/[escript]/trunk/finley/src/CPPAdapter/MeshAdapter.cpp
ViewVC logotype

Diff of /trunk/finley/src/CPPAdapter/MeshAdapter.cpp

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1375 by gross, Wed Jan 9 00:15:05 2008 UTC revision 4255 by jfenwick, Wed Feb 27 03:06:21 2013 UTC
# Line 1  Line 1 
1    
2  /* $Id$ */  /*****************************************************************************
3    *
4  /*******************************************************  * Copyright (c) 2003-2013 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);  
   
      // Points_Id  
      if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )  
         throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);  
      int_ptr = &mesh->Points->Id[0];  
      if (! (ids->put(int_ptr, num_Points)) )  
         throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);  
   
      // Points_Tag  
      if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )  
         throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);  
      int_ptr = &mesh->Points->Tag[0];  
      if (! (ids->put(int_ptr, num_Points)) )  
         throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);  
   
      // Points_Owner  
      if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )  
         throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);  
      int_ptr = &mesh->Points->Owner[0];  
      if (! (ids->put(int_ptr, num_Points)) )  
         throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);  
   
      // Points_Color  
      if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )  
         throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);  
      int_ptr = &mesh->Points->Color[0];  
      if (! (ids->put(int_ptr, num_Points)) )  
         throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);  
   
      // Points_Nodes  
      // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]  
      for (int i=0; i<num_Points; i++)  
        Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];  
      if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(Points_Nodes[0]), num_Points)) )  
         throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);  
451    
452       TMPMEMFREE(Points_Nodes);        // Points_Id
453          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
454             throw DataException(msgPrefix+"add_var(Points_Id)");
455          int_ptr = &mesh->Points->Id[0];
456          if (! (ids->put(int_ptr, num_Points)) )
457             throw DataException(msgPrefix+"put(Points_Id)");
458    
459          // Points_Tag
460          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
461             throw DataException(msgPrefix+"add_var(Points_Tag)");
462          int_ptr = &mesh->Points->Tag[0];
463          if (! (ids->put(int_ptr, num_Points)) )
464             throw DataException(msgPrefix+"put(Points_Tag)");
465    
466          // Points_Owner
467          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
468             throw DataException(msgPrefix+"add_var(Points_Owner)");
469          int_ptr = &mesh->Points->Owner[0];
470          if (! (ids->put(int_ptr, num_Points)) )
471             throw DataException(msgPrefix+"put(Points_Owner)");
472    
473          // Points_Color
474          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
475             throw DataException(msgPrefix+"add_var(Points_Color)");
476          int_ptr = &mesh->Points->Color[0];
477          if (! (ids->put(int_ptr, num_Points)) )
478             throw DataException(msgPrefix+"put(Points_Color)");
479    
480          // Points_Nodes
481          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
482          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
483             throw DataException(msgPrefix+"add_var(Points_Nodes)");
484          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
485             throw DataException(msgPrefix+"put(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();     checkFinleyError();
804    
805     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, smat->getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
806     checkFinleyError();     checkFinleyError();
807    
808     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
809       checkFinleyError();
810    
811        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  // adds PDE of second order into a transport problem
870  //  //
871  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
872                       TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,                                             AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,
873                       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,
874                       const escript::Data& d, const escript::Data& y,                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
875                       const escript::Data& d_contact,const escript::Data& y_contact) const                                             const escript::Data& d, const escript::Data& y,
876  {                                             const escript::Data& d_contact,const escript::Data& y_contact,
877     DataArrayView::ShapeType shape;                                             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();     source.expand();
    escript:: Data tmp(0.0,M.getDataPointShape(),tp.getFunctionSpace(),true);  
888     escriptDataC _source=source.getDataC();     escriptDataC _source=source.getDataC();
    escriptDataC _tmp=tmp.getDataC();  
889     escriptDataC _M=M.getDataC();     escriptDataC _M=M.getDataC();
890     escriptDataC _A=A.getDataC();     escriptDataC _A=A.getDataC();
891     escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
# Line 834  void MeshAdapter::addPDEToTransportProbl Line 897  void MeshAdapter::addPDEToTransportProbl
897     escriptDataC _y=y.getDataC();     escriptDataC _y=y.getDataC();
898     escriptDataC _d_contact=d_contact.getDataC();     escriptDataC _d_contact=d_contact.getDataC();
899     escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
900       escriptDataC _d_dirac=d_dirac.getDataC();
901       escriptDataC _y_dirac=y_dirac.getDataC();
902    
    Finley_Mesh* mesh=m_finleyMesh.get();  
    Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();  
     
903    
904     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_tmp, &_M);     Finley_Mesh* mesh=m_finleyMesh.get();
905     checkFinleyError();     Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
    /* add mass matix to lumped mass matrix of transport problem */  
    double* tmp_prt=getSampleData(&_tmp,0);  
    int i;  
    int n=Paso_FCTransportProblem_getTotalNumRows(_tp);  
    #pragma omp parallel for private(i) schedule(static)  
    for (i=0;i<n ;++i) _tp->lumped_mass_matrix[i]+=tmp_prt[i];  
906    
907     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, 0, 0, &_D, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
908     checkFinleyError();     checkFinleyError();
909    
910     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->flux_matrix, &_source, 0, &_B, &_C, 0, 0, 0 );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
911     checkFinleyError();     checkFinleyError();
912    
913     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
# Line 859  void MeshAdapter::addPDEToTransportProbl Line 915  void MeshAdapter::addPDEToTransportProbl
915    
916     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
917     checkFinleyError();     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 866  void MeshAdapter::addPDEToTransportProbl Line 926  void MeshAdapter::addPDEToTransportProbl
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()==ReducedFaceElements) {        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          }        }
1056          break;        break;
1057       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1058       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1059          if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1060             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1061          } else {        } else {
1062             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1063          }        }
