {                  case ReducedFaceElements:
1088           escript::Data temp=escript::Data(in);                      if (getMPISize()>1) {
1089           temp.expand();                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1090           escriptDataC _in2 = temp.getDataC();                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1091           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                      } else {
1092        } else {                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1093           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      }
1094        }                      break;
1095        break;                  case Points:
1096        case(DegreesOfFreedom):                      if (getMPISize()>1) {
1097        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1098        break;                          Assemble_interpolate(mesh->Nodes, mesh->Points, in2, target);
1099        case(ReducedDegreesOfFreedom):                      } else {
1100        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1101        break;                      }
1102        case(Elements):                      break;
1103        case(ReducedElements):                  case ContactElementsZero:
1104        if (getMPISize()>1) {                  case ContactElementsOne:
1105           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );                  case ReducedContactElementsZero:
1106           escriptDataC _in2 = temp.getDataC();                  case ReducedContactElementsOne:
1107           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                      if (getMPISize()>1) {
1108        } else {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1109           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1110        }                      } else {
1111        break;                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1112        case(FaceElements):                      }
1113        case(ReducedFaceElements):                      break;
1114        if (getMPISize()>1) {                  default:
1115           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );                      stringstream temp;
1116           escriptDataC _in2 = temp.getDataC();                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1117           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      throw FinleyAdapterException(temp.str());
1118        } else {                      break;
1119           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);              }
1120        }              break;
1121        break;          default:
1122        case(Points):              stringstream temp;
1123        if (getMPISize()>1) {              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1124           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );              throw FinleyAdapterException(temp.str());
1125           escriptDataC _in2 = temp.getDataC();              break;
1126           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);      }
1127        } else {      checkFinleyError();
          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);  
       }  
       break;  
       case(ContactElementsZero):  
       case(ContactElementsOne):  
       case(ReducedContactElementsZero):  
       case(ReducedContactElementsOne):  
       if (getMPISize()>1) {  
          escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );  
          escriptDataC _in2 = temp.getDataC();  
          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);  
       } else {  
          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);  
       }  
       break;  
       default:  
          stringstream temp;  
          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();  
          throw FinleyAdapterException(temp.str());  
          break;  
       }  
       break;  
    default:  
       stringstream temp;  
       temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1128  }  }
1129    
1130  //  //
1131  // copies the locations of sample points into x:  // copies the locations of sample points into x
1132  //  //
1133  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1134  {  {
1135     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1136     if (argDomain!=*this)      if (argDomain!=*this)
1137        throw FinleyAdapterException("Error - Illegal domain of data point locations");          throw FinleyAdapterException("Error - Illegal domain of data point locations");
1138     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1139     // in case of values node coordinates we can do the job directly:      // in case of appropriate function space we can do the job directly:
1140     if (arg.getFunctionSpace().getTypeCode()==Nodes) {      if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1141        escriptDataC _arg=arg.getDataC();          Assemble_NodeCoordinates(mesh->Nodes, arg);
1142        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);      } else {
1143     } else {          escript::Data tmp_data=Vector(0., continuousFunction(*this), true);
1144        escript::Data tmp_data=Vector(0.0,continuousFunction(*this),true);          Assemble_NodeCoordinates(mesh->Nodes, tmp_data);
1145        escriptDataC _tmp_data=tmp_data.getDataC();          // this is then interpolated onto arg:
1146        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);          interpolateOnDomain(arg, tmp_data);
1147        // this is then interpolated onto arg:      }
1148        interpolateOnDomain(arg,tmp_data);      checkFinleyError();
    }  
    checkFinleyError();  
1149  }  }
1150    
1151  //  //
1152  // return the normal vectors at the location of data points as a Data object:  // return the normal vectors at the location of data points as a Data object
1153  //  //
1154  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1155  {  {
1156  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/      const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1157     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));      if (normalDomain!=*this)
1158     if (normalDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of normal locations");
1159        throw FinleyAdapterException("Error - Illegal domain of normal locations");      Finley_Mesh* mesh=m_finleyMesh.get();
1160     Finley_Mesh* mesh=m_finleyMesh.get();      switch(normal.getFunctionSpace().getTypeCode()) {
1161     escriptDataC _normal=normal.getDataC();          case Nodes:
1162     switch(normal.getFunctionSpace().getTypeCode()) {              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1163     case(Nodes):              break;
1164     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");          case ReducedNodes:
1165     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1166     case(ReducedNodes):              break;
1167     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");          case Elements:
1168     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1169     case(Elements):              break;
1170     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");          case ReducedElements:
1171     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1172     case(ReducedElements):              break;
1173     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");          case FaceElements:
1174     break;          case ReducedFaceElements:
1175     case (FaceElements):              Assemble_setNormal(mesh->Nodes, mesh->FaceElements, normal);
1176     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              break;
1177     break;          case Points:
1178     case (ReducedFaceElements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1179     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              break;
1180     break;          case ContactElementsOne:
1181     case(Points):          case ContactElementsZero:
1182     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");          case ReducedContactElementsOne:
1183     break;          case ReducedContactElementsZero:
1184     case (ContactElementsOne):              Assemble_setNormal(mesh->Nodes, mesh->ContactElements, normal);
1185     case (ContactElementsZero):              break;
1186     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);          case DegreesOfFreedom:
1187     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1188     case (ReducedContactElementsOne):              break;
1189     case (ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1190     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1191     break;              break;
1192     case(DegreesOfFreedom):          default:
1193     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");              stringstream temp;
1194     break;              temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1195     case(ReducedDegreesOfFreedom):              throw FinleyAdapterException(temp.str());
1196     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");              break;
1197     break;      }
1198     default:      checkFinleyError();
       stringstream temp;  
       temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
 }  
   
 //  
 // interpolates data to other domain:  
 //  
 void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  
 {  
    const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();  
    const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());  
    if (targetDomain!=this)  
       throw FinleyAdapterException("Error - Illegal domain of interpolation target");  
   
    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");  
 }  
   
 //  
 // calculates the integral of a function defined of arg:  
 //  
 void MeshAdapter::setToIntegrals(vector<double>& integrals,const escript::Data& arg) const  
 {  
    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));  
    if (argDomain!=*this)  
       throw FinleyAdapterException("Error - Illegal domain of integration kernel");  
   
    double blocktimer_start = blocktimer_time();  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    escriptDataC _temp;  
    escript::Data temp;  
    escriptDataC _arg=arg.getDataC();  
    switch(arg.getFunctionSpace().getTypeCode()) {  
    case(Nodes):  
    temp=escript::Data( arg, escript::function(*this) );  
    _temp=temp.getDataC();  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
    break;  
    case(ReducedNodes):  
    temp=escript::Data( arg, escript::function(*this) );  
    _temp=temp.getDataC();  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
    break;  
    case(Elements):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);  
    break;  
    case(ReducedElements):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);  
    break;  
    case(FaceElements):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);  
    break;  
    case(ReducedFaceElements):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);  
    break;  
    case(Points):  
    throw FinleyAdapterException("Error - Integral of data on points is not supported.");  
    break;  
    case(ContactElementsZero):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  
    break;  
    case(ReducedContactElementsZero):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  
    break;  
    case(ContactElementsOne):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  
    break;  
    case(ReducedContactElementsOne):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  
    break;  
    case(DegreesOfFreedom):  
    temp=escript::Data( arg, escript::function(*this) );  
    _temp=temp.getDataC();  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
    break;  
    case(ReducedDegreesOfFreedom):  
    temp=escript::Data( arg, escript::function(*this) );  
    _temp=temp.getDataC();  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
    blocktimer_increment("integrate()", blocktimer_start);  
 }  
   
