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

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revision 2385 by gross, Wed Apr 15 03:52:38 2009 UTC revision 3355 by caltinay, Tue Nov 16 06:35:06 2010 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*******************************************************
3  *  *
4  * Copyright (c) 2003-2008 by University of Queensland  * Copyright (c) 2003-2010 by University of Queensland
5  * Earth Systems Science Computational Center (ESSCC)  * Earth Systems Science Computational Center (ESSCC)
6  * http://www.uq.edu.au/esscc  * http://www.uq.edu.au/esscc
7  *  *
# Line 18  Line 18 
18  #ifdef USE_NETCDF  #ifdef USE_NETCDF
19  #include <netcdfcpp.h>  #include <netcdfcpp.h>
20  #endif  #endif
 #ifdef PASO_MPI  
 #include <mpi.h>  
 #include "paso/Paso_MPI.h"  
 #endif  
21  extern "C" {  extern "C" {
22  #include "esysUtils/blocktimer.h"  #include "esysUtils/blocktimer.h"
23  }  }
24    
25    #include <boost/python/import.hpp>
26    
27  using namespace std;  using namespace std;
28  using namespace escript;  using namespace escript;
29    
# Line 85  int MeshAdapter::getMPIRank() const Line 83  int MeshAdapter::getMPIRank() const
83  }  }
84  void MeshAdapter::MPIBarrier() const  void MeshAdapter::MPIBarrier() const
85  {  {
86  #ifdef PASO_MPI  #ifdef ESYS_MPI
87     MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);     MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
88  #endif  #endif
89     return;     return;
# Line 96  bool MeshAdapter::onMasterProcessor() co Line 94  bool MeshAdapter::onMasterProcessor() co
94  }  }
95    
96    
97    #ifdef ESYS_MPI
98      MPI_Comm
99    #else
100      unsigned int
101    #endif
102    MeshAdapter::getMPIComm() const
103    {
104    #ifdef ESYS_MPI
105        return m_finleyMesh->MPIInfo->comm;
106    #else
107        return 0;
108    #endif
109    }
110    
111    
112  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
113     return m_finleyMesh.get();     return m_finleyMesh.get();
114  }  }
115    
116  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
117  {  {
118     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;
119     strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
# Line 109  void MeshAdapter::write(const std::strin Line 122  void MeshAdapter::write(const std::strin
122     TMPMEMFREE(fName);     TMPMEMFREE(fName);
123  }  }
124    
125  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  void MeshAdapter::Print_Mesh_Info(const bool full) const
126  {  {
127     Finley_PrintMesh_Info(m_finleyMesh.get(), full);     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
128  }  }
129    
130  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const string& fileName) const
131  {  {
132  #ifdef USE_NETCDF  #ifdef USE_NETCDF
133     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
# Line 134  void MeshAdapter::dump(const std::string Line 147  void MeshAdapter::dump(const std::string
147     int num_Elements_numNodes        = mesh->Elements->numNodes;     int num_Elements_numNodes        = mesh->Elements->numNodes;
148     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
149     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
150  #ifdef PASO_MPI  #ifdef ESYS_MPI
151     MPI_Status status;     MPI_Status status;
152  #endif  #endif
153    
154  /* Incoming token indicates it's my turn to write */  /* Incoming token indicates it's my turn to write */
155  #ifdef PASO_MPI  #ifdef ESYS_MPI
156     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
157  #endif  #endif
158    
159     char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),     char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
160                                                       mpi_size, mpi_rank);                                                       mpi_size, mpi_rank);
161    
162     /* Figure out how much storage is required for tags */     /* Figure out how much storage is required for tags */
163     tag_map = mesh->TagMap;     tag_map = mesh->TagMap;
164     num_Tags = 0;     num_Tags = 0;
165     if (tag_map) {     while (tag_map) {
166        while (tag_map) {        num_Tags++;
167           num_Tags++;        tag_map=tag_map->next;
          tag_map=tag_map->next;  
       }  
168     }     }
169    
170     // NetCDF error handler     // NetCDF error handler
171     NcError err(NcError::verbose_nonfatal);     NcError err(NcError::verbose_nonfatal);
172     // Create the file.     // Create the file.