1064          break;        break;
1065       case(DegreesOfFreedom):           case(DegreesOfFreedom):      
1066          switch(target.getFunctionSpace().getTypeCode()) {        switch(target.getFunctionSpace().getTypeCode()) {
1067             case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
1068             case(DegreesOfFreedom):        case(DegreesOfFreedom):
1069                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1070                break;        break;
1071      
1072             case(Nodes):        case(Nodes):
1073             case(ReducedNodes):        case(ReducedNodes):
1074                if (getMPISize()>1) {        if (getMPISize()>1) {
1075                    escript::Data temp=escript::Data(in);           escript::Data temp=escript::Data(in);
1076                    temp.expand();           temp.expand();
1077                    escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1078                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1079                } else {        } else {
1080                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1081                }        }
1082                break;        break;
1083             case(Elements):        case(Elements):
1084             case(ReducedElements):        case(ReducedElements):
1085                if (getMPISize()>1) {        if (getMPISize()>1) {
1086                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1087                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1088                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1089                } else {        } else {
1090                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1091                }        }
1092                break;        break;
1093             case(FaceElements):        case(FaceElements):
1094             case(ReducedFaceElements):        case(ReducedFaceElements):
1095                if (getMPISize()>1) {        if (getMPISize()>1) {
1096                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1097                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1098                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1099      
1100                } else {        } else {
1101                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1102                }        }
1103                break;        break;
1104             case(Points):        case(Points):
1105                if (getMPISize()>1) {        if (getMPISize()>1) {
1106                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           //escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1107                   escriptDataC _in2 = temp.getDataC();           //escriptDataC _in2 = temp.getDataC();
1108                } else {        } else {
1109                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1110                }        }
1111                break;        break;
1112             case(ContactElementsZero):        case(ContactElementsZero):
1113             case(ContactElementsOne):        case(ContactElementsOne):
1114             case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
1115             case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
1116                if (getMPISize()>1) {        if (getMPISize()>1) {
1117                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1118                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1119                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1120                } else {        } else {
1121                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1122                }        }
1123               break;        break;
1124             default:        default:
1125               stringstream temp;           stringstream temp;
1126               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();
1127               throw FinleyAdapterException(temp.str());           throw FinleyAdapterException(temp.str());
1128               break;           break;
1129          }        }
1130          break;        break;
1131       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1132         switch(target.getFunctionSpace().getTypeCode()) {        switch(target.getFunctionSpace().getTypeCode()) {
1133            case(Nodes):        case(Nodes):
1134               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1135               break;        break;
1136            case(ReducedNodes):        case(ReducedNodes):
1137                if (getMPISize()>1) {        if (getMPISize()>1) {
1138                    escript::Data temp=escript::Data(in);           escript::Data temp=escript::Data(in);
1139                    temp.expand();           temp.expand();
1140                    escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1141                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1142                } else {        } else {
1143                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1144                }        }
1145                break;        break;
1146            case(DegreesOfFreedom):        case(DegreesOfFreedom):
1147               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1148               break;        break;
1149            case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
1150               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1151               break;        break;
1152            case(Elements):        case(Elements):
1153            case(ReducedElements):        case(ReducedElements):
1154                if (getMPISize()>1) {        if (getMPISize()>1) {
1155                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1156                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1157                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1158                } else {        } else {
1159                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1160               }        }
1161               break;        break;
1162            case(FaceElements):        case(FaceElements):
1163            case(ReducedFaceElements):        case(ReducedFaceElements):
1164                if (getMPISize()>1) {        if (getMPISize()>1) {
1165                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1166                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1167                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1168                } else {        } else {
1169                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1170                }        }
1171               break;        break;
1172            case(Points):        case(Points):
1173                if (getMPISize()>1) {        if (getMPISize()>1) {
1174                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1175                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1176                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1177                } else {        } else {
1178                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1179               }        }
1180               break;        break;
1181            case(ContactElementsZero):        case(ContactElementsZero):
1182            case(ContactElementsOne):        case(ContactElementsOne):
1183            case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
1184            case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
1185                if (getMPISize()>1) {        if (getMPISize()>1) {
1186                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1187                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1188                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1189                } else {        } else {
1190                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1191               }        }
1192               break;        break;
1193            default:        default:
1194               stringstream temp;           stringstream temp;
1195               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();
