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

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

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

revision 2315 by gross, Wed Mar 18 00:38:48 2009 UTC revision 4612 by gross, Thu Jan 9 05:30:27 2014 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*****************************************************************************
3  *  *
4  * Copyright (c) 2003-2008 by University of Queensland  * Copyright (c) 2003-2013 by University of Queensland
5  * Earth Systems Science Computational Center (ESSCC)  * http://www.uq.edu.au
 * http://www.uq.edu.au/esscc  
6  *  *
7  * Primary Business: Queensland, Australia  * Primary Business: Queensland, Australia
8  * Licensed under the Open Software License version 3.0  * Licensed under the Open Software License version 3.0
9  * http://www.opensource.org/licenses/osl-3.0.php  * http://www.opensource.org/licenses/osl-3.0.php
10  *  *
11  *******************************************************/  * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12    * Development since 2012 by School of Earth Sciences
13    *
14    *****************************************************************************/
15    
16    #include <pasowrap/PasoException.h>
17    #include <pasowrap/TransportProblemAdapter.h>
18  #include "MeshAdapter.h"  #include "MeshAdapter.h"
19  #include "escript/Data.h"  #include "escript/Data.h"
20  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
21    #include "esysUtils/blocktimer.h"
22    
23    #include <boost/python/import.hpp>
24  #ifdef USE_NETCDF  #ifdef USE_NETCDF
25  #include <netcdfcpp.h>  #include <netcdfcpp.h>
26  #endif  #endif
 #ifdef PASO_MPI  
 #include <mpi.h>  
 #include "paso/Paso_MPI.h"  
 #endif  
 extern "C" {  
 #include "esysUtils/blocktimer.h"  
 }  
27    
28  using namespace std;  using namespace std;
29  using namespace escript;  using namespace paso;
30    
31  namespace finley {  namespace finley {
32    
 //  
33  // define the static constants  // define the static constants
34  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
35  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
# Line 48  const int MeshAdapter::ReducedContactEle Line 46  const int MeshAdapter::ReducedContactEle
46  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
47  const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;  const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
48    
49  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Mesh* finleyMesh)
50  {  {
51     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
52     //      // need to use a null_deleter as Finley_Mesh_free deletes the pointer
53     // need to use a null_deleter as Finley_Mesh_free deletes the pointer      // for us.
54     // for us.      m_finleyMesh.reset(finleyMesh, null_deleter());
    m_finleyMesh.reset(finleyMesh,null_deleter());  
55  }  }
56    
57  //  //
58  // The copy constructor should just increment the use count  // The copy constructor should just increment the use count
59  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in) :
60  m_finleyMesh(in.m_finleyMesh)      m_finleyMesh(in.m_finleyMesh)
61  {  {
62     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
63  }  }
64    
65  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
66  {  {
67     //      // I hope the case for the pointer being zero has been taken care of
68     // I hope the case for the pointer being zero has been taken care of.      if (m_finleyMesh.unique()) {
69     //  cout << "In MeshAdapter destructor." << endl;          delete m_finleyMesh.get();
70     if (m_finleyMesh.unique()) {      }
       Finley_Mesh_free(m_finleyMesh.get());  
    }  
71  }  }
72    
73  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
74  {  {
75     return m_finleyMesh.get()->MPIInfo->size;      return m_finleyMesh.get()->MPIInfo->size;
76  }  }
77    
78  int MeshAdapter::getMPIRank() const  int MeshAdapter::getMPIRank() const
79  {  {
80     return m_finleyMesh.get()->MPIInfo->rank;      return m_finleyMesh.get()->MPIInfo->rank;
81  }  }
82    
83  void MeshAdapter::MPIBarrier() const  void MeshAdapter::MPIBarrier() const
84  {  {
85  #ifdef PASO_MPI  #ifdef ESYS_MPI
86     MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);      MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
87  #endif  #endif
    return;  
88  }  }
89    
90  bool MeshAdapter::onMasterProcessor() const  bool MeshAdapter::onMasterProcessor() const
91  {  {
92     return m_finleyMesh.get()->MPIInfo->rank == 0;      return m_finleyMesh.get()->MPIInfo->rank == 0;
93  }  }
94    
95    #ifdef ESYS_MPI
96    MPI_Comm
97    #else
98    unsigned int
99    #endif
100    MeshAdapter::getMPIComm() const
101    {
102    #ifdef ESYS_MPI
103        return m_finleyMesh->MPIInfo->comm;
104    #else
105        return 0;
106    #endif
107    }
108    
109  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Mesh* MeshAdapter::getFinley_Mesh() const
110     return m_finleyMesh.get();  {
111        return m_finleyMesh.get();
112  }  }
113    
114  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
115  {  {
116     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;      m_finleyMesh.get()->write(fileName);
117     strcpy(fName,fileName.c_str());      checkFinleyError();
    Finley_Mesh_write(m_finleyMesh.get(),fName);  
    checkFinleyError();  
    TMPMEMFREE(fName);  
118  }  }
119    
120  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  void MeshAdapter::Print_Mesh_Info(const bool full) const
121  {  {
122     Finley_PrintMesh_Info(m_finleyMesh.get(), full);      m_finleyMesh.get()->printInfo(full);
123  }  }
124    
125  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const string& fileName) const
126  {  {
127  #ifdef USE_NETCDF  #ifdef USE_NETCDF
128     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};      const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
129     NcVar *ids;      NcVar *ids;
130     int *int_ptr;      int *int_ptr;
131     Finley_Mesh *mesh = m_finleyMesh.get();      Mesh *mesh = m_finleyMesh.get();
132     Finley_TagMap* tag_map;      int num_Tags = 0;
133     int num_Tags = 0;      int mpi_size                         = mesh->MPIInfo->size;
134     int mpi_size             = mesh->MPIInfo->size;      int mpi_rank                         = mesh->MPIInfo->rank;
135     int mpi_rank             = mesh->MPIInfo->rank;      int numDim                           = mesh->Nodes->numDim;
136     int numDim               = mesh->Nodes->numDim;      int numNodes                         = mesh->Nodes->numNodes;
137     int numNodes             = mesh->Nodes->numNodes;      int num_Elements                     = mesh->Elements->numElements;
138     int num_Elements         = mesh->Elements->numElements;      int num_FaceElements                 = mesh->FaceElements->numElements;
139     int num_FaceElements         = mesh->FaceElements->numElements;      int num_ContactElements              = mesh->ContactElements->numElements;
140     int num_ContactElements      = mesh->ContactElements->numElements;      int num_Points                       = mesh->Points->numElements;
141     int num_Points           = mesh->Points->numElements;      int num_Elements_numNodes            = mesh->Elements->numNodes;
142     int num_Elements_numNodes        = mesh->Elements->numNodes;      int num_FaceElements_numNodes        = mesh->FaceElements->numNodes;
143     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;      int num_ContactElements_numNodes     = mesh->ContactElements->numNodes;
