/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 2748 by gross, Tue Nov 17 07:32:59 2009 UTC revision 4437 by caltinay, Tue Jun 4 05:37:18 2013 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*****************************************************************************
3  *  *
4  * Copyright (c) 2003-2009 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>
17    #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"
21    #include "esysUtils/blocktimer.h"
22    
23    #include <boost/python/import.hpp>
24  #ifdef USE_NETCDF  #ifdef USE_NETCDF
25  #include <netcdfcpp.h>  #include <netcdfcpp.h>
26  #endif  #endif
 #ifdef PASO_MPI  
 #include <mpi.h>  
 #include "paso/Paso_MPI.h"  
 #endif  
 extern "C" {  
 #include "esysUtils/blocktimer.h"  
 }  
27    
28  using namespace std;  using namespace std;
29  using namespace escript;  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 PASO_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
96  #ifdef PASO_MPI  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 PASO_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 std::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 std::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;
144     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;  #ifdef ESYS_MPI
145  #ifdef PASO_MPI      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 PASO_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 = Paso_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();
160     num_Tags = 0;  
161     if (tag_map) {      // NetCDF error handler
162        while (tag_map) {      NcError err(NcError::verbose_nonfatal);
163           num_Tags++;      // Create the file.
164           tag_map=tag_map->next;      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     // NetCDF error handler          throw FinleyAdapterException(msgPrefix+"Open file for output");
169     NcError err(NcError::verbose_nonfatal);  
170     // Create the file.      // Define dimensions (num_Elements and dim_Elements are identical,
171     NcFile dataFile(newFileName, NcFile::Replace);      // dim_Elements only appears if > 0)
172     // check if writing was successful      if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
173     if (!dataFile.is_valid())          throw FinleyAdapterException(msgPrefix+"add_dim(numNodes)");
174        throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);      if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
175            throw FinleyAdapterException(msgPrefix+"add_dim(numDim)");
176     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)      if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
177     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )          throw FinleyAdapterException(msgPrefix+"add_dim(mpi_size)");
178        throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);      if (num_Elements>0)
179     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
180        throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements)");
181     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )      if (num_FaceElements>0)
182        throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
183     if (num_Elements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements)");
184        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )      if (num_ContactElements>0)
185           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
186     if (num_FaceElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements)");
187        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )      if (num_Points>0)
188           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
189     if (num_ContactElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Points)");
190        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )      if (num_Elements>0)
191           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
192     if (num_Points>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements_Nodes)");
193        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )      if (num_FaceElements>0)
194           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
195     if (num_Elements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
196        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )      if (num_ContactElements>0)
197           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
198     if (num_FaceElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
199        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )      if (num_Tags>0)
200           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
201     if (num_ContactElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Tags)");
202        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )  
203           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);      // Attributes: MPI size, MPI rank, Name, order, reduced_order
204     if (num_Tags>0)      if (!dataFile.add_att("mpi_size", mpi_size) )
205        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )          throw FinleyAdapterException(msgPrefix+"add_att(mpi_size)");
206           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);      if (!dataFile.add_att("mpi_rank", mpi_rank) )
207            throw FinleyAdapterException(msgPrefix+"add_att(mpi_rank)");
208     // Attributes: MPI size, MPI rank, Name, order, reduced_order      if (!dataFile.add_att("Name",mesh->Name) )
209     if (!dataFile.add_att("mpi_size", mpi_size) )          throw FinleyAdapterException(msgPrefix+"add_att(Name)");
210        throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("numDim",numDim) )
211     if (!dataFile.add_att("mpi_rank", mpi_rank) )          throw FinleyAdapterException(msgPrefix+"add_att(order)");
212        throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("order",mesh->integrationOrder) )
213     if (!dataFile.add_att("Name",mesh->Name) )          throw FinleyAdapterException(msgPrefix+"add_att(order)");
214        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
215     if (!dataFile.add_att("numDim",numDim) )          throw FinleyAdapterException(msgPrefix+"add_att(reduced_order)");
216        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("numNodes",numNodes) )
217     if (!dataFile.add_att("order",mesh->order) )          throw FinleyAdapterException(msgPrefix+"add_att(numNodes)");
218        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Elements",num_Elements) )
219     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements)");
220        throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
221     if (!dataFile.add_att("numNodes",numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements)");
222        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
223     if (!dataFile.add_att("num_Elements",num_Elements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements)");
224        throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Points",num_Points) )
225     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Points)");
226        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
227     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements_numNodes)");
228        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
229     if (!dataFile.add_att("num_Points",num_Points) )          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements_numNodes)");
230        throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
231     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements_numNodes)");
232        throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
233     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(Elements_TypeId)");
234        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
235     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(FaceElements_TypeId)");
236        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
237     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(ContactElements_TypeId)");
238        throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
239     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(Points_TypeId)");
240        throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Tags", num_Tags) )
241     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Tags)");
242        throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);  
243     if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )      // // // // // Nodes // // // // //
244        throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);  
245     if (!dataFile.add_att("num_Tags", num_Tags) )      // Nodes nodeDistribution
246        throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);      if (! (ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
247            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_NodeDistribution)");
248     // // // // // Nodes // // // // //      int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
249        if (! (ids->put(int_ptr, mpi_size+1)) )
250     // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)          throw FinleyAdapterException(msgPrefix+"put(Nodes_NodeDistribution)");
251     if (numNodes>0) {  
252        // Nodes degreesOfFreedomDistribution
253        // Nodes Id      if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
254        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )          throw FinleyAdapterException(msgPrefix+"add_var(Nodes_DofDistribution)");
255           throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);      int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
256        int_ptr = &mesh->Nodes->Id[0];      if (! (ids->put(int_ptr, mpi_size+1)) )
257        if (! (ids->put(int_ptr, numNodes)) )          throw FinleyAdapterException(msgPrefix+"put(Nodes_DofDistribution)");
258           throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);  
259        // Only write nodes if non-empty because NetCDF doesn't like empty arrays
260        // Nodes Tag      // (it treats them as NC_UNLIMITED)
261        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )      if (numNodes>0) {
262           throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);          // Nodes Id
263        int_ptr = &mesh->Nodes->Tag[0];          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
264        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Id)");
265           throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->Id[0];
266            if (! (ids->put(int_ptr, numNodes)) )
267        // Nodes gDOF              throw FinleyAdapterException(msgPrefix+"put(Nodes_Id)");
268        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )  
269           throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);          // Nodes Tag
270        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
271        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Tag)");
272           throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->Tag[0];
273            if (! (ids->put(int_ptr, numNodes)) )
274        // Nodes global node index              throw FinleyAdapterException(msgPrefix+"put(Nodes_Tag)");
275        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )  
276           throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);          // Nodes gDOF
277        int_ptr = &mesh->Nodes->globalNodesIndex[0];          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
278        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gDOF)");
279           throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
280            if (! (ids->put(int_ptr, numNodes)) )
281        // Nodes grDof              throw FinleyAdapterException(msgPrefix+"put(Nodes_gDOF)");
282        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )  
283           throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);          // Nodes global node index
284        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
285        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gNI)");
286           throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalNodesIndex[0];
287            if (! (ids->put(int_ptr, numNodes)) )
288        // Nodes grNI              throw FinleyAdapterException(msgPrefix+"put(Nodes_gNI)");
289        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )  
290           throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);          // Nodes grDof
291        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
292        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grDfI)");
293           throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
294            if (! (ids->put(int_ptr, numNodes)) )
295        // Nodes Coordinates              throw FinleyAdapterException(msgPrefix+"put(Nodes_grDfI)");
296        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )  
297           throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);          // Nodes grNI
298        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
299           throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grNI)");
300            int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
301        // Nodes degreesOfFreedomDistribution          if (! (ids->put(int_ptr, numNodes)) )
302        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_grNI)");
303           throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);  
304        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];          // Nodes Coordinates
305        if (! (ids->put(int_ptr, mpi_size+1)) )          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
306           throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Coordinates)");
307            if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
308        // Nodes nodeDistribution              throw FinleyAdapterException(msgPrefix+"put(Nodes_Coordinates)");
309        if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )      }
310           throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);  
311        int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];      // // // // // Elements // // // // //
312        if (! (ids->put(int_ptr, mpi_size+1)) )      if (num_Elements>0) {
313           throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);          // 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     // // // // // Elements // // // // //          if (! (ids->put(int_ptr, num_Elements)) )
318                throw FinleyAdapterException(msgPrefix+"put(Elements_Id)");
319     if (num_Elements>0) {  
320            // Elements_Tag
321        // Elements_Id          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
322        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Tag)");
323           throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Tag[0];
324        int_ptr = &mesh->Elements->Id[0];          if (! (ids->put(int_ptr, num_Elements)) )
325        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Tag)");
326           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);  
327            // Elements_Owner
328        // Elements_Tag          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
329        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Owner)");
330           throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Owner[0];
331        int_ptr = &mesh->Elements->Tag[0];          if (! (ids->put(int_ptr, num_Elements)) )
332        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Owner)");
333           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);  
334            // Elements_Color
335        // Elements_Owner          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
336        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Color)");
337           throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Color[0];
338        int_ptr = &mesh->Elements->Owner[0];          if (! (ids->put(int_ptr, num_Elements)) )
339        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Color)");
340           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);  
341            // Elements_Nodes
342        // Elements_Color          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
343        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Nodes)");
344           throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
345        int_ptr = &mesh->Elements->Color[0];              throw FinleyAdapterException(msgPrefix+"put(Elements_Nodes)");
346        if (! (ids->put(int_ptr, num_Elements)) )      }
347           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);  
348        // // // // // Face_Elements // // // // //
349        // Elements_Nodes      if (num_FaceElements>0) {
350        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )          // FaceElements_Id
351           throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
352        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Id)");
353           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->FaceElements->Id[0];
354            if (! (ids->put(int_ptr, num_FaceElements)) )
355     }              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Id)");
356    
357     // // // // // Face_Elements // // // // //          // FaceElements_Tag
358            if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
