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

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revision 1347 by ksteube, Fri Nov 16 05:37:07 2007 UTC revision 3998 by caltinay, Thu Sep 27 01:17:28 2012 UTC
# Line 1  Line 1 
1    
2  /* $Id$ */  /*****************************************************************************
3    *
4  /*******************************************************  * Copyright (c) 2003-2012 by University of Queensland
5   *  * http://www.uq.edu.au
6   *           Copyright 2003-2007 by ACceSS MNRF  *
7   *       Copyright 2007 by University of Queensland  * Primary Business: Queensland, Australia
8   *  * Licensed under the Open Software License version 3.0
9   *                http://esscc.uq.edu.au  * http://www.opensource.org/licenses/osl-3.0.php
10   *        Primary Business: Queensland, Australia  *
11   *  Licensed under the Open Software License version 3.0  * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12   *     http://www.opensource.org/licenses/osl-3.0.php  * 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"
# Line 20  Line 22 
22  #include <netcdfcpp.h>  #include <netcdfcpp.h>
23  #endif  #endif
24  extern "C" {  extern "C" {
25  #include "escript/blocktimer.h"  #include "esysUtils/blocktimer.h"
26  }  }
27  #include <vector>  
28    #include <boost/python/import.hpp>
29    
30  using namespace std;  using namespace std;
31  using namespace escript;  using namespace escript;
32    using namespace paso;
33    
34  namespace finley {  namespace finley {
35    
# Line 48  const int MeshAdapter::ReducedContactEle Line 52  const int MeshAdapter::ReducedContactEle
52    
53  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
54  {  {
55    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
56    //     //
57    // need to use a null_deleter as Finley_Mesh_free deletes the pointer     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
58    // for us.     // for us.
59    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
60  }  }
61    
62  //  //
# Line 60  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 64  MeshAdapter::MeshAdapter(Finley_Mesh* fi
64  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
65  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
66  {  {
67    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
68  }  }
69    
70  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
71  {  {
72    //     //
73    // I hope the case for the pointer being zero has been taken care of.     // I hope the case for the pointer being zero has been taken care of.
74    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
75    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
76      Finley_Mesh_free(m_finleyMesh.get());        Finley_Mesh_free(m_finleyMesh.get());
77    }     }
78  }  }
79    
80  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
# Line 81  int MeshAdapter::getMPIRank() const Line 85  int MeshAdapter::getMPIRank() const
85  {  {
86     return m_finleyMesh.get()->MPIInfo->rank;     return m_finleyMesh.get()->MPIInfo->rank;
87  }  }
88    void MeshAdapter::MPIBarrier() const
89    {
90    #ifdef ESYS_MPI
91       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
92    #endif
93       return;
94    }
95    bool MeshAdapter::onMasterProcessor() const
96    {
97       return m_finleyMesh.get()->MPIInfo->rank == 0;
98    }
99    
100    
101    #ifdef ESYS_MPI
102      MPI_Comm
103    #else
104      unsigned int
105    #endif
106    MeshAdapter::getMPIComm() const
107    {
108    #ifdef ESYS_MPI
109        return m_finleyMesh->MPIInfo->comm;
110    #else
111        return 0;
112    #endif
113    }
114    
115    
116  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
117     return m_finleyMesh.get();     return m_finleyMesh.get();
118  }  }
119    
120  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
121  {  {
122    char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
123    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
124    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
125    checkFinleyError();     checkFinleyError();
126    TMPMEMFREE(fName);     TMPMEMFREE(fName);
127  }  }
128    
129  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  void MeshAdapter::Print_Mesh_Info(const bool full) const
130  {  {
131    Finley_PrintMesh_Info(m_finleyMesh.get(), full);     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
132  }  }
133    
134  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const string& fileName) const
135  {  {
136  #ifdef USE_NETCDF  #ifdef USE_NETCDF
137     const NcDim* ncdims[12];     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
138     NcVar *ids, *data;     NcVar *ids;
139     int *int_ptr;     int *int_ptr;
140     Finley_Mesh *mesh = m_finleyMesh.get();     Finley_Mesh *mesh = m_finleyMesh.get();
141     Finley_TagMap* tag_map;     Finley_TagMap* tag_map;
# Line 121  void MeshAdapter::dump(const std::string Line 151  void MeshAdapter::dump(const std::string
151     int num_Elements_numNodes        = mesh->Elements->numNodes;     int num_Elements_numNodes        = mesh->Elements->numNodes;
152     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
153     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
154     char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank);  #ifdef ESYS_MPI
155       MPI_Status status;
156    #endif
157    
158    /* Incoming token indicates it's my turn to write */
159    #ifdef ESYS_MPI
160       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
161    #endif
162    
163       char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
164                                                         mpi_size, mpi_rank);
165    
166     /* Figure out how much storage is required for tags */     /* Figure out how much storage is required for tags */
167     tag_map = mesh->TagMap;     tag_map = mesh->TagMap;
168     if (tag_map) {     num_Tags = 0;
169       while (tag_map) {     while (tag_map) {
170      num_Tags++;        num_Tags++;
171          tag_map=tag_map->next;        tag_map=tag_map->next;
      }  
172     }     }
173    
174     // NetCDF error handler     // NetCDF error handler
175     NcError err(NcError::verbose_nonfatal);     NcError err(NcError::verbose_nonfatal);
176     // Create the file.     // Create the file.
177     NcFile dataFile(newFileName, NcFile::Replace);     NcFile dataFile(newFileName, NcFile::Replace);
178       string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
179     // check if writing was successful     // check if writing was successful
180     if (!dataFile.is_valid())     if (!dataFile.is_valid())
181          throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);        throw DataException(msgPrefix+"Open file for output");
182    
183     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)     // Define dimensions (num_Elements and dim_Elements are identical,
184       // dim_Elements only appears if > 0)
185     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
186          throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_dim(numNodes)");
187     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
188          throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_dim(numDim)");
189     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
190          throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_dim(mpi_size)");
191     if (num_Elements>0)     if (num_Elements>0)
192        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
193          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_Elements)");
194     if (num_FaceElements>0)     if (num_FaceElements>0)
195        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
196          throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_FaceElements)");
197     if (num_ContactElements>0)     if (num_ContactElements>0)
198        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
199          throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_ContactElements)");
200     if (num_Points>0)     if (num_Points>0)
201        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
202          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_Points)");
203     if (num_Elements>0)     if (num_Elements>0)
204        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
205          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_Elements_Nodes)");
206     if (num_FaceElements>0)     if (num_FaceElements>0)
207        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
208          throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
209     if (num_ContactElements>0)     if (num_ContactElements>0)
210        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
211          throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
212     if (num_Tags>0)     if (num_Tags>0)
213        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
214          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_Tags)");
215    
216     // Attributes: MPI size, MPI rank, Name, order, reduced_order     // Attributes: MPI size, MPI rank, Name, order, reduced_order
217     if (!dataFile.add_att("mpi_size", mpi_size) )     if (!dataFile.add_att("mpi_size", mpi_size) )
218          throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(mpi_size)");
219     if (!dataFile.add_att("mpi_rank", mpi_rank) )     if (!dataFile.add_att("mpi_rank", mpi_rank) )
220          throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(mpi_rank)");
221     if (!dataFile.add_att("Name",mesh->Name) )     if (!dataFile.add_att("Name",mesh->Name) )
222          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(Name)");
223     if (!dataFile.add_att("numDim",numDim) )     if (!dataFile.add_att("numDim",numDim) )
224          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(order)");
225     if (!dataFile.add_att("order",mesh->order) )     if (!dataFile.add_att("order",mesh->integrationOrder) )
226          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(order)");
227     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )     if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
228          throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(reduced_order)");
229     if (!dataFile.add_att("numNodes",numNodes) )     if (!dataFile.add_att("numNodes",numNodes) )
230          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(numNodes)");
231     if (!dataFile.add_att("num_Elements",num_Elements) )     if (!dataFile.add_att("num_Elements",num_Elements) )
232          throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_Elements)");
233     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
234          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_FaceElements)");
235     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
236          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_ContactElements)");
237     if (!dataFile.add_att("num_Points",num_Points) )     if (!dataFile.add_att("num_Points",num_Points) )
238          throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_Points)");
239     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
240          throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_Elements_numNodes)");
241     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
242          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_FaceElements_numNodes)");
243     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
244          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_ContactElements_numNodes)");
245     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
246        throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(Elements_TypeId)");
247     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
248        throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(FaceElements_TypeId)");
249     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
250        throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(ContactElements_TypeId)");
251     if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
252        throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(Points_TypeId)");
253     if (!dataFile.add_att("num_Tags", num_Tags) )     if (!dataFile.add_att("num_Tags", num_Tags) )
254        throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_Tags)");
255    
256     // // // // // Nodes // // // // //     // // // // // Nodes // // // // //
257    
258     // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)     // Nodes nodeDistribution
259     if (numNodes>0) {     if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
260          throw DataException(msgPrefix+"add_var(Nodes_NodeDistribution)");
261     // Nodes Id     int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
262     if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )     if (! (ids->put(int_ptr, mpi_size+1)) )
263          throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"put(Nodes_NodeDistribution)");
    int_ptr = &mesh->Nodes->Id[0];  
    if (! (ids->put(int_ptr, numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);  
   
    // Nodes Tag  
    if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )  
         throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);  
    int_ptr = &mesh->Nodes->Tag[0];  
    if (! (ids->put(int_ptr, numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);  
   
    // Nodes gDOF  
    if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )  
         throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);  
    int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];  
    if (! (ids->put(int_ptr, numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);  
   
    // Nodes global node index  
    if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )  
         throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);  
    int_ptr = &mesh->Nodes->globalNodesIndex[0];  
    if (! (ids->put(int_ptr, numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);  
   
    // Nodes grDof  
    if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )  
         throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);  
    int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];  
    if (! (ids->put(int_ptr, numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);  
   
    // Nodes grNI  
    if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )  
         throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);  
    int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];  
    if (! (ids->put(int_ptr, numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);  
   
    // Nodes Coordinates  
    if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);  
    if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )  
         throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);  
264    
265     // Nodes degreesOfFreedomDistribution     // Nodes degreesOfFreedomDistribution
266     if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )     if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
267          throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_var(Nodes_DofDistribution)");
268     int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];     int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
269     if (! (ids->put(int_ptr, mpi_size+1)) )     if (! (ids->put(int_ptr, mpi_size+1)) )
270          throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);        throw DataException(msgPrefix+"put(Nodes_DofDistribution)");
271    
272       // Only write nodes if non-empty because NetCDF doesn't like empty arrays
273       // (it treats them as NC_UNLIMITED)
274       if (numNodes>0) {
275    
276          // Nodes Id
277          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
278             throw DataException(msgPrefix+"add_var(Nodes_Id)");
279          int_ptr = &mesh->Nodes->Id[0];
280          if (! (ids->put(int_ptr, numNodes)) )
281             throw DataException(msgPrefix+"put(Nodes_Id)");
282    
283          // Nodes Tag
284          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
285             throw DataException(msgPrefix+"add_var(Nodes_Tag)");
286          int_ptr = &mesh->Nodes->Tag[0];
287          if (! (ids->put(int_ptr, numNodes)) )
288             throw DataException(msgPrefix+"put(Nodes_Tag)");
289    
290          // Nodes gDOF
291          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
292             throw DataException(msgPrefix+"add_var(Nodes_gDOF)");
293          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
294          if (! (ids->put(int_ptr, numNodes)) )
295             throw DataException(msgPrefix+"put(Nodes_gDOF)");
296    
297          // Nodes global node index
298          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
299             throw DataException(msgPrefix+"add_var(Nodes_gNI)");
300          int_ptr = &mesh->Nodes->globalNodesIndex[0];
301          if (! (ids->put(int_ptr, numNodes)) )
302             throw DataException(msgPrefix+"put(Nodes_gNI)");
303    
304          // Nodes grDof
305          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