144     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;  #ifdef ESYS_MPI
145  #ifdef PASO_MPI      MPI_Status status;
    MPI_Status status;  
146  #endif  #endif
147    
148  /* Incoming token indicates it's my turn to write */  /* Incoming token indicates it's my turn to write */
149  #ifdef PASO_MPI  #ifdef ESYS_MPI
150     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);      if (mpi_rank>0) {
151            MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
152        }
153  #endif  #endif
154    
155     char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),      const std::string newFileName(esysUtils::appendRankToFileName(fileName,
156                                                       mpi_size, mpi_rank);                                                       mpi_size, mpi_rank));
157    
158        // Figure out how much storage is required for tags
159        num_Tags = mesh->tagMap.size();
160    
161     /* Figure out how much storage is required for tags */      // NetCDF error handler
162     tag_map = mesh->TagMap;      NcError err(NcError::verbose_nonfatal);
163     num_Tags = 0;      // Create the file.
164     if (tag_map) {      NcFile dataFile(newFileName.c_str(), NcFile::Replace);
165        while (tag_map) {      string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
166           num_Tags++;      // check if writing was successful
167           tag_map=tag_map->next;      if (!dataFile.is_valid())
168        }          throw FinleyAdapterException(msgPrefix+"Open file for output");
169     }  
170        // Define dimensions (num_Elements and dim_Elements are identical,
171     // NetCDF error handler      // dim_Elements only appears if > 0)
172     NcError err(NcError::verbose_nonfatal);      if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
173     // Create the file.          throw FinleyAdapterException(msgPrefix+"add_dim(numNodes)");
174     NcFile dataFile(newFileName, NcFile::Replace);      if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
175     // check if writing was successful          throw FinleyAdapterException(msgPrefix+"add_dim(numDim)");
176     if (!dataFile.is_valid())      if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
177        throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_dim(mpi_size)");
178        if (num_Elements>0)
179     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
180     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements)");
181        throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);      if (num_FaceElements>0)
182     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
183        throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements)");
184     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )      if (num_ContactElements>0)
185        throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
186     if (num_Elements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements)");
187        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )      if (num_Points>0)
188           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
189     if (num_FaceElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Points)");
190        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )      if (num_Elements>0)
191           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
192     if (num_ContactElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements_Nodes)");
193        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )      if (num_FaceElements>0)
194           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
195     if (num_Points>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
196        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )      if (num_ContactElements>0)
197           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
198     if (num_Elements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
199        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )      if (num_Tags>0)
200           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
201     if (num_FaceElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Tags)");
202        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )  
203           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);      // Attributes: MPI size, MPI rank, Name, order, reduced_order
204     if (num_ContactElements>0)      if (!dataFile.add_att("mpi_size", mpi_size))
205        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )          throw FinleyAdapterException(msgPrefix+"add_att(mpi_size)");
206           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);      if (!dataFile.add_att("mpi_rank", mpi_rank))
207     if (num_Tags>0)          throw FinleyAdapterException(msgPrefix+"add_att(mpi_rank)");
208        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )      if (!dataFile.add_att("Name",mesh->m_name.c_str()))
209           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(Name)");
210        if (!dataFile.add_att("numDim",numDim))
211     // Attributes: MPI size, MPI rank, Name, order, reduced_order          throw FinleyAdapterException(msgPrefix+"add_att(order)");
212     if (!dataFile.add_att("mpi_size", mpi_size) )      if (!dataFile.add_att("order",mesh->integrationOrder))
213        throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(order)");
214     if (!dataFile.add_att("mpi_rank", mpi_rank) )      if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder))
215        throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(reduced_order)");
216     if (!dataFile.add_att("Name",mesh->Name) )      if (!dataFile.add_att("numNodes",numNodes))
217        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(numNodes)");
218     if (!dataFile.add_att("numDim",numDim) )      if (!dataFile.add_att("num_Elements",num_Elements))
219        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements)");
220     if (!dataFile.add_att("order",mesh->order) )      if (!dataFile.add_att("num_FaceElements",num_FaceElements))
221        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements)");
222     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )      if (!dataFile.add_att("num_ContactElements",num_ContactElements))
223        throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements)");
224     if (!dataFile.add_att("numNodes",numNodes) )      if (!dataFile.add_att("num_Points",num_Points))
225        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_Points)");
226     if (!dataFile.add_att("num_Elements",num_Elements) )      if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes))
227        throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements_numNodes)");
228     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )      if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
229        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements_numNodes)");
230     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )      if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
231        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements_numNodes)");
232     if (!dataFile.add_att("num_Points",num_Points) )      if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
233        throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(Elements_TypeId)");
234     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )      if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
235        throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(FaceElements_TypeId)");