359     if (num_FaceElements>0) {              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Tag)");
360            int_ptr = &mesh->FaceElements->Tag[0];
361        // FaceElements_Id          if (! (ids->put(int_ptr, num_FaceElements)) )
362        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Tag)");
363           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);  
364        int_ptr = &mesh->FaceElements->Id[0];          // FaceElements_Owner
365        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
366           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Owner)");
367            int_ptr = &mesh->FaceElements->Owner[0];
368        // FaceElements_Tag          if (! (ids->put(int_ptr, num_FaceElements)) )
369        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Owner)");
370           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);  
371        int_ptr = &mesh->FaceElements->Tag[0];          // FaceElements_Color
372        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
373           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Color)");
374            int_ptr = &mesh->FaceElements->Color[0];
375        // FaceElements_Owner          if (! (ids->put(int_ptr, num_FaceElements)) )
376        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Color)");
377           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);  
378        int_ptr = &mesh->FaceElements->Owner[0];          // FaceElements_Nodes
379        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
380           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Nodes)");
381            if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
382        // FaceElements_Color              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Nodes)");
383        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )      }
384           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);  
385        int_ptr = &mesh->FaceElements->Color[0];      // // // // // Contact_Elements // // // // //
386        if (! (ids->put(int_ptr, num_FaceElements)) )      if (num_ContactElements>0) {
387           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);  
388            // ContactElements_Id
389        // FaceElements_Nodes          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
390        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Id)");
391           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);          int_ptr = &mesh->ContactElements->Id[0];
392        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )          if (! (ids->put(int_ptr, num_ContactElements)) )
393           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Id)");
394    
395     }          // ContactElements_Tag
396            if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
397     // // // // // Contact_Elements // // // // //              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Tag)");
398            int_ptr = &mesh->ContactElements->Tag[0];
399     if (num_ContactElements>0) {          if (! (ids->put(int_ptr, num_ContactElements)) )
400                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Tag)");
401        // ContactElements_Id  
402        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )          // ContactElements_Owner
403           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
404        int_ptr = &mesh->ContactElements->Id[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Owner)");
405        if (! (ids->put(int_ptr, num_ContactElements)) )          int_ptr = &mesh->ContactElements->Owner[0];
406           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_ContactElements)) )
407                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Owner)");
408        // ContactElements_Tag  
409        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )          // ContactElements_Color
410           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
411        int_ptr = &mesh->ContactElements->Tag[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Color)");
412        if (! (ids->put(int_ptr, num_ContactElements)) )          int_ptr = &mesh->ContactElements->Color[0];
413           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_ContactElements)) )
414                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Color)");
415        // ContactElements_Owner  
416        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )          // ContactElements_Nodes
417           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
418        int_ptr = &mesh->ContactElements->Owner[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Nodes)");
419        if (! (ids->put(int_ptr, num_ContactElements)) )          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
420           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Nodes)");
421        }
422        // ContactElements_Color  
423        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )      // // // // // Points // // // // //
424           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);      if (num_Points>0) {
425        int_ptr = &mesh->ContactElements->Color[0];          // Points_Id
426        if (! (ids->put(int_ptr, num_ContactElements)) )          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
427           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Id)");
428            int_ptr = &mesh->Points->Id[0];
429        // ContactElements_Nodes          if (! (ids->put(int_ptr, num_Points)) )
430        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )              throw FinleyAdapterException(msgPrefix+"put(Points_Id)");
431           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);  
432        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )          // Points_Tag
433           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);          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     // // // // // Points // // // // //              throw FinleyAdapterException(msgPrefix+"put(Points_Tag)");
438    
439     if (num_Points>0) {          // Points_Owner
440            if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
441        fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");              throw FinleyAdapterException(msgPrefix+"add_var(Points_Owner)");
442            int_ptr = &mesh->Points->Owner[0];
443        // Points_Id          if (! (ids->put(int_ptr, num_Points)) )
444        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Owner)");
445           throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);  
446        int_ptr = &mesh->Points->Id[0];          // Points_Color
447        if (! (ids->put(int_ptr, num_Points)) )          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
448           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Color)");
449            int_ptr = &mesh->Points->Color[0];
450        // Points_Tag          if (! (ids->put(int_ptr, num_Points)) )
451        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Color)");
452           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);  
453        int_ptr = &mesh->Points->Tag[0];          // Points_Nodes
454        if (! (ids->put(int_ptr, num_Points)) )          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
455           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
456                throw FinleyAdapterException(msgPrefix+"add_var(Points_Nodes)");
457        // Points_Owner          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
458        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Nodes)");
459           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);      }
460        int_ptr = &mesh->Points->Owner[0];  
461        if (! (ids->put(int_ptr, num_Points)) )      // // // // // TagMap // // // // //
462           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);      if (num_Tags>0) {
463            // Temp storage to gather node IDs
464        // Points_Color          vector<int> Tags_keys;
465        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )  
466           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);          // Copy tag data into temp arrays
467        int_ptr = &mesh->Points->Color[0];          TagMap::const_iterator it;
468        if (! (ids->put(int_ptr, num_Points)) )          for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++) {
469           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);              Tags_keys.push_back(it->second);
470            }
471        // Points_Nodes  
472        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]          // Tags_keys
473        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )          if (! (ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
474           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Tags_keys)");
475        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )          int_ptr = &Tags_keys[0];
476           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_Tags)) )
477                throw FinleyAdapterException(msgPrefix+"put(Tags_keys)");
478     }  
479            // Tags_names_*
480     // // // // // TagMap // // // // //          // 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     if (num_Tags>0) {          // manual doesn't tell how to do an array of strings
483            int i = 0;
484        // Temp storage to gather node IDs          for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++, i++) {
485        int *Tags_keys = TMPMEMALLOC(num_Tags, int);              stringstream tagnamestream;
486        char name_temp[4096];              tagnamestream << "Tags_name_" << i;
487                const string tagname = tagnamestream.str();
488        /* Copy tag data into temp arrays */              if (!dataFile.add_att(tagname.c_str(), it->first.c_str()))
489        tag_map = mesh->TagMap;                  throw FinleyAdapterException(msgPrefix+"add_att(Tags_names_X)");
490        if (tag_map) {          }
491           int i = 0;      }
492           while (tag_map) {  
493              Tags_keys[i++] = tag_map->tag_key;      // Send token to next MPI process so he can take his turn
494              tag_map=tag_map->next;  #ifdef ESYS_MPI
495           }      if (mpi_rank<mpi_size-1) {
496        }          MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
497        }
       // Tags_keys  
       if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )  
          throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);  
       int_ptr = &Tags_keys[0];  
       if (! (ids->put(int_ptr, num_Tags)) )  
          throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);  
   
       // 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("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);  
             tag_map=tag_map->next;  
             i++;  
          }  
       }  
   
       TMPMEMFREE(Tags_keys);  
   
    }  
   
 /* Send token to next MPI process so he can take his turn */  
 #ifdef PASO_MPI  
    if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);  
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::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
622  {  {
623     return Points;      return Points;
624  }  }
625    
626  //  //
# Line 658  int MeshAdapter::getDiracDeltaFunctionCo Line 628  int MeshAdapter::getDiracDeltaFunctionCo
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 669  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 678  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                                   SystemMatrixAdapter& 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          const escript::Data& d, const escript::Data& y,
747  {          const escript::Data& d_contact, const escript::Data& y_contact,
748     escriptDataC _rhs=rhs.getDataC();          const escript::Data& d_dirac, const escript::Data& y_dirac) const
749     escriptDataC _A  =A.getDataC();  {
750     escriptDataC _B=B.getDataC();      SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
751     escriptDataC _C=C.getDataC();      if (!smat)
752     escriptDataC _D=D.getDataC();          throw FinleyAdapterException("finley only supports Paso system matrices.");
753     escriptDataC _X=X.getDataC();  
754     escriptDataC _Y=Y.getDataC();      escriptDataC _rhs=rhs.getDataC();
755     escriptDataC _d=d.getDataC();      escriptDataC _A  =A.getDataC();
756     escriptDataC _y=y.getDataC();      escriptDataC _B=B.getDataC();
757     escriptDataC _d_contact=d_contact.getDataC();      escriptDataC _C=C.getDataC();
758     escriptDataC _y_contact=y_contact.getDataC();      escriptDataC _D=D.getDataC();
759        escriptDataC _X=X.getDataC();
760     Finley_Mesh* mesh=m_finleyMesh.get();      escriptDataC _Y=Y.getDataC();
761        escriptDataC _d=d.getDataC();
762     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );      escriptDataC _y=y.getDataC();
763     checkFinleyError();      escriptDataC _d_contact=d_contact.getDataC();
764        escriptDataC _y_contact=y_contact.getDataC();
765     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );      escriptDataC _d_dirac=d_dirac.getDataC();
766     checkFinleyError();      escriptDataC _y_dirac=y_dirac.getDataC();
767    
768     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );      Finley_Mesh* mesh=m_finleyMesh.get();
769     checkFinleyError();      Paso_SystemMatrix* S = smat->getPaso_SystemMatrix();
770  }  
771        Finley_Assemble_PDE(mesh->Nodes, mesh->Elements, S, &_rhs, &_A, &_B, &_C,
772  void  MeshAdapter::addPDEToLumpedSystem(                          &_D, &_X, &_Y);
773                                          escript::Data& mat,      checkFinleyError();
774                                          const escript::Data& D,  
775                                          const escript::Data& d) const      Finley_Assemble_PDE(mesh->Nodes, mesh->FaceElements, S, &_rhs, 0, 0, 0,
776  {                          &_d, 0, &_y);
777     escriptDataC _mat=mat.getDataC();      checkFinleyError();
778     escriptDataC _D=D.getDataC();  
779     escriptDataC _d=d.getDataC();      Finley_Assemble_PDE(mesh->Nodes, mesh->ContactElements, S, &_rhs, 0, 0, 0,
780                &_d_contact, 0, &_y_contact);
781        checkFinleyError();
782    
783        Finley_Assemble_PDE(mesh->Nodes, mesh->Points, S, &_rhs, 0, 0, 0,
784                            &_d_dirac, 0, &_y_dirac );
785        checkFinleyError();
786    }
787    
788    void MeshAdapter::addPDEToLumpedSystem(escript::Data& mat,
789            const escript::Data& D, const escript::Data& d,
790            const escript::Data& d_dirac, const bool useHRZ) const
791    {
792        escriptDataC _mat=mat.getDataC();
793        escriptDataC _D=D.getDataC();
794        escriptDataC _d=d.getDataC();
795        escriptDataC _d_dirac=d_dirac.getDataC();
796    
797        Finley_Mesh* mesh=m_finleyMesh.get();
798    
799     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Assemble_LumpedSystem(mesh->Nodes, mesh->Elements, &_mat, &_D, useHRZ);
800        checkFinleyError();
801    
802     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);      Finley_Assemble_LumpedSystem(mesh->Nodes, mesh->FaceElements, &_mat, &_d, useHRZ);
803     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);      checkFinleyError();
804    
805     checkFinleyError();      Finley_Assemble_LumpedSystem(mesh->Nodes, mesh->Points, &_mat, &_d_dirac, useHRZ);
806        checkFinleyError();
807  }  }
808    
   
809  //  //
810  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
811  //  //
812  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const  void MeshAdapter::addPDEToRHS(escript::Data& rhs, const escript::Data& X,
813  {          const escript::Data& Y, const escript::Data& y,
814     Finley_Mesh* mesh=m_finleyMesh.get();          const escript::Data& y_contact, const escript::Data& y_dirac) const
815    {
816     escriptDataC _rhs=rhs.getDataC();      Finley_Mesh* mesh=m_finleyMesh.get();
817     escriptDataC _X=X.getDataC();  
818     escriptDataC _Y=Y.getDataC();      escriptDataC _rhs=rhs.getDataC();
819     escriptDataC _y=y.getDataC();      escriptDataC _X=X.getDataC();
820     escriptDataC _y_contact=y_contact.getDataC();      escriptDataC _Y=Y.getDataC();
821        escriptDataC _y=y.getDataC();
822        escriptDataC _y_contact=y_contact.getDataC();
823        escriptDataC _y_dirac=y_dirac.getDataC();
824    
825        Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y);
826        checkFinleyError();
827    
828     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );      Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y);
829     checkFinleyError();      checkFinleyError();
830    
831     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );      Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y_contact);
832     checkFinleyError();      checkFinleyError();
833    
834     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );      Finley_Assemble_PDE(mesh->Nodes,mesh->Points, 0, &_rhs, 0, 0, 0, 0, 0, &_y_dirac);
835     checkFinleyError();      checkFinleyError();
836  }  }
837    
838  //  //
839  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
840  //  //
841  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
842                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,          escript::AbstractTransportProblem& tp, escript::Data& source,