306             throw DataException(msgPrefix+"add_var(Nodes_grDfI)");
307          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
308          if (! (ids->put(int_ptr, numNodes)) )
309             throw DataException(msgPrefix+"put(Nodes_grDfI)");
310    
311          // Nodes grNI
312          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
313             throw DataException(msgPrefix+"add_var(Nodes_grNI)");
314          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
315          if (! (ids->put(int_ptr, numNodes)) )
316             throw DataException(msgPrefix+"put(Nodes_grNI)");
317    
318          // Nodes Coordinates
319          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
320             throw DataException(msgPrefix+"add_var(Nodes_Coordinates)");
321          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
322             throw DataException(msgPrefix+"put(Nodes_Coordinates)");
323    
324     }     }
325    
# Line 278  void MeshAdapter::dump(const std::string Line 327  void MeshAdapter::dump(const std::string
327    
328     if (num_Elements>0) {     if (num_Elements>0) {
329    
330       // Temp storage to gather node IDs        // Elements_Id
331       int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
332             throw DataException(msgPrefix+"add_var(Elements_Id)");
333       // Elements_Id        int_ptr = &mesh->Elements->Id[0];
334       if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
335          throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Id)");
336       int_ptr = &mesh->Elements->Id[0];  
337       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Tag
338          throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
339             throw DataException(msgPrefix+"add_var(Elements_Tag)");
340       // Elements_Tag        int_ptr = &mesh->Elements->Tag[0];
341       if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
342          throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Tag)");
343       int_ptr = &mesh->Elements->Tag[0];  
344       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Owner
345          throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
346             throw DataException(msgPrefix+"add_var(Elements_Owner)");
347       // Elements_Owner        int_ptr = &mesh->Elements->Owner[0];
348       if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
349          throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Owner)");
350       int_ptr = &mesh->Elements->Owner[0];  
351       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Color
352          throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
353             throw DataException(msgPrefix+"add_var(Elements_Color)");
354       // Elements_Color        int_ptr = &mesh->Elements->Color[0];
355       if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
356          throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Color)");
357       int_ptr = &mesh->Elements->Color[0];  
358       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Nodes
359          throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
360             throw DataException(msgPrefix+"add_var(Elements_Nodes)");
361       // Elements_Nodes        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
362       for (int i=0; i<num_Elements; i++)           throw DataException(msgPrefix+"put(Elements_Nodes)");
        for (int j=0; j<num_Elements_numNodes; j++)  
          Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]];  
      if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(Elements_Nodes);  
363    
364     }     }
365    
# Line 326  void MeshAdapter::dump(const std::string Line 367  void MeshAdapter::dump(const std::string
367    
368     if (num_FaceElements>0) {     if (num_FaceElements>0) {
369    
370       // Temp storage to gather node IDs        // FaceElements_Id
371       int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
372             throw DataException(msgPrefix+"add_var(FaceElements_Id)");
373       // FaceElements_Id        int_ptr = &mesh->FaceElements->Id[0];
374       if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
375          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Id)");
376       int_ptr = &mesh->FaceElements->Id[0];  
377       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Tag
378          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
379             throw DataException(msgPrefix+"add_var(FaceElements_Tag)");
380       // FaceElements_Tag        int_ptr = &mesh->FaceElements->Tag[0];
381       if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
382          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Tag)");
383       int_ptr = &mesh->FaceElements->Tag[0];  
384       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Owner
385          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
386             throw DataException(msgPrefix+"add_var(FaceElements_Owner)");
387       // FaceElements_Owner        int_ptr = &mesh->FaceElements->Owner[0];
388       if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
389          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Owner)");
390       int_ptr = &mesh->FaceElements->Owner[0];  
391       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Color
392          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
393             throw DataException(msgPrefix+"add_var(FaceElements_Color)");
394       // FaceElements_Color        int_ptr = &mesh->FaceElements->Color[0];
395       if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
396          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Color)");
397       int_ptr = &mesh->FaceElements->Color[0];  
398       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Nodes
399          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
400             throw DataException(msgPrefix+"add_var(FaceElements_Nodes)");
401       // FaceElements_Nodes        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
402       for (int i=0; i<num_FaceElements; i++)           throw DataException(msgPrefix+"put(FaceElements_Nodes)");
        for (int j=0; j<num_FaceElements_numNodes; j++)  
          FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]];  
      if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(FaceElements_Nodes);  
403    
404     }     }
405    
# Line 374  void MeshAdapter::dump(const std::string Line 407  void MeshAdapter::dump(const std::string
407    
408     if (num_ContactElements>0) {     if (num_ContactElements>0) {
409    
410       // Temp storage to gather node IDs        // ContactElements_Id
411       int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
412             throw DataException(msgPrefix+"add_var(ContactElements_Id)");
413       // ContactElements_Id        int_ptr = &mesh->ContactElements->Id[0];
414       if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
415          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Id)");
416       int_ptr = &mesh->ContactElements->Id[0];  
417       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Tag
418          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
419             throw DataException(msgPrefix+"add_var(ContactElements_Tag)");
420       // ContactElements_Tag        int_ptr = &mesh->ContactElements->Tag[0];
421       if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
422          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Tag)");
423       int_ptr = &mesh->ContactElements->Tag[0];  
424       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Owner
425          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
426             throw DataException(msgPrefix+"add_var(ContactElements_Owner)");
427       // ContactElements_Owner        int_ptr = &mesh->ContactElements->Owner[0];
428       if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
429          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Owner)");
430       int_ptr = &mesh->ContactElements->Owner[0];  
431       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Color
432          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
433             throw DataException(msgPrefix+"add_var(ContactElements_Color)");
434       // ContactElements_Color        int_ptr = &mesh->ContactElements->Color[0];
435       if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
436          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Color)");
437       int_ptr = &mesh->ContactElements->Color[0];  
438       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Nodes
439          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
440             throw DataException(msgPrefix+"add_var(ContactElements_Nodes)");
441       // ContactElements_Nodes        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
442       for (int i=0; i<num_ContactElements; i++)           throw DataException(msgPrefix+"put(ContactElements_Nodes)");
        for (int j=0; j<num_ContactElements_numNodes; j++)  
          ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]];  
      if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(ContactElements_Nodes);  
443    
444     }     }
445    
# Line 422  void MeshAdapter::dump(const std::string Line 447  void MeshAdapter::dump(const std::string
447    
448     if (num_Points>0) {     if (num_Points>0) {
449    
450       fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");        fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
   
      // Temp storage to gather node IDs  
      int *Points_Nodes = TMPMEMALLOC(num_Points,int);  
451    
452       // Points_Id        // Points_Id
453       if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
454          throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Id)");
455       int_ptr = &mesh->Points->Id[0];        int_ptr = &mesh->Points->Id[0];
456       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
457          throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Id)");
458    
459       // Points_Tag        // Points_Tag
460       if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
461          throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Tag)");
462       int_ptr = &mesh->Points->Tag[0];        int_ptr = &mesh->Points->Tag[0];
463       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
464          throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Tag)");
465    
466       // Points_Owner        // Points_Owner
467       if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
468          throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Owner)");
469       int_ptr = &mesh->Points->Owner[0];        int_ptr = &mesh->Points->Owner[0];
470       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
471          throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Owner)");
472    
473       // Points_Color        // Points_Color
474       if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
475          throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Color)");
476       int_ptr = &mesh->Points->Color[0];        int_ptr = &mesh->Points->Color[0];
477       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
478          throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Color)");
479    
480       // Points_Nodes        // Points_Nodes
481       // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
482       for (int i=0; i<num_Points; i++)        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
483         Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];           throw DataException(msgPrefix+"add_var(Points_Nodes)");
484       if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
485          throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Nodes)");
      if (! (ids->put(&(Points_Nodes[0]), num_Points)) )  
         throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(Points_Nodes);  
486    
487     }     }
488    
# Line 472  void MeshAdapter::dump(const std::string Line 490  void MeshAdapter::dump(const std::string
490    
491     if (num_Tags>0) {     if (num_Tags>0) {
492    
493       // Temp storage to gather node IDs        // Temp storage to gather node IDs
494       int *Tags_keys = TMPMEMALLOC(num_Tags, int);        int *Tags_keys = TMPMEMALLOC(num_Tags, int);
495       char name_temp[4096];        char name_temp[4096];
496    
497       /* Copy tag data into temp arrays */        /* Copy tag data into temp arrays */
498       tag_map = mesh->TagMap;        tag_map = mesh->TagMap;
499       if (tag_map) {        if (tag_map) {
500         int i = 0;           int i = 0;
501         while (tag_map) {           while (tag_map) {
502      Tags_keys[i++] = tag_map->tag_key;              Tags_keys[i++] = tag_map->tag_key;
503          tag_map=tag_map->next;              tag_map=tag_map->next;
504         }           }
505       }        }
   
      // 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++;  
        }  
      }  
506    
507       TMPMEMFREE(Tags_keys);        // Tags_keys
508          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
509             throw DataException(msgPrefix+"add_var(Tags_keys)");
510          int_ptr = &Tags_keys[0];
511          if (! (ids->put(int_ptr, num_Tags)) )
512             throw DataException(msgPrefix+"put(Tags_keys)");
513    
514          // Tags_names_*
515          // This is an array of strings, it should be stored as an array but
516          // instead I have hacked in one attribute per string because the NetCDF
517          // manual doesn't tell how to do an array of strings
518          tag_map = mesh->TagMap;
519          if (tag_map) {
520             int i = 0;
521             while (tag_map) {
522                sprintf(name_temp, "Tags_name_%d", i);
523                if (!dataFile.add_att(name_temp, tag_map->name) )
524                   throw DataException(msgPrefix+"add_att(Tags_names_XX)");
525                tag_map=tag_map->next;
526                i++;
527             }
528          }
529    
530          TMPMEMFREE(Tags_keys);
531     }     }
532    
533    /* Send token to next MPI process so he can take his turn */
534    #ifdef ESYS_MPI
535       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
536    #endif
537    
538     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
539    
540  #else  #else
541     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.");
542  #endif  /* USE_NETCDF */  #endif  /* USE_NETCDF */
# Line 522  void MeshAdapter::dump(const std::string Line 545  void MeshAdapter::dump(const std::string
545    
546  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
547  {  {
548    return "FinleyMesh";     return "FinleyMesh";
549  }  }
550    
551  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
552  {  {
553    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
554    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
555    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
556      return "Invalid function space type code.";        return "Invalid function space type code.";
557    } else {     } else {
558      return loc->second;        return loc->second;
559    }     }
560  }  }
561    
562  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
563  {  {
564    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
565    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
566    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
567  }  }
568    
569  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
570  {  {
571    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
572      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
573    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
574      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
575    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
576      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
577    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
578      (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
579    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
580      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
581    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
582      (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
583    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
584      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
585    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
586      (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
587    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
588      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
589    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
590      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
591    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
592      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
593    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
594      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
595    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
596      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