236     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )      if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
237        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(ContactElements_TypeId)");
238     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )      if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
239        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(Points_TypeId)");
240     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )      if (!dataFile.add_att("num_Tags", num_Tags) )
241        throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_Tags)");
242     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )  
243        throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);      // // // // // Nodes // // // // //
244     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )  
245        throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);      // Nodes nodeDistribution
246     if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )      if (! (ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
247        throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_var(Nodes_NodeDistribution)");
248     if (!dataFile.add_att("num_Tags", num_Tags) )      int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
249        throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);      if (! (ids->put(int_ptr, mpi_size+1)) )
250            throw FinleyAdapterException(msgPrefix+"put(Nodes_NodeDistribution)");
251     // // // // // Nodes // // // // //  
252        // Nodes degreesOfFreedomDistribution
253     // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)      if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
254     if (numNodes>0) {          throw FinleyAdapterException(msgPrefix+"add_var(Nodes_DofDistribution)");
255        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
256        // Nodes Id      if (! (ids->put(int_ptr, mpi_size+1)) )
257        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )          throw FinleyAdapterException(msgPrefix+"put(Nodes_DofDistribution)");
258           throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);  
259        int_ptr = &mesh->Nodes->Id[0];      // Only write nodes if non-empty because NetCDF doesn't like empty arrays
260        if (! (ids->put(int_ptr, numNodes)) )      // (it treats them as NC_UNLIMITED)
261           throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);      if (numNodes>0) {
262            // Nodes Id
263        // Nodes Tag          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
264        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Id)");
265           throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Nodes->Id[0];
266        int_ptr = &mesh->Nodes->Tag[0];          if (! (ids->put(int_ptr, numNodes)) )
267        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_Id)");
268           throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);  
269            // Nodes Tag
270        // Nodes gDOF          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
271        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Tag)");
272           throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Nodes->Tag[0];
273        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];          if (! (ids->put(int_ptr, numNodes)) )
274        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_Tag)");
275           throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);  
276            // Nodes gDOF
277        // Nodes global node index          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
278        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gDOF)");
279           throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
280        int_ptr = &mesh->Nodes->globalNodesIndex[0];          if (! (ids->put(int_ptr, numNodes)) )
281        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_gDOF)");
282           throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);  
283            // Nodes global node index
284        // Nodes grDof          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
285        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gNI)");
286           throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalNodesIndex[0];
287        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];          if (! (ids->put(int_ptr, numNodes)) )
288        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_gNI)");
289           throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);  
290            // Nodes grDof
291        // Nodes grNI          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
292        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grDfI)");
293           throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
294        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];          if (! (ids->put(int_ptr, numNodes)) )
295        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_grDfI)");
296           throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);  
297            // Nodes grNI
298        // Nodes Coordinates          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
299        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grNI)");
300           throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
301        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )          if (! (ids->put(int_ptr, numNodes)) )
302           throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Nodes_grNI)");
303    
304        // Nodes degreesOfFreedomDistribution          // Nodes Coordinates
305        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
306           throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Coordinates)");
307        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
308        if (! (ids->put(int_ptr, mpi_size+1)) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_Coordinates)");
309           throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);      }
310    
311        // Nodes nodeDistribution      // // // // // Elements // // // // //
312        if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )      if (num_Elements>0) {
313           throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);          // Elements_Id
314        int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
315        if (! (ids->put(int_ptr, mpi_size+1)) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Id)");
316           throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Elements->Id[0];
317            if (! (ids->put(int_ptr, num_Elements)) )
318     }              throw FinleyAdapterException(msgPrefix+"put(Elements_Id)");
319    
320     // // // // // Elements // // // // //          // Elements_Tag
321            if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
322     if (num_Elements>0) {              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Tag)");
323            int_ptr = &mesh->Elements->Tag[0];
324        // Elements_Id          if (! (ids->put(int_ptr, num_Elements)) )
325        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Tag)");
326           throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);  
327        int_ptr = &mesh->Elements->Id[0];          // Elements_Owner
328        if (! (ids->put(int_ptr, num_Elements)) )          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
329           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Owner)");