1196               throw FinleyAdapterException(temp.str());           throw FinleyAdapterException(temp.str());
1197               break;           break;
1198         }        }
1199         break;        break;
1200       default:     default:
1201          stringstream temp;        stringstream temp;
1202          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1203          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1204          break;        break;
1205    }     }
1206    checkFinleyError();     checkFinleyError();
1207  }  }
1208    
1209  //  //
# Line 1151  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 1174  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 1229  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 1313  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 1391  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();
   /* 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;  
   }  
   
   char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  
   escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  
   escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
   boost::python::list keys=arg.keys();  
   for (int i=0;i<num_data;++i) {  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
     checkFinleyError();  
       
       /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
   
     return;  
1523  }  }
1524    
1525  // saves a data array in openVTK format:  bool MeshAdapter::ownSample(int fs_code, index_t id) const
 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  
1526  {  {
1527      int MAX_namelength=256;      if (getMPISize() > 1) {
1528      const int num_data=boost::python::extract<int>(arg.attr("__len__")());  #ifdef ESYS_MPI
1529    /* win32 refactor */          index_t myFirstNode=0, myLastNode=0, k=0;
1530    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;          index_t* globalNodeIndex=0;
1531    for(int i=0;i<num_data;i++)          Finley_Mesh* mesh_p=m_finleyMesh.get();
1532    {          /*
1533      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;           * this method is only used by saveDataCSV which would use the returned
1534    }           * values for reduced nodes wrongly so this case is disabled for now
1535            if (fs_code == FINLEY_REDUCED_NODES)
1536            {
1537                myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1538                myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1539                globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1540            }
1541            else
1542            */
1543            if (fs_code == FINLEY_NODES)
1544            {
1545                myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1546                myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1547                globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
1548            }
1549            else
1550            {
1551                throw FinleyAdapterException("Unsupported function space type for ownSample()");
1552            }
1553    
1554    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;          k=globalNodeIndex[id];
1555    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;          return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1556    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  #endif
   
     boost::python::list keys=arg.keys();  
     for (int i=0;i<num_data;++i) {  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
1557      }      }
1558      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);      return true;
1559    }
1560    
   checkFinleyError();  
   /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1561    
1562      return;  //
1563  }  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1564                                                                                                                                                                            //
1565                                                                                                                                                                            ASM_ptr MeshAdapter::newSystemMatrix(
1566  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:                                                   const int row_blocksize,
1567  SystemMatrixAdapter MeshAdapter::newSystemMatrix(                                                   const escript::FunctionSpace& row_functionspace,
1568                        const int row_blocksize,                                                   const int column_blocksize,
1569                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1570                        const int column_blocksize,                                                   const int type) const
1571                        const escript::FunctionSpace& column_functionspace,  {
1572                        const int type) const     int reduceRowOrder=0;
1573  {     int reduceColOrder=0;
1574      int reduceRowOrder=0;     // is the domain right?
1575      int reduceColOrder=0;     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1576      // is the domain right?     if (row_domain!=*this)
1577      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.");
1578      if (row_domain!=*this)     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1579            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");     if (col_domain!=*this)
1580      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.");
1581      if (col_domain!=*this)     // is the function space type right
1582            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1583      // is the function space type right        reduceRowOrder=0;
1584      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1585          reduceRowOrder=0;        reduceRowOrder=1;
1586      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else {
1587          reduceRowOrder=1;        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1588      } else {     }
1589          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1590      }        reduceColOrder=0;
1591      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1592          reduceColOrder=0;        reduceColOrder=1;
1593      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else {
1594          reduceColOrder=1;        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1595      } else {     }
1596          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");     // generate matrix:
1597      }  
1598      // generate matrix:     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1599           checkFinleyError();
1600      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrix* fsystemMatrix;
1601      checkFinleyError();     int trilinos = 0;
1602      Paso_SystemMatrix* fsystemMatrix;     if (trilinos) {
     int trilinos = 0;  
     if (trilinos) {  
1603  #ifdef TRILINOS  #ifdef TRILINOS
1604        /* Allocation Epetra_VrbMatrix here */        /* Allocation Epetra_VrbMatrix here */
1605  #endif  #endif
1606      }     }
1607      else {     else {
1608        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1609      }     }
1610      checkPasoError();     checkPasoError();
1611      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1612      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1613       return ASM_ptr(sma);
1614    //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1615  }  }
1616    
1617    //
1618  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1619  TransportProblemAdapter MeshAdapter::newTransportProblem(  //
1620                        const double theta,  ATP_ptr MeshAdapter::newTransportProblem(
1621                        const double dt_max,                                                           const int blocksize,
1622                        const int blocksize,                                                           const escript::FunctionSpace& functionspace,
1623                        const escript::FunctionSpace& functionspace,                                                           const int type) const
1624                        const int type) const  {
1625  {     int reduceOrder=0;
1626      int reduceOrder=0;     // is the domain right?