597  }  }
598    
599  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
600  {  {
601    return Nodes;     return Nodes;
602  }  }
603  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
604  {  {
605    return ReducedNodes;     return ReducedNodes;
606  }  }
607    
608  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
609  {  {
610    return Elements;     return Elements;
611  }  }
612  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
613  {  {
614    return ReducedElements;     return ReducedElements;
615  }  }
616    
617  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
618  {  {
619    return FaceElements;     return FaceElements;
620  }  }
621  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
622  {  {
623    return ReducedFaceElements;     return ReducedFaceElements;
624  }  }
625    
626  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
627  {  {
628    return ContactElementsZero;     return ContactElementsZero;
629  }  }
630  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
631  {  {
632    return ReducedContactElementsZero;     return ReducedContactElementsZero;
633  }  }
634    
635  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
636  {  {
637    return ContactElementsOne;     return ContactElementsOne;
638  }  }
639  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
640  {  {
641    return ReducedContactElementsOne;     return ReducedContactElementsOne;
642  }  }
643    
644  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
645  {  {
646    return DegreesOfFreedom;     return DegreesOfFreedom;
647  }  }
648    
649  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
650  {  {
651    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
652  }  }
653    
654  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
655  {  {
656    return Points;     return Points;
657  }  }
658    
659  //  //
# Line 638  int MeshAdapter::getDiracDeltaFunctionCo Line 661  int MeshAdapter::getDiracDeltaFunctionCo
661  //  //
662  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
663  {  {
664    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     Finley_Mesh* mesh=m_finleyMesh.get();
665    checkFinleyError();     int numDim=Finley_Mesh_getDim(mesh);
666    return numDim;     checkFinleyError();
667       return numDim;
668    }
669    
670    //
671    // Return the number of data points summed across all MPI processes
672    //
673    int MeshAdapter::getNumDataPointsGlobal() const
674    {
675       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
676  }  }
677    
678  //  //
# Line 653  pair<int,int> MeshAdapter::getDataShape( Line 685  pair<int,int> MeshAdapter::getDataShape(
685     int numSamples=0;     int numSamples=0;
686     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
687     switch (functionSpaceCode) {     switch (functionSpaceCode) {
688        case(Nodes):     case(Nodes):
689             numDataPointsPerSample=1;     numDataPointsPerSample=1;
690             numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
691             break;     break;
692        case(ReducedNodes):     case(ReducedNodes):
693             numDataPointsPerSample=1;     numDataPointsPerSample=1;
694             numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
695             break;     break;
696        case(Elements):     case(Elements):
697             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
698               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
699               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
700             }     }
701             break;     break;
702        case(ReducedElements):     case(ReducedElements):
703             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
704               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
705               numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
706             }     }
707             break;     break;
708        case(FaceElements):     case(FaceElements):
709             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
710                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
711                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
712             }     }
713             break;     break;
714        case(ReducedFaceElements):     case(ReducedFaceElements):
715             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
716                  numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
717                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
718             }     }
719             break;     break;
720        case(Points):     case(Points):
721             if (mesh->Points!=NULL) {     if (mesh->Points!=NULL) {
722               numDataPointsPerSample=1;        numDataPointsPerSample=1;
723               numSamples=mesh->Points->numElements;        numSamples=mesh->Points->numElements;
724             }     }
725             break;     break;
726        case(ContactElementsZero):     case(ContactElementsZero):
727             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
728               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
729               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
730             }     }
731             break;     break;
732        case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
733             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
734               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
735               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
736             }     }
737             break;     break;
738        case(ContactElementsOne):     case(ContactElementsOne):
739             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
740               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
741               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
742             }     }
743             break;     break;
744        case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
745             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
746               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
747               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
748             }     }
749             break;     break;
750        case(DegreesOfFreedom):     case(DegreesOfFreedom):
751             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
752               numDataPointsPerSample=1;        numDataPointsPerSample=1;
753               numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
754             }     }
755             break;     break;
756        case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
757             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
758               numDataPointsPerSample=1;        numDataPointsPerSample=1;
759               numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
760             }     }
761             break;     break;
762        default:     default:
763          stringstream temp;        stringstream temp;
764          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
765          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
766          break;        break;
767        }     }
768        return pair<int,int>(numDataPointsPerSample,numSamples);     return pair<int,int>(numDataPointsPerSample,numSamples);
769  }  }
770    
771  //  //
772  // adds linear PDE of second order into a given stiffness matrix and right hand side:  // adds linear PDE of second order into a given stiffness matrix and right hand side:
773  //  //
774  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
775                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   AbstractSystemMatrix& mat, escript::Data& rhs,
776                       const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,                                   const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
777                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
778                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact,
779  {                                   const escript::Data& d_dirac,const escript::Data& y_dirac) const
780    {
781       SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
782       if (smat==0)
783       {
784        throw FinleyAdapterException("finley only supports Paso system matrices.");
785       }
786     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
787     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
788     escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
# Line 756  void MeshAdapter::addPDEToSystem( Line 794  void MeshAdapter::addPDEToSystem(
794     escriptDataC _y=y.getDataC();     escriptDataC _y=y.getDataC();
795     escriptDataC _d_contact=d_contact.getDataC();     escriptDataC _d_contact=d_contact.getDataC();
796     escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
797       escriptDataC _d_dirac=d_dirac.getDataC();
798       escriptDataC _y_dirac=y_dirac.getDataC();
799    
800     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
801    
802     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,smat->getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
803       checkFinleyError();
804    
805       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, smat->getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
806     checkFinleyError();     checkFinleyError();
807    
808     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
809     checkFinleyError();     checkFinleyError();
810    
811     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );      Finley_Assemble_PDE(mesh->Nodes,mesh->Points, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
812     checkFinleyError();     checkFinleyError();
813  }  }
814    
815  void  MeshAdapter::addPDEToLumpedSystem(  void  MeshAdapter::addPDEToLumpedSystem(
816                       escript::Data& mat,                                          escript::Data& mat,
817                       const escript::Data& D,                                          const escript::Data& D,
818                       const escript::Data& d) const                                          const escript::Data& d,
819                                            const escript::Data& d_dirac,
820                                            const bool useHRZ) const
821  {  {
822     escriptDataC _mat=mat.getDataC();     escriptDataC _mat=mat.getDataC();
823     escriptDataC _D=D.getDataC();     escriptDataC _D=D.getDataC();
824     escriptDataC _d=d.getDataC();     escriptDataC _d=d.getDataC();
825       escriptDataC _d_dirac=d_dirac.getDataC();
826    
827     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
828    
829     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D, useHRZ);
830     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);     checkFinleyError();
831      
832       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d, useHRZ);
833       checkFinleyError();
834    
835       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Points,&_mat, &_d_dirac, useHRZ);
836     checkFinleyError();     checkFinleyError();
837    
838  }  }
839    
840    
841  //  //
842  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
843  //  //
844  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,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact,  const escript::Data& y_dirac) const
845  {  {
846     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
847    
# Line 799  void MeshAdapter::addPDEToRHS( escript:: Line 850  void MeshAdapter::addPDEToRHS( escript::
850     escriptDataC _Y=Y.getDataC();     escriptDataC _Y=Y.getDataC();
851     escriptDataC _y=y.getDataC();     escriptDataC _y=y.getDataC();
852     escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
853       escriptDataC _y_dirac=y_dirac.getDataC();
854    
855     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
856     checkFinleyError();     checkFinleyError();
# Line 808  void MeshAdapter::addPDEToRHS( escript:: Line 860  void MeshAdapter::addPDEToRHS( escript::
860    
861     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
862     checkFinleyError();     checkFinleyError();
863    
864       Finley_Assemble_PDE(mesh->Nodes,mesh->Points, 0, &_rhs , 0, 0, 0, 0, 0, &_y_dirac );
865       checkFinleyError();
866    
867    }
868    //
869    // adds PDE of second order into a transport problem
870    //
871    void MeshAdapter::addPDEToTransportProblem(
872                                               AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,
873                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
874                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
875                                               const escript::Data& d, const escript::Data& y,
876                                               const escript::Data& d_contact,const escript::Data& y_contact,
877                                               const escript::Data& d_dirac, const escript::Data& y_dirac) const
878    {
879       TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
880       if (tpa==0)
881       {
882        throw FinleyAdapterException("finley only supports Paso transport problems.");
883       }
884    
885    
886       DataTypes::ShapeType shape;
887       source.expand();
888       escriptDataC _source=source.getDataC();
889       escriptDataC _M=M.getDataC();
890       escriptDataC _A=A.getDataC();
891       escriptDataC _B=B.getDataC();
892       escriptDataC _C=C.getDataC();
893       escriptDataC _D=D.getDataC();
894       escriptDataC _X=X.getDataC();
895       escriptDataC _Y=Y.getDataC();
896       escriptDataC _d=d.getDataC();
897       escriptDataC _y=y.getDataC();
898       escriptDataC _d_contact=d_contact.getDataC();
899       escriptDataC _y_contact=y_contact.getDataC();
900       escriptDataC _d_dirac=d_dirac.getDataC();
901       escriptDataC _y_dirac=y_dirac.getDataC();
902    
903    
904       Finley_Mesh* mesh=m_finleyMesh.get();
905       Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
906    
907       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
908       checkFinleyError();
909    
910       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
911       checkFinleyError();
912    
913       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
914       checkFinleyError();
915    
916       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
917       checkFinleyError();
918    
919       Finley_Assemble_PDE(mesh->Nodes,mesh->Points, _tp->transport_matrix, &_source , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
920       checkFinleyError();
921    
922  }  }
923    
924  //  //
# Line 815  void MeshAdapter::addPDEToRHS( escript:: Line 926  void MeshAdapter::addPDEToRHS( escript::
926  //  //
927  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
928  {  {
929    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
930    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
931    if (inDomain!=*this)       if (inDomain!=*this)  
932      throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
933    if (targetDomain!=*this)     if (targetDomain!=*this)
934      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
935    
936    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
937    escriptDataC _target=target.getDataC();     escriptDataC _target=target.getDataC();
938    escriptDataC _in=in.getDataC();     escriptDataC _in=in.getDataC();
939    switch(in.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
940       case(Nodes):     case(Nodes):
941          switch(target.getFunctionSpace().getTypeCode()) {        switch(target.getFunctionSpace().getTypeCode()) {
942             case(Nodes):        case(Nodes):
943             case(ReducedNodes):        case(ReducedNodes):
944             case(DegreesOfFreedom):        case(DegreesOfFreedom):
945             case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
946                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
947                 break;        break;
948             case(Elements):        case(Elements):
949             case(ReducedElements):        case(ReducedElements):
950                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
951                 break;        break;
952             case(FaceElements):        case(FaceElements):
953             case(ReducedFaceElements):        case(ReducedFaceElements):
954                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
955                 break;        break;
956             case(Points):        case(Points):
957                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
958                 break;        break;
959             case(ContactElementsZero):        case(ContactElementsZero):
960             case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
961                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
962                 break;        break;
963             case(ContactElementsOne):        case(ContactElementsOne):
964             case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