 //  
 // calculates the gradient of arg:  
 //  
 void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  
 {  
    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));  
    if (argDomain!=*this)  
       throw FinleyAdapterException("Error - Illegal domain of gradient argument");  
    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));  
    if (gradDomain!=*this)  
       throw FinleyAdapterException("Error - Illegal domain of gradient");  
   
    Finley_Mesh* mesh=m_finleyMesh.get();  
    escriptDataC _grad=grad.getDataC();  
    escriptDataC nodeDataC;  
    escript::Data temp;  
    if (getMPISize()>1) {  
       if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {  
          temp=escript::Data( arg,  continuousFunction(*this) );  
          nodeDataC = temp.getDataC();  
       } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {  
          temp=escript::Data( arg,  reducedContinuousFunction(*this) );  
          nodeDataC = temp.getDataC();  
       } else {  
          nodeDataC = arg.getDataC();  
       }  
    } else {  
       nodeDataC = arg.getDataC();  
    }  
    switch(grad.getFunctionSpace().getTypeCode()) {  
    case(Nodes):  
    throw FinleyAdapterException("Error - Gradient at nodes is not supported.");  
    break;  
    case(ReducedNodes):  
    throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");  
    break;  
    case(Elements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);  
    break;  
    case(ReducedElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);  
    break;  
    case(FaceElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedFaceElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);  
    break;  
    case(Points):  
    throw FinleyAdapterException("Error - Gradient at points is not supported.");  
    break;  
    case(ContactElementsZero):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedContactElementsZero):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ContactElementsOne):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedContactElementsOne):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(DegreesOfFreedom):  
    throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");  
    break;  
    case(ReducedDegreesOfFreedom):  
    throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1199  }  }
1200    
1201  //  //
1202  // returns the size of elements:  // interpolates data to other domain
1203    //
1204    void MeshAdapter::interpolateACross(escript::Data& target, const escript::Data& source) const
1205    {
1206        throw FinleyAdapterException("Error - Finley does not allow interpolation across domains.");
1207    }
1208    
1209    //
1210    // calculates the integral of a function defined on arg
1211    //
1212    void MeshAdapter::setToIntegrals(vector<double>& integrals, const escript::Data& arg) const
1213    {
1214        const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1215        if (argDomain!=*this)
1216            throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1217    
1218        double blocktimer_start = blocktimer_time();
1219        Finley_Mesh* mesh=m_finleyMesh.get();
1220        switch(arg.getFunctionSpace().getTypeCode()) {
1221            case Nodes:
1222                {
1223                    escript::Data temp(arg, escript::function(*this));
1224                    Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1225                }
1226                break;
1227            case ReducedNodes:
1228                {
1229                    escript::Data temp(arg, escript::function(*this));
1230                    Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1231                }
1232                break;
1233            case Elements:
1234            case ReducedElements:
1235                Assemble_integrate(mesh->Nodes, mesh->Elements, arg, &integrals[0]);
1236                break;
1237            case FaceElements:
1238            case ReducedFaceElements:
1239                Assemble_integrate(mesh->Nodes, mesh->FaceElements, arg, &integrals[0]);
1240                break;
1241            case Points:
1242                throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1243                break;
1244            case ContactElementsZero:
1245            case ReducedContactElementsZero:
1246            case ContactElementsOne:
1247            case ReducedContactElementsOne:
1248                Assemble_integrate(mesh->Nodes, mesh->ContactElements, arg, &integrals[0]);
1249                break;
1250            case DegreesOfFreedom:
1251            case ReducedDegreesOfFreedom:
1252                {
1253                    escript::Data temp(arg, escript::function(*this));
1254                    Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1255                }
1256                break;
1257            default:
1258                stringstream temp;
1259                temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1260                throw FinleyAdapterException(temp.str());
1261                break;
1262        }
1263        checkFinleyError();
1264        blocktimer_increment("integrate()", blocktimer_start);
1265    }
1266    
1267    //
1268    // calculates the gradient of arg
1269    //
1270    void MeshAdapter::setToGradient(escript::Data& grad, const escript::Data& arg) const
1271    {
1272        const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1273        if (argDomain!=*this)
1274            throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1275        const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1276        if (gradDomain!=*this)
1277            throw FinleyAdapterException("Error - Illegal domain of gradient");
1278    
1279        Finley_Mesh* mesh=m_finleyMesh.get();
1280        escript::Data nodeData;
1281        if (getMPISize()>1) {
1282            if (arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom) {
1283                nodeData=escript::Data(arg, continuousFunction(*this));
1284            } else if(arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom) {
1285                nodeData=escript::Data(arg, reducedContinuousFunction(*this));
1286            } else {
1287                nodeData = arg;
1288            }
1289        } else {
1290            nodeData = arg;
1291        }
1292        switch(grad.getFunctionSpace().getTypeCode()) {
1293            case Nodes:
1294                throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1295                break;
1296            case ReducedNodes:
1297                throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1298                break;
1299            case Elements:
1300            case ReducedElements:
1301                Assemble_gradient(mesh->Nodes, mesh->Elements, grad, nodeData);
1302                break;
1303            case FaceElements:
1304            case ReducedFaceElements:
1305                Assemble_gradient(mesh->Nodes, mesh->FaceElements, grad, nodeData);
1306                break;
1307            case Points:
1308                throw FinleyAdapterException("Error - Gradient at points is not supported.");
1309                break;
1310            case ContactElementsZero:
1311            case ReducedContactElementsZero:
1312            case ContactElementsOne:
1313            case ReducedContactElementsOne:
1314                Assemble_gradient(mesh->Nodes, mesh->ContactElements, grad, nodeData);
1315                break;
1316            case DegreesOfFreedom:
1317                throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1318                break;
1319            case ReducedDegreesOfFreedom:
1320                throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1321                break;
1322            default:
1323                stringstream temp;
1324                temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1325                throw FinleyAdapterException(temp.str());
1326                break;
1327        }
1328        checkFinleyError();
1329    }
1330    
1331    //
1332    // returns the size of elements
1333  //  //
1334  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1335  {  {
1336     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1337     escriptDataC tmp=size.getDataC();      switch(size.getFunctionSpace().getTypeCode()) {
1338     switch(size.getFunctionSpace().getTypeCode()) {          case Nodes:
1339     case(Nodes):              throw FinleyAdapterException("Error - Size of nodes is not supported.");
1340     throw FinleyAdapterException("Error - Size of nodes is not supported.");              break;
1341     break;          case ReducedNodes:
1342     case(ReducedNodes):              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1343     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");              break;
1344     break;          case Elements:
1345     case(Elements):          case ReducedElements:
1346     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);              Assemble_getSize(mesh->Nodes, mesh->Elements, size);
1347     break;              break;
1348     case(ReducedElements):          case FaceElements:
1349     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case ReducedFaceElements:
1350     break;              Assemble_getSize(mesh->Nodes, mesh->FaceElements, size);
1351     case(FaceElements):              break;
1352     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case Points:
1353     break;              throw FinleyAdapterException("Error - Size of point elements is not supported.");
1354     case(ReducedFaceElements):              break;
1355     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case ContactElementsZero:
1356     break;          case ContactElementsOne:
1357     case(Points):          case ReducedContactElementsZero:
1358     throw FinleyAdapterException("Error - Size of point elements is not supported.");          case ReducedContactElementsOne:
1359     break;              Assemble_getSize(mesh->Nodes,mesh->ContactElements,size);
1360     case(ContactElementsZero):              break;
1361     case(ContactElementsOne):          case DegreesOfFreedom:
1362     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1363     break;              break;
1364     case(ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1365     case(ReducedContactElementsOne):              throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1366     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              break;
1367     break;          default:
1368     case(DegreesOfFreedom):              stringstream temp;
1369     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");              temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1370     break;              throw FinleyAdapterException(temp.str());
1371     case(ReducedDegreesOfFreedom):              break;
1372     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");      }
1373     break;      checkFinleyError();
    default:  
       stringstream temp;  
       temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1374  }  }
1375    
1376  //  //
# Line 1503  void MeshAdapter::setToSize(escript::Dat Line 1378  void MeshAdapter::setToSize(escript::Dat
1378  //  //
1379  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1380  {  {
1381     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1382     escriptDataC tmp;      const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1383     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));      if (newDomain!=*this)
1384     if (newDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of new point locations");
1385        throw FinleyAdapterException("Error - Illegal domain of new point locations");      if (new_x.getFunctionSpace() == continuousFunction(*this)) {
1386     if ( new_x.getFunctionSpace() == continuousFunction(*this) ) {          Finley_Mesh_setCoordinates(mesh, new_x);
1387         tmp = new_x.getDataC();      } else {
1388         Finley_Mesh_setCoordinates(mesh,&tmp);          throw FinleyAdapterException("As of escript version 3.3 SetX() only accepts ContinuousFunction arguments. Please interpolate.");
1389     } else {      }
1390         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(*this) );      checkFinleyError();
        tmp = new_x_inter.getDataC();  
        Finley_Mesh_setCoordinates(mesh,&tmp);  
    }  
    checkFinleyError();  
 }  
   