843                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,          const escript::Data& M, const escript::Data& A, const escript::Data& B,
844                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& C, const escript::Data& D, const escript::Data& X,
845                                             const escript::Data& d, const escript::Data& y,          const escript::Data& Y, const escript::Data& d, const escript::Data& y,
846                                             const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d_contact, const escript::Data& y_contact,
847  {          const escript::Data& d_dirac, const escript::Data& y_dirac) const
848     DataTypes::ShapeType shape;  {
849     source.expand();      TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
850     escriptDataC _source=source.getDataC();      if (!tpa)
851     escriptDataC _M=M.getDataC();          throw FinleyAdapterException("finley only supports Paso transport problems.");
852     escriptDataC _A=A.getDataC();  
853     escriptDataC _B=B.getDataC();      source.expand();
854     escriptDataC _C=C.getDataC();      escriptDataC _source=source.getDataC();
855     escriptDataC _D=D.getDataC();      escriptDataC _M=M.getDataC();
856     escriptDataC _X=X.getDataC();      escriptDataC _A=A.getDataC();
857     escriptDataC _Y=Y.getDataC();      escriptDataC _B=B.getDataC();
858     escriptDataC _d=d.getDataC();      escriptDataC _C=C.getDataC();
859     escriptDataC _y=y.getDataC();      escriptDataC _D=D.getDataC();
860     escriptDataC _d_contact=d_contact.getDataC();      escriptDataC _X=X.getDataC();
861     escriptDataC _y_contact=y_contact.getDataC();      escriptDataC _Y=Y.getDataC();
862        escriptDataC _d=d.getDataC();
863     Finley_Mesh* mesh=m_finleyMesh.get();      escriptDataC _y=y.getDataC();
864     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();      escriptDataC _d_contact=d_contact.getDataC();
865        escriptDataC _y_contact=y_contact.getDataC();
866     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );      escriptDataC _d_dirac=d_dirac.getDataC();
867     checkFinleyError();      escriptDataC _y_dirac=y_dirac.getDataC();
868    
869     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );      Finley_Mesh* mesh=m_finleyMesh.get();
870     checkFinleyError();      Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
871    
872     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );      Finley_Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->mass_matrix,
873     checkFinleyError();                          &_source, 0, 0, 0, &_M, 0, 0);
874        checkFinleyError();
875     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );  
876     checkFinleyError();      Finley_Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->transport_matrix,
877  }                          &_source, &_A, &_B, &_C, &_D, &_X, &_Y);
878        checkFinleyError();
879  //  
880  // interpolates data between different function spaces:      Finley_Assemble_PDE(mesh->Nodes, mesh->FaceElements, _tp->transport_matrix,
881  //                          &_source, 0, 0, 0, &_d, 0, &_y);
882  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const      checkFinleyError();
883  {  
884     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));      Finley_Assemble_PDE(mesh->Nodes, mesh->ContactElements,
885     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));                          _tp->transport_matrix, &_source, 0, 0, 0, &_d_contact, 0, &_y_contact);
886     if (inDomain!=*this)        checkFinleyError();
887        throw FinleyAdapterException("Error - Illegal domain of interpolant.");  
888     if (targetDomain!=*this)      Finley_Assemble_PDE(mesh->Nodes, mesh->Points, _tp->transport_matrix,
889        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");                          &_source, 0, 0, 0, &_d_dirac, 0, &_y_dirac);
890        checkFinleyError();
891     Finley_Mesh* mesh=m_finleyMesh.get();  }
892     escriptDataC _target=target.getDataC();  
893     escriptDataC _in=in.getDataC();  //
894     switch(in.getFunctionSpace().getTypeCode()) {  // interpolates data between different function spaces
895     case(Nodes):  //
896        switch(target.getFunctionSpace().getTypeCode()) {  void MeshAdapter::interpolateOnDomain(escript::Data& target, const escript::Data& in) const
897        case(Nodes):  {
898        case(ReducedNodes):      const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
899        case(DegreesOfFreedom):      const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
900        case(ReducedDegreesOfFreedom):      if (inDomain!=*this)
901        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);          throw FinleyAdapterException("Error - Illegal domain of interpolant.");
902        break;      if (targetDomain!=*this)
903        case(Elements):          throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
904        case(ReducedElements):  
905        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);      Finley_Mesh* mesh=m_finleyMesh.get();
906        break;      escriptDataC _target=target.getDataC();
907        case(FaceElements):      escriptDataC _in=in.getDataC();
908        case(ReducedFaceElements):      switch(in.getFunctionSpace().getTypeCode()) {
909        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);          case Nodes:
910        break;              switch(target.getFunctionSpace().getTypeCode()) {
911        case(Points):                  case Nodes:
912        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedNodes:
913        break;                  case DegreesOfFreedom:
914        case(ContactElementsZero):                  case ReducedDegreesOfFreedom:
915        case(ReducedContactElementsZero):                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
916        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
917        break;                  case Elements:
918        case(ContactElementsOne):                  case ReducedElements:
919        case(ReducedContactElementsOne):                      Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
920        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
921        break;                  case FaceElements:
922        default:                  case ReducedFaceElements:
923           stringstream temp;                      Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
924           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      break;
925           throw FinleyAdapterException(temp.str());                  case Points:
926           break;                      Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
927        }                      break;
928        break;                  case ContactElementsZero:
929     case(ReducedNodes):                  case ReducedContactElementsZero:
930        switch(target.getFunctionSpace().getTypeCode()) {                  case ContactElementsOne:
931        case(Nodes):                  case ReducedContactElementsOne:
932        case(ReducedNodes):                      Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
933        case(DegreesOfFreedom):                      break;
934        case(ReducedDegreesOfFreedom):                  default:
935        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      stringstream temp;
936        break;                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
937        case(Elements):                      throw FinleyAdapterException(temp.str());
938        case(ReducedElements):                      break;
939        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);              }
940        break;              break;
941        case(FaceElements):          case ReducedNodes:
942        case(ReducedFaceElements):              switch(target.getFunctionSpace().getTypeCode()) {
943        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case Nodes:
944        break;                  case ReducedNodes:
945        case(Points):                  case DegreesOfFreedom:
946        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedDegreesOfFreedom:
947        break;                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
948        case(ContactElementsZero):                      break;
949        case(ReducedContactElementsZero):                  case Elements:
950        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedElements:
951        break;                      Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
952        case(ContactElementsOne):                      break;
953        case(ReducedContactElementsOne):                  case FaceElements:
954        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedFaceElements:
955        break;                      Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
956        default:                      break;
957           stringstream temp;                  case Points:
958           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
959           throw FinleyAdapterException(temp.str());                      break;
960           break;                  case ContactElementsZero:
961        }                  case ReducedContactElementsZero:
962        break;                  case ContactElementsOne:
963     case(Elements):                  case ReducedContactElementsOne:
964        if (target.getFunctionSpace().getTypeCode()==Elements) {                      Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
965           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);                      break;
966        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  default:
967           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);                      stringstream temp;
968        } else {                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
969           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");                      throw FinleyAdapterException(temp.str());
970        }                      break;
971        break;              }
972     case(ReducedElements):              break;
973        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {          case Elements:
974           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              if (target.getFunctionSpace().getTypeCode()==Elements) {
975        } else {                  Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
976           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");              } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
977        }                  Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
978        break;              } else {
979     case(FaceElements):                  throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
980        if (target.getFunctionSpace().getTypeCode()==FaceElements) {              }
981           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              break;
982        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {          case ReducedElements:
983           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);              if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
984        } else {                  Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
985           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");              } else {
986        }                  throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
987        break;              }
988     case(ReducedFaceElements):              break;
989        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {          case FaceElements:
990           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              if (target.getFunctionSpace().getTypeCode()==FaceElements) {
991        } else {                  Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
992           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");              } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
993        }                  Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
994        break;              } else {
995     case(Points):                  throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
996        if (target.getFunctionSpace().getTypeCode()==Points) {              }
997           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);              break;
998        } else {          case ReducedFaceElements:
999           throw FinleyAdapterException("Error - No interpolation with data on points possible.");              if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1000        }                  Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1001        break;              } else {
1002     case(ContactElementsZero):                  throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
1003     case(ContactElementsOne):              }
1004        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {              break;
1005           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);          case Points:
1006        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {              if (target.getFunctionSpace().getTypeCode()==Points) {
1007           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);                  Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1008        } else {              } else {
1009           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");                  throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1010        }              }
1011        break;              break;
1012     case(ReducedContactElementsZero):          case ContactElementsZero:
1013     case(ReducedContactElementsOne):          case ContactElementsOne:
1014        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {              if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1015           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);                  Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1016        } else {              } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1017           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");                  Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
1018        }              } else {
1019        break;                  throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1020     case(DegreesOfFreedom):                    }
1021        switch(target.getFunctionSpace().getTypeCode()) {              break;
1022        case(ReducedDegreesOfFreedom):          case ReducedContactElementsZero:
1023        case(DegreesOfFreedom):          case ReducedContactElementsOne:
1024        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);              if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1025        break;                  Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1026                  } else {
1027        case(Nodes):                  throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1028        case(ReducedNodes):              }
1029        if (getMPISize()>1) {              break;
1030           escript::Data temp=escript::Data(in);          case DegreesOfFreedom:
1031           temp.expand();              switch(target.getFunctionSpace().getTypeCode()) {
1032           escriptDataC _in2 = temp.getDataC();                  case ReducedDegreesOfFreedom:
1033           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                  case DegreesOfFreedom:
1034        } else {                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1035           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1036        }  
1037        break;                  case Nodes:
1038        case(Elements):                  case ReducedNodes:
1039        case(ReducedElements):                      if (getMPISize()>1) {
1040        if (getMPISize()>1) {                          escript::Data temp=escript::Data(in);
1041           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          temp.expand();
1042           escriptDataC _in2 = temp.getDataC();                          escriptDataC _in2 = temp.getDataC();
1043           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1044        } else {                      } else {
1045           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1046        }                      }
1047        break;                      break;
1048        case(FaceElements):                  case Elements:
1049        case(ReducedFaceElements):                  case ReducedElements:
1050        if (getMPISize()>1) {                      if (getMPISize()>1) {
1051           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          escript::Data temp=escript::Data(in, continuousFunction(*this));
1052           escriptDataC _in2 = temp.getDataC();                          escriptDataC _in2 = temp.getDataC();
1053           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1054                          } else {
1055        } else {                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1056           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      }
1057        }                      break;
1058        break;                  case FaceElements:
1059        case(Points):                  case ReducedFaceElements:
1060        if (getMPISize()>1) {                      if (getMPISize()>1) {
1061           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          escript::Data temp=escript::Data(in, continuousFunction(*this));
1062           escriptDataC _in2 = temp.getDataC();                          escriptDataC _in2 = temp.getDataC();
1063        } else {                          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1064           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      } else {
1065        }                          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1066        break;                      }
1067        case(ContactElementsZero):                      break;
1068        case(ContactElementsOne):                  case Points:
1069        case(ReducedContactElementsZero):                      if (getMPISize()>1) {
1070        case(ReducedContactElementsOne):                          //escript::Data temp=escript::Data(in, continuousFunction(*this) );
1071        if (getMPISize()>1) {                          //escriptDataC _in2 = temp.getDataC();
1072           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                      } else {
1073           escriptDataC _in2 = temp.getDataC();                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1074           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);                      }
1075        } else {                      break;
1076           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ContactElementsZero:
1077        }                  case ContactElementsOne:
1078        break;                  case ReducedContactElementsZero:
1079        default:                  case ReducedContactElementsOne:
1080           stringstream temp;                      if (getMPISize()>1) {
1081           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                          escript::Data temp=escript::Data(in, continuousFunction(*this));
1082           throw FinleyAdapterException(temp.str());                          escriptDataC _in2 = temp.getDataC();
1083           break;                          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1084        }                      } else {
1085        break;                          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1086     case(ReducedDegreesOfFreedom):                      }
1087        switch(target.getFunctionSpace().getTypeCode()) {                      break;
1088        case(Nodes):                  default:
1089        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                      stringstream temp;
1090        break;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1091        case(ReducedNodes):                      throw FinleyAdapterException(temp.str());
1092        if (getMPISize()>1) {                      break;
1093           escript::Data temp=escript::Data(in);              }
1094           temp.expand();              break;
1095           escriptDataC _in2 = temp.getDataC();          case ReducedDegreesOfFreedom:
1096           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);              switch(target.getFunctionSpace().getTypeCode()) {
1097        } else {                  case Nodes:
1098           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1099        }                      break;
1100        break;                  case ReducedNodes:
1101        case(DegreesOfFreedom):                      if (getMPISize()>1) {
1102        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                          escript::Data temp=escript::Data(in);
1103        break;                          temp.expand();
1104        case(ReducedDegreesOfFreedom):                          escriptDataC _in2 = temp.getDataC();
1105        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1106        break;                      } else {
1107        case(Elements):                          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1108        case(ReducedElements):                      }
1109        if (getMPISize()>1) {                      break;
1110           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                  case DegreesOfFreedom:
1111           escriptDataC _in2 = temp.getDataC();                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1112           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                      break;
1113        } else {                  case ReducedDegreesOfFreedom:
1114           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1115        }                      break;
1116        break;                  case Elements:
1117        case(FaceElements):                  case ReducedElements:
1118        case(ReducedFaceElements):                      if (getMPISize()>1) {
1119        if (getMPISize()>1) {                          escript::Data temp=escript::Data(in, reducedContinuousFunction(*this) );
1120           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          escriptDataC _in2 = temp.getDataC();
1121           escriptDataC _in2 = temp.getDataC();                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1122           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      } else {
1123        } else {                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1124           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      }
1125        }                      break;
1126        break;                  case FaceElements:
1127        case(Points):                  case ReducedFaceElements:
1128        if (getMPISize()>1) {                      if (getMPISize()>1) {
1129           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          escript::Data temp=escript::Data(in, reducedContinuousFunction(*this) );
1130           escriptDataC _in2 = temp.getDataC();                          escriptDataC _in2 = temp.getDataC();
1131           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);                          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1132        } else {                      } else {
1133           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1134        }                      }
1135        break;                      break;
1136        case(ContactElementsZero):                  case Points:
1137        case(ContactElementsOne):                      if (getMPISize()>1) {
1138        case(ReducedContactElementsZero):                          escript::Data temp=escript::Data(in, reducedContinuousFunction(*this));
1139        case(ReducedContactElementsOne):                          escriptDataC _in2 = temp.getDataC();
1140        if (getMPISize()>1) {                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1141           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                      } else {
1142           escriptDataC _in2 = temp.getDataC();                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1143           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);                      }
1144        } else {                      break;
1145           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ContactElementsZero:
1146        }                  case ContactElementsOne:
1147        break;                  case ReducedContactElementsZero:
1148        default:                  case ReducedContactElementsOne:
1149           stringstream temp;                      if (getMPISize()>1) {
1150           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                          escript::Data temp=escript::Data(in, reducedContinuousFunction(*this));
1151           throw FinleyAdapterException(temp.str());                          escriptDataC _in2 = temp.getDataC();
1152           break;                          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1153        }                      } else {
1154        break;                          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1155     default:                      }
1156        stringstream temp;                      break;
1157        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();                  default:
1158        throw FinleyAdapterException(temp.str());                      stringstream temp;
1159        break;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1160     }                      throw FinleyAdapterException(temp.str());
1161     checkFinleyError();                      break;
1162                }
1163                break;
1164            default:
1165                stringstream temp;
1166                temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1167                throw FinleyAdapterException(temp.str());
1168                break;
1169        }
1170        checkFinleyError();
1171  }  }
1172    
1173  //  //
1174  // copies the locations of sample points into x:  // copies the locations of sample points into x
1175  //  //
1176  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1177  {  {
1178     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1179     if (argDomain!=*this)      if (argDomain!=*this)
1180        throw FinleyAdapterException("Error - Illegal domain of data point locations");          throw FinleyAdapterException("Error - Illegal domain of data point locations");
1181     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1182     // in case of values node coordinates we can do the job directly:      // in case of appropriate function space we can do the job directly:
1183     if (arg.getFunctionSpace().getTypeCode()==Nodes) {      if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1184        escriptDataC _arg=arg.getDataC();          escriptDataC _arg=arg.getDataC();
1185        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);          Finley_Assemble_NodeCoordinates(mesh->Nodes, &_arg);
1186     } else {      } else {
1187        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);          escript::Data tmp_data=Vector(0., continuousFunction(*this), true);
1188        escriptDataC _tmp_data=tmp_data.getDataC();          escriptDataC _tmp_data=tmp_data.getDataC();
1189        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);          Finley_Assemble_NodeCoordinates(mesh->Nodes, &_tmp_data);
1190        // this is then interpolated onto arg:          // this is then interpolated onto arg:
1191        interpolateOnDomain(arg,tmp_data);          interpolateOnDomain(arg, tmp_data);
1192     }      }
1193     checkFinleyError();      checkFinleyError();
1194  }  }
1195    
1196  //  //
1197  // 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
1198  //  //
1199  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1200  {  {
1201  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/      const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1202     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));      if (normalDomain!=*this)
1203     if (normalDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of normal locations");
1204        throw FinleyAdapterException("Error - Illegal domain of normal locations");      Finley_Mesh* mesh=m_finleyMesh.get();
1205     Finley_Mesh* mesh=m_finleyMesh.get();      escriptDataC _normal=normal.getDataC();
1206     escriptDataC _normal=normal.getDataC();      switch(normal.getFunctionSpace().getTypeCode()) {
1207     switch(normal.getFunctionSpace().getTypeCode()) {          case Nodes:
1208     case(Nodes):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1209     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");              break;
1210     break;          case ReducedNodes:
1211     case(ReducedNodes):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1212     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");              break;
1213     break;          case Elements:
1214     case(Elements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1215     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");              break;
1216     break;          case ReducedElements:
1217     case(ReducedElements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1218     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");              break;
1219     break;          case FaceElements:
1220     case (FaceElements):          case ReducedFaceElements:
1221     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1222     break;              break;
1223     case (ReducedFaceElements):          case Points:
1224     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1225     break;              break;
1226     case(Points):          case ContactElementsOne:
1227     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");          case ContactElementsZero:
1228     break;          case ReducedContactElementsOne:
1229     case (ContactElementsOne):          case ReducedContactElementsZero:
1230     case (ContactElementsZero):              Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1231     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              break;
1232     break;          case DegreesOfFreedom:
1233     case (ReducedContactElementsOne):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1234     case (ReducedContactElementsZero):              break;
1235     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);          case ReducedDegreesOfFreedom:
1236     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1237     case(DegreesOfFreedom):              break;
1238     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");          default:
1239     break;              stringstream temp;
1240     case(ReducedDegreesOfFreedom):              temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1241     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");              throw FinleyAdapterException(temp.str());
1242     break;              break;
1243     default:      }
1244        stringstream temp;      checkFinleyError();
       temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1245  }  }
1246    
1247  //  //
1248  // interpolates data to other domain:  // interpolates data to other domain
1249  //  //
1250  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1251  {  {
1252     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();      escript::const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1253     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());      const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1254     if (targetDomain!=this)      if (targetDomain!=this)
1255        throw FinleyAdapterException("Error - Illegal domain of interpolation target");          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1256    
1257     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");      throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1258  }  }
1259    
1260  //  //
1261  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined on arg
1262  //  //
1263  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(vector<double>& integrals, const escript::Data& arg) const
1264  {  {
1265     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1266     if (argDomain!=*this)      if (argDomain!=*this)
1267        throw FinleyAdapterException("Error - Illegal domain of integration kernel");          throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1268    
1269     double blocktimer_start = blocktimer_time();      double blocktimer_start = blocktimer_time();
1270     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1271     escriptDataC _temp;      escriptDataC _temp;
1272     escript::Data temp;      escript::Data temp;
1273     escriptDataC _arg=arg.getDataC();      escriptDataC _arg=arg.getDataC();
1274     switch(arg.getFunctionSpace().getTypeCode()) {      switch(arg.getFunctionSpace().getTypeCode()) {
1275     case(Nodes):          case Nodes:
1276     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );              temp=escript::Data(arg, escript::function(*this));
1277     _temp=temp.getDataC();              _temp=temp.getDataC();
1278     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);              Finley_Assemble_integrate(mesh->Nodes, mesh->Elements, &_temp, &integrals[0]);
1279     break;              break;
1280     case(ReducedNodes):          case ReducedNodes:
1281     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );              temp=escript::Data( arg, escript::function(*this) );
1282     _temp=temp.getDataC();              _temp=temp.getDataC();
1283     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);              Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1284     break;              break;
1285     case(Elements):          case Elements:
1286     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case ReducedElements:
1287     break;              Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1288     case(ReducedElements):              break;
1289     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case FaceElements:
1290     break;          case ReducedFaceElements:
1291     case(FaceElements):              Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1292     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);              break;
1293     break;          case Points:
1294     case(ReducedFaceElements):              throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1295     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);              break;