173     NcFile dataFile(newFileName, NcFile::Replace);     NcFile dataFile(newFileName, NcFile::Replace);
174       string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
175     // check if writing was successful     // check if writing was successful
176     if (!dataFile.is_valid())     if (!dataFile.is_valid())
177        throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);        throw DataException(msgPrefix+"Open file for output");
178    
179     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)     // Define dimensions (num_Elements and dim_Elements are identical,
180       // dim_Elements only appears if > 0)
181     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
182        throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_dim(numNodes)");
183     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
184        throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_dim(numDim)");
185     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)) )
186        throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_dim(mpi_size)");
187     if (num_Elements>0)     if (num_Elements>0)
188        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
189           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_Elements)");
190     if (num_FaceElements>0)     if (num_FaceElements>0)
191        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
192           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_FaceElements)");
193     if (num_ContactElements>0)     if (num_ContactElements>0)
194        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
195           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_ContactElements)");
196     if (num_Points>0)     if (num_Points>0)
197        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
198           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_Points)");
199     if (num_Elements>0)     if (num_Elements>0)
200        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
201           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_Elements_Nodes)");
202     if (num_FaceElements>0)     if (num_FaceElements>0)
203        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
204           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
205     if (num_ContactElements>0)     if (num_ContactElements>0)
206        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
207           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
208     if (num_Tags>0)     if (num_Tags>0)
209        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
210           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_dim(dim_Tags)");
211    
212     // Attributes: MPI size, MPI rank, Name, order, reduced_order     // Attributes: MPI size, MPI rank, Name, order, reduced_order
213     if (!dataFile.add_att("mpi_size", mpi_size) )     if (!dataFile.add_att("mpi_size", mpi_size) )
214        throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(mpi_size)");
215     if (!dataFile.add_att("mpi_rank", mpi_rank) )     if (!dataFile.add_att("mpi_rank", mpi_rank) )
216        throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(mpi_rank)");
217     if (!dataFile.add_att("Name",mesh->Name) )     if (!dataFile.add_att("Name",mesh->Name) )
218        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(Name)");
219     if (!dataFile.add_att("numDim",numDim) )     if (!dataFile.add_att("numDim",numDim) )
220        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(order)");
221     if (!dataFile.add_att("order",mesh->order) )     if (!dataFile.add_att("order",mesh->integrationOrder) )
222        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(order)");
223     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )     if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
224        throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(reduced_order)");
225     if (!dataFile.add_att("numNodes",numNodes) )     if (!dataFile.add_att("numNodes",numNodes) )
226        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(numNodes)");
227     if (!dataFile.add_att("num_Elements",num_Elements) )     if (!dataFile.add_att("num_Elements",num_Elements) )
228        throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_Elements)");
229     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
230        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_FaceElements)");
231     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
232        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_ContactElements)");
233     if (!dataFile.add_att("num_Points",num_Points) )     if (!dataFile.add_att("num_Points",num_Points) )
234        throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_Points)");
235     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
236        throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_Elements_numNodes)");
237     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
238        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_FaceElements_numNodes)");
239     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
240        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_ContactElements_numNodes)");
241     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
242        throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(Elements_TypeId)");
243     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
244        throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(FaceElements_TypeId)");
245     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
246        throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(ContactElements_TypeId)");
247     if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
248        throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(Points_TypeId)");
249     if (!dataFile.add_att("num_Tags", num_Tags) )     if (!dataFile.add_att("num_Tags", num_Tags) )
250        throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);        throw DataException(msgPrefix+"add_att(num_Tags)");
251    
252     // // // // // Nodes // // // // //     // // // // // Nodes // // // // //
253    
254     // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)     // Nodes nodeDistribution
255       if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
256          throw DataException(msgPrefix+"add_var(Nodes_NodeDistribution)");
257       int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
258       if (! (ids->put(int_ptr, mpi_size+1)) )
259          throw DataException(msgPrefix+"put(Nodes_NodeDistribution)");
260    
261       // Nodes degreesOfFreedomDistribution
262       if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
263          throw DataException(msgPrefix+"add_var(Nodes_DofDistribution)");
264       int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
265       if (! (ids->put(int_ptr, mpi_size+1)) )
266          throw DataException(msgPrefix+"put(Nodes_DofDistribution)");
267    
268       // Only write nodes if non-empty because NetCDF doesn't like empty arrays
269       // (it treats them as NC_UNLIMITED)
270     if (numNodes>0) {     if (numNodes>0) {
271    
272        // Nodes Id        // Nodes Id
273        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
274           throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Nodes_Id)");
275        int_ptr = &mesh->Nodes->Id[0];        int_ptr = &mesh->Nodes->Id[0];
276        if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
277           throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Nodes_Id)");
278    
279        // Nodes Tag        // Nodes Tag
280        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
281           throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Nodes_Tag)");
282        int_ptr = &mesh->Nodes->Tag[0];        int_ptr = &mesh->Nodes->Tag[0];
283        if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
284           throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Nodes_Tag)");
285    
286        // Nodes gDOF        // Nodes gDOF
287        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
288           throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Nodes_gDOF)");
289        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
290        if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
291           throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Nodes_gDOF)");
292    
293        // Nodes global node index        // Nodes global node index
294        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
295           throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Nodes_gNI)");
296        int_ptr = &mesh->Nodes->globalNodesIndex[0];        int_ptr = &mesh->Nodes->globalNodesIndex[0];