1627      // is the domain right?     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1628      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());     if (domain!=*this)
1629      if (domain!=*this)        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1630            throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");     // is the function space type right
1631      // is the function space type right     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1632      if (functionspace.getTypeCode()==DegreesOfFreedom) {        reduceOrder=0;
1633          reduceOrder=0;     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1634      } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {        reduceOrder=1;
1635          reduceOrder=1;     } else {
1636      } else {        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1637          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");     }
1638      }     // generate matrix:
1639      // generate matrix:  
1640           Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1641      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);     checkFinleyError();
1642      checkFinleyError();     Paso_TransportProblem* transportProblem;
1643      Paso_FCTransportProblem* transportProblem;     transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern,blocksize);
1644      transportProblem=Paso_FCTransportProblem_alloc(theta,dt_max,fsystemMatrixPattern,blocksize);     checkPasoError();
1645      checkPasoError();     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1646      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,blocksize,functionspace);
1647      return TransportProblemAdapter(transportProblem,theta,dt_max,blocksize,functionspace);     return ATP_ptr(tpa);
1648    //   return TransportProblemAdapter(transportProblem, blocksize,functionspace);
1649  }  }
1650    
1651  //  //
# Line 1639  TransportProblemAdapter MeshAdapter::new Line 1657  TransportProblemAdapter MeshAdapter::new
1657  // 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:
1658  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1659  {  {
1660    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1661         case(Nodes):     case(Nodes):
1662         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1663         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1664            return false;     return false;
1665            break;     break;
1666         case(Elements):     case(Elements):
1667         case(FaceElements):     case(FaceElements):
1668         case(Points):     case(Points):
1669         case(ContactElementsZero):     case(ContactElementsZero):
1670         case(ContactElementsOne):     case(ContactElementsOne):
1671         case(ReducedElements):     case(ReducedElements):
1672         case(ReducedFaceElements):     case(ReducedFaceElements):
1673         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1674         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1675            return true;     return true;
1676            break;     break;
1677         default:     default:
1678            stringstream temp;        stringstream temp;
1679            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;
1680            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1681            break;        break;
1682    }     }
1683    checkFinleyError();     checkFinleyError();
1684    return false;     return false;
1685    }
1686    
1687    bool
1688    MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1689    {
1690       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1691        class 1: DOF <-> Nodes
1692        class 2: ReducedDOF <-> ReducedNodes
1693        class 3: Points
1694        class 4: Elements
1695        class 5: ReducedElements
1696        class 6: FaceElements
1697        class 7: ReducedFaceElements
1698        class 8: ContactElementZero <-> ContactElementOne
1699        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1700    
1701       There is also a set of lines. Interpolation is possible down a line but not between lines.
1702       class 1 and 2 belong to all lines so aren't considered.
1703        line 0: class 3
1704        line 1: class 4,5
1705        line 2: class 6,7
1706        line 3: class 8,9
1707    
1708       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1709       eg hasnodes is true if we have at least one instance of Nodes.
1710       */
1711        if (fs.empty())
1712        {
1713            return false;
1714        }
1715        vector<int> hasclass(10);
1716        vector<int> hasline(4);
1717        bool hasnodes=false;
1718        bool hasrednodes=false;
1719        bool hascez=false;
1720        bool hasrcez=false;
1721        for (int i=0;i<fs.size();++i)
1722        {
1723        switch(fs[i])
1724        {
1725        case(Nodes):   hasnodes=true;   // no break is deliberate
1726        case(DegreesOfFreedom):
1727            hasclass[1]=1;
1728            break;
1729        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1730        case(ReducedDegreesOfFreedom):
1731            hasclass[2]=1;
1732            break;
1733        case(Points):
1734            hasline[0]=1;
1735            hasclass[3]=1;
1736            break;
1737        case(Elements):
1738            hasclass[4]=1;
1739            hasline[1]=1;
1740            break;
1741        case(ReducedElements):
1742            hasclass[5]=1;
1743            hasline[1]=1;
1744            break;
1745        case(FaceElements):
1746            hasclass[6]=1;
1747            hasline[2]=1;
1748            break;
1749        case(ReducedFaceElements):
1750            hasclass[7]=1;
1751            hasline[2]=1;
1752            break;
1753        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1754        case(ContactElementsOne):
1755            hasclass[8]=1;
1756            hasline[3]=1;
1757            break;
1758        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1759        case(ReducedContactElementsOne):
1760            hasclass[9]=1;
1761            hasline[3]=1;
1762            break;
1763        default:
1764            return false;
1765        }
1766        }
1767        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1768        // fail if we have more than one leaf group
1769    
1770        if (totlines>1)
1771        {
1772        return false;   // there are at least two branches we can't interpolate between
1773        }
1774        else if (totlines==1)
1775        {
1776        if (hasline[0]==1)      // we have points
1777        {
1778            resultcode=Points;
1779        }
1780        else if (hasline[1]==1)
1781        {
1782            if (hasclass[5]==1)
1783            {
1784            resultcode=ReducedElements;
1785            }
1786            else
1787            {
1788            resultcode=Elements;
1789            }
1790        }
1791        else if (hasline[2]==1)
1792        {
1793            if (hasclass[7]==1)
1794            {
1795            resultcode=ReducedFaceElements;
1796            }
1797            else
1798            {
1799            resultcode=FaceElements;
1800            }
1801        }
1802        else    // so we must be in line3
1803        {
1804            if (hasclass[9]==1)
1805            {
1806            // need something from class 9
1807            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1808            }
1809            else
1810            {
1811            // something from class 8
1812            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1813            }