965                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
966                 break;        break;
967             default:        default:
968                 stringstream temp;           stringstream temp;
969                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
970                 throw FinleyAdapterException(temp.str());           throw FinleyAdapterException(temp.str());
971                 break;           break;
972          }        }
973          break;        break;
974       case(ReducedNodes):     case(ReducedNodes):
975          switch(target.getFunctionSpace().getTypeCode()) {        switch(target.getFunctionSpace().getTypeCode()) {
976             case(Nodes):        case(Nodes):
977             case(ReducedNodes):        case(ReducedNodes):
978             case(DegreesOfFreedom):        case(DegreesOfFreedom):
979             case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
980                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
981                 break;        break;
982             case(Elements):        case(Elements):
983             case(ReducedElements):        case(ReducedElements):
984                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
985                 break;        break;
986             case(FaceElements):        case(FaceElements):
987             case(ReducedFaceElements):        case(ReducedFaceElements):
988                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
989                 break;        break;
990             case(Points):        case(Points):
991                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
992                 break;        break;
993             case(ContactElementsZero):        case(ContactElementsZero):
994             case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
995                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
996                 break;        break;
997             case(ContactElementsOne):        case(ContactElementsOne):
998             case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
999                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1000                 break;        break;
1001             default:        default:
1002                 stringstream temp;           stringstream temp;
1003                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1004                 throw FinleyAdapterException(temp.str());           throw FinleyAdapterException(temp.str());
1005                 break;           break;
1006          }        }
1007          break;        break;
1008       case(Elements):     case(Elements):
1009          if (target.getFunctionSpace().getTypeCode()==Elements) {        if (target.getFunctionSpace().getTypeCode()==Elements) {
1010             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
1011          } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
1012             Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
1013          } else {        } else {
1014             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
1015          }        }
1016          break;        break;
1017       case(ReducedElements):     case(ReducedElements):
1018          if (target.getFunctionSpace().getTypeCode()==ReducedElements) {        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
1019             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
1020          } else {        } else {
1021             throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
1022          }        }
1023          break;        break;
1024       case(FaceElements):     case(FaceElements):
1025          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
1026             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1027          } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1028             Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
1029          } else {        } else {
1030             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
1031         }        }
1032         break;        break;
1033       case(ReducedFaceElements):     case(ReducedFaceElements):
1034          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1035             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1036          } else {        } else {
1037             throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
1038         }        }
1039         break;        break;
1040       case(Points):     case(Points):
1041          if (target.getFunctionSpace().getTypeCode()==Points) {        if (target.getFunctionSpace().getTypeCode()==Points) {
1042             Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1043          } else {        } else {
1044             throw FinleyAdapterException("Error - No interpolation with data on points possible.");           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1045          }        }
1046          break;        break;
1047       case(ContactElementsZero):     case(ContactElementsZero):
1048       case(ContactElementsOne):     case(ContactElementsOne):
1049          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1050             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1051          } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1052             Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
1053          } else {        } else {
1054             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1055             break;        }
1056          }        break;
1057          break;     case(ReducedContactElementsZero):
1058       case(ReducedContactElementsZero):     case(ReducedContactElementsOne):
1059       case(ReducedContactElementsOne):        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1060          if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1061             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);        } else {
1062          } else {           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1063             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");        }
1064             break;        break;
1065          }     case(DegreesOfFreedom):      
1066          break;        switch(target.getFunctionSpace().getTypeCode()) {
1067       case(DegreesOfFreedom):              case(ReducedDegreesOfFreedom):
1068          switch(target.getFunctionSpace().getTypeCode()) {        case(DegreesOfFreedom):
1069             case(ReducedDegreesOfFreedom):        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1070             case(DegreesOfFreedom):        break;
1071                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);    
1072                break;        case(Nodes):
1073          case(ReducedNodes):
1074             case(Nodes):        if (getMPISize()>1) {
1075             case(ReducedNodes):           escript::Data temp=escript::Data(in);
1076                if (getMPISize()>1) {           temp.expand();
1077                    escript::Data temp=escript::Data(in);           escriptDataC _in2 = temp.getDataC();
1078                    temp.expand();           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1079                    escriptDataC _in2 = temp.getDataC();        } else {
1080                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1081                } else {        }
1082                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        break;
1083                }        case(Elements):
1084                break;        case(ReducedElements):
1085             case(Elements):        if (getMPISize()>1) {
1086             case(ReducedElements):           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1087                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1088                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1089                   escriptDataC _in2 = temp.getDataC();        } else {
1090                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1091                } else {        }
1092                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        break;
1093                }        case(FaceElements):
1094                break;        case(ReducedFaceElements):
1095             case(FaceElements):        if (getMPISize()>1) {
1096             case(ReducedFaceElements):           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1097                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1098                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1099                   escriptDataC _in2 = temp.getDataC();    
1100                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);        } else {
1101             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1102                } else {        }
1103                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        break;
1104                }        case(Points):
1105                break;        if (getMPISize()>1) {
1106             case(Points):           //escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1107                if (getMPISize()>1) {           //escriptDataC _in2 = temp.getDataC();
1108                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        } else {
1109                   escriptDataC _in2 = temp.getDataC();           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1110                } else {        }
1111                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        break;
1112                }        case(ContactElementsZero):
1113                break;        case(ContactElementsOne):
1114             case(ContactElementsZero):        case(ReducedContactElementsZero):
1115             case(ContactElementsOne):        case(ReducedContactElementsOne):
1116             case(ReducedContactElementsZero):        if (getMPISize()>1) {
1117             case(ReducedContactElementsOne):           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1118                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1119                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1120                   escriptDataC _in2 = temp.getDataC();        } else {
1121                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1122                } else {        }
1123                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        break;
1124                }        default:
1125               break;           stringstream temp;
1126             default:           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1127               stringstream temp;           throw FinleyAdapterException(temp.str());
1128               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           break;
1129               throw FinleyAdapterException(temp.str());        }
1130               break;        break;
1131          }     case(ReducedDegreesOfFreedom):
1132          break;        switch(target.getFunctionSpace().getTypeCode()) {
1133       case(ReducedDegreesOfFreedom):        case(Nodes):
1134         switch(target.getFunctionSpace().getTypeCode()) {        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1135            case(Nodes):        break;
1136               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");        case(ReducedNodes):
1137               break;        if (getMPISize()>1) {
1138            case(ReducedNodes):           escript::Data temp=escript::Data(in);
1139                if (getMPISize()>1) {           temp.expand();
1140                    escript::Data temp=escript::Data(in);           escriptDataC _in2 = temp.getDataC();
1141                    temp.expand();           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1142                    escriptDataC _in2 = temp.getDataC();        } else {
1143                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1144                } else {        }
1145                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        break;
1146                }        case(DegreesOfFreedom):
1147                break;        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1148            case(DegreesOfFreedom):        break;
1149               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");        case(ReducedDegreesOfFreedom):
1150               break;        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1151            case(ReducedDegreesOfFreedom):        break;
1152               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        case(Elements):
1153               break;        case(ReducedElements):
1154            case(Elements):        if (getMPISize()>1) {
1155            case(ReducedElements):           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1156                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1157                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1158                   escriptDataC _in2 = temp.getDataC();        } else {
1159                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1160                } else {        }
1161                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        break;
1162               }        case(FaceElements):
1163               break;        case(ReducedFaceElements):
1164            case(FaceElements):        if (getMPISize()>1) {
1165            case(ReducedFaceElements):           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1166                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1167                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1168                   escriptDataC _in2 = temp.getDataC();        } else {
1169                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1170                } else {        }
1171                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        break;
1172                }        case(Points):
1173               break;        if (getMPISize()>1) {
1174            case(Points):           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1175                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1176                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1177                   escriptDataC _in2 = temp.getDataC();        } else {
1178                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1179                } else {        }
1180                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        break;
1181               }        case(ContactElementsZero):
1182               break;        case(ContactElementsOne):
1183            case(ContactElementsZero):        case(ReducedContactElementsZero):
1184            case(ContactElementsOne):        case(ReducedContactElementsOne):
1185            case(ReducedContactElementsZero):        if (getMPISize()>1) {
1186            case(ReducedContactElementsOne):           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1187                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1188                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1189                   escriptDataC _in2 = temp.getDataC();        } else {
1190                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1191                } else {        }
1192                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        break;
1193               }        default:
1194               break;           stringstream temp;
1195            default:           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1196               stringstream temp;           throw FinleyAdapterException(temp.str());
1197               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           break;
1198               throw FinleyAdapterException(temp.str());        }
1199               break;        break;
1200         }     default:
1201         break;        stringstream temp;
1202       default:        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1203          stringstream temp;        throw FinleyAdapterException(temp.str());
1204          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        break;
1205          throw FinleyAdapterException(temp.str());     }
1206          break;     checkFinleyError();
   }  
   checkFinleyError();  
1207  }  }
1208    
1209  //  //
# Line 1102  void MeshAdapter::interpolateOnDomain(es Line 1211  void MeshAdapter::interpolateOnDomain(es
1211  //  //
1212  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1213  {  {
1214    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1215    if (argDomain!=*this)     if (argDomain!=*this)
1216       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1217    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1218    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1219    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1220       escriptDataC _arg=arg.getDataC();        escriptDataC _arg=arg.getDataC();
1221       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1222    } else {     } else {