 //  
 // Helper for the save* methods. Extracts optional data variable names and the  
 // corresponding pointers from python dictionary. Caller must free arrays.  
 //  
 void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const  
 {  
    numData = boost::python::extract<int>(arg.attr("__len__")());  
    /* win32 refactor */  
    names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;  
    data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;  
    dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;  
   
    boost::python::list keys=arg.keys();  
    for (int i=0; i<numData; ++i) {  
       string n=boost::python::extract<string>(keys[i]);  
       escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
       if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)  
          throw FinleyAdapterException("Error: Data must be defined on same Domain");  
       data[i] = d.getDataC();  
       dataPtr[i] = &(data[i]);  
       names[i] = TMPMEMALLOC(n.length()+1, char);  
       strcpy(names[i], n.c_str());  
    }  
 }  
   
 //  
 // saves mesh and optionally data arrays in openDX format  
 //  
 void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const  
 {  
    int num_data;  
    char **names;  
    escriptDataC *data;  
    escriptDataC **ptr_data;  
   
    extractArgsFromDict(arg, num_data, names, data, ptr_data);  
    Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);  
    checkFinleyError();  
   
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0; i<num_data; i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
   
    return;  
 }  
   
 //  
 // saves mesh and optionally data arrays in VTK format  
 //  
 void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const  
 {  
     boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("_saveVTK");  
     pySaveVTK(filename, const_cast<MeshAdapter*>(this)->getPtr(),  
               metadata, metadata_schema, arg);  
1391  }  }
1392    
1393  bool MeshAdapter::ownSample(int fs_code, index_t id) const  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1394  {  {
1395        if (getMPISize() > 1) {
1396  #ifdef ESYS_MPI  #ifdef ESYS_MPI
1397      index_t myFirstNode=0, myLastNode=0, k=0;          int myFirstNode=0, myLastNode=0, k=0;
1398      index_t* globalNodeIndex=0;          int* globalNodeIndex=0;
1399      Finley_Mesh* mesh_p=m_finleyMesh.get();          Finley_Mesh* mesh_p=m_finleyMesh.get();
1400      if (fs_code == FINLEY_REDUCED_NODES)          /*
1401      {           * this method is only used by saveDataCSV which would use the returned
1402      myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);           * values for reduced nodes wrongly so this case is disabled for now
1403      myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);          if (fs_code == FINLEY_REDUCED_NODES) {
1404      globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);              myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1405      }              myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1406      else              globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1407      {          } else
1408      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);          */
1409      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);          if (fs_code == FINLEY_NODES) {
1410      globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);              myFirstNode = mesh_p->Nodes->getFirstNode();
1411      }              myLastNode = mesh_p->Nodes->getLastNode();
1412      k=globalNodeIndex[id];              globalNodeIndex = mesh_p->Nodes->borrowGlobalNodesIndex();
1413      return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );          } else {
1414                throw FinleyAdapterException("Unsupported function space type for ownSample()");
1415            }
1416    
1417            k=globalNodeIndex[id];
1418            return ((myFirstNode <= k) && (k < myLastNode));
1419  #endif  #endif
1420        }
1421      return true;      return true;
1422  }  }
1423    
1424    
   
1425  //  //
1426  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1427  //  //
1428  ASM_ptr MeshAdapter::newSystemMatrix(  escript::ASM_ptr MeshAdapter::newSystemMatrix(const int row_blocksize,
1429                                                   const int row_blocksize,                              const escript::FunctionSpace& row_functionspace,
1430                                                   const escript::FunctionSpace& row_functionspace,                              const int column_blocksize,
1431                                                   const int column_blocksize,                              const escript::FunctionSpace& column_functionspace,
1432                                                   const escript::FunctionSpace& column_functionspace,                              const int type) const
1433                                                   const int type) const  {
1434  {      // is the domain right?
1435     int reduceRowOrder=0;      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1436     int reduceColOrder=0;      if (row_domain!=*this)
1437     // is the domain right?          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1438     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1439     if (row_domain!=*this)      if (col_domain!=*this)
1440        throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");          throw FinleyAdapterException("Error - domain of column function space does not match the domain of matrix generator.");
1441     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));  
1442     if (col_domain!=*this)      int reduceRowOrder=0;
1443        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");      int reduceColOrder=0;
1444     // is the function space type right      // is the function space type right?
1445     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {      if (row_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1446        reduceRowOrder=0;          reduceRowOrder=1;
1447     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      } else if (row_functionspace.getTypeCode() != DegreesOfFreedom) {
1448        reduceRowOrder=1;          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1449     } else {      }
1450        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      if (column_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1451     }          reduceColOrder=1;
1452     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (column_functionspace.getTypeCode() != DegreesOfFreedom) {
1453        reduceColOrder=0;          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1454     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1455        reduceColOrder=1;  
1456     } else {      // generate matrix:
1457        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(
1458     }              getFinley_Mesh(), reduceRowOrder, reduceColOrder);
1459     // generate matrix:      checkFinleyError();
1460        Paso_SystemMatrix* fsystemMatrix;
1461     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);      const int trilinos = 0;
1462     checkFinleyError();      if (trilinos) {
    Paso_SystemMatrix* fsystemMatrix;  
    int trilinos = 0;  
    if (trilinos) {  
1463  #ifdef TRILINOS  #ifdef TRILINOS
1464        /* Allocation Epetra_VrbMatrix here */          // FIXME: Allocation Epetra_VrbMatrix here...
1465  #endif  #endif
1466     }      } else {
1467     else {          fsystemMatrix=Paso_SystemMatrix_alloc(type, fsystemMatrixPattern,
1468        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);                  row_blocksize, column_blocksize, FALSE);
1469     }      }
1470     checkPasoError();      checkPasoError();
1471     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1472     SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);      SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1473     return ASM_ptr(sma);      return escript::ASM_ptr(sma);
 //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  
1474  }  }
1475    
1476  //  //
1477  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1478  //  //
1479  ATP_ptr MeshAdapter::newTransportProblem(  escript::ATP_ptr MeshAdapter::newTransportProblem(const int blocksize,
1480                                                           const bool useBackwardEuler,          const escript::FunctionSpace& functionspace, const int type) const
1481                                                           const int blocksize,  {
1482                                                           const escript::FunctionSpace& functionspace,      // is the domain right?
1483                                                           const int type) const      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1484  {      if (domain!=*this)
1485     int reduceOrder=0;          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1486     // is the domain right?  
1487     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));      // is the function space type right?
1488     if (domain!=*this)      int reduceOrder=0;
1489        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");      if (functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1490     // is the function space type right          reduceOrder=1;
1491     if (functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (functionspace.getTypeCode() != DegreesOfFreedom) {
1492        reduceOrder=0;          throw FinleyAdapterException("Error - illegal function space type for transport problem.");
1493     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1494        reduceOrder=1;  
1495     } else {      // generate transport problem:
1496        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(
1497     }              getFinley_Mesh(), reduceOrder, reduceOrder);
1498     // generate matrix:      checkFinleyError();
1499        Paso_TransportProblem* transportProblem;
1500     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);      transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern, blocksize);
1501     checkFinleyError();      checkPasoError();
1502     Paso_TransportProblem* transportProblem;      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1503     transportProblem=Paso_TransportProblem_alloc(useBackwardEuler,fsystemMatrixPattern,blocksize);      TransportProblemAdapter* tpa=new TransportProblemAdapter(
1504     checkPasoError();              transportProblem, blocksize, functionspace);
1505     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      return escript::ATP_ptr(tpa);
    TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);  
    return ATP_ptr(tpa);  
 //   return TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);  
1506  }  }
1507    
1508  //  //
1509  // vtkObject MeshAdapter::createVtkObject() const  // returns true if data on functionSpaceCode is considered as being cell centered
 // TODO:  
1510  //  //
   