297        if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
298           throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Nodes_gNI)");
299    
300        // Nodes grDof        // Nodes grDof
301        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
302           throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Nodes_grDfI)");
303        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
304        if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
305           throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Nodes_grDfI)");
306    
307        // Nodes grNI        // Nodes grNI
308        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
309           throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Nodes_grNI)");
310        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
311        if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
312           throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Nodes_grNI)");
313    
314        // Nodes Coordinates        // Nodes Coordinates
315        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
316           throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Nodes_Coordinates)");
317        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
318           throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Nodes_Coordinates)");
   
       // Nodes degreesOfFreedomDistribution  
       if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];  
       if (! (ids->put(int_ptr, mpi_size+1)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);  
   
       // Nodes nodeDistribution  
       if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )  
          throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);  
       int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];  
       if (! (ids->put(int_ptr, mpi_size+1)) )  
          throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);  
319    
320     }     }
321    
# Line 311  void MeshAdapter::dump(const std::string Line 325  void MeshAdapter::dump(const std::string
325    
326        // Elements_Id        // Elements_Id
327        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
328           throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Elements_Id)");
329        int_ptr = &mesh->Elements->Id[0];        int_ptr = &mesh->Elements->Id[0];
330        if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
331           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Id)");
332    
333        // Elements_Tag        // Elements_Tag
334        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
335           throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Elements_Tag)");
336        int_ptr = &mesh->Elements->Tag[0];        int_ptr = &mesh->Elements->Tag[0];
337        if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
338           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Tag)");
339    
340        // Elements_Owner        // Elements_Owner
341        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
342           throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Elements_Owner)");
343        int_ptr = &mesh->Elements->Owner[0];        int_ptr = &mesh->Elements->Owner[0];
344        if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
345           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Owner)");
346    
347        // Elements_Color        // Elements_Color
348        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
349           throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Elements_Color)");
350        int_ptr = &mesh->Elements->Color[0];        int_ptr = &mesh->Elements->Color[0];
351        if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
352           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Color)");
353    
354        // Elements_Nodes        // Elements_Nodes
355        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
356           throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Elements_Nodes)");
357        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
358           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Elements_Nodes)");
359    
360     }     }
361    
# Line 351  void MeshAdapter::dump(const std::string Line 365  void MeshAdapter::dump(const std::string
365    
366        // FaceElements_Id        // FaceElements_Id
367        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
368           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(FaceElements_Id)");
369        int_ptr = &mesh->FaceElements->Id[0];        int_ptr = &mesh->FaceElements->Id[0];
370        if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
371           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Id)");
372    
373        // FaceElements_Tag        // FaceElements_Tag
374        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
375           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(FaceElements_Tag)");
376        int_ptr = &mesh->FaceElements->Tag[0];        int_ptr = &mesh->FaceElements->Tag[0];
377        if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
378           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Tag)");
379    
380        // FaceElements_Owner        // FaceElements_Owner
381        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
382           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(FaceElements_Owner)");
383        int_ptr = &mesh->FaceElements->Owner[0];        int_ptr = &mesh->FaceElements->Owner[0];
384        if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
385           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Owner)");
386    
387        // FaceElements_Color        // FaceElements_Color
388        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
389           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(FaceElements_Color)");
390        int_ptr = &mesh->FaceElements->Color[0];        int_ptr = &mesh->FaceElements->Color[0];
391        if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
392           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Color)");
393    
394        // FaceElements_Nodes        // FaceElements_Nodes
395        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
396           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(FaceElements_Nodes)");
397        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
398           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(FaceElements_Nodes)");
399    
400     }     }
401    
# Line 391  void MeshAdapter::dump(const std::string Line 405  void MeshAdapter::dump(const std::string
405    
406        // ContactElements_Id        // ContactElements_Id
407        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
408           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(ContactElements_Id)");
409        int_ptr = &mesh->ContactElements->Id[0];        int_ptr = &mesh->ContactElements->Id[0];
410        if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
411           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Id)");
412    
413        // ContactElements_Tag        // ContactElements_Tag
414        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
415           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(ContactElements_Tag)");
416        int_ptr = &mesh->ContactElements->Tag[0];        int_ptr = &mesh->ContactElements->Tag[0];
417        if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
418           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Tag)");
419    
420        // ContactElements_Owner        // ContactElements_Owner
421        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
422           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(ContactElements_Owner)");
423        int_ptr = &mesh->ContactElements->Owner[0];        int_ptr = &mesh->ContactElements->Owner[0];
424        if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
425           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Owner)");
426    
427        // ContactElements_Color        // ContactElements_Color
428        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
429           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(ContactElements_Color)");
430        int_ptr = &mesh->ContactElements->Color[0];        int_ptr = &mesh->ContactElements->Color[0];
431        if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
432           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Color)");
433    
434        // ContactElements_Nodes        // ContactElements_Nodes
435        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