1296     break;          case ContactElementsZero:
1297     case(Points):          case ReducedContactElementsZero:
1298     throw FinleyAdapterException("Error - Integral of data on points is not supported.");          case ContactElementsOne:
1299     break;          case ReducedContactElementsOne:
1300     case(ContactElementsZero):              Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1301     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              break;
1302     break;          case DegreesOfFreedom:
1303     case(ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1304     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              temp=escript::Data(arg, escript::function(*this));
1305     break;              _temp=temp.getDataC();
1306     case(ContactElementsOne):              Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1307     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              break;
1308     break;          default:
1309     case(ReducedContactElementsOne):              stringstream temp;
1310     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1311     break;              throw FinleyAdapterException(temp.str());
1312     case(DegreesOfFreedom):              break;
1313     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );      }
1314     _temp=temp.getDataC();      checkFinleyError();
1315     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);      blocktimer_increment("integrate()", blocktimer_start);
1316     break;  }
1317     case(ReducedDegreesOfFreedom):  
1318     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );  //
1319     _temp=temp.getDataC();  // calculates the gradient of arg
1320     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  //
1321     break;  void MeshAdapter::setToGradient(escript::Data& grad, const escript::Data& arg) const
1322     default:  {
1323        stringstream temp;      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1324        temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();      if (argDomain!=*this)
1325        throw FinleyAdapterException(temp.str());          throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1326        break;      const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1327     }      if (gradDomain!=*this)
1328     checkFinleyError();          throw FinleyAdapterException("Error - Illegal domain of gradient");
1329     blocktimer_increment("integrate()", blocktimer_start);  
1330  }      Finley_Mesh* mesh=m_finleyMesh.get();
1331        escriptDataC _grad=grad.getDataC();
1332  //      escriptDataC nodeDataC;
1333  // calculates the gradient of arg:      escript::Data temp;
1334  //      if (getMPISize()>1) {
1335  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const          if (arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom) {
1336  {              temp=escript::Data(arg, continuousFunction(*this));
1337     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));              nodeDataC = temp.getDataC();
1338     if (argDomain!=*this)          } else if(arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom) {
1339        throw FinleyAdapterException("Error - Illegal domain of gradient argument");              temp=escript::Data(arg, reducedContinuousFunction(*this));
1340     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));              nodeDataC = temp.getDataC();
1341     if (gradDomain!=*this)          } else {
1342        throw FinleyAdapterException("Error - Illegal domain of gradient");              nodeDataC = arg.getDataC();
1343            }
1344     Finley_Mesh* mesh=m_finleyMesh.get();      } else {
1345     escriptDataC _grad=grad.getDataC();          nodeDataC = arg.getDataC();
1346     escriptDataC nodeDataC;      }
1347     escript::Data temp;      switch(grad.getFunctionSpace().getTypeCode()) {
1348     if (getMPISize()>1) {          case Nodes:
1349        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {              throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1350           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );              break;
1351           nodeDataC = temp.getDataC();          case ReducedNodes:
1352        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {              throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1353           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );              break;
1354           nodeDataC = temp.getDataC();          case Elements:
1355        } else {          case ReducedElements:
1356           nodeDataC = arg.getDataC();              Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1357        }              break;
1358     } else {          case FaceElements:
1359        nodeDataC = arg.getDataC();          case ReducedFaceElements:
1360     }              Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1361     switch(grad.getFunctionSpace().getTypeCode()) {              break;
1362     case(Nodes):          case Points:
1363     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");              throw FinleyAdapterException("Error - Gradient at points is not supported.");
1364     break;              break;
1365     case(ReducedNodes):          case ContactElementsZero:
1366     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");          case ReducedContactElementsZero:
1367     break;          case ContactElementsOne:
1368     case(Elements):          case ReducedContactElementsOne:
1369     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);              Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1370     break;              break;
1371     case(ReducedElements):          case DegreesOfFreedom:
1372     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);              throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1373     break;              break;
1374     case(FaceElements):          case ReducedDegreesOfFreedom:
1375     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);              throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1376     break;              break;
1377     case(ReducedFaceElements):          default:
1378     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);              stringstream temp;
1379     break;              temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1380     case(Points):              throw FinleyAdapterException(temp.str());
1381     throw FinleyAdapterException("Error - Gradient at points is not supported.");              break;
1382     break;      }
1383     case(ContactElementsZero):      checkFinleyError();
    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();  
1384  }  }
1385    
1386  //  //
1387  // returns the size of elements:  // returns the size of elements
1388  //  //
1389  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1390  {  {
1391     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1392     escriptDataC tmp=size.getDataC();      escriptDataC tmp=size.getDataC();
1393     switch(size.getFunctionSpace().getTypeCode()) {      switch(size.getFunctionSpace().getTypeCode()) {
1394     case(Nodes):          case Nodes:
1395     throw FinleyAdapterException("Error - Size of nodes is not supported.");              throw FinleyAdapterException("Error - Size of nodes is not supported.");
1396     break;              break;
1397     case(ReducedNodes):          case ReducedNodes:
1398     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1399     break;              break;
1400     case(Elements):          case Elements:
1401     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case ReducedElements:
1402     break;              Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1403     case(ReducedElements):              break;
1404     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case FaceElements:
1405     break;          case ReducedFaceElements:
1406     case(FaceElements):              Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1407     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);              break;
1408     break;          case Points:
1409     case(ReducedFaceElements):              throw FinleyAdapterException("Error - Size of point elements is not supported.");
1410     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);              break;
1411     break;          case ContactElementsZero:
1412     case(Points):          case ContactElementsOne:
1413     throw FinleyAdapterException("Error - Size of point elements is not supported.");          case ReducedContactElementsZero:
1414     break;          case ReducedContactElementsOne:
1415     case(ContactElementsZero):              Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1416     case(ContactElementsOne):              break;
1417     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);          case DegreesOfFreedom:
1418     break;              throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1419     case(ReducedContactElementsZero):              break;
1420     case(ReducedContactElementsOne):          case ReducedDegreesOfFreedom:
1421     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1422     break;              break;
1423     case(DegreesOfFreedom):          default:
1424     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");              stringstream temp;
1425     break;              temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1426     case(ReducedDegreesOfFreedom):              throw FinleyAdapterException(temp.str());
1427     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");              break;
1428     break;      }
1429     default:      checkFinleyError();
       stringstream temp;  
       temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1430  }  }
1431    
1432  //  //
# Line 1463  void MeshAdapter::setToSize(escript::Dat Line 1434  void MeshAdapter::setToSize(escript::Dat
1434  //  //
1435  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1436  {  {
1437     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1438     escriptDataC tmp;      const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1439     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));      if (newDomain!=*this)
1440     if (newDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of new point locations");
1441        throw FinleyAdapterException("Error - Illegal domain of new point locations");      if (new_x.getFunctionSpace() == continuousFunction(*this)) {
1442     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {          Finley_Mesh_setCoordinates(mesh, new_x);
1443         tmp = new_x.getDataC();      } else {
1444         Finley_Mesh_setCoordinates(mesh,&tmp);          throw FinleyAdapterException("As of escript version 3.3 SetX() only accepts ContinuousFunction arguments. Please interpolate.");
1445     } else {          //escript::Data new_x_inter=escript::Data(new_x, continuousFunction(*this));
1446         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );          //Finley_Mesh_setCoordinates(mesh, new_x_inter);
1447         tmp = new_x_inter.getDataC();      }
1448         Finley_Mesh_setCoordinates(mesh,&tmp);      checkFinleyError();
    }  
    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) {  
       std::string n=boost::python::extract<std::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 std::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 std::string& filename,const boost::python::dict& arg,  const std::string& metadata, const std::string& metadata_schema) const  
 {  
    int num_data;  
    char **names;  
    escriptDataC *data;  
    escriptDataC **ptr_data;  
   
    extractArgsFromDict(arg, num_data, names, data, ptr_data);  
    Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data, metadata.c_str(), metadata_schema.c_str());  
    checkFinleyError();  
   
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0; i<num_data; i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
1449  }  }
1450    
1451  bool MeshAdapter::ownSample(int fs_code, index_t id) const  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1452  {  {
1453  #ifdef PASO_MPI      if (getMPISize() > 1) {
1454      index_t myFirstNode=0, myLastNode=0, k=0;  #ifdef ESYS_MPI
1455      index_t* globalNodeIndex=0;          index_t myFirstNode=0, myLastNode=0, k=0;
1456      Finley_Mesh* mesh_p=m_finleyMesh.get();          index_t* globalNodeIndex=0;
1457      if (fs_code == FINLEY_REDUCED_NODES)          Finley_Mesh* mesh_p=m_finleyMesh.get();
1458      {          /*
1459      myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);           * this method is only used by saveDataCSV which would use the returned
1460      myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);           * values for reduced nodes wrongly so this case is disabled for now
1461      globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);          if (fs_code == FINLEY_REDUCED_NODES) {
1462      }              myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1463      else              myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1464      {              globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1465      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);          } else
1466      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);          */
1467      globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);          if (fs_code == FINLEY_NODES) {
1468      }              myFirstNode = mesh_p->Nodes->getFirstNode();
1469      k=globalNodeIndex[id];              myLastNode = mesh_p->Nodes->getLastNode();
1470      return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );              globalNodeIndex = mesh_p->Nodes->borrowGlobalNodesIndex();
1471            } else {
1472                throw FinleyAdapterException("Unsupported function space type for ownSample()");
1473            }
1474    
1475            k=globalNodeIndex[id];
1476            return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1477  #endif  #endif
1478        }
1479      return true;      return true;
1480  }  }
1481    
1482    
   
1483  //  //
1484  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1485  //  //
1486  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  escript::ASM_ptr MeshAdapter::newSystemMatrix(const int row_blocksize,
1487                                                   const int row_blocksize,                              const escript::FunctionSpace& row_functionspace,
1488                                                   const escript::FunctionSpace& row_functionspace,                              const int column_blocksize,
1489                                                   const int column_blocksize,                              const escript::FunctionSpace& column_functionspace,
1490                                                   const escript::FunctionSpace& column_functionspace,                              const int type) const
1491                                                   const int type) const  {
1492  {      // is the domain right?
1493     int reduceRowOrder=0;      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1494     int reduceColOrder=0;      if (row_domain!=*this)
1495     // is the domain right?          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1496     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1497     if (row_domain!=*this)      if (col_domain!=*this)
1498        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.");
1499     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));  
1500     if (col_domain!=*this)      int reduceRowOrder=0;
1501        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");      int reduceColOrder=0;
1502     // is the function space type right      // is the function space type right?
1503     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {      if (row_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1504        reduceRowOrder=0;          reduceRowOrder=1;
1505     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      } else if (row_functionspace.getTypeCode() != DegreesOfFreedom) {
1506        reduceRowOrder=1;          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1507     } else {      }
1508        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      if (column_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1509     }          reduceColOrder=1;
1510     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (column_functionspace.getTypeCode() != DegreesOfFreedom) {
1511        reduceColOrder=0;          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1512     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1513        reduceColOrder=1;  
1514     } else {      // generate matrix:
1515        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(
1516     }              getFinley_Mesh(), reduceRowOrder, reduceColOrder);
1517     // generate matrix:      checkFinleyError();
1518        Paso_SystemMatrix* fsystemMatrix;
1519     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);      const int trilinos = 0;
1520     checkFinleyError();      if (trilinos) {
    Paso_SystemMatrix* fsystemMatrix;  
    int trilinos = 0;  
    if (trilinos) {  
1521  #ifdef TRILINOS  #ifdef TRILINOS
1522        /* Allocation Epetra_VrbMatrix here */          // FIXME: Allocation Epetra_VrbMatrix here...