 //  
 // returns true if data at the atom_type is considered as being cell centered:  
1511  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1512  {  {
1513     switch(functionSpaceCode) {      switch(functionSpaceCode) {
1514     case(Nodes):          case Nodes:
1515     case(DegreesOfFreedom):          case DegreesOfFreedom:
1516     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1517     return false;              return false;
1518     break;          case Elements:
1519     case(Elements):          case FaceElements:
1520     case(FaceElements):          case Points:
1521     case(Points):          case ContactElementsZero:
1522     case(ContactElementsZero):          case ContactElementsOne:
1523     case(ContactElementsOne):          case ReducedElements:
1524     case(ReducedElements):          case ReducedFaceElements:
1525     case(ReducedFaceElements):          case ReducedContactElementsZero:
1526     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
1527     case(ReducedContactElementsOne):              return true;
1528     return true;          default:
1529     break;              stringstream temp;
1530     default:              temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1531        stringstream temp;              throw FinleyAdapterException(temp.str());
1532        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;              break;
1533        throw FinleyAdapterException(temp.str());      }
1534        break;      return false;
    }  
    checkFinleyError();  
    return false;  
1535  }  }
1536    
1537  bool  bool
1538  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1539  {  {
1540     /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]      /* The idea is to use equivalence classes. [Types which can be interpolated
1541      class 1: DOF <-> Nodes         back and forth]:
1542      class 2: ReducedDOF <-> ReducedNodes          class 1: DOF <-> Nodes
1543      class 3: Points          class 2: ReducedDOF <-> ReducedNodes
1544      class 4: Elements          class 3: Points
1545      class 5: ReducedElements          class 4: Elements
1546      class 6: FaceElements          class 5: ReducedElements
1547      class 7: ReducedFaceElements          class 6: FaceElements
1548      class 8: ContactElementZero <-> ContactElementOne          class 7: ReducedFaceElements
1549      class 9: ReducedContactElementZero <-> ReducedContactElementOne          class 8: ContactElementZero <-> ContactElementOne
1550            class 9: ReducedContactElementZero <-> ReducedContactElementOne
1551     There is also a set of lines. Interpolation is possible down a line but not between lines.  
1552     class 1 and 2 belong to all lines so aren't considered.      There is also a set of lines. Interpolation is possible down a line but
1553      line 0: class 3      not between lines.
1554      line 1: class 4,5      class 1 and 2 belong to all lines so aren't considered.
1555      line 2: class 6,7          line 0: class 3
1556      line 3: class 8,9          line 1: class 4,5
1557            line 2: class 6,7
1558     For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.          line 3: class 8,9
1559     eg hasnodes is true if we have at least one instance of Nodes.  
1560     */      For classes with multiple members (eg class 2) we have vars to record if
1561        there is at least one instance.
1562        e.g. hasnodes is true if we have at least one instance of Nodes.
1563        */
1564      if (fs.empty())      if (fs.empty())
     {  
1565          return false;          return false;
1566      }  
1567      vector<int> hasclass(10);      vector<int> hasclass(10);
1568      vector<int> hasline(4);      vector<int> hasline(4);    
1569      bool hasnodes=false;      bool hasnodes=false;
1570      bool hasrednodes=false;      bool hasrednodes=false;
1571      bool hascez=false;      bool hascez=false;
1572      bool hasrcez=false;      bool hasrcez=false;
1573      for (int i=0;i<fs.size();++i)      for (int i=0;i<fs.size();++i) {
1574      {          switch(fs[i]) {
1575      switch(fs[i])              case Nodes:
1576      {                  hasnodes=true; // fall through
1577      case(Nodes):   hasnodes=true;   // no break is deliberate              case DegreesOfFreedom:
1578      case(DegreesOfFreedom):                  hasclass[1]=1;
1579          hasclass[1]=1;                  break;
1580          break;              case ReducedNodes:
1581      case(ReducedNodes):    hasrednodes=true;    // no break is deliberate                  hasrednodes=true; // fall through
1582      case(ReducedDegreesOfFreedom):              case ReducedDegreesOfFreedom:
1583          hasclass[2]=1;                  hasclass[2]=1;
1584          break;                  break;
1585      case(Points):              case Points:
1586          hasline[0]=1;                  hasline[0]=1;
1587          hasclass[3]=1;                  hasclass[3]=1;
1588          break;                  break;
1589      case(Elements):              case Elements:
1590          hasclass[4]=1;                  hasclass[4]=1;
1591          hasline[1]=1;                  hasline[1]=1;
1592          break;                  break;
1593      case(ReducedElements):              case ReducedElements:
1594          hasclass[5]=1;                  hasclass[5]=1;
1595          hasline[1]=1;                  hasline[1]=1;
1596          break;                  break;
1597      case(FaceElements):              case FaceElements:
1598          hasclass[6]=1;                  hasclass[6]=1;
1599          hasline[2]=1;                  hasline[2]=1;
1600          break;                  break;
1601      case(ReducedFaceElements):              case ReducedFaceElements:
1602          hasclass[7]=1;                  hasclass[7]=1;
1603          hasline[2]=1;                  hasline[2]=1;
1604          break;                  break;
1605      case(ContactElementsZero):  hascez=true;    // no break is deliberate              case ContactElementsZero:
1606      case(ContactElementsOne):                  hascez=true; // fall through
1607          hasclass[8]=1;              case ContactElementsOne:
1608          hasline[3]=1;                  hasclass[8]=1;
1609          break;                  hasline[3]=1;
1610      case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate                  break;
1611      case(ReducedContactElementsOne):              case ReducedContactElementsZero:
1612          hasclass[9]=1;                  hasrcez=true; // fall through
1613          hasline[3]=1;              case ReducedContactElementsOne:
1614          break;                  hasclass[9]=1;
1615      default:                  hasline[3]=1;
1616          return false;                  break;
1617      }              default:
1618                    return false;
1619            }
1620      }      }
1621      int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];      int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
     // fail if we have more than one leaf group  
1622    
1623        // fail if we have more than one leaf group
1624      if (totlines>1)      if (totlines>1)
1625      {          return false; // there are at least two branches we can't interpolate between
1626      return false;   // there are at least two branches we can't interpolate between      else if (totlines==1) {
1627      }          if (hasline[0]==1)              // we have points
1628      else if (totlines==1)              resultcode=Points;
1629      {          else if (hasline[1]==1) {
1630      if (hasline[0]==1)      // we have points              if (hasclass[5]==1)
1631      {                  resultcode=ReducedElements;
1632          resultcode=Points;              else
1633      }                  resultcode=Elements;
1634      else if (hasline[1]==1)          } else if (hasline[2]==1) {
1635      {              if (hasclass[7]==1)
1636          if (hasclass[5]==1)                  resultcode=ReducedFaceElements;
1637          {              else
1638          resultcode=ReducedElements;                  resultcode=FaceElements;
1639          }          } else {   // so we must be in line3
1640          else              if (hasclass[9]==1) {
1641          {                  // need something from class 9
1642          resultcode=Elements;                  resultcode=(hasrcez ? ReducedContactElementsZero : ReducedContactElementsOne);
1643          }              } else {
1644      }                  // something from class 8
1645      else if (hasline[2]==1)                  resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1646      {              }
1647          if (hasclass[7]==1)          }
1648          {      } else { // totlines==0
1649          resultcode=ReducedFaceElements;          if (hasclass[2]==1) {
1650          }              // something from class 2
1651          else              resultcode=(hasrednodes ? ReducedNodes : ReducedDegreesOfFreedom);
1652          {          } else {
1653          resultcode=FaceElements;              // something from class 1
1654          }              resultcode=(hasnodes ? Nodes : DegreesOfFreedom);
1655      }          }
     else    // so we must be in line3  
     {  
         if (hasclass[9]==1)  
         {  
         // need something from class 9  
         resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);  
         }  
         else  
         {  
         // something from class 8  
         resultcode=(hascez?ContactElementsZero:ContactElementsOne);  
         }  
     }  
     }  
     else    // totlines==0  
     {  
     if (hasclass[2]==1)  
     {  
         // something from class 2  
         resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);  
     }  
     else  
     {   // something from class 1  
         resultcode=(hasnodes?Nodes:DegreesOfFreedom);  
     }  
1656      }      }
1657      return true;      return true;
1658  }  }
1659    
1660  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,
1661                                                 int functionSpaceType_target) const
1662  {  {
1663     switch(functionSpaceType_source) {      switch(functionSpaceType_source) {