436           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(ContactElements_Nodes)");
437        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
438           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(ContactElements_Nodes)");
439    
440     }     }
441    
# Line 433  void MeshAdapter::dump(const std::string Line 447  void MeshAdapter::dump(const std::string
447    
448        // Points_Id        // Points_Id
449        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
450           throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Id)");
451        int_ptr = &mesh->Points->Id[0];        int_ptr = &mesh->Points->Id[0];
452        if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
453           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Id)");
454    
455        // Points_Tag        // Points_Tag
456        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
457           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Tag)");
458        int_ptr = &mesh->Points->Tag[0];        int_ptr = &mesh->Points->Tag[0];
459        if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
460           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Tag)");
461    
462        // Points_Owner        // Points_Owner
463        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
464           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Owner)");
465        int_ptr = &mesh->Points->Owner[0];        int_ptr = &mesh->Points->Owner[0];
466        if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
467           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Owner)");
468    
469        // Points_Color        // Points_Color
470        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
471           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Color)");
472        int_ptr = &mesh->Points->Color[0];        int_ptr = &mesh->Points->Color[0];
473        if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
474           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Color)");
475    
476        // Points_Nodes        // Points_Nodes
477        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
478        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
479           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Points_Nodes)");
480        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
481           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Points_Nodes)");
482    
483     }     }
484    
# Line 488  void MeshAdapter::dump(const std::string Line 502  void MeshAdapter::dump(const std::string
502    
503        // Tags_keys        // Tags_keys
504        if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )        if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
505           throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);           throw DataException(msgPrefix+"add_var(Tags_keys)");
506        int_ptr = &Tags_keys[0];        int_ptr = &Tags_keys[0];
507        if (! (ids->put(int_ptr, num_Tags)) )        if (! (ids->put(int_ptr, num_Tags)) )
508           throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);           throw DataException(msgPrefix+"put(Tags_keys)");
509    
510        // Tags_names_*        // Tags_names_*
511        // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string        // This is an array of strings, it should be stored as an array but
512        // because the NetCDF manual doesn't tell how to do an array of strings        // instead I have hacked in one attribute per string because the NetCDF
513          // manual doesn't tell how to do an array of strings
514        tag_map = mesh->TagMap;        tag_map = mesh->TagMap;
515        if (tag_map) {        if (tag_map) {
516           int i = 0;           int i = 0;
517           while (tag_map) {           while (tag_map) {
518              sprintf(name_temp, "Tags_name_%d", i);              sprintf(name_temp, "Tags_name_%d", i);
519              if (!dataFile.add_att(name_temp, tag_map->name) )              if (!dataFile.add_att(name_temp, tag_map->name) )
520                 throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);                 throw DataException(msgPrefix+"add_att(Tags_names_XX)");
521              tag_map=tag_map->next;              tag_map=tag_map->next;
522              i++;              i++;
523           }           }
524        }        }
525    
526        TMPMEMFREE(Tags_keys);        TMPMEMFREE(Tags_keys);
   
527     }     }
528    
529  /* Send token to next MPI process so he can take his turn */  /* Send token to next MPI process so he can take his turn */
530  #ifdef PASO_MPI  #ifdef ESYS_MPI
531     if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);     if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
532  #endif  #endif
533    
# Line 678  pair<int,int> MeshAdapter::getDataShape( Line 692  pair<int,int> MeshAdapter::getDataShape(
692     case(Elements):     case(Elements):
693     if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
694        numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
695        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
696     }     }
697     break;     break;
698     case(ReducedElements):     case(ReducedElements):
699     if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
700        numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
701        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
702     }     }
703     break;     break;
704     case(FaceElements):     case(FaceElements):
705     if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
706        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
707        numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
708     }     }
709     break;     break;
710     case(ReducedFaceElements):     case(ReducedFaceElements):
711     if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
712        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
713        numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
714     }     }
715     break;     break;
# Line 707  pair<int,int> MeshAdapter::getDataShape( Line 721  pair<int,int> MeshAdapter::getDataShape(
721     break;     break;
722     case(ContactElementsZero):     case(ContactElementsZero):
723     if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
724        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
725        numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
726     }     }
727     break;     break;
728     case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
729     if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
730        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
731        numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
732     }     }
733     break;     break;
734     case(ContactElementsOne):     case(ContactElementsOne):
735     if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
736        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
737        numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
738     }     }
739     break;     break;
740     case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
741     if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
742        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
743        numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
744     }     }
745     break;     break;
# Line 754  pair<int,int> MeshAdapter::getDataShape( Line 768  pair<int,int> MeshAdapter::getDataShape(
768  // 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:
769  //  //
770  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
771                                   SystemMatrixAdapter& mat, escript::Data& rhs,                                   AbstractSystemMatrix& mat, escript::Data& rhs,
772                                   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,
773                                   const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
774                                   const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
775  {  {
776       SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
777       if (smat==0)
778       {
779        throw FinleyAdapterException("finley only supports its own system matrices.");
780       }
781     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
782     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
783     escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
# Line 773  void MeshAdapter::addPDEToSystem( Line 792  void MeshAdapter::addPDEToSystem(
792    
793     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
794    