1814        }
1815        }
1816        else    // totlines==0
1817        {
1818        if (hasclass[2]==1)
1819        {
1820            // something from class 2
1821            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1822        }
1823        else
1824        {   // something from class 1
1825            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1826        }
1827        }
1828        return true;
1829  }  }
1830    
1831  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1832  {  {
1833    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1834       case(Nodes):     case(Nodes):
1835          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1836             case(Nodes):      case(Nodes):
1837             case(ReducedNodes):      case(ReducedNodes):
1838             case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1839             case(DegreesOfFreedom):      case(DegreesOfFreedom):
1840             case(Elements):      case(Elements):
1841             case(ReducedElements):      case(ReducedElements):
1842             case(FaceElements):      case(FaceElements):
1843             case(ReducedFaceElements):      case(ReducedFaceElements):
1844             case(Points):      case(Points):
1845             case(ContactElementsZero):      case(ContactElementsZero):
1846             case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1847             case(ContactElementsOne):      case(ContactElementsOne):
1848             case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1849                 return true;      return true;
1850             default:      default:
1851                 stringstream temp;            stringstream temp;
1852                 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;
1853                 throw FinleyAdapterException(temp.str());            throw FinleyAdapterException(temp.str());
1854          }     }
1855          break;     break;
1856       case(ReducedNodes):     case(ReducedNodes):
1857          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1858             case(ReducedNodes):      case(ReducedNodes):
1859             case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1860             case(Elements):      case(Elements):
1861             case(ReducedElements):      case(ReducedElements):
1862             case(FaceElements):      case(FaceElements):
1863             case(ReducedFaceElements):      case(ReducedFaceElements):
1864             case(Points):      case(Points):
1865             case(ContactElementsZero):      case(ContactElementsZero):
1866             case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1867             case(ContactElementsOne):      case(ContactElementsOne):
1868             case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1869                 return true;      return true;
1870            case(Nodes):      case(Nodes):
1871            case(DegreesOfFreedom):      case(DegreesOfFreedom):
1872               return false;      return false;
1873             default:      default:
1874                 stringstream temp;          stringstream temp;
1875                 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;
1876                 throw FinleyAdapterException(temp.str());          throw FinleyAdapterException(temp.str());
1877          }     }
1878          break;     break;
1879       case(Elements):     case(Elements):
1880          if (functionSpaceType_target==Elements) {      if (functionSpaceType_target==Elements) {
1881             return true;        return true;
1882          } else if (functionSpaceType_target==ReducedElements) {      } else if (functionSpaceType_target==ReducedElements) {
1883             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;  
1884          } else {          } else {
1885             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());  
1886          }          }
1887          break;     case(ReducedElements):
1888       case(ReducedDegreesOfFreedom):      if (functionSpaceType_target==ReducedElements) {
1889         switch(functionSpaceType_target) {        return true;
1890            case(ReducedDegreesOfFreedom):      } else {
1891            case(ReducedNodes):            return false;
1892            case(Elements):      }
1893            case(ReducedElements):     case(FaceElements):
1894            case(FaceElements):      if (functionSpaceType_target==FaceElements) {
1895            case(ReducedFaceElements):              return true;
1896            case(Points):      } else if (functionSpaceType_target==ReducedFaceElements) {
1897            case(ContactElementsZero):              return true;
1898            case(ReducedContactElementsZero):      } else {
1899            case(ContactElementsOne):              return false;
1900            case(ReducedContactElementsOne):      }
1901                return true;     case(ReducedFaceElements):
1902            case(Nodes):      if (functionSpaceType_target==ReducedFaceElements) {
1903            case(DegreesOfFreedom):              return true;
1904               return false;      } else {
1905            default:          return false;
1906               stringstream temp;      }
1907               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1908               throw FinleyAdapterException(temp.str());      if (functionSpaceType_target==Points) {
1909         }              return true;
1910         break;      } else {
1911       default:              return false;
1912          stringstream temp;      }
1913          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1914          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1915          break;      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1916    }              return true;
1917    checkFinleyError();      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1918    return false;              return true;
1919        } else {
1920                return false;
1921        }
1922       case(ReducedContactElementsZero):
1923       case(ReducedContactElementsOne):
1924        if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1925                return true;
1926        } else {
1927                return false;
1928        }
1929       case(DegreesOfFreedom):
1930        switch(functionSpaceType_target) {
1931        case(ReducedDegreesOfFreedom):
1932        case(DegreesOfFreedom):
1933        case(Nodes):
1934        case(ReducedNodes):
1935        case(Elements):
1936        case(ReducedElements):
1937        case(Points):
1938        case(FaceElements):
1939        case(ReducedFaceElements):
1940        case(ContactElementsZero):
1941        case(ReducedContactElementsZero):
1942        case(ContactElementsOne):
1943        case(ReducedContactElementsOne):
1944        return true;
1945        default:
1946            stringstream temp;
1947            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1948            throw FinleyAdapterException(temp.str());
1949        }
1950        break;
1951       case(ReducedDegreesOfFreedom):
1952       switch(functionSpaceType_target) {
1953        case(ReducedDegreesOfFreedom):
1954        case(ReducedNodes):
1955        case(Elements):
1956        case(ReducedElements):
1957        case(FaceElements):
1958        case(ReducedFaceElements):
1959        case(Points):
1960        case(ContactElementsZero):
1961        case(ReducedContactElementsZero):
1962        case(ContactElementsOne):
1963        case(ReducedContactElementsOne):
1964        return true;
1965        case(Nodes):
1966        case(DegreesOfFreedom):
1967        return false;