1664     case(Nodes):          case Nodes:
1665      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1666      case(Nodes):                  case Nodes:
1667      case(ReducedNodes):                  case ReducedNodes:
1668      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1669      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1670      case(Elements):                  case Elements:
1671      case(ReducedElements):                  case ReducedElements:
1672      case(FaceElements):                  case FaceElements:
1673      case(ReducedFaceElements):                  case ReducedFaceElements:
1674      case(Points):                  case Points:
1675      case(ContactElementsZero):                  case ContactElementsZero:
1676      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1677      case(ContactElementsOne):                  case ContactElementsOne:
1678      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1679      return true;                      return true;
1680      default:                  default:
1681            stringstream temp;                      stringstream temp;
1682            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1683            throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1684     }              }
1685     break;              break;
1686     case(ReducedNodes):          case ReducedNodes:
1687      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1688      case(ReducedNodes):                  case ReducedNodes:
1689      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1690      case(Elements):                  case Elements:
1691      case(ReducedElements):                  case ReducedElements:
1692      case(FaceElements):                  case FaceElements:
1693      case(ReducedFaceElements):                  case ReducedFaceElements:
1694      case(Points):                  case Points:
1695      case(ContactElementsZero):                  case ContactElementsZero:
1696      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1697      case(ContactElementsOne):                  case ContactElementsOne:
1698      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1699      return true;                      return true;
1700      case(Nodes):                  case Nodes:
1701      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1702      return false;                      return false;
1703      default:                  default:
1704          stringstream temp;                      stringstream temp;
1705          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1706          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1707     }              }
1708     break;              break;
1709     case(Elements):          case Elements:
1710      if (functionSpaceType_target==Elements) {              if (functionSpaceType_target==Elements) {
1711        return true;                  return true;
1712      } else if (functionSpaceType_target==ReducedElements) {              } else if (functionSpaceType_target==ReducedElements) {
1713        return true;                  return true;
1714          } else {              } else {
1715            return false;                  return false;
1716          }              }
1717     case(ReducedElements):          case ReducedElements:
1718      if (functionSpaceType_target==ReducedElements) {              if (functionSpaceType_target==ReducedElements) {
1719        return true;                  return true;
1720      } else {              } else {
1721            return false;                  return false;
1722      }              }
1723     case(FaceElements):          case FaceElements:
1724      if (functionSpaceType_target==FaceElements) {              if (functionSpaceType_target==FaceElements) {
1725              return true;                  return true;
1726      } else if (functionSpaceType_target==ReducedFaceElements) {              } else if (functionSpaceType_target==ReducedFaceElements) {
1727              return true;                  return true;
1728      } else {              } else {
1729              return false;                  return false;
1730      }              }
1731     case(ReducedFaceElements):          case ReducedFaceElements:
1732      if (functionSpaceType_target==ReducedFaceElements) {              if (functionSpaceType_target==ReducedFaceElements) {
1733              return true;                  return true;
1734      } else {              } else {
1735          return false;                  return false;
1736      }              }
1737     case(Points):          case Points:
1738      if (functionSpaceType_target==Points) {              if (functionSpaceType_target==Points) {
1739              return true;                  return true;
1740      } else {              } else {
1741              return false;                  return false;
1742      }              }
1743     case(ContactElementsZero):          case ContactElementsZero:
1744     case(ContactElementsOne):          case ContactElementsOne:
1745      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {              if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1746              return true;                  return true;
1747      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {              } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1748              return true;                  return true;
1749      } else {              } else {
1750              return false;                  return false;
1751      }              }
1752     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
1753     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
1754      if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {              if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1755              return true;                  return true;
1756      } else {              } else {
1757              return false;                  return false;
1758      }              }
1759     case(DegreesOfFreedom):          case DegreesOfFreedom:
1760      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1761      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1762      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1763      case(Nodes):                  case Nodes:
1764      case(ReducedNodes):                  case ReducedNodes:
1765      case(Elements):                  case Elements:
1766      case(ReducedElements):                  case ReducedElements:
1767      case(Points):                  case Points:
1768      case(FaceElements):                  case FaceElements:
1769      case(ReducedFaceElements):                  case ReducedFaceElements:
1770      case(ContactElementsZero):                  case ContactElementsZero:
1771      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1772      case(ContactElementsOne):                  case ContactElementsOne:
1773      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1774      return true;                      return true;
1775      default:                  default:
1776          stringstream temp;                      stringstream temp;
1777          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1778          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1779      }              }
1780      break;              break;
1781     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1782     switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1783      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1784      case(ReducedNodes):                  case ReducedNodes:
1785      case(Elements):                  case Elements:
1786      case(ReducedElements):                  case ReducedElements:
1787      case(FaceElements):                  case FaceElements:
1788      case(ReducedFaceElements):                  case ReducedFaceElements:
1789      case(Points):                  case Points:
1790      case(ContactElementsZero):                  case ContactElementsZero:
1791      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1792      case(ContactElementsOne):                  case ContactElementsOne:
1793      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1794      return true;                      return true;
1795      case(Nodes):                  case Nodes:
1796      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1797      return false;                      return false;
1798      default:                  default:
1799          stringstream temp;                      stringstream temp;
1800          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1801          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1802      }              }
1803      break;              break;
1804     default:          default:
1805        stringstream temp;              stringstream temp;
1806        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1807        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
1808        break;              break;
1809     }      }
1810     checkFinleyError();      return false;
1811     return false;  }
1812  }  
1813    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
1814  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const  {
1815  {      if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1816     return false;          return 1;
1817  }  
1818        if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1819  bool MeshAdapter::operator==(const AbstractDomain& other) const          return -1;
1820  {  
1821     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);      return 0;
    if (temp!=0) {  
       return (m_finleyMesh==temp->m_finleyMesh);  
    } else {  
       return false;  
    }  
1822  }  }
1823    
1824  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,
1825            const escript::AbstractDomain& targetDomain,
1826            int functionSpaceType_target) const
1827  {  {
1828     return !(operator==(other));      return false;
1829    }
1830    
1831    bool MeshAdapter::operator==(const escript::AbstractDomain& other) const
1832    {
1833        const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1834        if (temp) {