1223       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);        escript::Data tmp_data=Vector(0.0,continuousFunction(*this),true);
1224       escriptDataC _tmp_data=tmp_data.getDataC();        escriptDataC _tmp_data=tmp_data.getDataC();
1225       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1226       // this is then interpolated onto arg:        // this is then interpolated onto arg:
1227       interpolateOnDomain(arg,tmp_data);        interpolateOnDomain(arg,tmp_data);
1228    }     }
1229    checkFinleyError();     checkFinleyError();
1230  }  }
1231    
1232  //  //
# Line 1125  void MeshAdapter::setToX(escript::Data& Line 1234  void MeshAdapter::setToX(escript::Data&
1234  //  //
1235  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1236  {  {
1237    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1238    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1239       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1240    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1241    escriptDataC _normal=normal.getDataC();     Finley_Mesh* mesh=m_finleyMesh.get();
1242    switch(normal.getFunctionSpace().getTypeCode()) {     escriptDataC _normal=normal.getDataC();
1243      case(Nodes):     switch(normal.getFunctionSpace().getTypeCode()) {
1244        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     case(Nodes):
1245        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1246      case(ReducedNodes):     break;
1247        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");     case(ReducedNodes):
1248        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1249      case(Elements):     break;
1250        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     case(Elements):
1251        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1252      case(ReducedElements):     break;
1253        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");     case(ReducedElements):
1254        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1255      case (FaceElements):     break;
1256        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     case (FaceElements):
1257        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1258      case (ReducedFaceElements):     break;
1259        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     case (ReducedFaceElements):
1260        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1261      case(Points):     break;
1262        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     case(Points):
1263        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1264      case (ContactElementsOne):     break;
1265      case (ContactElementsZero):     case (ContactElementsOne):
1266        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     case (ContactElementsZero):
1267        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1268      case (ReducedContactElementsOne):     break;
1269      case (ReducedContactElementsZero):     case (ReducedContactElementsOne):
1270        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     case (ReducedContactElementsZero):
1271        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1272      case(DegreesOfFreedom):     break;
1273        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case(DegreesOfFreedom):
1274        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1275      case(ReducedDegreesOfFreedom):     break;
1276        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(ReducedDegreesOfFreedom):
1277        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1278      default:     break;
1279       default:
1280        stringstream temp;        stringstream temp;
1281        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1282        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1283        break;        break;
1284    }     }
1285    checkFinleyError();     checkFinleyError();
1286  }  }
1287    
1288  //  //
# Line 1180  void MeshAdapter::setToNormal(escript::D Line 1290  void MeshAdapter::setToNormal(escript::D
1290  //  //
1291  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1292  {  {
1293    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1294    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1295       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1296          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1297    
1298    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1299  }  }
1300    
1301  //  //
1302  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined of arg:
1303  //  //
1304  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(vector<double>& integrals,const escript::Data& arg) const
1305  {  {
1306    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1307    if (argDomain!=*this)     if (argDomain!=*this)
1308       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1309    
1310    double blocktimer_start = blocktimer_time();     double blocktimer_start = blocktimer_time();
1311    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1312    escriptDataC _temp;     escriptDataC _temp;
1313    escript::Data temp;     escript::Data temp;
1314    escriptDataC _arg=arg.getDataC();     escriptDataC _arg=arg.getDataC();
1315    switch(arg.getFunctionSpace().getTypeCode()) {     switch(arg.getFunctionSpace().getTypeCode()) {
1316       case(Nodes):     case(Nodes):
1317          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1318          _temp=temp.getDataC();     _temp=temp.getDataC();
1319          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1320          break;     break;
1321       case(ReducedNodes):     case(ReducedNodes):
1322          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1323          _temp=temp.getDataC();     _temp=temp.getDataC();
1324          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1325          break;     break;
1326       case(Elements):     case(Elements):
1327          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1328          break;     break;
1329       case(ReducedElements):     case(ReducedElements):
1330          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1331          break;     break;
1332       case(FaceElements):     case(FaceElements):
1333          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1334          break;     break;
1335       case(ReducedFaceElements):     case(ReducedFaceElements):
1336          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1337          break;     break;
1338       case(Points):     case(Points):
1339          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1340          break;     break;
1341       case(ContactElementsZero):     case(ContactElementsZero):
1342          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1343          break;     break;
1344       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1345          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1346          break;     break;
1347       case(ContactElementsOne):     case(ContactElementsOne):
1348          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1349          break;     break;
1350       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1351          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1352          break;     break;
1353       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1354          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1355          _temp=temp.getDataC();     _temp=temp.getDataC();
1356          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1357          break;     break;
1358       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1359          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1360          _temp=temp.getDataC();     _temp=temp.getDataC();
1361          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1362          break;     break;
1363       default:     default:
1364          stringstream temp;        stringstream temp;
1365          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();        temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1366          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1367          break;        break;
1368    }     }
1369    checkFinleyError();     checkFinleyError();
1370    blocktimer_increment("integrate()", blocktimer_start);     blocktimer_increment("integrate()", blocktimer_start);
1371  }  }
1372    
1373  //  //
# Line 1264  void MeshAdapter::setToIntegrals(std::ve Line 1375  void MeshAdapter::setToIntegrals(std::ve
1375  //  //
1376  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1377  {  {
1378    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1379    if (argDomain!=*this)     if (argDomain!=*this)
1380      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1381    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1382    if (gradDomain!=*this)     if (gradDomain!=*this)
1383       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1384    
1385    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1386    escriptDataC _grad=grad.getDataC();     escriptDataC _grad=grad.getDataC();
1387    escriptDataC nodeDataC;     escriptDataC nodeDataC;
1388    escript::Data temp;     escript::Data temp;
1389    if (getMPISize()>1) {     if (getMPISize()>1) {
1390        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1391          temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  continuousFunction(*this) );
1392          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1393        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1394          temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  reducedContinuousFunction(*this) );
1395          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1396        } else {        } else {
1397          nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1398        }        }
1399    } else {     } else {
1400       nodeDataC = arg.getDataC();        nodeDataC = arg.getDataC();
1401    }     }
1402    switch(grad.getFunctionSpace().getTypeCode()) {     switch(grad.getFunctionSpace().getTypeCode()) {
1403         case(Nodes):     case(Nodes):
1404            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1405            break;     break;
1406         case(ReducedNodes):     case(ReducedNodes):
1407            throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1408            break;     break;
1409         case(Elements):     case(Elements):
1410            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1411            break;     break;
1412         case(ReducedElements):     case(ReducedElements):
1413            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1414            break;     break;
1415         case(FaceElements):     case(FaceElements):
1416            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1417            break;     break;
1418         case(ReducedFaceElements):     case(ReducedFaceElements):
1419            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1420            break;     break;
1421         case(Points):     case(Points):
1422            throw FinleyAdapterException("Error - Gradient at points is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1423            break;     break;
1424         case(ContactElementsZero):     case(ContactElementsZero):
1425            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1426            break;     break;
1427         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1428            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1429            break;     break;
1430         case(ContactElementsOne):     case(ContactElementsOne):
1431            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1432            break;     break;
1433         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1434            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1435            break;     break;
1436         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1437            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1438            break;     break;
1439         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1440            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1441            break;     break;
1442         default:     default:
1443            stringstream temp;        stringstream temp;
1444            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();        temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1445            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1446            break;        break;
1447    }     }
1448    checkFinleyError();     checkFinleyError();
1449  }  }
1450    
1451  //  //
# Line 1342  void MeshAdapter::setToGradient(escript: Line 1453  void MeshAdapter::setToGradient(escript:
1453  //  //
1454  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1455  {  {
1456    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1457    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1458    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1459         case(Nodes):     case(Nodes):
1460            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1461            break;     break;
1462         case(ReducedNodes):     case(ReducedNodes):
1463            throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1464            break;     break;
1465         case(Elements):     case(Elements):
1466            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1467            break;     break;
1468         case(ReducedElements):     case(ReducedElements):
1469            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1470            break;     break;
1471         case(FaceElements):     case(FaceElements):
1472            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1473            break;     break;
1474         case(ReducedFaceElements):     case(ReducedFaceElements):
1475            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1476            break;     break;
1477         case(Points):     case(Points):
1478            throw FinleyAdapterException("Error - Size of point elements is not supported.");     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1479            break;     break;
1480         case(ContactElementsZero):     case(ContactElementsZero):
1481         case(ContactElementsOne):     case(ContactElementsOne):
1482            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1483            break;     break;
1484         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1485         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1486            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1487            break;     break;
1488         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1489            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1490            break;     break;
1491         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1492            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1493            break;     break;
1494         default:     default:
1495            stringstream temp;        stringstream temp;
1496            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();        temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1497            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1498            break;        break;
1499    }     }
1500    checkFinleyError();     checkFinleyError();
1501  }  }
1502    
1503  // sets the location of nodes:  //
1504    // sets the location of nodes
1505    //
1506  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1507  {  {
1508    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1509    escriptDataC tmp;     escriptDataC tmp;
1510    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1511    if (newDomain!=*this)     if (newDomain!=*this)
1512       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1513    tmp = new_x.getDataC();     if ( new_x.getFunctionSpace() == continuousFunction(*this) ) {
1514    Finley_Mesh_setCoordinates(mesh,&tmp);         tmp = new_x.getDataC();
1515    checkFinleyError();         Finley_Mesh_setCoordinates(mesh,&tmp);
1516  }     } else {
1517           throw FinleyAdapterException("As of version escript3.3 - SetNewX only accepts ContinuousFunction arguments please interpolate.");    
1518  // saves a data array in openDX format:  /*       escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(*this) );
1519  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const         tmp = new_x_inter.getDataC();
1520  {         Finley_Mesh_setCoordinates(mesh,&tmp);*/
1521      int MAX_namelength=256;     }
1522      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     checkFinleyError();
1523    /* win32 refactor */  }
   char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
1524    
1525    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  //
1526    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  // Helper for the save* methods. Extracts optional data variable names and the
1527    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  // corresponding pointers from python dictionary. Caller must free arrays.