330            int_ptr = &mesh->Elements->Owner[0];
331        // Elements_Tag          if (! (ids->put(int_ptr, num_Elements)) )
332        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Owner)");
333           throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);  
334        int_ptr = &mesh->Elements->Tag[0];          // Elements_Color
335        if (! (ids->put(int_ptr, num_Elements)) )          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
336           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Color)");
337            int_ptr = &mesh->Elements->Color[0];
338        // Elements_Owner          if (! (ids->put(int_ptr, num_Elements)) )
339        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Color)");
340           throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);  
341        int_ptr = &mesh->Elements->Owner[0];          // Elements_Nodes
342        if (! (ids->put(int_ptr, num_Elements)) )          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
343           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Nodes)");
344            if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
345        // Elements_Color              throw FinleyAdapterException(msgPrefix+"put(Elements_Nodes)");
346        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )      }
347           throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);  
348        int_ptr = &mesh->Elements->Color[0];      // // // // // Face_Elements // // // // //
349        if (! (ids->put(int_ptr, num_Elements)) )      if (num_FaceElements>0) {
350           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);          // FaceElements_Id
351            if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
352        // Elements_Nodes              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Id)");
353        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )          int_ptr = &mesh->FaceElements->Id[0];
354           throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);          if (! (ids->put(int_ptr, num_FaceElements)) )
355        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Id)");
356           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);  
357            // FaceElements_Tag
358     }          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
359                throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Tag)");
360     // // // // // Face_Elements // // // // //          int_ptr = &mesh->FaceElements->Tag[0];
361            if (! (ids->put(int_ptr, num_FaceElements)) )
362     if (num_FaceElements>0) {              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Tag)");
363    
364        // FaceElements_Id          // FaceElements_Owner
365        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
366           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Owner)");
367        int_ptr = &mesh->FaceElements->Id[0];          int_ptr = &mesh->FaceElements->Owner[0];
368        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! (ids->put(int_ptr, num_FaceElements)) )
369           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Owner)");
370    
371        // FaceElements_Tag          // FaceElements_Color
372        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
373           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Color)");
374        int_ptr = &mesh->FaceElements->Tag[0];          int_ptr = &mesh->FaceElements->Color[0];
375        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! (ids->put(int_ptr, num_FaceElements)) )
376           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Color)");
377    
378        // FaceElements_Owner          // FaceElements_Nodes
379        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
380           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Nodes)");
381        int_ptr = &mesh->FaceElements->Owner[0];          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
382        if (! (ids->put(int_ptr, num_FaceElements)) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Nodes)");
383           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);      }
384    
385        // FaceElements_Color      // // // // // Contact_Elements // // // // //
386        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )      if (num_ContactElements>0) {
387           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);  
388        int_ptr = &mesh->FaceElements->Color[0];          // ContactElements_Id
389        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
390           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Id)");
391            int_ptr = &mesh->ContactElements->Id[0];
392        // FaceElements_Nodes          if (! (ids->put(int_ptr, num_ContactElements)) )
393        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Id)");
394           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);  
395        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )          // ContactElements_Tag
396           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
397                throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Tag)");
398     }          int_ptr = &mesh->ContactElements->Tag[0];
399            if (! (ids->put(int_ptr, num_ContactElements)) )
400     // // // // // Contact_Elements // // // // //              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Tag)");
401    
402     if (num_ContactElements>0) {          // ContactElements_Owner
403            if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
404        // ContactElements_Id              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Owner)");
405        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )          int_ptr = &mesh->ContactElements->Owner[0];
406           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);          if (! (ids->put(int_ptr, num_ContactElements)) )
407        int_ptr = &mesh->ContactElements->Id[0];              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Owner)");
408        if (! (ids->put(int_ptr, num_ContactElements)) )  
409           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);          // ContactElements_Color
410            if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
411        // ContactElements_Tag              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Color)");
412        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )          int_ptr = &mesh->ContactElements->Color[0];
413           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);          if (! (ids->put(int_ptr, num_ContactElements)) )
414        int_ptr = &mesh->ContactElements->Tag[0];              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Color)");
415        if (! (ids->put(int_ptr, num_ContactElements)) )  
416           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);          // ContactElements_Nodes
417            if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
418        // ContactElements_Owner              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Nodes)");
419        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
420           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Nodes)");
421        int_ptr = &mesh->ContactElements->Owner[0];      }
422        if (! (ids->put(int_ptr, num_ContactElements)) )  
423           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);      // // // // // Points // // // // //
424        if (num_Points>0) {