1968        default:
1969            stringstream temp;
1970            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1971            throw FinleyAdapterException(temp.str());
1972        }
1973        break;
1974       default:
1975          stringstream temp;
1976          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1977          throw FinleyAdapterException(temp.str());
1978          break;
1979       }
1980       checkFinleyError();
1981       return false;
1982  }  }
1983    
1984    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1985    {
1986        if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1987        {
1988            return 1;
1989        }
1990        else if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1991        {
1992            return -1;
1993        }
1994        return 0;
1995    }  
1996      
1997  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
1998  {  {
1999      return false;     return false;
2000  }  }
2001    
2002  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
2003  {  {
2004    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
2005    if (temp!=0) {     if (temp!=0) {
2006      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
2007    } else {     } else {
2008      return false;        return false;
2009    }     }
2010  }  }
2011    
2012  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
2013  {  {
2014    return !(operator==(other));     return !(operator==(other));
2015  }  }
2016    
2017  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
2018  {  {
2019     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
2020     checkPasoError();     return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
2021     return out;             package, symmetry, mesh->MPIInfo);
2022    }
2023    
2024    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2025    {
2026       Finley_Mesh* mesh=m_finleyMesh.get();
2027       return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
2028               package, symmetry, mesh->MPIInfo);
2029  }  }
2030    
2031  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2032  {  {
2033    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(*this).getX();
2034  }  }
2035    
2036  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2037  {  {
2038    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(*this).getNormal();
2039  }  }
2040    
2041  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2042  {  {
2043    return function(asAbstractContinuousDomain()).getSize();     return escript::function(*this).getSize();
2044  }  }
2045    
2046  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2047  {  {
2048    int *out=0,i;     int *out = NULL;
2049    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2050    switch (functionSpaceType) {     switch (functionSpaceType) {
2051      case(Nodes):     case(Nodes):
2052        out=mesh->Nodes->Id;     out=mesh->Nodes->Id;
2053        break;     break;
2054      case(ReducedNodes):     case(ReducedNodes):
2055        out=mesh->Nodes->reducedNodesId;     out=mesh->Nodes->reducedNodesId;
2056        break;     break;
2057      case(Elements):     case(Elements):
2058        out=mesh->Elements->Id;     out=mesh->Elements->Id;
2059        break;     break;
2060      case(ReducedElements):     case(ReducedElements):
2061        out=mesh->Elements->Id;     out=mesh->Elements->Id;
2062        break;     break;
2063      case(FaceElements):     case(FaceElements):
2064        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
2065        break;     break;
2066      case(ReducedFaceElements):     case(ReducedFaceElements):
2067        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
2068        break;     break;
2069      case(Points):     case(Points):
2070        out=mesh->Points->Id;     out=mesh->Points->Id;
2071        break;     break;
2072      case(ContactElementsZero):     case(ContactElementsZero):
2073        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2074        break;     break;
2075      case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
2076        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2077        break;     break;
2078      case(ContactElementsOne):     case(ContactElementsOne):
2079        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2080        break;     break;
2081      case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
2082        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2083        break;     break;
2084      case(DegreesOfFreedom):     case(DegreesOfFreedom):
2085        out=mesh->Nodes->degreesOfFreedomId;     out=mesh->Nodes->degreesOfFreedomId;
2086        break;     break;
2087      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2088        out=mesh->Nodes->reducedDegreesOfFreedomId;     out=mesh->Nodes->reducedDegreesOfFreedomId;
2089        break;     break;
2090      default:     default:
2091        stringstream temp;        stringstream temp;
2092        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2093        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2094        break;        break;
2095    }     }
2096    return out;     return out;
2097  }  }
2098  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2099  {  {
2100    int out=0;     int out=0;
2101    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2102    switch (functionSpaceType) {     switch (functionSpaceType) {
2103    case(Nodes):     case(Nodes):
2104      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
2105      break;     break;
2106    case(ReducedNodes):     case(ReducedNodes):
2107      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
2108      break;     break;
2109    case(Elements):     case(Elements):
2110      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
2111      break;     break;
2112    case(ReducedElements):     case(ReducedElements):
2113      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
2114      break;     break;
2115    case(FaceElements):     case(FaceElements):
2116      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
2117      break;     break;
2118    case(ReducedFaceElements):     case(ReducedFaceElements):
2119      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
2120      break;     break;
2121    case(Points):     case(Points):
2122      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
2123      break;     break;
2124    case(ContactElementsZero):     case(ContactElementsZero):
2125      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2126      break;     break;
2127    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
2128      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2129      break;     break;
2130    case(ContactElementsOne):     case(ContactElementsOne):
2131      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2132      break;     break;
2133    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
2134      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2135      break;     break;
2136    case(DegreesOfFreedom):     case(DegreesOfFreedom):
2137      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2138      break;     break;
2139    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2140      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2141      break;     break;
2142    default:     default:
2143      stringstream temp;        stringstream temp;
2144      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2145      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2146      break;        break;
2147    }     }