1835            return (m_finleyMesh==temp->m_finleyMesh);
1836        } else {
1837            return false;
1838        }
1839    }
1840    
1841    bool MeshAdapter::operator!=(const escript::AbstractDomain& other) const
1842    {
1843        return !(operator==(other));
1844  }  }
1845    
1846  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1847  {  {
1848     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1849     return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,      return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
1850             package, symmetry, mesh->MPIInfo);                 package, symmetry, mesh->MPIInfo);
1851  }  }
1852    
1853  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
1854  {  {
1855     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1856     return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,      return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
1857             package, symmetry, mesh->MPIInfo);                  package, symmetry, mesh->MPIInfo);
1858  }  }
1859    
1860  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1861  {  {
1862     return continuousFunction(*this).getX();      return continuousFunction(*this).getX();
1863  }  }
1864    
1865  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1866  {  {
1867     return functionOnBoundary(*this).getNormal();      return functionOnBoundary(*this).getNormal();
1868  }  }
1869    
1870  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1871  {  {
1872     return escript::function(*this).getSize();      return escript::function(*this).getSize();
1873  }  }
1874    
1875  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1876  {  {
1877     int *out = NULL;      int *out = NULL;
1878     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1879     switch (functionSpaceType) {      switch (functionSpaceType) {
1880     case(Nodes):          case Nodes:
1881     out=mesh->Nodes->Id;              out=mesh->Nodes->Id;
1882     break;              break;
1883     case(ReducedNodes):          case ReducedNodes:
1884     out=mesh->Nodes->reducedNodesId;              out=mesh->Nodes->reducedNodesId;
1885     break;              break;
1886     case(Elements):          case Elements:
1887     out=mesh->Elements->Id;          case ReducedElements:
1888     break;              out=mesh->Elements->Id;
1889     case(ReducedElements):              break;
1890     out=mesh->Elements->Id;          case FaceElements:
1891     break;          case ReducedFaceElements:
1892     case(FaceElements):              out=mesh->FaceElements->Id;
1893     out=mesh->FaceElements->Id;              break;
1894     break;          case Points:
1895     case(ReducedFaceElements):              out=mesh->Points->Id;
1896     out=mesh->FaceElements->Id;              break;
1897     break;          case ContactElementsZero:
1898     case(Points):          case ReducedContactElementsZero:
1899     out=mesh->Points->Id;          case ContactElementsOne:
1900     break;          case ReducedContactElementsOne:
1901     case(ContactElementsZero):              out=mesh->ContactElements->Id;
1902     out=mesh->ContactElements->Id;              break;
1903     break;          case DegreesOfFreedom:
1904     case(ReducedContactElementsZero):              out=mesh->Nodes->degreesOfFreedomId;
1905     out=mesh->ContactElements->Id;              break;
1906     break;          case ReducedDegreesOfFreedom:
1907     case(ContactElementsOne):              out=mesh->Nodes->reducedDegreesOfFreedomId;
1908     out=mesh->ContactElements->Id;              break;
1909     break;          default:
1910     case(ReducedContactElementsOne):              stringstream temp;
1911     out=mesh->ContactElements->Id;              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1912     break;              throw FinleyAdapterException(temp.str());
1913     case(DegreesOfFreedom):              break;
1914     out=mesh->Nodes->degreesOfFreedomId;      }
1915     break;      return out;
    case(ReducedDegreesOfFreedom):  
    out=mesh->Nodes->reducedDegreesOfFreedomId;  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    return out;  
1916  }  }
1917  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1918  {  {
1919     int out=0;      int out=0;
1920     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1921     switch (functionSpaceType) {      switch (functionSpaceType) {
1922     case(Nodes):          case Nodes:
1923     out=mesh->Nodes->Tag[sampleNo];              out=mesh->Nodes->Tag[sampleNo];
1924     break;              break;
1925     case(ReducedNodes):          case ReducedNodes:
1926     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");              throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1927     break;              break;
1928     case(Elements):          case Elements:
1929     out=mesh->Elements->Tag[sampleNo];          case ReducedElements:
1930     break;              out=mesh->Elements->Tag[sampleNo];
1931     case(ReducedElements):              break;
1932     out=mesh->Elements->Tag[sampleNo];          case FaceElements:
1933     break;          case ReducedFaceElements:
1934     case(FaceElements):              out=mesh->FaceElements->Tag[sampleNo];
1935     out=mesh->FaceElements->Tag[sampleNo];              break;
1936     break;          case Points:
1937     case(ReducedFaceElements):              out=mesh->Points->Tag[sampleNo];
1938     out=mesh->FaceElements->Tag[sampleNo];              break;
1939     break;          case ContactElementsZero:
1940     case(Points):          case ReducedContactElementsZero:
1941     out=mesh->Points->Tag[sampleNo];          case ContactElementsOne:
1942     break;          case ReducedContactElementsOne:
1943     case(ContactElementsZero):              out=mesh->ContactElements->Tag[sampleNo];
1944     out=mesh->ContactElements->Tag[sampleNo];              break;
1945     break;          case DegreesOfFreedom:
1946     case(ReducedContactElementsZero):              throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1947     out=mesh->ContactElements->Tag[sampleNo];              break;
1948     break;          case ReducedDegreesOfFreedom:
1949     case(ContactElementsOne):              throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1950     out=mesh->ContactElements->Tag[sampleNo];              break;
1951     break;          default:
1952     case(ReducedContactElementsOne):              stringstream temp;
1953     out=mesh->ContactElements->Tag[sampleNo];              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1954     break;              throw FinleyAdapterException(temp.str());
1955     case(DegreesOfFreedom):              break;
1956     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");      }
1957     break;      return out;
    case(ReducedDegreesOfFreedom):  
    throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    return out;  
1958  }  }
1959    
1960    
1961  void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const  void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1962  {  {
1963     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1964     escriptDataC tmp=mask.getDataC();      switch(functionSpaceType) {
1965     switch(functionSpaceType) {          case Nodes:
1966     case(Nodes):              mesh->Nodes->setTags(newTag, mask);
1967     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);              break;
1968     break;          case ReducedNodes:
1969     case(ReducedNodes):              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1970     throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case DegreesOfFreedom:
1971     break;              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1972     case(DegreesOfFreedom):          case ReducedDegreesOfFreedom:
1973     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1974     break;          case Elements:
1975     case(ReducedDegreesOfFreedom):          case ReducedElements:
1976     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");              mesh->Elements->setTags(newTag, mask);
1977     break;              break;
1978     case(Elements):          case FaceElements:
1979     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case ReducedFaceElements:
1980     break;              mesh->FaceElements->setTags(newTag, mask);
1981     case(ReducedElements):              break;
1982     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case Points:
1983     break;              mesh->Points->setTags(newTag, mask);
1984     case(FaceElements):              break;
1985     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ContactElementsZero:
1986     break;          case ReducedContactElementsZero:
1987     case(ReducedFaceElements):          case ContactElementsOne:
1988     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ReducedContactElementsOne:
1989     break;              mesh->ContactElements->setTags(newTag, mask);
1990     case(Points):              break;
1991     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);          default:
1992     break;              stringstream temp;
1993     case(ContactElementsZero):              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
1994     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              throw FinleyAdapterException(temp.str());
1995     break;      }
1996     case(ReducedContactElementsZero):      checkFinleyError();
1997     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  }
1998     break;  
1999     case(ContactElementsOne):  void MeshAdapter::setTagMap(const string& name, int tag)
2000     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  {
2001     break;      Finley_Mesh* mesh=m_finleyMesh.get();
2002     case(ReducedContactElementsOne):      Finley_Mesh_addTagMap(mesh, name.c_str(), tag);
2003     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);      checkFinleyError();
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Finley does not know anything about function space type " << functionSpaceType;  
       throw FinleyAdapterException(temp.str());  
    }  
    checkFinleyError();  
    return;  
 }  
   