1523  #endif  #endif
1524     }      } else {
1525     else {          fsystemMatrix=Paso_SystemMatrix_alloc(type, fsystemMatrixPattern,
1526        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);                  row_blocksize, column_blocksize, FALSE);
1527     }      }
1528     checkPasoError();      checkPasoError();
1529     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1530     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);      SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1531        return escript::ASM_ptr(sma);
1532  }  }
1533    
1534  //  //
1535  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1536  //  //
1537  TransportProblemAdapter MeshAdapter::newTransportProblem(  escript::ATP_ptr MeshAdapter::newTransportProblem(const int blocksize,
1538                                                           const double theta,          const escript::FunctionSpace& functionspace, const int type) const
1539                                                           const int blocksize,  {
1540                                                           const escript::FunctionSpace& functionspace,      // is the domain right?
1541                                                           const int type) const      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1542  {      if (domain!=*this)
1543     int reduceOrder=0;          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1544     // is the domain right?  
1545     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));      // is the function space type right?
1546     if (domain!=*this)      int reduceOrder=0;
1547        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");      if (functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1548     // is the function space type right          reduceOrder=1;
1549     if (functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (functionspace.getTypeCode() != DegreesOfFreedom) {
1550        reduceOrder=0;          throw FinleyAdapterException("Error - illegal function space type for transport problem.");
1551     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1552        reduceOrder=1;  
1553     } else {      // generate transport problem:
1554        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(
1555     }              getFinley_Mesh(), reduceOrder, reduceOrder);
1556     // generate matrix:      checkFinleyError();
1557        Paso_TransportProblem* transportProblem;
1558     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);      transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern, blocksize);
1559     checkFinleyError();      checkPasoError();
1560     Paso_FCTransportProblem* transportProblem;      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1561     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);      TransportProblemAdapter* tpa=new TransportProblemAdapter(
1562     checkPasoError();              transportProblem, blocksize, functionspace);
1563     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      return escript::ATP_ptr(tpa);
    return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);  
1564  }  }
1565    
1566  //  //
1567  // vtkObject MeshAdapter::createVtkObject() const  // returns true if data on functionSpaceCode is considered as being cell centered
 // TODO:  
1568  //  //
   
 //  
 // returns true if data at the atom_type is considered as being cell centered:  
1569  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1570  {  {
1571     switch(functionSpaceCode) {      switch(functionSpaceCode) {
1572     case(Nodes):          case Nodes:
1573     case(DegreesOfFreedom):          case DegreesOfFreedom:
1574     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1575     return false;              return false;
1576     break;          case Elements:
1577     case(Elements):          case FaceElements:
1578     case(FaceElements):          case Points:
1579     case(Points):          case ContactElementsZero:
1580     case(ContactElementsZero):          case ContactElementsOne:
1581     case(ContactElementsOne):          case ReducedElements:
1582     case(ReducedElements):          case ReducedFaceElements:
1583     case(ReducedFaceElements):          case ReducedContactElementsZero:
1584     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
1585     case(ReducedContactElementsOne):              return true;
1586     return true;          default:
1587     break;              stringstream temp;
1588     default:              temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1589        stringstream temp;              throw FinleyAdapterException(temp.str());
1590        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;              break;
1591        throw FinleyAdapterException(temp.str());      }
1592        break;      return false;
    }  
    checkFinleyError();  
    return false;  
1593  }  }
1594    
1595  bool  bool
1596  MeshAdapter::commonFunctionSpace(const std::vector<int>& fs, int& resultcode) const  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1597  {  {
1598     /* 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
1599      class 1: DOF <-> Nodes         back and forth]:
1600      class 2: ReducedDOF <-> ReducedNodes          class 1: DOF <-> Nodes
1601      class 3: Points          class 2: ReducedDOF <-> ReducedNodes
1602      class 4: Elements          class 3: Points
1603      class 5: ReducedElements          class 4: Elements
1604      class 6: FaceElements          class 5: ReducedElements
1605      class 7: ReducedFaceElements          class 6: FaceElements
1606      class 8: ContactElementZero <-> ContactElementOne          class 7: ReducedFaceElements
1607      class 9: ReducedContactElementZero <-> ReducedContactElementOne          class 8: ContactElementZero <-> ContactElementOne
1608            class 9: ReducedContactElementZero <-> ReducedContactElementOne
1609     There is also a set of lines. Interpolation is possible down a line but not between lines.  
1610     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
1611      line 0: class 3      not between lines.
1612      line 1: class 4,5      class 1 and 2 belong to all lines so aren't considered.
1613      line 2: class 6,7          line 0: class 3
1614      line 3: class 8,9          line 1: class 4,5
1615            line 2: class 6,7
1616     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
1617     eg hasnodes is true if we have at least one instance of Nodes.  
1618     */      For classes with multiple members (eg class 2) we have vars to record if
1619      if (fs.size()==0)      there is at least one instance.
1620      {      e.g. hasnodes is true if we have at least one instance of Nodes.
1621      return false;      */
1622      }      if (fs.empty())
1623      std::vector<int> hasclass(10);          return false;
1624      std::vector<int> hasline(4);      
1625        vector<int> hasclass(10);
1626        vector<int> hasline(4);    
1627      bool hasnodes=false;      bool hasnodes=false;
1628      bool hasrednodes=false;      bool hasrednodes=false;
1629      bool hascez=false;      bool hascez=false;
1630      bool hasrcez=false;      bool hasrcez=false;
1631      for (int i=0;i<fs.size();++i)      for (int i=0;i<fs.size();++i) {
1632      {          switch(fs[i]) {
1633      switch(fs[i])              case Nodes:
1634      {                  hasnodes=true; // fall through
1635      case(Nodes):   hasnodes=true;   // no break is deliberate              case DegreesOfFreedom:
1636      case(DegreesOfFreedom):                  hasclass[1]=1;
1637          hasclass[1]=1;                  break;
1638          break;              case ReducedNodes:
1639      case(ReducedNodes):    hasrednodes=true;    // no break is deliberate                  hasrednodes=true; // fall through
1640      case(ReducedDegreesOfFreedom):              case ReducedDegreesOfFreedom:
1641          hasclass[2]=1;                  hasclass[2]=1;
1642          break;                  break;
1643      case(Points):              case Points:
1644          hasline[0]=1;                  hasline[0]=1;
1645          hasclass[3]=1;                  hasclass[3]=1;
1646          break;                  break;
1647      case(Elements):              case Elements:
1648          hasclass[4]=1;                  hasclass[4]=1;
1649          hasline[1]=1;                  hasline[1]=1;
1650          break;                  break;
1651      case(ReducedElements):              case ReducedElements:
1652          hasclass[5]=1;                  hasclass[5]=1;
1653          hasline[1]=1;                  hasline[1]=1;
1654          break;                  break;
1655      case(FaceElements):              case FaceElements:
1656          hasclass[6]=1;                  hasclass[6]=1;
1657          hasline[2]=1;                  hasline[2]=1;
1658          break;                  break;
1659      case(ReducedFaceElements):              case ReducedFaceElements:
1660          hasclass[7]=1;                  hasclass[7]=1;
1661          hasline[2]=1;                  hasline[2]=1;
1662          break;                  break;
1663      case(ContactElementsZero):  hascez=true;    // no break is deliberate              case ContactElementsZero:
1664      case(ContactElementsOne):                  hascez=true; // fall through
1665          hasclass[8]=1;              case ContactElementsOne:
1666          hasline[3]=1;                  hasclass[8]=1;
1667          break;                  hasline[3]=1;
1668      case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate                  break;
1669      case(ReducedContactElementsOne):              case ReducedContactElementsZero:
1670          hasclass[9]=1;                  hasrcez=true; // fall through
1671          hasline[3]=1;              case ReducedContactElementsOne:
1672          break;                  hasclass[9]=1;
1673      default:                  hasline[3]=1;
1674          return false;                  break;
1675      }              default:
1676                    return false;
1677            }
1678      }      }
1679      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  
1680    
1681        // fail if we have more than one leaf group
1682      if (totlines>1)      if (totlines>1)
1683      {          return false; // there are at least two branches we can't interpolate between
1684      return false;   // there are at least two branches we can't interpolate between      else if (totlines==1) {
1685      }          if (hasline[0]==1)              // we have points
1686      else if (totlines==1)              resultcode=Points;
1687      {          else if (hasline[1]==1) {
1688      if (hasline[0]==1)      // we have points              if (hasclass[5]==1)
1689      {                  resultcode=ReducedElements;
1690          resultcode=Points;              else
1691      }                  resultcode=Elements;
1692      else if (hasline[1]==1)          } else if (hasline[2]==1) {
1693      {              if (hasclass[7]==1)
1694          if (hasclass[5]==1)                  resultcode=ReducedFaceElements;
1695          {              else
1696          resultcode=ReducedElements;                  resultcode=FaceElements;
1697          }          } else {   // so we must be in line3
1698          else              if (hasclass[9]==1) {
1699          {                  // need something from class 9
1700          resultcode=Elements;                  resultcode=(hasrcez ? ReducedContactElementsZero : ReducedContactElementsOne);
1701          }              } else {
1702      }                  // something from class 8
1703      else if (hasline[2]==1)                  resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1704      {              }
1705          if (hasclass[7]==1)          }
1706          {      } else { // totlines==0
1707          resultcode=ReducedFaceElements;          if (hasclass[2]==1) {
1708          }              // something from class 2
1709          else              resultcode=(hasrednodes ? ReducedNodes : ReducedDegreesOfFreedom);
1710          {          } else {
1711          resultcode=FaceElements;              // something from class 1
1712          }              resultcode=(hasnodes ? Nodes : DegreesOfFreedom);
1713      }          }
     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);  
     }  
1714      }      }
1715      return true;      return true;
1716  }  }
1717    
1718  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,
1719                                                 int functionSpaceType_target) const
1720  {  {
1721     switch(functionSpaceType_source) {      switch(functionSpaceType_source) {
1722     case(Nodes):          case Nodes:
1723      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1724      case(Nodes):                  case Nodes:
1725      case(ReducedNodes):                  case ReducedNodes:
1726      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1727      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1728      case(Elements):                  case Elements:
1729      case(ReducedElements):                  case ReducedElements:
1730      case(FaceElements):                  case FaceElements:
1731      case(ReducedFaceElements):                  case ReducedFaceElements:
1732      case(Points):                  case Points:
1733      case(ContactElementsZero):                  case ContactElementsZero:
1734      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1735      case(ContactElementsOne):                  case ContactElementsOne:
1736      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1737      return true;                      return true;
1738      default:                  default:
1739            stringstream temp;                      stringstream temp;
1740            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;
1741            throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1742     }              }
1743     break;              break;
1744     case(ReducedNodes):          case ReducedNodes:
1745      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1746      case(ReducedNodes):                  case ReducedNodes:
1747      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1748      case(Elements):                  case Elements:
1749      case(ReducedElements):                  case ReducedElements:
1750      case(FaceElements):                  case FaceElements:
1751      case(ReducedFaceElements):                  case ReducedFaceElements:
1752      case(Points):                  case Points:
1753      case(ContactElementsZero):                  case ContactElementsZero:
1754      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1755      case(ContactElementsOne):                  case ContactElementsOne:
1756      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1757      return true;                      return true;
1758      case(Nodes):                  case Nodes:
1759      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1760      return false;                      return false;
1761      default:                  default:
1762          stringstream temp;                      stringstream temp;
1763          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;
1764          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1765     }              }