425        // ContactElements_Color          // Points_Id
426        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
427           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Id)");
428        int_ptr = &mesh->ContactElements->Color[0];          int_ptr = &mesh->Points->Id[0];
429        if (! (ids->put(int_ptr, num_ContactElements)) )          if (! (ids->put(int_ptr, num_Points)) )
430           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Points_Id)");
431    
432        // ContactElements_Nodes          // Points_Tag
433        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
434           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Tag)");
435        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )          int_ptr = &mesh->Points->Tag[0];
436           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_Points)) )
437                throw FinleyAdapterException(msgPrefix+"put(Points_Tag)");
438     }  
439            // Points_Owner
440     // // // // // Points // // // // //          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
441                throw FinleyAdapterException(msgPrefix+"add_var(Points_Owner)");
442     if (num_Points>0) {          int_ptr = &mesh->Points->Owner[0];
443            if (! (ids->put(int_ptr, num_Points)) )
444        fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");              throw FinleyAdapterException(msgPrefix+"put(Points_Owner)");
445    
446        // Points_Id          // Points_Color
447        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
448           throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Color)");
449        int_ptr = &mesh->Points->Id[0];          int_ptr = &mesh->Points->Color[0];
450        if (! (ids->put(int_ptr, num_Points)) )          if (! (ids->put(int_ptr, num_Points)) )
451           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Points_Color)");
452    
453        // Points_Tag          // Points_Nodes
454        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
455           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
456        int_ptr = &mesh->Points->Tag[0];              throw FinleyAdapterException(msgPrefix+"add_var(Points_Nodes)");
457        if (! (ids->put(int_ptr, num_Points)) )          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
458           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Points_Nodes)");
459        }
460        // Points_Owner  
461        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )      // // // // // TagMap // // // // //
462           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);      if (num_Tags>0) {
463        int_ptr = &mesh->Points->Owner[0];          // Temp storage to gather node IDs
464        if (! (ids->put(int_ptr, num_Points)) )          vector<int> Tags_keys;
465           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);  
466            // Copy tag data into temp arrays
467        // Points_Color          TagMap::const_iterator it;
468        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )          for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++) {
469           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);              Tags_keys.push_back(it->second);
470        int_ptr = &mesh->Points->Color[0];          }
471        if (! (ids->put(int_ptr, num_Points)) )  
472           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);          // Tags_keys
473            if (! (ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
474        // Points_Nodes              throw FinleyAdapterException(msgPrefix+"add_var(Tags_keys)");
475        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]          int_ptr = &Tags_keys[0];
476        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )          if (! (ids->put(int_ptr, num_Tags)) )
477           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Tags_keys)");
478        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )  
479           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);          // Tags_names_*
480            // This is an array of strings, it should be stored as an array but
481     }          // instead I have hacked in one attribute per string because the NetCDF
482            // manual doesn't tell how to do an array of strings
483     // // // // // TagMap // // // // //          int i = 0;
484            for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++, i++) {
485     if (num_Tags>0) {              stringstream tagnamestream;
486                tagnamestream << "Tags_name_" << i;
487        // Temp storage to gather node IDs              const string tagname = tagnamestream.str();
488        int *Tags_keys = TMPMEMALLOC(num_Tags, int);              if (!dataFile.add_att(tagname.c_str(), it->first.c_str()))
489        char name_temp[4096];                  throw FinleyAdapterException(msgPrefix+"add_att(Tags_names_X)");
490            }
491        /* Copy tag data into temp arrays */      }
492        tag_map = mesh->TagMap;  
493        if (tag_map) {      // Send token to next MPI process so he can take his turn
494           int i = 0;  #ifdef ESYS_MPI
495           while (tag_map) {      if (mpi_rank<mpi_size-1) {
496              Tags_keys[i++] = tag_map->tag_key;          MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
497              tag_map=tag_map->next;      }
          }  
       }  
   
       // Tags_keys  
       if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )  
          throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);  
       int_ptr = &Tags_keys[0];  
       if (! (ids->put(int_ptr, num_Tags)) )  
          throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);  
   
       // Tags_names_*  
       // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string  
       // because the NetCDF manual doesn't tell how to do an array of strings  
       tag_map = mesh->TagMap;  
       if (tag_map) {  
          int i = 0;  
          while (tag_map) {  
             sprintf(name_temp, "Tags_name_%d", i);  
             if (!dataFile.add_att(name_temp, tag_map->name) )  
                throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);  
             tag_map=tag_map->next;  
             i++;  
          }  
       }  
   
       TMPMEMFREE(Tags_keys);  
   
    }  
   
 /* Send token to next MPI process so he can take his turn */  
 #ifdef PASO_MPI  
    if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);  
498  #endif  #endif
499    
500     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
501    
502  #else  #else // USE_NETCDF
503     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");      setError(IO_ERROR, "MeshAdapter::dump: not configured with netCDF. Please contact your installation manager.");
504  #endif  /* USE_NETCDF */  #endif // USE_NETCDF
505     checkFinleyError();      checkFinleyError();
506  }  }
507    
508  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
509  {  {
510     return "FinleyMesh";      return "FinleyMesh";
511  }  }
512    
513  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
514  {  {
515     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
516     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
517     if (loc==m_functionSpaceTypeNames.end()) {      if (loc==m_functionSpaceTypeNames.end()) {
518        return "Invalid function space type code.";          return "Invalid function space type code.";
519     } else {      } else {
520        return loc->second;          return loc->second;