 void MeshAdapter::setTagMap(const string& name,  int tag)  
 {  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    Finley_Mesh_addTagMap(mesh, name.c_str(),tag);  
    checkFinleyError();  
    // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
2004  }  }
2005    
2006  int MeshAdapter::getTag(const string& name) const  int MeshAdapter::getTag(const string& name) const
2007  {  {
2008     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2009     int tag=0;      int tag = Finley_Mesh_getTag(mesh, name.c_str());
2010     tag=Finley_Mesh_getTag(mesh, name.c_str());      checkFinleyError();
2011     checkFinleyError();      return tag;
    // throwStandardException("MeshAdapter::getTag is not implemented.");  
    return tag;  
2012  }  }
2013    
2014  bool MeshAdapter::isValidTagName(const string& name) const  bool MeshAdapter::isValidTagName(const string& name) const
2015  {  {
2016     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2017     return Finley_Mesh_isValidTagName(mesh,name.c_str());      return Finley_Mesh_isValidTagName(mesh, name.c_str());
2018  }  }
2019    
2020  string MeshAdapter::showTagNames() const  string MeshAdapter::showTagNames() const
2021  {  {
2022     stringstream temp;      stringstream temp;
2023     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2024     Finley_TagMap* tag_map=mesh->TagMap;      TagMap::const_iterator it = mesh->tagMap.begin();
2025     while (tag_map) {      while (it != mesh->tagMap.end()) {
2026        temp << tag_map->name;          temp << it->first;
2027        tag_map=tag_map->next;          ++it;
2028        if (tag_map) temp << ", ";          if (it != mesh->tagMap.end())
2029     }              temp << ", ";
2030     return temp.str();      }
2031        return temp.str();
2032  }  }
2033    
2034  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2035  {  {
2036    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2037    dim_t numTags=0;      switch(functionSpaceCode) {
2038    switch(functionSpaceCode) {          case Nodes:
2039     case(Nodes):              return mesh->Nodes->tagsInUse.size();
2040            numTags=mesh->Nodes->numTagsInUse;          case ReducedNodes:
2041            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2042     case(ReducedNodes):          case DegreesOfFreedom:
2043            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2044            break;          case ReducedDegreesOfFreedom:
2045     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2046            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2047            break;          case ReducedElements:
2048     case(ReducedDegreesOfFreedom):              return mesh->Elements->tagsInUse.size();
2049            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2050            break;          case ReducedFaceElements:
2051     case(Elements):              return mesh->FaceElements->tagsInUse.size();
2052     case(ReducedElements):          case Points:
2053            numTags=mesh->Elements->numTagsInUse;              return mesh->Points->tagsInUse.size();
2054            break;          case ContactElementsZero:
2055     case(FaceElements):          case ReducedContactElementsZero:
2056     case(ReducedFaceElements):          case ContactElementsOne:
2057            numTags=mesh->FaceElements->numTagsInUse;          case ReducedContactElementsOne:
2058            break;              return mesh->ContactElements->tagsInUse.size();
2059     case(Points):          default:
2060            numTags=mesh->Points->numTagsInUse;              stringstream ss;
2061            break;              ss << "Finley does not know anything about function space type "
2062     case(ContactElementsZero):                   << functionSpaceCode;
2063     case(ReducedContactElementsZero):              throw FinleyAdapterException(ss.str());
2064     case(ContactElementsOne):      }
2065     case(ReducedContactElementsOne):      return 0;
           numTags=mesh->ContactElements->numTagsInUse;  
           break;  
    default:  
       stringstream temp;  
       temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;  
       throw FinleyAdapterException(temp.str());  
   }  
   return numTags;  
2066  }  }
2067    
2068  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2069  {  {
2070    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2071    index_t* tags=NULL;      switch(functionSpaceCode) {
2072    switch(functionSpaceCode) {          case Nodes:
2073     case(Nodes):              return &mesh->Nodes->tagsInUse[0];
2074            tags=mesh->Nodes->tagsInUse;          case ReducedNodes:
2075            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2076     case(ReducedNodes):          case DegreesOfFreedom:
2077            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2078            break;          case ReducedDegreesOfFreedom:
2079     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2080            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2081            break;          case ReducedElements:
2082     case(ReducedDegreesOfFreedom):              return &mesh->Elements->tagsInUse[0];
2083            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2084            break;          case ReducedFaceElements:
2085     case(Elements):              return &mesh->FaceElements->tagsInUse[0];
2086     case(ReducedElements):          case Points:
2087            tags=mesh->Elements->tagsInUse;              return &mesh->Points->tagsInUse[0];
2088            break;          case ContactElementsZero:
2089     case(FaceElements):          case ReducedContactElementsZero:
2090     case(ReducedFaceElements):          case ContactElementsOne:
2091            tags=mesh->FaceElements->tagsInUse;          case ReducedContactElementsOne:
2092            break;              return &mesh->ContactElements->tagsInUse[0];
2093     case(Points):          default:
2094            tags=mesh->Points->tagsInUse;              stringstream temp;
2095            break;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2096     case(ContactElementsZero):              throw FinleyAdapterException(temp.str());
2097     case(ReducedContactElementsZero):      }
2098     case(ContactElementsOne):      return NULL;
    case(ReducedContactElementsOne):  
           tags=mesh->ContactElements->tagsInUse;  
           break;  
    default:  
       stringstream temp;  
       temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;  
       throw FinleyAdapterException(temp.str());  
   }  
   return tags;  
2099  }  }
2100    
2101    
2102  bool MeshAdapter::canTag(int functionSpaceCode) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2103  {  {
2104    switch(functionSpaceCode) {      switch(functionSpaceCode) {
2105     case(Nodes):          case Nodes:
2106     case(Elements):          case Elements:
2107     case(ReducedElements):          case ReducedElements:
2108     case(FaceElements):          case FaceElements:
2109     case(ReducedFaceElements):          case ReducedFaceElements:
2110     case(Points):          case Points:
2111     case(ContactElementsZero):          case ContactElementsZero:
2112     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
2113     case(ContactElementsOne):          case ContactElementsOne:
2114     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
2115            return true;              return true;
2116     case(ReducedNodes):          default:
2117     case(DegreesOfFreedom):              return false;
2118     case(ReducedDegreesOfFreedom):      }
       return false;  
    default:  
     return false;  
   }  
2119  }  }
2120    
2121  AbstractDomain::StatusType MeshAdapter::getStatus() const  escript::AbstractDomain::StatusType MeshAdapter::getStatus() const
2122  {  {
2123    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2124    return Finley_Mesh_getStatus(mesh);      return Finley_Mesh_getStatus(mesh);
2125  }  }
2126    
2127  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2128  {  {
2129          Finley_Mesh* mesh=m_finleyMesh.get();
2130    Finley_Mesh* mesh=m_finleyMesh.get();      int order =-1;
2131    int order =-1;      switch(functionSpaceCode) {
2132    switch(functionSpaceCode) {          case Nodes:
2133     case(Nodes):          case DegreesOfFreedom:
2134     case(DegreesOfFreedom):              order=mesh->approximationOrder;
2135            order=mesh->approximationOrder;              break;
2136            break;          case ReducedNodes:
2137     case(ReducedNodes):          case ReducedDegreesOfFreedom:
2138     case(ReducedDegreesOfFreedom):              order=mesh->reducedApproximationOrder;
2139            order=mesh->reducedApproximationOrder;              break;
2140            break;          case Elements:
2141     case(Elements):          case FaceElements:
2142     case(FaceElements):          case Points:
2143     case(Points):          case ContactElementsZero:
2144     case(ContactElementsZero):          case ContactElementsOne:
2145     case(ContactElementsOne):              order=mesh->integrationOrder;
2146            order=mesh->integrationOrder;              break;
2147            break;          case ReducedElements:
2148     case(ReducedElements):          case ReducedFaceElements:
2149     case(ReducedFaceElements):          case ReducedContactElementsZero:
2150     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
2151     case(ReducedContactElementsOne):              order=mesh->reducedIntegrationOrder;
2152            order=mesh->reducedIntegrationOrder;              break;
2153            break;          default:
2154     default:              stringstream temp;
2155        stringstream temp;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2156        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;              throw FinleyAdapterException(temp.str());
2157        throw FinleyAdapterException(temp.str());      }
2158    }      return order;
   return order;  
2159  }  }
2160    
2161  bool MeshAdapter::supportsContactElements() const  bool MeshAdapter::supportsContactElements() const
2162  {  {
2163    return true;      return true;
2164  }  }
2165    
2166  ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)  ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id,
2167            index_t order, index_t reducedOrder)
2168  {  {
2169    m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);      m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2170  }  }
2171    
2172  ReferenceElementSetWrapper::~ReferenceElementSetWrapper()  ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2173  {  {
2174    Finley_ReferenceElementSet_dealloc(m_refSet);      Finley_ReferenceElementSet_dealloc(m_refSet);
2175  }  }
2176    
2177  // points will be flattened  void MeshAdapter::addDiracPoints(const vector<double>& points,
2178  void MeshAdapter:: addDiracPoints(const std::vector<double>& points, const std::vector<int>& tags) const                                   const vector<int>& tags) const
2179  {  {
2180        const int dim = getDim();      // points will be flattened
2181        int numPoints=points.size()/dim;      const int dim = getDim();
2182        int numTags=tags.size();      int numPoints=points.size()/dim;
2183        Finley_Mesh* mesh=m_finleyMesh.get();      int numTags=tags.size();
2184              Finley_Mesh* mesh=m_finleyMesh.get();
       if ( points.size() % dim != 0 )  
       {  
     throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");  
       }  
         