1528    //
1529    boost::python::list keys=arg.keys();  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1530    for (int i=0;i<num_data;++i) {  {
1531           std::string n=boost::python::extract<std::string>(keys[i]);     numData = boost::python::extract<int>(arg.attr("__len__")());
1532           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     /* win32 refactor */
1533           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1534               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1535           data[i]=d.getDataC();     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1536           ptr_data[i]=&(data[i]);  
1537           c_names[i]=&(names[i][0]);     boost::python::list keys=arg.keys();
1538           if (n.length()>MAX_namelength-1) {     for (int i=0; i<numData; ++i) {
1539              strncpy(c_names[i],n.c_str(),MAX_namelength-1);        string n=boost::python::extract<string>(keys[i]);
1540              c_names[i][MAX_namelength-1]='\0';        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1541           } else {        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1542              strcpy(c_names[i],n.c_str());           throw FinleyAdapterException("Error: Data must be defined on same Domain");
1543           }        data[i] = d.getDataC();
1544      }        dataPtr[i] = &(data[i]);
1545      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);        names[i] = TMPMEMALLOC(n.length()+1, char);
1546      checkFinleyError();        strcpy(names[i], n.c_str());
1547           }
1548        /* win32 refactor */  }
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1549    
1550      return;  //
1551    // saves mesh and optionally data arrays in openDX format
1552    //
1553    void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1554    {
1555       int num_data;
1556       char **names;
1557       escriptDataC *data;
1558       escriptDataC **ptr_data;
1559    
1560       extractArgsFromDict(arg, num_data, names, data, ptr_data);
1561       Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1562       checkFinleyError();
1563    
1564       /* win32 refactor */
1565       TMPMEMFREE(data);
1566       TMPMEMFREE(ptr_data);
1567       for(int i=0; i<num_data; i++)
1568       {
1569          TMPMEMFREE(names[i]);
1570       }
1571       TMPMEMFREE(names);
1572  }  }
1573    
1574  // saves a data array in openVTK format:  //
1575  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  // saves mesh and optionally data arrays in VTK format
1576    //
1577    void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1578  {  {
1579      int MAX_namelength=256;      boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("_saveVTK");
1580      const int num_data=boost::python::extract<int>(arg.attr("__len__")());      pySaveVTK(filename, const_cast<MeshAdapter*>(this)->getPtr(),
1581    /* win32 refactor */                metadata, metadata_schema, arg);
1582    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  }
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
1583    
1584    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1585    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  {
1586    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;      if (getMPISize() > 1) {
1587    #ifdef ESYS_MPI
1588      boost::python::list keys=arg.keys();          index_t myFirstNode=0, myLastNode=0, k=0;
1589      for (int i=0;i<num_data;++i) {          index_t* globalNodeIndex=0;
1590           std::string n=boost::python::extract<std::string>(keys[i]);          Finley_Mesh* mesh_p=m_finleyMesh.get();
1591           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);          /*
1592           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)           * this method is only used by saveDataCSV which would use the returned
1593               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");           * values for reduced nodes wrongly so this case is disabled for now
1594           data[i]=d.getDataC();          if (fs_code == FINLEY_REDUCED_NODES)
1595           ptr_data[i]=&(data[i]);          {
1596           c_names[i]=&(names[i][0]);              myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1597           if (n.length()>MAX_namelength-1) {              myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1598              strncpy(c_names[i],n.c_str(),MAX_namelength-1);              globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1599              c_names[i][MAX_namelength-1]='\0';          }
1600           } else {          else
1601              strcpy(c_names[i],n.c_str());          */
1602           }          if (fs_code == FINLEY_NODES)
1603            {
1604                myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1605                myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1606                globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
1607            }
1608            else
1609            {
1610                throw FinleyAdapterException("Unsupported function space type for ownSample()");
1611            }
1612    
1613            k=globalNodeIndex[id];
1614            return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1615    #endif
1616      }      }
1617      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);      return true;
1618    }
1619    
   checkFinleyError();  
   /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1620    
1621      return;  //
1622  }  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1623                                                                                                                                                                            //
1624                                                                                                                                                                            ASM_ptr MeshAdapter::newSystemMatrix(
1625  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:                                                   const int row_blocksize,
1626  SystemMatrixAdapter MeshAdapter::newSystemMatrix(                                                   const escript::FunctionSpace& row_functionspace,
1627                        const int row_blocksize,                                                   const int column_blocksize,
1628                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1629                        const int column_blocksize,                                                   const int type) const
1630                        const escript::FunctionSpace& column_functionspace,  {
1631                        const int type) const     int reduceRowOrder=0;
1632  {     int reduceColOrder=0;
1633      int reduceRowOrder=0;     // is the domain right?
1634      int reduceColOrder=0;     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1635      // is the domain right?     if (row_domain!=*this)
1636      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());        throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1637      if (row_domain!=*this)     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1638            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");     if (col_domain!=*this)
1639      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1640      if (col_domain!=*this)     // is the function space type right
1641            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1642      // is the function space type right        reduceRowOrder=0;
1643      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1644          reduceRowOrder=0;        reduceRowOrder=1;
1645      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else {
1646          reduceRowOrder=1;        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1647      } else {     }
1648          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1649      }        reduceColOrder=0;
1650      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1651          reduceColOrder=0;        reduceColOrder=1;
1652      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else {
1653          reduceColOrder=1;        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1654      } else {     }
1655          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");     // generate matrix:
1656      }  
1657      // generate matrix:     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1658           checkFinleyError();
1659      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrix* fsystemMatrix;
1660      checkFinleyError();     int trilinos = 0;
1661      Paso_SystemMatrix* fsystemMatrix;     if (trilinos) {
     int trilinos = 0;  
     if (trilinos) {  
1662  #ifdef TRILINOS  #ifdef TRILINOS
1663        /* Allocation Epetra_VrbMatrix here */        /* Allocation Epetra_VrbMatrix here */
1664  #endif  #endif
1665      }     }
1666      else {     else {
1667        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1668      }     }
1669      checkPasoError();     checkPasoError();
1670      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1671      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1672       return ASM_ptr(sma);
1673    //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1674    }
1675    
1676    //
1677    // creates a TransportProblemAdapter
1678    //
1679    ATP_ptr MeshAdapter::newTransportProblem(
1680                                                             const int blocksize,
1681                                                             const escript::FunctionSpace& functionspace,
1682                                                             const int type) const
1683    {
1684       int reduceOrder=0;
1685       // is the domain right?
1686       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1687       if (domain!=*this)
1688          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1689       // is the function space type right
1690       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1691          reduceOrder=0;
1692       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1693          reduceOrder=1;
1694       } else {
1695          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1696       }
1697       // generate matrix:
1698    
1699       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1700       checkFinleyError();
1701       Paso_TransportProblem* transportProblem;
1702       transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern,blocksize);
1703       checkPasoError();
1704       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1705       TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,blocksize,functionspace);
1706       return ATP_ptr(tpa);
1707    //   return TransportProblemAdapter(transportProblem, blocksize,functionspace);
1708  }  }
1709    
1710  //  //
# Line 1559  SystemMatrixAdapter MeshAdapter::newSyst Line 1716  SystemMatrixAdapter MeshAdapter::newSyst
1716  // returns true if data at the atom_type is considered as being cell centered:  // returns true if data at the atom_type is considered as being cell centered:
1717  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1718  {  {
1719    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1720         case(Nodes):     case(Nodes):
1721         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1722         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1723            return false;     return false;
1724            break;     break;
1725         case(Elements):     case(Elements):
1726         case(FaceElements):     case(FaceElements):
1727         case(Points):     case(Points):
1728         case(ContactElementsZero):     case(ContactElementsZero):
1729         case(ContactElementsOne):     case(ContactElementsOne):
1730         case(ReducedElements):     case(ReducedElements):
1731         case(ReducedFaceElements):     case(ReducedFaceElements):
1732         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1733         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1734            return true;     return true;
1735            break;     break;
1736         default:     default:
1737            stringstream temp;        stringstream temp;
1738            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1739            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1740            break;        break;
1741    }     }
1742    checkFinleyError();     checkFinleyError();
1743    return false;     return false;
1744    }
1745    
1746    bool
1747    MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1748    {
1749       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1750        class 1: DOF <-> Nodes
1751        class 2: ReducedDOF <-> ReducedNodes
1752        class 3: Points
1753        class 4: Elements
1754        class 5: ReducedElements
1755        class 6: FaceElements
1756        class 7: ReducedFaceElements
1757        class 8: ContactElementZero <-> ContactElementOne
1758        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1759    
1760       There is also a set of lines. Interpolation is possible down a line but not between lines.
1761       class 1 and 2 belong to all lines so aren't considered.
1762        line 0: class 3
1763        line 1: class 4,5
1764        line 2: class 6,7
1765        line 3: class 8,9
1766    
1767       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1768       eg hasnodes is true if we have at least one instance of Nodes.
1769       */
1770        if (fs.empty())
1771        {
1772            return false;
1773        }
1774        vector<int> hasclass(10);
1775        vector<int> hasline(4);
1776        bool hasnodes=false;
1777        bool hasrednodes=false;
1778        bool hascez=false;
1779        bool hasrcez=false;
1780        for (int i=0;i<fs.size();++i)
1781        {
1782        switch(fs[i])
1783        {
1784        case(Nodes):   hasnodes=true;   // no break is deliberate
1785        case(DegreesOfFreedom):
1786            hasclass[1]=1;
1787            break;
1788        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1789        case(ReducedDegreesOfFreedom):
1790            hasclass[2]=1;
1791            break;
1792        case(Points):
1793            hasline[0]=1;
1794            hasclass[3]=1;
1795            break;
1796        case(Elements):
1797            hasclass[4]=1;
1798            hasline[1]=1;
1799            break;
1800        case(ReducedElements):
1801            hasclass[5]=1;
1802            hasline[1]=1;
1803            break;
1804        case(FaceElements):
1805            hasclass[6]=1;
1806            hasline[2]=1;
1807            break;
1808        case(ReducedFaceElements):
1809            hasclass[7]=1;
1810            hasline[2]=1;
1811            break;
1812        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1813        case(ContactElementsOne):
1814            hasclass[8]=1;
1815            hasline[3]=1;
1816            break;
1817        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1818        case(ReducedContactElementsOne):
1819            hasclass[9]=1;
1820            hasline[3]=1;
1821            break;
1822        default:
1823            return false;
1824        }
1825        }
1826        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1827        // fail if we have more than one leaf group
1828    
1829        if (totlines>1)
1830        {
1831        return false;   // there are at least two branches we can't interpolate between
1832        }
1833        else if (totlines==1)
1834        {
1835        if (hasline[0]==1)      // we have points
1836        {
1837            resultcode=Points;
1838        }
1839        else if (hasline[1]==1)
1840        {
1841            if (hasclass[5]==1)
1842            {
1843            resultcode=ReducedElements;
1844            }
1845            else
1846            {
1847            resultcode=Elements;
1848            }
1849        }
1850        else if (hasline[2]==1)
1851        {
1852            if (hasclass[7]==1)
1853            {
1854            resultcode=ReducedFaceElements;
1855            }
1856            else
1857            {
1858            resultcode=FaceElements;
1859            }
1860        }