521     }      }
522  }  }
523    
524  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
525  {  {
526     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
527     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
528     return (loc!=m_functionSpaceTypeNames.end());      return (loc!=m_functionSpaceTypeNames.end());
529  }  }
530    
531  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
532  {  {
533     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
534     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));                  DegreesOfFreedom,"Finley_DegreesOfFreedom"));
535     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
536     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));                  ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
537     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
538     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));                  Nodes,"Finley_Nodes"));
539     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
540     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));                  ReducedNodes,"Finley_Reduced_Nodes"));
541     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
542     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));                  Elements,"Finley_Elements"));
543     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
544     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));                  ReducedElements,"Finley_Reduced_Elements"));
545     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
546     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));                  FaceElements,"Finley_Face_Elements"));
547     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
548     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));                  ReducedFaceElements,"Finley_Reduced_Face_Elements"));
549     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
550     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));                  Points,"Finley_Points"));
551     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
552     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));                  ContactElementsZero,"Finley_Contact_Elements_0"));
553     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
554     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));                  ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
555     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
556     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));                  ContactElementsOne,"Finley_Contact_Elements_1"));
557     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
558     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));                  ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
559  }  }
560    
561  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
562  {  {
563     return Nodes;      return Nodes;
564  }  }
565    
566  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
567  {  {
568     return ReducedNodes;      return ReducedNodes;
569  }  }
570    
571  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
572  {  {
573     return Elements;      return Elements;
574  }  }
575    
576  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
577  {  {
578     return ReducedElements;      return ReducedElements;
579  }  }
580    
581  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
582  {  {
583     return FaceElements;      return FaceElements;
584  }  }
585    
586  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
587  {  {
588     return ReducedFaceElements;      return ReducedFaceElements;
589  }  }
590    
591  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
592  {  {
593     return ContactElementsZero;      return ContactElementsZero;
594  }  }
595    
596  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
597  {  {
598     return ReducedContactElementsZero;      return ReducedContactElementsZero;
599  }  }
600    
601  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
602  {  {
603     return ContactElementsOne;      return ContactElementsOne;
604  }  }
605    
606  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
607  {  {
608     return ReducedContactElementsOne;      return ReducedContactElementsOne;
609  }  }
610    
611  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
612  {  {
613     return DegreesOfFreedom;      return DegreesOfFreedom;
614  }  }
615    
616  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
617  {  {
618     return ReducedDegreesOfFreedom;      return ReducedDegreesOfFreedom;
619  }  }
620    
621  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
622  {  {
623     return Points;      return Points;
624  }  }
625    
626  //  //
# Line 643  int MeshAdapter::getDiracDeltaFunctionCo Line 628  int MeshAdapter::getDiracDeltaFunctionCo
628  //  //
629  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
630  {  {
631     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
632     int numDim=Finley_Mesh_getDim(mesh);      return mesh->getDim();
    checkFinleyError();  
    return numDim;  
633  }  }
634    
635  //  //
# Line 654  int MeshAdapter::getDim() const Line 637  int MeshAdapter::getDim() const
637  //  //
638  int MeshAdapter::getNumDataPointsGlobal() const  int MeshAdapter::getNumDataPointsGlobal() const
639  {  {
640     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);      return m_finleyMesh.get()->Nodes->getGlobalNumNodes();
641  }  }
642    
643  //  //
# Line 663  int MeshAdapter::getNumDataPointsGlobal( Line 646  int MeshAdapter::getNumDataPointsGlobal(
646  //  //
647  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const
648  {  {
649     int numDataPointsPerSample=0;      int numDataPointsPerSample=0;
650     int numSamples=0;      int numSamples=0;
651     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
652     switch (functionSpaceCode) {      switch (functionSpaceCode) {
653     case(Nodes):          case Nodes:
654     numDataPointsPerSample=1;              numDataPointsPerSample=1;
655     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumNodes();
656     break;              break;
657     case(ReducedNodes):          case ReducedNodes:
658     numDataPointsPerSample=1;              numDataPointsPerSample=1;
659     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumReducedNodes();
660     break;              break;
661     case(Elements):          case Elements:
662     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
663        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
664        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
665     }              }
666     break;              break;
667     case(ReducedElements):          case ReducedElements:
668     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
669        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
670        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
671     }              }
672     break;              break;
673     case(FaceElements):          case FaceElements:
674     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
675        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
676        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
677     }              }
678     break;              break;
679     case(ReducedFaceElements):          case ReducedFaceElements:
680     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
681        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