       if  ( (numTags > 0) && ( numPoints !=  numTags ) )  
      throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");  
         
       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);  
       int*    tags_ptr= TMPMEMALLOC(numPoints, int);  
         
       for (int i=0;i<numPoints;++i) {  
        points_ptr[ i * dim     ] = points[i * dim ];  
        if ( dim > 1 ) points_ptr[ i * dim + 1 ] = points[i * dim + 1];  
        if ( dim > 2 ) points_ptr[ i * dim + 2 ] = points[i * dim + 2];      
            tags_ptr[i]=tags[i];  
       }  
         
       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);  
       checkFinleyError();  
         
       TMPMEMFREE(points_ptr);  
       TMPMEMFREE(tags_ptr);  
 }  
2185    
2186        if ( points.size() % dim != 0 ) {
2187            throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2188        }
2189    
2190  // void MeshAdapter:: addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const      if ((numTags > 0) && (numPoints != numTags))
2191            throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2192    
2193        Finley_Mesh_addPoints(mesh, numPoints, &points[0], &tags[0]);
2194        checkFinleyError();
2195    }
2196    
2197    // void MeshAdapter::addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2198  // {  // {
2199  //       const int dim = getDim();  //       const int dim = getDim();
2200  //       int numPoints=boost::python::extract<int>(points.attr("__len__")());  //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2201  //       int numTags=boost::python::extract<int>(tags.attr("__len__")());  //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2202  //       Finley_Mesh* mesh=m_finleyMesh.get();  //       Finley_Mesh* mesh=m_finleyMesh.get();
2203  //        //
2204  //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )  //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2205  //   throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");  //       throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2206  //        //
2207  //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);  //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2208  //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);  //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2209  //        //
2210  //       for (int i=0;i<numPoints;++i) {  //       for (int i=0;i<numPoints;++i) {
2211  //     int tag_id=-1;  //         int tag_id=-1;
2212  //     int numComps=boost::python::extract<int>(points[i].attr("__len__")());  //         int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2213  //     if  ( numComps !=   dim ) {  //         if  ( numComps !=   dim ) {
2214  //                stringstream temp;              //                stringstream temp;
2215  //                temp << "Error - illegal number of components " << numComps << " for point " << i;                //                temp << "Error - illegal number of components " << numComps << " for point " << i;
2216  //                throw FinleyAdapterException(temp.str());  //                throw FinleyAdapterException(temp.str());
2217  //     }  //         }
2218  //     points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);  //         points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2219  //     if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);  //         if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2220  //     if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);  //         if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2221  //      //
2222  //     if ( numTags > 0) {  //         if ( numTags > 0) {
2223  //            boost::python::extract<string> ex_str(tags[i]);  //                boost::python::extract<string> ex_str(tags[i]);
2224  //        if  ( ex_str.check() ) {  //                if  ( ex_str.check() ) {
2225  //            tag_id=getTag( ex_str());  //                    tag_id=getTag( ex_str());
2226  //        } else {  //                } else {
2227  //             boost::python::extract<int> ex_int(tags[i]);  //                     boost::python::extract<int> ex_int(tags[i]);
2228  //             if ( ex_int.check() ) {  //                     if ( ex_int.check() ) {
2229  //                 tag_id=ex_int();  //                         tag_id=ex_int();
2230  //             } else {  //                     } else {
2231  //              stringstream temp;            //                          stringstream temp;
2232  //                  temp << "Error - unable to extract tag for point " << i;  //                          temp << "Error - unable to extract tag for point " << i;
2233  //              throw FinleyAdapterException(temp.str());  //                          throw FinleyAdapterException(temp.str());
2234  //            }  //                    }
2235  //        }  //                }
2236  //     }        //         }
2237  //            tags_ptr[i]=tag_id;  //            tags_ptr[i]=tag_id;
2238  //       }  //       }
2239  //        //
2240  //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);  //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2241  //       checkPasoError();  //       checkPasoError();
2242  //        //
2243  //       TMPMEMFREE(points_ptr);  //       TMPMEMFREE(points_ptr);
2244  //       TMPMEMFREE(tags_ptr);  //       TMPMEMFREE(tags_ptr);
2245  // }  // }
2246    
2247  /*  /*
2248  void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const  void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2249  {    {
2250      boost::python::list points =  boost::python::list();      boost::python::list points =  boost::python::list();
2251      boost::python::list tags =  boost::python::list();      boost::python::list tags =  boost::python::list();
2252      points.append(point);      points.append(point);
# Line 2534  void MeshAdapter:: addDiracPoint( const Line 2256  void MeshAdapter:: addDiracPoint( const
2256  */  */
2257    
2258  /*  /*
2259  void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const std::string& tag) const  void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const string& tag) const
2260  {  {
2261          boost::python::list points =   boost::python::list();      boost::python::list points =   boost::python::list();
2262          boost::python::list tags =   boost::python::list();      boost::python::list tags =   boost::python::list();
2263          points.append(point);      points.append(point);
2264          tags.append(tag);      tags.append(tag);
2265          addDiracPoints(points, tags);      addDiracPoints(points, tags);
2266  }  }
2267  */  */
2268  }  // end of namespace  }  // end of namespace
2269    

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