1766     break;              break;
1767     case(Elements):          case Elements:
1768      if (functionSpaceType_target==Elements) {              if (functionSpaceType_target==Elements) {
1769        return true;                  return true;
1770      } else if (functionSpaceType_target==ReducedElements) {              } else if (functionSpaceType_target==ReducedElements) {
1771        return true;                  return true;
1772          } else {              } else {
1773            return false;                  return false;
1774          }              }
1775     case(ReducedElements):          case ReducedElements:
1776      if (functionSpaceType_target==ReducedElements) {              if (functionSpaceType_target==ReducedElements) {
1777        return true;                  return true;
1778      } else {              } else {
1779            return false;                  return false;
1780      }              }
1781     case(FaceElements):          case FaceElements:
1782      if (functionSpaceType_target==FaceElements) {              if (functionSpaceType_target==FaceElements) {
1783              return true;                  return true;
1784      } else if (functionSpaceType_target==ReducedFaceElements) {              } else if (functionSpaceType_target==ReducedFaceElements) {
1785              return true;                  return true;
1786      } else {              } else {
1787              return false;                  return false;
1788      }              }
1789     case(ReducedFaceElements):          case ReducedFaceElements:
1790      if (functionSpaceType_target==ReducedFaceElements) {              if (functionSpaceType_target==ReducedFaceElements) {
1791              return true;                  return true;
1792      } else {              } else {
1793          return false;                  return false;
1794      }              }
1795     case(Points):          case Points:
1796      if (functionSpaceType_target==Points) {              if (functionSpaceType_target==Points) {
1797              return true;                  return true;
1798      } else {              } else {
1799              return false;                  return false;
1800      }              }
1801     case(ContactElementsZero):          case ContactElementsZero:
1802     case(ContactElementsOne):          case ContactElementsOne:
1803      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {              if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1804              return true;                  return true;
1805      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {              } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1806              return true;                  return true;
1807      } else {              } else {
1808              return false;                  return false;
1809      }              }
1810     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
1811     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
1812      if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {              if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1813              return true;                  return true;
1814      } else {              } else {
1815              return false;                  return false;
1816      }              }
1817     case(DegreesOfFreedom):          case DegreesOfFreedom:
1818      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1819      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1820      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1821      case(Nodes):                  case Nodes:
1822      case(ReducedNodes):                  case ReducedNodes:
1823      case(Elements):                  case Elements:
1824      case(ReducedElements):                  case ReducedElements:
1825      case(Points):                  case Points:
1826      case(FaceElements):                  case FaceElements:
1827      case(ReducedFaceElements):                  case ReducedFaceElements:
1828      case(ContactElementsZero):                  case ContactElementsZero:
1829      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1830      case(ContactElementsOne):                  case ContactElementsOne:
1831      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1832      return true;                      return true;
1833      default:                  default:
1834          stringstream temp;                      stringstream temp;
1835          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;
1836          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1837      }              }
1838      break;              break;
1839     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1840     switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1841      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1842      case(ReducedNodes):                  case ReducedNodes:
1843      case(Elements):                  case Elements:
1844      case(ReducedElements):                  case ReducedElements:
1845      case(FaceElements):                  case FaceElements:
1846      case(ReducedFaceElements):                  case ReducedFaceElements:
1847      case(Points):                  case Points:
1848      case(ContactElementsZero):                  case ContactElementsZero:
1849      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1850      case(ContactElementsOne):                  case ContactElementsOne:
1851      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1852      return true;                      return true;
1853      case(Nodes):                  case Nodes:
1854      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1855      return false;                      return false;
1856      default:                  default:
1857          stringstream temp;                      stringstream temp;
1858          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;
1859          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1860      }              }
1861      break;              break;
1862     default:          default:
1863        stringstream temp;              stringstream temp;
1864        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;
1865        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
1866        break;              break;
1867     }      }
1868     checkFinleyError();      return false;
1869     return false;  }
1870  }  
1871    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
1872  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const  {
1873  {      if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1874     return false;          return 1;
1875  }  
1876        if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1877  bool MeshAdapter::operator==(const AbstractDomain& other) const          return -1;
1878  {  
1879     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);      return 0;
1880     if (temp!=0) {  }
1881        return (m_finleyMesh==temp->m_finleyMesh);  
1882     } else {  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,
1883        return false;          const escript::AbstractDomain& targetDomain,
1884     }          int functionSpaceType_target) const
1885    {
1886        return false;
1887  }  }
1888    
1889  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator==(const escript::AbstractDomain& other) const
1890  {  {
1891     return !(operator==(other));      const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1892        if (temp) {
1893            return (m_finleyMesh==temp->m_finleyMesh);
1894        } else {
1895            return false;
1896        }
1897    }
1898    
1899    bool MeshAdapter::operator!=(const escript::AbstractDomain& other) const
1900    {
1901        return !(operator==(other));
1902  }  }
1903    
1904  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
1905  {  {
1906     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1907     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);      return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
1908     checkPasoError();                 package, symmetry, mesh->MPIInfo);
    return out;  
1909  }  }
1910    
1911  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
1912  {  {
1913     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1914     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);      return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
1915     checkPasoError();                  package, symmetry, mesh->MPIInfo);
    return out;  
1916  }  }
1917    
1918  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1919  {  {
1920     return continuousFunction(asAbstractContinuousDomain()).getX();      return continuousFunction(*this).getX();
1921  }  }
1922    
1923  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1924  {  {
1925     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();      return functionOnBoundary(*this).getNormal();
1926  }  }
1927    
1928  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1929  {  {
1930     return escript::function(asAbstractContinuousDomain()).getSize();      return escript::function(*this).getSize();
1931  }  }
1932    
1933  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1934  {  {
1935     int *out = NULL;      int *out = NULL;
1936     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1937     switch (functionSpaceType) {      switch (functionSpaceType) {
1938     case(Nodes):          case Nodes:
1939     out=mesh->Nodes->Id;              out=mesh->Nodes->Id;
1940     break;              break;
1941     case(ReducedNodes):          case ReducedNodes:
1942     out=mesh->Nodes->reducedNodesId;              out=mesh->Nodes->reducedNodesId;
1943     break;              break;
1944     case(Elements):          case Elements:
1945     out=mesh->Elements->Id;          case ReducedElements:
1946     break;              out=mesh->Elements->Id;
1947     case(ReducedElements):              break;
1948     out=mesh->Elements->Id;          case FaceElements:
1949     break;          case ReducedFaceElements:
1950     case(FaceElements):              out=mesh->FaceElements->Id;
1951     out=mesh->FaceElements->Id;              break;
1952     break;          case Points:
1953     case(ReducedFaceElements):              out=mesh->Points->Id;
1954     out=mesh->FaceElements->Id;              break;
1955     break;          case ContactElementsZero:
1956     case(Points):          case ReducedContactElementsZero:
1957     out=mesh->Points->Id;          case ContactElementsOne:
1958     break;          case ReducedContactElementsOne:
1959     case(ContactElementsZero):              out=mesh->ContactElements->Id;
1960     out=mesh->ContactElements->Id;              break;
1961     break;          case DegreesOfFreedom:
1962     case(ReducedContactElementsZero):              out=mesh->Nodes->degreesOfFreedomId;
1963     out=mesh->ContactElements->Id;              break;
1964     break;          case ReducedDegreesOfFreedom:
1965     case(ContactElementsOne):              out=mesh->Nodes->reducedDegreesOfFreedomId;
1966     out=mesh->ContactElements->Id;              break;
1967     break;          default:
1968     case(ReducedContactElementsOne):              stringstream temp;
1969     out=mesh->ContactElements->Id;              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1970     break;              throw FinleyAdapterException(temp.str());
1971     case(DegreesOfFreedom):              break;
1972     out=mesh->Nodes->degreesOfFreedomId;      }
1973     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;  
1974  }  }
1975  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1976  {  {
1977     int out=0;      int out=0;
1978     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1979     switch (functionSpaceType) {      switch (functionSpaceType) {
1980     case(Nodes):          case Nodes:
1981     out=mesh->Nodes->Tag[sampleNo];              out=mesh->Nodes->Tag[sampleNo];
1982     break;              break;
1983     case(ReducedNodes):          case ReducedNodes:
1984     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");              throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1985     break;              break;
1986     case(Elements):          case Elements:
1987     out=mesh->Elements->Tag[sampleNo];          case ReducedElements:
1988     break;              out=mesh->Elements->Tag[sampleNo];
1989     case(ReducedElements):              break;
1990     out=mesh->Elements->Tag[sampleNo];          case FaceElements:
1991     break;          case ReducedFaceElements:
1992     case(FaceElements):              out=mesh->FaceElements->Tag[sampleNo];
1993     out=mesh->FaceElements->Tag[sampleNo];              break;
1994     break;          case Points:
1995     case(ReducedFaceElements):              out=mesh->Points->Tag[sampleNo];
1996     out=mesh->FaceElements->Tag[sampleNo];              break;
1997     break;          case ContactElementsZero:
1998     case(Points):          case ReducedContactElementsZero:
1999     out=mesh->Points->Tag[sampleNo];          case ContactElementsOne:
2000     break;          case ReducedContactElementsOne:
2001     case(ContactElementsZero):              out=mesh->ContactElements->Tag[sampleNo];
2002     out=mesh->ContactElements->Tag[sampleNo];              break;
2003     break;          case DegreesOfFreedom:
2004     case(ReducedContactElementsZero):              throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2005     out=mesh->ContactElements->Tag[sampleNo];              break;
2006     break;          case ReducedDegreesOfFreedom:
2007     case(ContactElementsOne):              throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2008     out=mesh->ContactElements->Tag[sampleNo];              break;
2009     break;          default:
2010     case(ReducedContactElementsOne):              stringstream temp;
2011     out=mesh->ContactElements->Tag[sampleNo];              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2012     break;              throw FinleyAdapterException(temp.str());
2013     case(DegreesOfFreedom):              break;
2014     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");      }
2015     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;  
2016  }  }
2017    
2018    
2019  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
2020  {  {
2021     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2022     escriptDataC tmp=mask.getDataC();      switch(functionSpaceType) {
2023     switch(functionSpaceType) {          case Nodes:
2024     case(Nodes):              mesh->Nodes->setTags(newTag, mask);
2025     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);              break;
2026     break;          case ReducedNodes:
2027     case(ReducedNodes):              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2028     throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case DegreesOfFreedom:
2029     break;              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2030     case(DegreesOfFreedom):          case ReducedDegreesOfFreedom:
2031     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2032     break;          case Elements:
2033     case(ReducedDegreesOfFreedom):          case ReducedElements:
2034     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");              mesh->Elements->setTags(newTag, mask);
2035     break;              break;
2036     case(Elements):          case FaceElements:
2037     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case ReducedFaceElements:
2038     break;              mesh->FaceElements->setTags(newTag, mask);
2039     case(ReducedElements):              break;
2040     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case Points:
2041     break;              mesh->Points->setTags(newTag, mask);
2042     case(FaceElements):              break;
2043     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ContactElementsZero:
2044     break;          case ReducedContactElementsZero:
2045     case(ReducedFaceElements):          case ContactElementsOne:
2046     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ReducedContactElementsOne:
2047     break;              mesh->ContactElements->setTags(newTag, mask);
2048     case(Points):              break;
2049     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);          default:
2050     break;              stringstream temp;
2051     case(ContactElementsZero):              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2052     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              throw FinleyAdapterException(temp.str());
2053     break;      }
2054     case(ReducedContactElementsZero):      checkFinleyError();
2055     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  }
2056     break;  
2057     case(ContactElementsOne):  void MeshAdapter::setTagMap(const string& name, int tag)
2058     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  {
2059     break;      Finley_Mesh* mesh=m_finleyMesh.get();
2060     case(ReducedContactElementsOne):      Finley_Mesh_addTagMap(mesh, name.c_str(), tag);
2061     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);      checkFinleyError();
2062     break;  }
2063     default:  
2064        stringstream temp;  int MeshAdapter::getTag(const string& name) const
2065        temp << "Error - Finley does not know anything about function space type " << functionSpaceType;  {
2066        throw FinleyAdapterException(temp.str());      Finley_Mesh* mesh=m_finleyMesh.get();
2067     }      int tag = Finley_Mesh_getTag(mesh, name.c_str());
2068     checkFinleyError();      checkFinleyError();
2069     return;      return tag;
2070  }  }
2071    
2072  void MeshAdapter::setTagMap(const std::string& name,  int tag)  bool MeshAdapter::isValidTagName(const string& name) const
2073  {  {
2074     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2075     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);      return Finley_Mesh_isValidTagName(mesh, name.c_str());
2076     checkPasoError();  }
2077     // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
2078  }  string MeshAdapter::showTagNames() const
2079    {
2080  int MeshAdapter::getTag(const std::string& name) const      stringstream temp;
2081  {      Finley_Mesh* mesh=m_finleyMesh.get();
2082     Finley_Mesh* mesh=m_finleyMesh.get();      TagMap::const_iterator it = mesh->tagMap.begin();
2083     int tag=0;      while (it != mesh->tagMap.end()) {
2084     tag=Finley_Mesh_getTag(mesh, name.c_str());          temp << it->first;
2085     checkPasoError();          ++it;
2086     // throwStandardException("MeshAdapter::getTag is not implemented.");          if (it != mesh->tagMap.end())
2087     return tag;              temp << ", ";
2088  }      }
2089        return temp.str();
 bool MeshAdapter::isValidTagName(const std::string& name) const  
 {  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    return Finley_Mesh_isValidTagName(mesh,name.c_str());  
 }  
   
 std::string MeshAdapter::showTagNames() const  
 {  
    stringstream temp;  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    Finley_TagMap* tag_map=mesh->TagMap;  
    while (tag_map) {  
       temp << tag_map->name;  
       tag_map=tag_map->next;  
       if (tag_map) temp << ", ";  
    }  
    return temp.str();  
2090  }  }
2091    
2092  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2093  {  {
2094    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2095    dim_t numTags=0;      switch(functionSpaceCode) {
2096    switch(functionSpaceCode) {          case Nodes:
2097     case(Nodes):              return mesh->Nodes->tagsInUse.size();
2098            numTags=mesh->Nodes->numTagsInUse;          case ReducedNodes:
2099            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2100     case(ReducedNodes):          case DegreesOfFreedom:
2101            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2102            break;          case ReducedDegreesOfFreedom:
2103     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2104            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2105            break;          case ReducedElements:
2106     case(ReducedDegreesOfFreedom):              return mesh->Elements->tagsInUse.size();
2107            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2108            break;          case ReducedFaceElements:
2109     case(Elements):              return mesh->FaceElements->tagsInUse.size();
2110     case(ReducedElements):          case Points:
2111            numTags=mesh->Elements->numTagsInUse;              return mesh->Points->tagsInUse.size();
2112            break;          case ContactElementsZero:
2113     case(FaceElements):          case ReducedContactElementsZero:
2114     case(ReducedFaceElements):          case ContactElementsOne:
2115            numTags=mesh->FaceElements->numTagsInUse;          case ReducedContactElementsOne:
2116            break;              return mesh->ContactElements->tagsInUse.size();
2117     case(Points):          default:
2118            numTags=mesh->Points->numTagsInUse;              stringstream ss;
2119            break;              ss << "Finley does not know anything about function space type "
2120     case(ContactElementsZero):                   << functionSpaceCode;
2121     case(ReducedContactElementsZero):              throw FinleyAdapterException(ss.str());
2122     case(ContactElementsOne):      }
2123     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;  
2124  }  }
2125    
2126  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2127  {  {
2128    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2129    index_t* tags=NULL;      switch(functionSpaceCode) {
2130    switch(functionSpaceCode) {          case Nodes:
2131     case(Nodes):              return &mesh->Nodes->tagsInUse[0];
2132            tags=mesh->Nodes->tagsInUse;          case ReducedNodes:
2133            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2134     case(ReducedNodes):          case DegreesOfFreedom:
2135            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2136            break;          case ReducedDegreesOfFreedom:
2137     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2138            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2139            break;          case ReducedElements:
2140     case(ReducedDegreesOfFreedom):              return &mesh->Elements->tagsInUse[0];
2141            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2142            break;          case ReducedFaceElements:
2143     case(Elements):              return &mesh->FaceElements->tagsInUse[0];
2144     case(ReducedElements):          case Points:
2145            tags=mesh->Elements->tagsInUse;              return &mesh->Points->tagsInUse[0];
2146            break;          case ContactElementsZero:
2147     case(FaceElements):          case ReducedContactElementsZero:
2148     case(ReducedFaceElements):          case ContactElementsOne:
2149            tags=mesh->FaceElements->tagsInUse;          case ReducedContactElementsOne:
2150            break;              return &mesh->ContactElements->tagsInUse[0];
2151     case(Points):          default:
2152            tags=mesh->Points->tagsInUse;              stringstream temp;
2153            break;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2154     case(ContactElementsZero):              throw FinleyAdapterException(temp.str());
2155     case(ReducedContactElementsZero):      }
2156     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;  
2157  }  }
2158    
2159    
2160  bool MeshAdapter::canTag(int functionSpaceCode) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2161  {  {
2162    switch(functionSpaceCode) {      switch(functionSpaceCode) {
2163     case(Nodes):          case Nodes:
2164     case(Elements):          case Elements:
2165     case(ReducedElements):          case ReducedElements:
2166     case(FaceElements):          case FaceElements:
2167     case(ReducedFaceElements):          case ReducedFaceElements:
2168     case(Points):          case Points:
2169     case(ContactElementsZero):          case ContactElementsZero:
2170     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
2171     case(ContactElementsOne):          case ContactElementsOne:
2172     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
2173            return true;              return true;
2174     case(ReducedNodes):          default:
2175     case(DegreesOfFreedom):              return false;
2176     case(ReducedDegreesOfFreedom):      }
2177        return false;  }
2178     default:  
2179      return false;  escript::AbstractDomain::StatusType MeshAdapter::getStatus() const
2180    }  {
2181        Finley_Mesh* mesh=m_finleyMesh.get();
2182        return Finley_Mesh_getStatus(mesh);
2183  }  }
2184    
2185  AbstractDomain::StatusType MeshAdapter::getStatus() const  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2186  {  {
2187    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2188    return Finley_Mesh_getStatus(mesh);      int order =-1;
2189        switch(functionSpaceCode) {
2190            case Nodes:
2191            case DegreesOfFreedom:
2192                order=mesh->approximationOrder;
2193                break;
2194            case ReducedNodes:
2195            case ReducedDegreesOfFreedom:
2196                order=mesh->reducedApproximationOrder;
2197                break;
2198            case Elements:
2199            case FaceElements:
2200            case Points:
2201            case ContactElementsZero:
2202            case ContactElementsOne:
2203                order=mesh->integrationOrder;
2204                break;
2205            case ReducedElements:
2206            case ReducedFaceElements:
2207            case ReducedContactElementsZero:
2208            case ReducedContactElementsOne:
2209                order=mesh->reducedIntegrationOrder;
2210                break;
2211            default:
2212                stringstream temp;
2213                temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2214                throw FinleyAdapterException(temp.str());
2215        }
2216        return order;
2217    }
2218    
2219    bool MeshAdapter::supportsContactElements() const
2220    {
2221        return true;
2222    }
2223    
2224    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id,
2225            index_t order, index_t reducedOrder)
2226    {
2227        m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2228    }
2229    
2230    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2231    {
2232        Finley_ReferenceElementSet_dealloc(m_refSet);
2233  }  }
2234    
2235    void MeshAdapter::addDiracPoints(const vector<double>& points,
2236                                     const vector<int>& tags) const
2237    {
2238        // points will be flattened
2239        const int dim = getDim();
2240        int numPoints=points.size()/dim;
2241        int numTags=tags.size();
2242        Finley_Mesh* mesh=m_finleyMesh.get();
2243    
2244        if ( points.size() % dim != 0 ) {
2245            throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2246        }
2247    
2248        if ((numTags > 0) && (numPoints != numTags))
2249            throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2250    
2251        Finley_Mesh_addPoints(mesh, numPoints, &points[0], &tags[0]);
2252        checkFinleyError();
2253    }
2254    
2255    // void MeshAdapter::addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2256    // {
2257    //       const int dim = getDim();
2258    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2259    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2260    //       Finley_Mesh* mesh=m_finleyMesh.get();
2261    //
2262    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2263    //       throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2264    //
2265    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2266    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2267    //
2268    //       for (int i=0;i<numPoints;++i) {
2269    //         int tag_id=-1;
2270    //         int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2271    //         if  ( numComps !=   dim ) {
2272    //                stringstream temp;
2273    //                temp << "Error - illegal number of components " << numComps << " for point " << i;
2274    //                throw FinleyAdapterException(temp.str());
2275    //         }
2276    //         points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2277    //         if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2278    //         if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2279    //
2280    //         if ( numTags > 0) {
2281    //                boost::python::extract<string> ex_str(tags[i]);
2282    //                if  ( ex_str.check() ) {
2283    //                    tag_id=getTag( ex_str());
2284    //                } else {
2285    //                     boost::python::extract<int> ex_int(tags[i]);
2286    //                     if ( ex_int.check() ) {
2287    //                         tag_id=ex_int();
2288    //                     } else {
2289    //                          stringstream temp;
2290    //                          temp << "Error - unable to extract tag for point " << i;
2291    //                          throw FinleyAdapterException(temp.str());
2292    //                    }
2293    //                }
2294    //         }
2295    //            tags_ptr[i]=tag_id;
2296    //       }
2297    //
2298    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2299    //       checkPasoError();
2300    //
2301    //       TMPMEMFREE(points_ptr);
2302    //       TMPMEMFREE(tags_ptr);
2303    // }
2304    
2305    /*
2306    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2307    {
2308        boost::python::list points =  boost::python::list();
2309        boost::python::list tags =  boost::python::list();
2310        points.append(point);
2311        tags.append(tag);
2312        addDiracPoints(points, tags);
2313    }
2314    */
2315    
2316    /*
2317    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const string& tag) const
2318    {
2319        boost::python::list points =   boost::python::list();
2320        boost::python::list tags =   boost::python::list();
2321        points.append(point);
2322        tags.append(tag);
2323        addDiracPoints(points, tags);
2324    }
2325    */
2326  }  // end of namespace  }  // end of namespace
2327    

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