682        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
683     }              }
684     break;              break;
685     case(Points):          case Points:
686     if (mesh->Points!=NULL) {              if (mesh->Points!=NULL) {
687        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
688        numSamples=mesh->Points->numElements;                  numSamples=mesh->Points->numElements;
689     }              }
690     break;              break;
691     case(ContactElementsZero):          case ContactElementsZero:
692     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
693        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
694        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
695     }              }
696     break;              break;
697     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
698     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
699        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
700        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
701     }              }
702     break;              break;
703     case(ContactElementsOne):          case ContactElementsOne:
704     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
705        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
706        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
707     }              }
708     break;              break;
709     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
710     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
711        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
712        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
713     }              }
714     break;              break;
715     case(DegreesOfFreedom):          case DegreesOfFreedom:
716     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
717        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
718        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumDegreesOfFreedom();
719     }              }
720     break;              break;
721     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
722     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
723        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
724        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumReducedDegreesOfFreedom();
725     }              }
726     break;              break;
727     default:          default:
728        stringstream temp;              stringstream temp;
729        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();              temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
730        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
731        break;              break;
732     }      }
733     return pair<int,int>(numDataPointsPerSample,numSamples);      return pair<int,int>(numDataPointsPerSample,numSamples);
734  }  }
735    
736  //  //
737  // 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
738    // hand side:
739  //  //
740  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
741                                   SystemMatrixAdapter& mat, escript::Data& rhs,          escript::AbstractSystemMatrix& mat, escript::Data& rhs,
742                                   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,
743                                   const escript::Data& d, const escript::Data& y,          const escript::Data& D, const escript::Data& X, const escript::Data& Y,
744                                   const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d, const escript::Data& y,
745  {          const escript::Data& d_contact, const escript::Data& y_contact,
746     escriptDataC _rhs=rhs.getDataC();          const escript::Data& d_dirac, const escript::Data& y_dirac) const
747     escriptDataC _A  =A.getDataC();  {
748     escriptDataC _B=B.getDataC();      SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
749     escriptDataC _C=C.getDataC();      if (!smat)
750     escriptDataC _D=D.getDataC();          throw FinleyAdapterException("finley only supports Paso system matrices.");
751     escriptDataC _X=X.getDataC();  
752     escriptDataC _Y=Y.getDataC();      Mesh* mesh=m_finleyMesh.get();
753     escriptDataC _d=d.getDataC();      Paso_SystemMatrix* S = smat->getPaso_SystemMatrix();
754     escriptDataC _y=y.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, S, rhs, A, B, C, D, X, Y);
755     escriptDataC _d_contact=d_contact.getDataC();      checkFinleyError();
756     escriptDataC _y_contact=y_contact.getDataC();  
757    
758     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, S, rhs,
759                escript::Data(), escript::Data(), escript::Data(), d,
760     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );              escript::Data(), y);
761     checkFinleyError();      checkFinleyError();
762    
763     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );      Assemble_PDE(mesh->Nodes, mesh->ContactElements, S, rhs,
764     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), d_contact,
765                escript::Data(), y_contact);
766     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );      checkFinleyError();
767     checkFinleyError();  
768  }      Assemble_PDE(mesh->Nodes, mesh->Points, S, rhs, escript::Data(),
769                escript::Data(), escript::Data(), d_dirac, escript::Data(), y_dirac);
770  void  MeshAdapter::addPDEToLumpedSystem(      checkFinleyError();
771                                          escript::Data& mat,  }
772                                          const escript::Data& D,  
773                                          const escript::Data& d) const  void MeshAdapter::addPDEToLumpedSystem(escript::Data& mat,
774  {          const escript::Data& D, const escript::Data& d,
775     escriptDataC _mat=mat.getDataC();          const escript::Data& d_dirac, const bool useHRZ) const
776     escriptDataC _D=D.getDataC();  {
777     escriptDataC _d=d.getDataC();      Mesh* mesh=m_finleyMesh.get();
778        Assemble_LumpedSystem(mesh->Nodes, mesh->Elements, mat, D, useHRZ);
779        checkFinleyError();
780    
781     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_LumpedSystem(mesh->Nodes, mesh->FaceElements, mat, d, useHRZ);
782        checkFinleyError();
783    
784     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);      Assemble_LumpedSystem(mesh->Nodes, mesh->Points, mat, d_dirac, useHRZ);
785     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);      checkFinleyError();
   
    checkFinleyError();  
786  }  }
787    
   
788  //  //
789  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
790  //  //
791  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const  void MeshAdapter::addPDEToRHS(escript::Data& rhs, const escript::Data& X,
792  {          const escript::Data& Y, const escript::Data& y,
793     Finley_Mesh* mesh=m_finleyMesh.get();          const escript::Data& y_contact, const escript::Data& y_dirac) const
794    {
795     escriptDataC _rhs=rhs.getDataC();      Mesh* mesh=m_finleyMesh.get();
796     escriptDataC _X=X.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, 0, rhs,
797     escriptDataC _Y=Y.getDataC();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
798     escriptDataC _y=y.getDataC();              X, Y);
799     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
800    
801     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );      Assemble_PDE(mesh->Nodes, mesh->FaceElements, 0, rhs,
802     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