795     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 );
796     checkFinleyError();     checkFinleyError();
797    
798     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 );
799     checkFinleyError();     checkFinleyError();
800    
801     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 );
802     checkFinleyError();     checkFinleyError();
803  }  }
804    
# Line 795  void  MeshAdapter::addPDEToLumpedSystem( Line 814  void  MeshAdapter::addPDEToLumpedSystem(
814     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
815    
816     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
817       checkFinleyError();
818      
819     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
   
820     checkFinleyError();     checkFinleyError();
821    
822  }  }
823    
824    
# Line 827  void MeshAdapter::addPDEToRHS( escript:: Line 848  void MeshAdapter::addPDEToRHS( escript::
848  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
849  //  //
850  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
851                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,                                             AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,
852                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,
853                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
854                                             const escript::Data& d, const escript::Data& y,                                             const escript::Data& d, const escript::Data& y,
855                                             const escript::Data& d_contact,const escript::Data& y_contact) const                                             const escript::Data& d_contact,const escript::Data& y_contact) const
856  {  {
857       TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
858       if (tpa==0)
859       {
860        throw FinleyAdapterException("finley only supports its own transport problems.");
861       }
862    
863    
864     DataTypes::ShapeType shape;     DataTypes::ShapeType shape;
865     source.expand();     source.expand();
866     escriptDataC _source=source.getDataC();     escriptDataC _source=source.getDataC();
# Line 849  void MeshAdapter::addPDEToTransportProbl Line 877  void MeshAdapter::addPDEToTransportProbl
877     escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
878    
879     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
880     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();     Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
881    
882     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
883     checkFinleyError();     checkFinleyError();
# Line 1026  void MeshAdapter::interpolateOnDomain(es Line 1054  void MeshAdapter::interpolateOnDomain(es
1054        case(Elements):        case(Elements):
1055        case(ReducedElements):        case(ReducedElements):
1056        if (getMPISize()>1) {        if (getMPISize()>1) {
1057           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1058           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1059           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1060        } else {        } else {
# Line 1036  void MeshAdapter::interpolateOnDomain(es Line 1064  void MeshAdapter::interpolateOnDomain(es
1064        case(FaceElements):        case(FaceElements):
1065        case(ReducedFaceElements):        case(ReducedFaceElements):
1066        if (getMPISize()>1) {        if (getMPISize()>1) {
1067           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1068           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1069           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1070        
# Line 1046  void MeshAdapter::interpolateOnDomain(es Line 1074  void MeshAdapter::interpolateOnDomain(es
1074        break;        break;
1075        case(Points):        case(Points):
1076        if (getMPISize()>1) {        if (getMPISize()>1) {
1077           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1078           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1079        } else {        } else {
1080           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
# Line 1057  void MeshAdapter::interpolateOnDomain(es Line 1085  void MeshAdapter::interpolateOnDomain(es
1085        case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
1086        case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
1087        if (getMPISize()>1) {        if (getMPISize()>1) {
1088           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1089           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1090           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1091        } else {        } else {
# Line 1095  void MeshAdapter::interpolateOnDomain(es Line 1123  void MeshAdapter::interpolateOnDomain(es
1123        case(Elements):        case(Elements):
1124        case(ReducedElements):        case(ReducedElements):
1125        if (getMPISize()>1) {        if (getMPISize()>1) {
1126           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1127           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1128           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1129        } else {        } else {
# Line 1105  void MeshAdapter::interpolateOnDomain(es Line 1133  void MeshAdapter::interpolateOnDomain(es
1133        case(FaceElements):        case(FaceElements):
1134        case(ReducedFaceElements):        case(ReducedFaceElements):
1135        if (getMPISize()>1) {        if (getMPISize()>1) {
1136           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1137           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1138           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1139        } else {        } else {
# Line 1114  void MeshAdapter::interpolateOnDomain(es Line 1142  void MeshAdapter::interpolateOnDomain(es
1142        break;        break;
1143        case(Points):        case(Points):
1144        if (getMPISize()>1) {        if (getMPISize()>1) {
1145           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1146           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1147           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1148        } else {        } else {
# Line 1126  void MeshAdapter::interpolateOnDomain(es Line 1154  void MeshAdapter::interpolateOnDomain(es
1154        case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
1155        case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
1156        if (getMPISize()>1) {        if (getMPISize()>1) {
1157           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1158           escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1159           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1160        } else {        } else {
# Line 1163  void MeshAdapter::setToX(escript::Data& Line 1191  void MeshAdapter::setToX(escript::Data&
1191        escriptDataC _arg=arg.getDataC();        escriptDataC _arg=arg.getDataC();
1192        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1193     } else {     } else {
1194        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);        escript::Data tmp_data=Vector(0.0,continuousFunction(*this),true);
1195        escriptDataC _tmp_data=tmp_data.getDataC();        escriptDataC _tmp_data=tmp_data.getDataC();
1196        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1197        // this is then interpolated onto arg:        // this is then interpolated onto arg:
# Line 1244  void MeshAdapter::interpolateACross(escr Line 1272  void MeshAdapter::interpolateACross(escr
1272  //  //
1273  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined of arg:
1274  //  //
1275  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(vector<double>& integrals,const escript::Data& arg) const
1276  {  {
1277     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1278     if (argDomain!=*this)     if (argDomain!=*this)
# Line 1257  void MeshAdapter::setToIntegrals(std::ve Line 1285  void MeshAdapter::setToIntegrals(std::ve
1285     escriptDataC _arg=arg.getDataC();     escriptDataC _arg=arg.getDataC();
1286     switch(arg.getFunctionSpace().getTypeCode()) {     switch(arg.getFunctionSpace().getTypeCode()) {
1287     case(Nodes):     case(Nodes):
1288     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1289     _temp=temp.getDataC();     _temp=temp.getDataC();
1290     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1291     break;     break;
1292     case(ReducedNodes):     case(ReducedNodes):
1293     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1294     _temp=temp.getDataC();     _temp=temp.getDataC();
1295     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1296     break;     break;