1861        else    // so we must be in line3
1862        {
1863            if (hasclass[9]==1)
1864            {
1865            // need something from class 9
1866            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1867            }
1868            else
1869            {
1870            // something from class 8
1871            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1872            }
1873        }
1874        }
1875        else    // totlines==0
1876        {
1877        if (hasclass[2]==1)
1878        {
1879            // something from class 2
1880            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1881        }
1882        else
1883        {   // something from class 1
1884            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1885        }
1886        }
1887        return true;
1888  }  }
1889    
1890  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1891  {  {
1892    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1893       case(Nodes):     case(Nodes):
1894          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1895             case(Nodes):      case(Nodes):
1896             case(ReducedNodes):      case(ReducedNodes):
1897             case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1898             case(DegreesOfFreedom):      case(DegreesOfFreedom):
1899             case(Elements):      case(Elements):
1900             case(ReducedElements):      case(ReducedElements):
1901             case(FaceElements):      case(FaceElements):
1902             case(ReducedFaceElements):      case(ReducedFaceElements):
1903             case(Points):      case(Points):
1904             case(ContactElementsZero):      case(ContactElementsZero):
1905             case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1906             case(ContactElementsOne):      case(ContactElementsOne):
1907             case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1908                 return true;      return true;
1909             default:      default:
1910                 stringstream temp;            stringstream temp;
1911                 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;
1912                 throw FinleyAdapterException(temp.str());            throw FinleyAdapterException(temp.str());
1913          }     }
1914          break;     break;
1915       case(ReducedNodes):     case(ReducedNodes):
1916          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1917             case(ReducedNodes):      case(ReducedNodes):
1918             case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1919             case(Elements):      case(Elements):
1920             case(ReducedElements):      case(ReducedElements):
1921             case(FaceElements):      case(FaceElements):
1922             case(ReducedFaceElements):      case(ReducedFaceElements):
1923             case(Points):      case(Points):
1924             case(ContactElementsZero):      case(ContactElementsZero):
1925             case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1926             case(ContactElementsOne):      case(ContactElementsOne):
1927             case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1928                 return true;      return true;
1929            case(Nodes):      case(Nodes):
1930            case(DegreesOfFreedom):      case(DegreesOfFreedom):
1931               return false;      return false;
1932             default:      default:
1933                 stringstream temp;          stringstream temp;
1934                 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;
1935                 throw FinleyAdapterException(temp.str());          throw FinleyAdapterException(temp.str());
1936          }     }
1937          break;     break;
1938       case(Elements):     case(Elements):
1939          if (functionSpaceType_target==Elements) {      if (functionSpaceType_target==Elements) {
1940             return true;        return true;
1941          } else if (functionSpaceType_target==ReducedElements) {      } else if (functionSpaceType_target==ReducedElements) {
1942             return true;        return true;
         } else {  
            return false;  
         }  
      case(ReducedElements):  
         if (functionSpaceType_target==ReducedElements) {  
            return true;  
         } else {  
            return false;  
         }  
      case(FaceElements):  
         if (functionSpaceType_target==FaceElements) {  
            return true;  
         } else if (functionSpaceType_target==ReducedFaceElements) {  
            return true;  
         } else {  
            return false;  
         }  
      case(ReducedFaceElements):  
         if (functionSpaceType_target==ReducedFaceElements) {  
            return true;  
         } else {  
            return false;  
         }  
      case(Points):  
         if (functionSpaceType_target==Points) {  
            return true;  
         } else {  
            return false;  
         }  
      case(ContactElementsZero):  
      case(ContactElementsOne):  
         if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {  
            return true;  
         } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {  
            return true;  
         } else {  
            return false;  
         }  
      case(ReducedContactElementsZero):  
      case(ReducedContactElementsOne):  
         if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {  
            return true;  
1943          } else {          } else {
1944             return false;            return false;
         }  
      case(DegreesOfFreedom):  
         switch(functionSpaceType_target) {  
            case(ReducedDegreesOfFreedom):  
            case(DegreesOfFreedom):  
            case(Nodes):  
            case(ReducedNodes):  
            case(Elements):  
            case(ReducedElements):  
            case(Points):  
            case(FaceElements):  
            case(ReducedFaceElements):  
            case(ContactElementsZero):  
            case(ReducedContactElementsZero):  
            case(ContactElementsOne):  
            case(ReducedContactElementsOne):  
               return true;  
            default:  
              stringstream temp;  
              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;  
              throw FinleyAdapterException(temp.str());  
1945          }          }
1946          break;     case(ReducedElements):
1947       case(ReducedDegreesOfFreedom):      if (functionSpaceType_target==ReducedElements) {
1948         switch(functionSpaceType_target) {        return true;
1949            case(ReducedDegreesOfFreedom):      } else {
1950            case(ReducedNodes):            return false;
1951            case(Elements):      }
1952            case(ReducedElements):     case(FaceElements):
1953            case(FaceElements):      if (functionSpaceType_target==FaceElements) {
1954            case(ReducedFaceElements):              return true;
1955            case(Points):      } else if (functionSpaceType_target==ReducedFaceElements) {
1956            case(ContactElementsZero):              return true;
1957            case(ReducedContactElementsZero):      } else {
1958            case(ContactElementsOne):              return false;
1959            case(ReducedContactElementsOne):      }
1960                return true;     case(ReducedFaceElements):
1961            case(Nodes):      if (functionSpaceType_target==ReducedFaceElements) {
1962            case(DegreesOfFreedom):              return true;
1963               return false;      } else {
1964            default:          return false;
1965               stringstream temp;      }
1966               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1967               throw FinleyAdapterException(temp.str());      if (functionSpaceType_target==Points) {
1968         }              return true;
1969         break;      } else {
1970       default:              return false;
1971          stringstream temp;      }
1972          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1973          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1974          break;      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1975    }              return true;
1976    checkFinleyError();      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1977    return false;              return true;
1978        } else {
1979                return false;
1980        }
1981       case(ReducedContactElementsZero):
1982       case(ReducedContactElementsOne):
1983        if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1984                return true;
1985        } else {
1986                return false;
1987        }
1988       case(DegreesOfFreedom):
1989        switch(functionSpaceType_target) {
1990        case(ReducedDegreesOfFreedom):
1991        case(DegreesOfFreedom):
1992        case(Nodes):
1993        case(ReducedNodes):
1994        case(Elements):
1995        case(ReducedElements):
1996        case(Points):
1997        case(FaceElements):
1998        case(ReducedFaceElements):
1999        case(ContactElementsZero):
2000        case(ReducedContactElementsZero):
2001        case(ContactElementsOne):
2002        case(ReducedContactElementsOne):
2003        return true;
2004        default:
2005            stringstream temp;
2006            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
2007            throw FinleyAdapterException(temp.str());
2008        }
2009        break;
2010       case(ReducedDegreesOfFreedom):
2011       switch(functionSpaceType_target) {
2012        case(ReducedDegreesOfFreedom):
2013        case(ReducedNodes):
2014        case(Elements):
2015        case(ReducedElements):
2016        case(FaceElements):
2017        case(ReducedFaceElements):
2018        case(Points):
2019        case(ContactElementsZero):
2020        case(ReducedContactElementsZero):
2021        case(ContactElementsOne):
2022        case(ReducedContactElementsOne):
2023        return true;
2024        case(Nodes):
2025        case(DegreesOfFreedom):
2026        return false;
2027        default:
2028            stringstream temp;
2029            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
2030            throw FinleyAdapterException(temp.str());
2031        }
2032        break;
2033       default:
2034          stringstream temp;
2035          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
2036          throw FinleyAdapterException(temp.str());
2037          break;
2038       }
2039       checkFinleyError();
2040       return false;
2041  }  }
2042    
2043  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const
2044  {  {
2045      return false;     return false;
2046  }  }
2047    
2048  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
2049  {  {
2050    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
2051    if (temp!=0) {     if (temp!=0) {
2052      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
2053    } else {     } else {
2054      return false;        return false;
2055    }     }
2056  }  }
2057    
2058  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
2059  {  {
2060    return !(operator==(other));     return !(operator==(other));
2061  }  }
2062    
2063  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2064  {  {
2065     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
2066     checkPasoError();     return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
2067     return out;             package, symmetry, mesh->MPIInfo);
2068    }
2069    
2070    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2071    {
2072       Finley_Mesh* mesh=m_finleyMesh.get();
2073       return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
2074               package, symmetry, mesh->MPIInfo);
2075  }  }
2076    
2077  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2078  {  {
2079    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(*this).getX();
2080  }  }
2081    
2082  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2083  {  {
2084    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(*this).getNormal();
2085  }  }
2086    
2087  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2088  {  {
2089    return function(asAbstractContinuousDomain()).getSize();     return escript::function(*this).getSize();
2090  }  }
2091    
2092  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2093  {  {
2094    int *out=0,i;     int *out = NULL;
2095    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2096    switch (functionSpaceType) {     switch (functionSpaceType) {
2097      case(Nodes):     case(Nodes):
2098        out=mesh->Nodes->Id;     out=mesh->Nodes->Id;
2099        break;     break;
2100      case(ReducedNodes):     case(ReducedNodes):
2101        out=mesh->Nodes->reducedNodesId;     out=mesh->Nodes->reducedNodesId;
2102        break;     break;
2103      case(Elements):     case(Elements):
2104        out=mesh->Elements->Id;     out=mesh->Elements->Id;
2105        break;     break;
2106      case(ReducedElements):     case(ReducedElements):
2107        out=mesh->Elements->Id;     out=mesh->Elements->Id;
2108        break;     break;
2109      case(FaceElements):     case(FaceElements):
2110        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
2111        break;     break;
2112      case(ReducedFaceElements):     case(ReducedFaceElements):
2113        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
2114        break;     break;
2115      case(Points):     case(Points):
2116        out=mesh->Points->Id;     out=mesh->Points->Id;
2117        break;     break;
2118      case(ContactElementsZero):     case(ContactElementsZero):
2119        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2120        break;     break;
2121      case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
2122        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2123        break;     break;
2124      case(ContactElementsOne):     case(ContactElementsOne):
2125        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2126        break;     break;
2127      case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
2128        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2129        break;     break;
2130      case(DegreesOfFreedom):     case(DegreesOfFreedom):
2131        out=mesh->Nodes->degreesOfFreedomId;     out=mesh->Nodes->degreesOfFreedomId;
2132        break;     break;
2133      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2134        out=mesh->Nodes->reducedDegreesOfFreedomId;     out=mesh->Nodes->reducedDegreesOfFreedomId;
2135        break;     break;
2136      default:     default:
2137        stringstream temp;        stringstream temp;
2138        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2139        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2140        break;        break;
2141    }     }
2142    return out;     return out;
2143  }  }
2144  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2145  {  {
2146    int out=0;     int out=0;
2147    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2148    switch (functionSpaceType) {     switch (functionSpaceType) {
2149    case(Nodes):     case(Nodes):
2150      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
2151      break;     break;
2152    case(ReducedNodes):     case(ReducedNodes):
2153      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
2154      break;     break;
2155    case(Elements):     case(Elements):
2156      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
2157      break;     break;
2158    case(ReducedElements):     case(ReducedElements):
2159      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
2160      break;     break;
2161    case(FaceElements):     case(FaceElements):
2162      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
2163      break;     break;
2164    case(ReducedFaceElements):     case(ReducedFaceElements):
2165      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
2166      break;     break;
2167    case(Points):     case(Points):
2168      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
2169      break;     break;
2170    case(ContactElementsZero):     case(ContactElementsZero):