2148    return out;     return out;
2149  }  }
2150    
2151    
2152  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
2153  {  {
2154       Finley_Mesh* mesh=m_finleyMesh.get();
2155       escriptDataC tmp=mask.getDataC();
2156       switch(functionSpaceType) {
2157       case(Nodes):
2158       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
2159       break;
2160       case(ReducedNodes):
2161       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2162       break;
2163       case(DegreesOfFreedom):
2164       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2165       break;
2166       case(ReducedDegreesOfFreedom):
2167       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2168       break;
2169       case(Elements):
2170       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2171       break;
2172       case(ReducedElements):
2173       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2174       break;
2175       case(FaceElements):
2176       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2177       break;
2178       case(ReducedFaceElements):
2179       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2180       break;
2181       case(Points):
2182       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2183       break;
2184       case(ContactElementsZero):
2185       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2186       break;
2187       case(ReducedContactElementsZero):
2188       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2189       break;
2190       case(ContactElementsOne):
2191       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2192       break;
2193       case(ReducedContactElementsOne):
2194       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2195       break;
2196       default:
2197          stringstream temp;
2198          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2199          throw FinleyAdapterException(temp.str());
2200       }
2201       checkFinleyError();
2202       return;
2203    }
2204    
2205    void MeshAdapter::setTagMap(const string& name,  int tag)
2206    {
2207       Finley_Mesh* mesh=m_finleyMesh.get();
2208       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2209       checkFinleyError();
2210       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2211    }
2212    
2213    int MeshAdapter::getTag(const string& name) const
2214    {
2215       Finley_Mesh* mesh=m_finleyMesh.get();
2216       int tag=0;
2217       tag=Finley_Mesh_getTag(mesh, name.c_str());
2218       checkFinleyError();
2219       // throwStandardException("MeshAdapter::getTag is not implemented.");
2220       return tag;
2221    }
2222    
2223    bool MeshAdapter::isValidTagName(const string& name) const
2224    {
2225       Finley_Mesh* mesh=m_finleyMesh.get();
2226       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2227    }
2228    
2229    string MeshAdapter::showTagNames() const
2230    {
2231       stringstream temp;
2232       Finley_Mesh* mesh=m_finleyMesh.get();
2233       Finley_TagMap* tag_map=mesh->TagMap;
2234       while (tag_map) {
2235          temp << tag_map->name;
2236          tag_map=tag_map->next;
2237          if (tag_map) temp << ", ";
2238       }
2239       return temp.str();
2240    }
2241    
2242    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2243    {
2244    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2245    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2246    switch(functionSpaceType) {    switch(functionSpaceCode) {
2247         case(Nodes):     case(Nodes):
2248            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2249            break;            break;
2250         case(ReducedNodes):     case(ReducedNodes):
2251            throw FinleyAdapterException("Error - ReducedNodes does not support tags");            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2252            break;            break;
2253         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2254            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2255            break;            break;
2256         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2257            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2258            break;            break;
2259         case(Elements):     case(Elements):
2260            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2261            break;            numTags=mesh->Elements->numTagsInUse;
2262         case(ReducedElements):            break;
2263            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(FaceElements):
2264            break;     case(ReducedFaceElements):
2265         case(FaceElements):            numTags=mesh->FaceElements->numTagsInUse;
2266            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);            break;
2267       case(Points):
2268              numTags=mesh->Points->numTagsInUse;
2269              break;
2270       case(ContactElementsZero):
2271       case(ReducedContactElementsZero):
2272       case(ContactElementsOne):
2273       case(ReducedContactElementsOne):
2274              numTags=mesh->ContactElements->numTagsInUse;
2275            break;            break;
2276         case(ReducedFaceElements):     default:
2277            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);        stringstream temp;
2278            break;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2279         case(Points):        throw FinleyAdapterException(temp.str());
2280            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);    }
2281      return numTags;
2282    }
2283    
2284    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2285    {
2286      Finley_Mesh* mesh=m_finleyMesh.get();
2287      index_t* tags=NULL;
2288      switch(functionSpaceCode) {
2289       case(Nodes):
2290              tags=mesh->Nodes->tagsInUse;
2291            break;            break;
2292         case(ContactElementsZero):     case(ReducedNodes):
2293            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2294            break;            break;
2295         case(ReducedContactElementsZero):     case(DegreesOfFreedom):
2296            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2297            break;            break;
2298         case(ContactElementsOne):     case(ReducedDegreesOfFreedom):
2299            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2300            break;            break;
2301         case(ReducedContactElementsOne):     case(Elements):
2302            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2303              tags=mesh->Elements->tagsInUse;
2304              break;
2305       case(FaceElements):
2306       case(ReducedFaceElements):
2307              tags=mesh->FaceElements->tagsInUse;
2308              break;
2309       case(Points):
2310              tags=mesh->Points->tagsInUse;
2311              break;
2312       case(ContactElementsZero):
2313       case(ReducedContactElementsZero):
2314       case(ContactElementsOne):
2315       case(ReducedContactElementsOne):
2316              tags=mesh->ContactElements->tagsInUse;
2317            break;            break;
2318         default:     default:
2319            stringstream temp;        stringstream temp;
2320            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2321            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2322    }    }
2323    checkFinleyError();    return tags;
   return;  
2324  }  }
2325    
2326  void MeshAdapter::setTagMap(const std::string& name,  int tag)  
2327    bool MeshAdapter::canTag(int functionSpaceCode) const