# Line 1294  void MeshAdapter::setToIntegrals(std::ve Line 1322  void MeshAdapter::setToIntegrals(std::ve
1322     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1323     break;     break;
1324     case(DegreesOfFreedom):     case(DegreesOfFreedom):
1325     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1326     _temp=temp.getDataC();     _temp=temp.getDataC();
1327     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1328     break;     break;
1329     case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1330     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1331     _temp=temp.getDataC();     _temp=temp.getDataC();
1332     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1333     break;     break;
# Line 1331  void MeshAdapter::setToGradient(escript: Line 1359  void MeshAdapter::setToGradient(escript:
1359     escript::Data temp;     escript::Data temp;
1360     if (getMPISize()>1) {     if (getMPISize()>1) {
1361        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1362           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  continuousFunction(*this) );
1363           nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1364        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1365           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  reducedContinuousFunction(*this) );
1366           nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1367        } else {        } else {
1368           nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
# Line 1453  void MeshAdapter::setNewX(const escript: Line 1481  void MeshAdapter::setNewX(const escript:
1481     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1482     if (newDomain!=*this)     if (newDomain!=*this)
1483        throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1484     tmp = new_x.getDataC();     if ( new_x.getFunctionSpace() == continuousFunction(*this) ) {
1485     Finley_Mesh_setCoordinates(mesh,&tmp);         tmp = new_x.getDataC();
1486           Finley_Mesh_setCoordinates(mesh,&tmp);
1487       } else {
1488           escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(*this) );
1489           tmp = new_x_inter.getDataC();
1490           Finley_Mesh_setCoordinates(mesh,&tmp);
1491       }
1492     checkFinleyError();     checkFinleyError();
1493  }  }
1494    
# Line 1472  void MeshAdapter::extractArgsFromDict(co Line 1506  void MeshAdapter::extractArgsFromDict(co
1506    
1507     boost::python::list keys=arg.keys();     boost::python::list keys=arg.keys();
1508     for (int i=0; i<numData; ++i) {     for (int i=0; i<numData; ++i) {
1509        std::string n=boost::python::extract<std::string>(keys[i]);        string n=boost::python::extract<string>(keys[i]);
1510        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1511        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1512           throw FinleyAdapterException("Error: Data must be defined on same Domain");           throw FinleyAdapterException("Error: Data must be defined on same Domain");
# Line 1486  void MeshAdapter::extractArgsFromDict(co Line 1520  void MeshAdapter::extractArgsFromDict(co
1520  //  //
1521  // saves mesh and optionally data arrays in openDX format  // saves mesh and optionally data arrays in openDX format
1522  //  //
1523  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1524  {  {
1525     int num_data;     int num_data;
1526     char **names;     char **names;
# Line 1512  void MeshAdapter::saveDX(const std::stri Line 1546  void MeshAdapter::saveDX(const std::stri
1546  //  //
1547  // saves mesh and optionally data arrays in VTK format  // saves mesh and optionally data arrays in VTK format
1548  //  //
1549  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1550  {  {
1551     int num_data;      boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("_saveVTK");
1552     char **names;      pySaveVTK(filename, const_cast<MeshAdapter*>(this)->getPtr(),
1553     escriptDataC *data;                metadata, metadata_schema, arg);
1554     escriptDataC **ptr_data;  }
1555    
1556    bool MeshAdapter::ownSample(int fs_code, index_t id) const
1557    {
1558    #ifdef ESYS_MPI
1559        index_t myFirstNode=0, myLastNode=0, k=0;
1560        index_t* globalNodeIndex=0;
1561        Finley_Mesh* mesh_p=m_finleyMesh.get();
1562        if (fs_code == FINLEY_REDUCED_NODES)
1563        {
1564        myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1565        myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1566        globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1567        }
1568        else
1569        {
1570        myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1571        myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1572        globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
1573        }
1574        k=globalNodeIndex[id];
1575        return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1576    #endif
1577        return true;
1578    }
1579    
    extractArgsFromDict(arg, num_data, names, data, ptr_data);  
    Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);  
    checkFinleyError();  
1580    
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0; i<num_data; i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
 }  
1581    
1582  //  //
1583  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1584  //  //
1585  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  ASM_ptr MeshAdapter::newSystemMatrix(
1586                                                   const int row_blocksize,                                                   const int row_blocksize,
1587                                                   const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1588                                                   const int column_blocksize,                                                   const int column_blocksize,
# Line 1579  SystemMatrixAdapter MeshAdapter::newSyst Line 1625  SystemMatrixAdapter MeshAdapter::newSyst
1625  #endif  #endif
1626     }     }
1627     else {     else {
1628        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1629     }     }
1630     checkPasoError();     checkPasoError();
1631     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1632     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1633       return ASM_ptr(sma);
1634    //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1635  }  }
1636    
1637  //  //
1638  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1639  //  //
1640  TransportProblemAdapter MeshAdapter::newTransportProblem(  ATP_ptr MeshAdapter::newTransportProblem(
1641                                                           const double theta,                                                           const bool useBackwardEuler,
1642                                                           const int blocksize,                                                           const int blocksize,
1643                                                           const escript::FunctionSpace& functionspace,                                                           const escript::FunctionSpace& functionspace,
1644                                                           const int type) const                                                           const int type) const
# Line 1612  TransportProblemAdapter MeshAdapter::new Line 1660  TransportProblemAdapter MeshAdapter::new
1660    
1661     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1662     checkFinleyError();     checkFinleyError();
1663     Paso_FCTransportProblem* transportProblem;     Paso_TransportProblem* transportProblem;
1664     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);     transportProblem=Paso_TransportProblem_alloc(useBackwardEuler,fsystemMatrixPattern,blocksize);
1665     checkPasoError();     checkPasoError();
1666     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1667     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);     TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1668       return ATP_ptr(tpa);
1669    //   return TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1670  }  }
1671    
1672  //  //
# Line 1655  bool MeshAdapter::isCellOriented(int fun Line 1705  bool MeshAdapter::isCellOriented(int fun
1705     return false;     return false;
1706  }  }
1707    
1708    bool
1709    MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1710    {
1711       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1712        class 1: DOF <-> Nodes
1713        class 2: ReducedDOF <-> ReducedNodes
1714        class 3: Points
1715        class 4: Elements
1716        class 5: ReducedElements
1717        class 6: FaceElements
1718        class 7: ReducedFaceElements