2171      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2172      break;     break;
2173    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
2174      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2175      break;     break;
2176    case(ContactElementsOne):     case(ContactElementsOne):
2177      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2178      break;     break;
2179    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
2180      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2181      break;     break;
2182    case(DegreesOfFreedom):     case(DegreesOfFreedom):
2183      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2184      break;     break;
2185    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2186      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2187      break;     break;
2188    default:     default:
2189      stringstream temp;        stringstream temp;
2190      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2191      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2192      break;        break;
2193    }     }
2194    return out;     return out;
2195  }  }
2196    
2197    
2198  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
2199  {  {
2200       Finley_Mesh* mesh=m_finleyMesh.get();
2201       escriptDataC tmp=mask.getDataC();
2202       switch(functionSpaceType) {
2203       case(Nodes):
2204       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
2205       break;
2206       case(ReducedNodes):
2207       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2208       break;
2209       case(DegreesOfFreedom):
2210       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2211       break;
2212       case(ReducedDegreesOfFreedom):
2213       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2214       break;
2215       case(Elements):
2216       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2217       break;
2218       case(ReducedElements):
2219       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2220       break;
2221       case(FaceElements):
2222       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2223       break;
2224       case(ReducedFaceElements):
2225       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2226       break;
2227       case(Points):
2228       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2229       break;
2230       case(ContactElementsZero):
2231       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2232       break;
2233       case(ReducedContactElementsZero):
2234       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2235       break;
2236       case(ContactElementsOne):
2237       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2238       break;
2239       case(ReducedContactElementsOne):
2240       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2241       break;
2242       default:
2243          stringstream temp;
2244          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2245          throw FinleyAdapterException(temp.str());
2246       }
2247       checkFinleyError();
2248       return;
2249    }
2250    
2251    void MeshAdapter::setTagMap(const string& name,  int tag)
2252    {
2253       Finley_Mesh* mesh=m_finleyMesh.get();
2254       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2255       checkFinleyError();
2256       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2257    }
2258    
2259    int MeshAdapter::getTag(const string& name) const
2260    {
2261       Finley_Mesh* mesh=m_finleyMesh.get();
2262       int tag=0;
2263       tag=Finley_Mesh_getTag(mesh, name.c_str());
2264       checkFinleyError();
2265       // throwStandardException("MeshAdapter::getTag is not implemented.");
2266       return tag;
2267    }
2268    
2269    bool MeshAdapter::isValidTagName(const string& name) const
2270    {
2271       Finley_Mesh* mesh=m_finleyMesh.get();
2272       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2273    }
2274    
2275    string MeshAdapter::showTagNames() const
2276    {
2277       stringstream temp;
2278       Finley_Mesh* mesh=m_finleyMesh.get();
2279       Finley_TagMap* tag_map=mesh->TagMap;
2280       while (tag_map) {
2281          temp << tag_map->name;
2282          tag_map=tag_map->next;
2283          if (tag_map) temp << ", ";
2284       }
2285       return temp.str();
2286    }
2287    
2288    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2289    {
2290    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2291    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2292    switch(functionSpaceType) {    switch(functionSpaceCode) {
2293         case(Nodes):     case(Nodes):
2294            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2295            break;            break;
2296         case(ReducedNodes):     case(ReducedNodes):
2297            throw FinleyAdapterException("Error - ReducedNodes does not support tags");            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2298            break;            break;
2299         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2300            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2301            break;            break;
2302         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2303            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2304            break;            break;
2305         case(Elements):     case(Elements):
2306            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2307            break;            numTags=mesh->Elements->numTagsInUse;
2308         case(ReducedElements):            break;
2309            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(FaceElements):
2310            break;     case(ReducedFaceElements):
2311         case(FaceElements):            numTags=mesh->FaceElements->numTagsInUse;
2312            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);            break;
2313            break;     case(Points):
2314         case(ReducedFaceElements):            numTags=mesh->Points->numTagsInUse;
2315            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);            break;
2316       case(ContactElementsZero):
2317       case(ReducedContactElementsZero):
2318       case(ContactElementsOne):
2319       case(ReducedContactElementsOne):
2320              numTags=mesh->ContactElements->numTagsInUse;
2321            break;            break;
2322         case(Points):     default:
2323            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);        stringstream temp;
2324          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2325          throw FinleyAdapterException(temp.str());
2326      }
2327      return numTags;
2328    }
2329    
2330    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2331    {
2332      Finley_Mesh* mesh=m_finleyMesh.get();
2333      index_t* tags=NULL;
2334      switch(functionSpaceCode) {
2335       case(Nodes):
2336              tags=mesh->Nodes->tagsInUse;
2337            break;            break;
2338         case(ContactElementsZero):     case(ReducedNodes):
2339            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2340            break;            break;
2341         case(ReducedContactElementsZero):     case(DegreesOfFreedom):
2342            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2343            break;            break;
2344         case(ContactElementsOne):     case(ReducedDegreesOfFreedom):
2345            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2346            break;            break;
2347         case(ReducedContactElementsOne):     case(Elements):
2348            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2349              tags=mesh->Elements->tagsInUse;
2350              break;
2351       case(FaceElements):
2352       case(ReducedFaceElements):
2353              tags=mesh->FaceElements->tagsInUse;
2354              break;
2355       case(Points):
2356              tags=mesh->Points->tagsInUse;
2357              break;
2358       case(ContactElementsZero):
2359       case(ReducedContactElementsZero):
2360       case(ContactElementsOne):
2361       case(ReducedContactElementsOne):
2362              tags=mesh->ContactElements->tagsInUse;
2363            break;            break;
2364         default:     default:
2365            stringstream temp;        stringstream temp;
2366            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2367            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2368    }    }
2369    checkFinleyError();    return tags;
   return;  
2370  }  }
2371    
2372  void MeshAdapter::setTagMap(const std::string& name,  int tag)  
2373    bool MeshAdapter::canTag(int functionSpaceCode) const
2374  {  {
2375    Finley_Mesh* mesh=m_finleyMesh.get();    switch(functionSpaceCode) {
2376    Finley_Mesh_addTagMap(mesh, name.c_str(),tag);     case(Nodes):
2377    checkPasoError();     case(Elements):
2378    // throwStandardException("MeshAdapter::set TagMap is not implemented.");     case(ReducedElements):
2379       case(FaceElements):
2380       case(ReducedFaceElements):
2381       case(Points):
2382       case(ContactElementsZero):
2383       case(ReducedContactElementsZero):
2384       case(ContactElementsOne):
2385       case(ReducedContactElementsOne):
2386              return true;
2387       case(ReducedNodes):
2388       case(DegreesOfFreedom):
2389       case(ReducedDegreesOfFreedom):
2390          return false;
2391       default:
2392        return false;
2393      }
2394  }  }
2395    
2396  int MeshAdapter::getTag(const std::string& name) const  AbstractDomain::StatusType MeshAdapter::getStatus() const
2397  {  {
2398    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2399    int tag=0;    return Finley_Mesh_getStatus(mesh);
   tag=Finley_Mesh_getTag(mesh, name.c_str());  
   checkPasoError();  
   // throwStandardException("MeshAdapter::getTag is not implemented.");  
   return tag;  
2400  }  }
2401    
2402  bool MeshAdapter::isValidTagName(const std::string& name) const  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2403  {  {
2404      
2405    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2406    return Finley_Mesh_isValidTagName(mesh,name.c_str());    int order =-1;
2407      switch(functionSpaceCode) {
2408       case(Nodes):
2409       case(DegreesOfFreedom):
2410              order=mesh->approximationOrder;
2411              break;
2412       case(ReducedNodes):
2413       case(ReducedDegreesOfFreedom):
2414              order=mesh->reducedApproximationOrder;
2415              break;
2416       case(Elements):
2417       case(FaceElements):
2418       case(Points):
2419       case(ContactElementsZero):
2420       case(ContactElementsOne):
2421              order=mesh->integrationOrder;
2422              break;
2423       case(ReducedElements):
2424       case(ReducedFaceElements):
2425       case(ReducedContactElementsZero):
2426       case(ReducedContactElementsOne):
2427              order=mesh->reducedIntegrationOrder;
2428              break;
2429       default:
2430          stringstream temp;
2431          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2432          throw FinleyAdapterException(temp.str());
2433      }
2434      return order;
2435  }  }
2436    
2437  std::string MeshAdapter::showTagNames() const  bool MeshAdapter::supportsContactElements() const
2438  {  {
2439    stringstream temp;    return true;
   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();  
2440  }  }
2441    
2442    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2443    {
2444      m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2445    }
2446    
2447    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2448    {
2449      Finley_ReferenceElementSet_dealloc(m_refSet);
2450    }
2451    
2452    // points will be flattened
2453    void MeshAdapter:: addDiracPoints(const std::vector<double>& points, const std::vector<int>& tags) const
2454    {
2455          const int dim = getDim();
2456          int numPoints=points.size()/dim;
2457          int numTags=tags.size();
2458          Finley_Mesh* mesh=m_finleyMesh.get();
2459          
2460          if ( points.size() % dim != 0 )
2461          {
2462        throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2463          }
2464          
2465          if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2466         throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2467          
2468          double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2469          int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2470          
2471          for (int i=0;i<numPoints;++i) {
2472           points_ptr[ i * dim     ] = points[i * dim ];
2473           if ( dim > 1 ) points_ptr[ i * dim + 1 ] = points[i * dim + 1];
2474           if ( dim > 2 ) points_ptr[ i * dim + 2 ] = points[i * dim + 2];    
2475               tags_ptr[i]=tags[i];
2476          }
2477          
2478          Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2479          checkFinleyError();
2480          
2481          TMPMEMFREE(points_ptr);
2482          TMPMEMFREE(tags_ptr);
2483    }
2484    
2485    
2486    // void MeshAdapter:: addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2487    // {
2488    //       const int dim = getDim();
2489    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2490    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2491    //       Finley_Mesh* mesh=m_finleyMesh.get();
2492    //      
2493    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2494    //   throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2495    //      
2496    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2497    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2498    //      
2499    //       for (int i=0;i<numPoints;++i) {
2500    //     int tag_id=-1;
2501    //     int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2502    //     if  ( numComps !=   dim ) {
2503    //                stringstream temp;            
2504    //                temp << "Error - illegal number of components " << numComps << " for point " << i;              
2505    //                throw FinleyAdapterException(temp.str());
2506    //     }
2507    //     points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2508    //     if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2509    //     if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2510    //    
2511    //     if ( numTags > 0) {
2512    //            boost::python::extract<string> ex_str(tags[i]);
2513    //        if  ( ex_str.check() ) {
2514    //            tag_id=getTag( ex_str());
2515    //        } else {
2516    //             boost::python::extract<int> ex_int(tags[i]);
2517    //             if ( ex_int.check() ) {
2518    //                 tag_id=ex_int();
2519    //             } else {
2520    //              stringstream temp;          
2521    //                  temp << "Error - unable to extract tag for point " << i;
2522    //              throw FinleyAdapterException(temp.str());
2523    //            }
2524    //        }
2525    //     }      
2526    //            tags_ptr[i]=tag_id;
2527    //       }
2528    //      
2529    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2530    //       checkPasoError();
2531    //      
2532    //       TMPMEMFREE(points_ptr);
2533    //       TMPMEMFREE(tags_ptr);
2534    // }
2535    
2536    /*
2537    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2538    {  
2539        boost::python::list points =  boost::python::list();
2540        boost::python::list tags =  boost::python::list();
2541        points.append(point);
2542        tags.append(tag);
2543        addDiracPoints(points, tags);
2544    }
2545    */
2546    
2547    /*
2548    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const std::string& tag) const
2549    {
2550            boost::python::list points =   boost::python::list();
2551            boost::python::list tags =   boost::python::list();
2552            points.append(point);
2553            tags.append(tag);
2554            addDiracPoints(points, tags);
2555    }
2556    */
2557  }  // end of namespace  }  // end of namespace

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