2328  {  {
2329    Finley_Mesh* mesh=m_finleyMesh.get();    switch(functionSpaceCode) {
2330    Finley_Mesh_addTagMap(mesh, name.c_str(),tag);     case(Nodes):
2331    checkPasoError();     case(Elements):
2332    // throwStandardException("MeshAdapter::set TagMap is not implemented.");     case(ReducedElements):
2333       case(FaceElements):
2334       case(ReducedFaceElements):
2335       case(Points):
2336       case(ContactElementsZero):
2337       case(ReducedContactElementsZero):
2338       case(ContactElementsOne):
2339       case(ReducedContactElementsOne):
2340              return true;
2341       case(ReducedNodes):
2342       case(DegreesOfFreedom):
2343       case(ReducedDegreesOfFreedom):
2344          return false;
2345       default:
2346        return false;
2347      }
2348  }  }
2349    
2350  int MeshAdapter::getTag(const std::string& name) const  AbstractDomain::StatusType MeshAdapter::getStatus() const
2351  {  {
2352    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2353    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;  
2354  }  }
2355    
2356  bool MeshAdapter::isValidTagName(const std::string& name) const  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2357  {  {
2358      
2359    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2360    return Finley_Mesh_isValidTagName(mesh,name.c_str());    int order =-1;
2361      switch(functionSpaceCode) {
2362       case(Nodes):
2363       case(DegreesOfFreedom):
2364              order=mesh->approximationOrder;
2365              break;
2366       case(ReducedNodes):
2367       case(ReducedDegreesOfFreedom):
2368              order=mesh->reducedApproximationOrder;
2369              break;
2370       case(Elements):
2371       case(FaceElements):
2372       case(Points):
2373       case(ContactElementsZero):
2374       case(ContactElementsOne):
2375              order=mesh->integrationOrder;
2376              break;
2377       case(ReducedElements):
2378       case(ReducedFaceElements):
2379       case(ReducedContactElementsZero):
2380       case(ReducedContactElementsOne):
2381              order=mesh->reducedIntegrationOrder;
2382              break;
2383       default:
2384          stringstream temp;
2385          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2386          throw FinleyAdapterException(temp.str());
2387      }
2388      return order;
2389  }  }
2390    
2391  std::string MeshAdapter::showTagNames() const  bool MeshAdapter::supportsContactElements() const
2392  {  {
2393    stringstream temp;    return true;
2394    Finley_Mesh* mesh=m_finleyMesh.get();  }
2395    Finley_TagMap* tag_map=mesh->TagMap;  
2396    while (tag_map) {  ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2397       temp << tag_map->name;  {
2398       tag_map=tag_map->next;    m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2399       if (tag_map) temp << ", ";  }
2400    }  
2401    return temp.str();  ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2402    {
2403      Finley_ReferenceElementSet_dealloc(m_refSet);
2404  }  }
2405    
2406    // points will be flattened
2407    void MeshAdapter:: addDiracPoints(const std::vector<double>& points, const std::vector<int>& tags) const
2408    {
2409          const int dim = getDim();
2410          int numPoints=points.size()/dim;
2411          int numTags=tags.size();
2412          Finley_Mesh* mesh=m_finleyMesh.get();
2413          
2414          if ( points.size() % dim != 0 )
2415          {
2416        throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2417          }
2418          
2419          if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2420         throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2421          
2422          double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2423          int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2424          
2425          for (int i=0;i<numPoints;++i) {
2426           points_ptr[ i * dim     ] = points[i * dim ];
2427           if ( dim > 1 ) points_ptr[ i * dim + 1 ] = points[i * dim + 1];
2428           if ( dim > 2 ) points_ptr[ i * dim + 2 ] = points[i * dim + 2];    
2429               tags_ptr[i]=tags[i];
2430          }
2431          
2432          Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2433          checkFinleyError();
2434          
2435          TMPMEMFREE(points_ptr);
2436          TMPMEMFREE(tags_ptr);
2437    }
2438    
2439    
2440    // void MeshAdapter:: addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2441    // {
2442    //       const int dim = getDim();
2443    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2444    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2445    //       Finley_Mesh* mesh=m_finleyMesh.get();
2446    //      
2447    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2448    //   throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2449    //      
2450    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2451    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2452    //      
2453    //       for (int i=0;i<numPoints;++i) {
2454    //     int tag_id=-1;
2455    //     int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2456    //     if  ( numComps !=   dim ) {
2457    //                stringstream temp;            
2458    //                temp << "Error - illegal number of components " << numComps << " for point " << i;              
2459    //                throw FinleyAdapterException(temp.str());
2460    //     }
2461    //     points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2462    //     if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2463    //     if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2464    //    
2465    //     if ( numTags > 0) {
2466    //            boost::python::extract<string> ex_str(tags[i]);
2467    //        if  ( ex_str.check() ) {
2468    //            tag_id=getTag( ex_str());
2469    //        } else {
2470    //             boost::python::extract<int> ex_int(tags[i]);
2471    //             if ( ex_int.check() ) {
2472    //                 tag_id=ex_int();
2473    //             } else {
2474    //              stringstream temp;          
2475    //                  temp << "Error - unable to extract tag for point " << i;
2476    //              throw FinleyAdapterException(temp.str());
2477    //            }
2478    //        }
2479    //     }      
2480    //            tags_ptr[i]=tag_id;
2481    //       }
2482    //      
2483    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2484    //       checkPasoError();
2485    //      
2486    //       TMPMEMFREE(points_ptr);
2487    //       TMPMEMFREE(tags_ptr);
2488    // }
2489    
2490    /*
2491    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2492    {  
2493        boost::python::list points =  boost::python::list();
2494        boost::python::list tags =  boost::python::list();
2495        points.append(point);
2496        tags.append(tag);
2497        addDiracPoints(points, tags);
2498    }
2499    */
2500    
2501    /*
2502    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const std::string& tag) const
2503    {
2504            boost::python::list points =   boost::python::list();
2505            boost::python::list tags =   boost::python::list();
2506            points.append(point);
2507            tags.append(tag);
2508            addDiracPoints(points, tags);
2509    }
2510    */
2511  }  // end of namespace  }  // end of namespace

Legend:
Removed from v.1375  
changed lines
  Added in v.4255

  ViewVC Help
Powered by ViewVC 1.1.26