1719        class 8: ContactElementZero <-> ContactElementOne
1720        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1721    
1722       There is also a set of lines. Interpolation is possible down a line but not between lines.
1723       class 1 and 2 belong to all lines so aren't considered.
1724        line 0: class 3
1725        line 1: class 4,5
1726        line 2: class 6,7
1727        line 3: class 8,9
1728    
1729       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1730       eg hasnodes is true if we have at least one instance of Nodes.
1731       */
1732        if (fs.empty())
1733        {
1734            return false;
1735        }
1736        vector<int> hasclass(10);
1737        vector<int> hasline(4);
1738        bool hasnodes=false;
1739        bool hasrednodes=false;
1740        bool hascez=false;
1741        bool hasrcez=false;
1742        for (int i=0;i<fs.size();++i)
1743        {
1744        switch(fs[i])
1745        {
1746        case(Nodes):   hasnodes=true;   // no break is deliberate
1747        case(DegreesOfFreedom):
1748            hasclass[1]=1;
1749            break;
1750        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1751        case(ReducedDegreesOfFreedom):
1752            hasclass[2]=1;
1753            break;
1754        case(Points):
1755            hasline[0]=1;
1756            hasclass[3]=1;
1757            break;
1758        case(Elements):
1759            hasclass[4]=1;
1760            hasline[1]=1;
1761            break;
1762        case(ReducedElements):
1763            hasclass[5]=1;
1764            hasline[1]=1;
1765            break;
1766        case(FaceElements):
1767            hasclass[6]=1;
1768            hasline[2]=1;
1769            break;
1770        case(ReducedFaceElements):
1771            hasclass[7]=1;
1772            hasline[2]=1;
1773            break;
1774        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1775        case(ContactElementsOne):
1776            hasclass[8]=1;
1777            hasline[3]=1;
1778            break;
1779        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1780        case(ReducedContactElementsOne):
1781            hasclass[9]=1;
1782            hasline[3]=1;
1783            break;
1784        default:
1785            return false;
1786        }
1787        }
1788        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1789        // fail if we have more than one leaf group
1790    
1791        if (totlines>1)
1792        {
1793        return false;   // there are at least two branches we can't interpolate between
1794        }
1795        else if (totlines==1)
1796        {
1797        if (hasline[0]==1)      // we have points
1798        {
1799            resultcode=Points;
1800        }
1801        else if (hasline[1]==1)
1802        {
1803            if (hasclass[5]==1)
1804            {
1805            resultcode=ReducedElements;
1806            }
1807            else
1808            {
1809            resultcode=Elements;
1810            }
1811        }
1812        else if (hasline[2]==1)
1813        {
1814            if (hasclass[7]==1)
1815            {
1816            resultcode=ReducedFaceElements;
1817            }
1818            else
1819            {
1820            resultcode=FaceElements;
1821            }
1822        }
1823        else    // so we must be in line3
1824        {
1825            if (hasclass[9]==1)
1826            {
1827            // need something from class 9
1828            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1829            }
1830            else
1831            {
1832            // something from class 8
1833            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1834            }
1835        }
1836        }
1837        else    // totlines==0
1838        {
1839        if (hasclass[2]==1)
1840        {
1841            // something from class 2
1842            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1843        }
1844        else
1845        {   // something from class 1
1846            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1847        }
1848        }
1849        return true;
1850    }
1851    
1852  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1853  {  {
1854     switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1855     case(Nodes):     case(Nodes):
1856     switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1857     case(Nodes):      case(Nodes):
1858     case(ReducedNodes):      case(ReducedNodes):
1859     case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1860     case(DegreesOfFreedom):      case(DegreesOfFreedom):
1861     case(Elements):      case(Elements):
1862     case(ReducedElements):      case(ReducedElements):
1863     case(FaceElements):      case(FaceElements):
1864     case(ReducedFaceElements):      case(ReducedFaceElements):
1865     case(Points):      case(Points):
1866     case(ContactElementsZero):      case(ContactElementsZero):
1867     case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1868     case(ContactElementsOne):      case(ContactElementsOne):
1869     case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1870     return true;      return true;
1871     default:      default:
1872        stringstream temp;            stringstream temp;
1873        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;
1874        throw FinleyAdapterException(temp.str());            throw FinleyAdapterException(temp.str());
1875     }     }
1876     break;     break;
1877     case(ReducedNodes):     case(ReducedNodes):
1878     switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1879     case(ReducedNodes):      case(ReducedNodes):
1880     case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1881     case(Elements):      case(Elements):
1882     case(ReducedElements):      case(ReducedElements):
1883     case(FaceElements):      case(FaceElements):
1884     case(ReducedFaceElements):      case(ReducedFaceElements):
1885     case(Points):      case(Points):
1886     case(ContactElementsZero):      case(ContactElementsZero):
1887     case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1888     case(ContactElementsOne):      case(ContactElementsOne):
1889     case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1890     return true;      return true;
1891     case(Nodes):      case(Nodes):
1892     case(DegreesOfFreedom):      case(DegreesOfFreedom):
1893     return false;      return false;
1894     default:      default:
1895        stringstream temp;          stringstream temp;
1896        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;
1897        throw FinleyAdapterException(temp.str());          throw FinleyAdapterException(temp.str());
1898     }     }
1899     break;     break;
1900     case(Elements):     case(Elements):
1901     if (functionSpaceType_target==Elements) {      if (functionSpaceType_target==Elements) {
1902        return true;        return true;
1903     } else if (functionSpaceType_target==ReducedElements) {      } else if (functionSpaceType_target==ReducedElements) {
1904        return true;        return true;
1905     } else {          } else {
1906        return false;            return false;
1907     }          }
1908     case(ReducedElements):     case(ReducedElements):
1909     if (functionSpaceType_target==ReducedElements) {      if (functionSpaceType_target==ReducedElements) {
1910        return true;        return true;
1911     } else {      } else {
1912        return false;            return false;
1913     }      }
1914     case(FaceElements):     case(FaceElements):
1915     if (functionSpaceType_target==FaceElements) {      if (functionSpaceType_target==FaceElements) {
1916        return true;              return true;
1917     } else if (functionSpaceType_target==ReducedFaceElements) {      } else if (functionSpaceType_target==ReducedFaceElements) {
1918        return true;              return true;
1919     } else {      } else {
1920        return false;              return false;
1921     }      }
1922     case(ReducedFaceElements):     case(ReducedFaceElements):
1923     if (functionSpaceType_target==ReducedFaceElements) {      if (functionSpaceType_target==ReducedFaceElements) {
1924        return true;              return true;
1925     } else {      } else {
1926        return false;          return false;
1927     }      }
1928     case(Points):     case(Points):
1929     if (functionSpaceType_target==Points) {      if (functionSpaceType_target==Points) {
1930        return true;              return true;
1931     } else {      } else {
1932        return false;              return false;
1933     }      }
1934     case(ContactElementsZero):     case(ContactElementsZero):
1935     case(ContactElementsOne):     case(ContactElementsOne):
1936     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1937        return true;              return true;
1938     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1939        return true;              return true;
1940     } else {      } else {
1941        return false;              return false;
1942     }      }
1943     case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1944     case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1945     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {      if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1946        return true;              return true;
1947     } else {      } else {
1948        return false;              return false;
1949     }      }
1950     case(DegreesOfFreedom):     case(DegreesOfFreedom):
1951     switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1952     case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1953     case(DegreesOfFreedom):      case(DegreesOfFreedom):
1954     case(Nodes):      case(Nodes):
1955     case(ReducedNodes):      case(ReducedNodes):
1956     case(Elements):      case(Elements):
1957     case(ReducedElements):      case(ReducedElements):
1958     case(Points):      case(Points):
1959     case(FaceElements):      case(FaceElements):
1960     case(ReducedFaceElements):      case(ReducedFaceElements):
1961     case(ContactElementsZero):      case(ContactElementsZero):
1962     case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1963     case(ContactElementsOne):      case(ContactElementsOne):
1964     case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1965     return true;      return true;
1966     default:      default:
1967        stringstream temp;          stringstream temp;
1968        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;
1969        throw FinleyAdapterException(temp.str());          throw FinleyAdapterException(temp.str());
1970     }      }
1971     break;      break;
1972     case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1973     switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1974     case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1975     case(ReducedNodes):      case(ReducedNodes):
1976     case(Elements):      case(Elements):
1977     case(ReducedElements):      case(ReducedElements):
1978     case(FaceElements):      case(FaceElements):
1979     case(ReducedFaceElements):      case(ReducedFaceElements):
1980     case(Points):      case(Points):
1981     case(ContactElementsZero):      case(ContactElementsZero):
1982     case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1983     case(ContactElementsOne):      case(ContactElementsOne):
1984     case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1985     return true;      return true;
1986     case(Nodes):      case(Nodes):
1987     case(DegreesOfFreedom):      case(DegreesOfFreedom):
1988     return false;      return false;
1989     default:      default:
1990        stringstream temp;          stringstream temp;
1991        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;
1992        throw FinleyAdapterException(temp.str());          throw FinleyAdapterException(temp.str());
1993     }      }
1994     break;      break;
1995     default:     default:
1996        stringstream temp;        stringstream temp;
1997        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
# Line 1838  int MeshAdapter::getSystemMatrixTypeId(c Line 2032  int MeshAdapter::getSystemMatrixTypeId(c
2032  int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const  int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2033  {  {
2034     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2035     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);     int out=Paso_TransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2036     checkPasoError();     checkPasoError();
2037     return out;     return out;
2038  }  }
2039    
2040  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2041  {  {
2042     return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(*this).getX();
2043  }  }
2044    
2045  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2046  {  {
2047     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(*this).getNormal();
2048  }  }
2049    
2050  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2051  {  {
2052     return escript::function(asAbstractContinuousDomain()).getSize();     return escript::function(*this).getSize();
2053  }  }
2054    
2055  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2056  {  {
2057     int *out = NULL;     int *out = NULL;
2058     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
# Line 2017  void MeshAdapter::setTags(const int func Line 2211  void MeshAdapter::setTags(const int func
2211     return;     return;
2212  }  }
2213    
2214  void MeshAdapter::setTagMap(const std::string& name,  int tag)  void MeshAdapter::setTagMap(const string& name,  int tag)
2215  {  {
2216     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2217     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
# Line 2025  void MeshAdapter::setTagMap(const std::s Line 2219  void MeshAdapter::setTagMap(const std::s
2219     // throwStandardException("MeshAdapter::set TagMap is not implemented.");     // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2220  }  }
2221    
2222  int MeshAdapter::getTag(const std::string& name) const  int MeshAdapter::getTag(const string& name) const
2223  {  {
2224     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2225     int tag=0;     int tag=0;
# Line 2035  int MeshAdapter::getTag(const std::strin Line 2229  int MeshAdapter::getTag(const std::strin
2229     return tag;     return tag;
2230  }  }
2231    
2232  bool MeshAdapter::isValidTagName(const std::string& name) const  bool MeshAdapter::isValidTagName(const string& name) const
2233  {  {
2234     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2235     return Finley_Mesh_isValidTagName(mesh,name.c_str());     return Finley_Mesh_isValidTagName(mesh,name.c_str());
2236  }  }
2237    
2238  std::string MeshAdapter::showTagNames() const  string MeshAdapter::showTagNames() const
2239  {  {
2240     stringstream temp;     stringstream temp;
2241     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
# Line 2095  int MeshAdapter::getNumberOfTagsInUse(in Line 2289  int MeshAdapter::getNumberOfTagsInUse(in
2289    }    }
2290    return numTags;    return numTags;
2291  }  }
2292  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const  
2293    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2294  {  {
2295    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2296    index_t* tags=NULL;    index_t* tags=NULL;
# Line 2161  bool MeshAdapter::canTag(int functionSpa Line 2356  bool MeshAdapter::canTag(int functionSpa
2356    }    }
2357  }  }
2358    
2359    AbstractDomain::StatusType MeshAdapter::getStatus() const
2360    {
2361      Finley_Mesh* mesh=m_finleyMesh.get();
2362      return Finley_Mesh_getStatus(mesh);
2363    }
2364    
2365    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2366    {
2367      
2368      Finley_Mesh* mesh=m_finleyMesh.get();
2369      int order =-1;
2370      switch(functionSpaceCode) {
2371       case(Nodes):
2372       case(DegreesOfFreedom):
2373              order=mesh->approximationOrder;
2374              break;
2375       case(ReducedNodes):
2376       case(ReducedDegreesOfFreedom):
2377              order=mesh->reducedApproximationOrder;
2378              break;
2379       case(Elements):
2380       case(FaceElements):
2381       case(Points):
2382       case(ContactElementsZero):
2383       case(ContactElementsOne):
2384              order=mesh->integrationOrder;
2385              break;
2386       case(ReducedElements):
2387       case(ReducedFaceElements):
2388       case(ReducedContactElementsZero):
2389       case(ReducedContactElementsOne):
2390              order=mesh->reducedIntegrationOrder;
2391              break;
2392       default:
2393          stringstream temp;
2394          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2395          throw FinleyAdapterException(temp.str());
2396      }
2397      return order;
2398    }
2399    
2400    bool MeshAdapter::supportsContactElements() const
2401    {
2402      return true;
2403    }
2404    
2405    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2406    {
2407      m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2408    }
2409    
2410    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2411    {
2412      Finley_ReferenceElementSet_dealloc(m_refSet);
2413    }
2414    
2415  }  // end of namespace  }  // end of namespace

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