803                escript::Data(), y);
804     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );      checkFinleyError();
805     checkFinleyError();  
806        Assemble_PDE(mesh->Nodes, mesh->ContactElements, 0, rhs,
807     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );              escript::Data(), escript::Data(), escript::Data(),
808     checkFinleyError();              escript::Data(), escript::Data(), y_contact);
809        checkFinleyError();
810    
811        Assemble_PDE(mesh->Nodes, mesh->Points, 0, rhs,
812                escript::Data(), escript::Data(), escript::Data(), escript::Data(),
813                escript::Data(), y_dirac);
814        checkFinleyError();
815  }  }
816    
817  //  //
818  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
819  //  //
820  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
821                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,          escript::AbstractTransportProblem& tp, escript::Data& source,
822                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,          const escript::Data& M, const escript::Data& A, const escript::Data& B,
823                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& C, const escript::Data& D, const escript::Data& X,
824                                             const escript::Data& d, const escript::Data& y,          const escript::Data& Y, const escript::Data& d, const escript::Data& y,
825                                             const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d_contact, const escript::Data& y_contact,
826  {          const escript::Data& d_dirac, const escript::Data& y_dirac) const
827     DataTypes::ShapeType shape;  {
828     source.expand();      TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
829     escriptDataC _source=source.getDataC();      if (!tpa)
830     escriptDataC _M=M.getDataC();          throw FinleyAdapterException("finley only supports Paso transport problems.");
831     escriptDataC _A=A.getDataC();  
832     escriptDataC _B=B.getDataC();      source.expand();
833     escriptDataC _C=C.getDataC();  
834     escriptDataC _D=D.getDataC();      Mesh* mesh=m_finleyMesh.get();
835     escriptDataC _X=X.getDataC();      Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
836     escriptDataC _Y=Y.getDataC();  
837     escriptDataC _d=d.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->mass_matrix, source,
838     escriptDataC _y=y.getDataC();                          escript::Data(), escript::Data(), escript::Data(),
839     escriptDataC _d_contact=d_contact.getDataC();                          M, escript::Data(), escript::Data());
840     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
841    
842     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->transport_matrix,
843     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();                          source, A, B, C, D, X, Y);
844        checkFinleyError();
845     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );  
846     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, _tp->transport_matrix,
847                            source, escript::Data(), escript::Data(),
848     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );                          escript::Data(), d, escript::Data(), y);
849     checkFinleyError();      checkFinleyError();
850    
851     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );      Assemble_PDE(mesh->Nodes, mesh->ContactElements,
852     checkFinleyError();                          _tp->transport_matrix, source, escript::Data(),
853                            escript::Data(), escript::Data(), d_contact,
854     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );                          escript::Data(), y_contact);
855     checkFinleyError();      checkFinleyError();
856  }  
857        Assemble_PDE(mesh->Nodes, mesh->Points, _tp->transport_matrix,
858  //                          source, escript::Data(), escript::Data(),
859  // interpolates data between different function spaces:                          escript::Data(), d_dirac, escript::Data(), y_dirac);
860  //      checkFinleyError();
861  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  }
862  {  
863     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));  //
864     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));  // interpolates data between different function spaces
865     if (inDomain!=*this)    //
866        throw FinleyAdapterException("Error - Illegal domain of interpolant.");  void MeshAdapter::interpolateOnDomain(escript::Data& target, const escript::Data& in) const
867     if (targetDomain!=*this)  {
868        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");      const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
869        const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
870     Finley_Mesh* mesh=m_finleyMesh.get();      if (inDomain!=*this)
871     escriptDataC _target=target.getDataC();          throw FinleyAdapterException("Error - Illegal domain of interpolant.");
872     escriptDataC _in=in.getDataC();      if (targetDomain!=*this)
873     switch(in.getFunctionSpace().getTypeCode()) {          throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
874     case(Nodes):  
875     switch(target.getFunctionSpace().getTypeCode()) {      Mesh* mesh=m_finleyMesh.get();
876     case(Nodes):      switch(in.getFunctionSpace().getTypeCode()) {
877     case(ReducedNodes):          case Nodes:
878     case(DegreesOfFreedom):              switch(target.getFunctionSpace().getTypeCode()) {
879     case(ReducedDegreesOfFreedom):                  case Nodes:
880     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedNodes:
881     break;                  case DegreesOfFreedom:
882     case(Elements):                  case ReducedDegreesOfFreedom:
883     case(ReducedElements):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
884     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
885     break;                  case Elements:
886     case(FaceElements):                  case ReducedElements:
887     case(ReducedFaceElements):                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in,target);
888     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      break;
889     break;                  case FaceElements:
890     case(Points):                  case ReducedFaceElements:
891     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
892     break;                      break;
893     case(ContactElementsZero):                  case Points:
894     case(ReducedContactElementsZero):                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
895     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
896     break;                  case ContactElementsZero:
897     case(ContactElementsOne):                  case ReducedContactElementsZero:
898     case(ReducedContactElementsOne):                  case ContactElementsOne:
899     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsOne:
900     break;                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
901     default:                      break;
902        stringstream temp;                  default:
903        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      stringstream temp;
904        throw FinleyAdapterException(temp.str());                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
905        break;                      throw FinleyAdapterException(temp.str());
906     }                      break;
907     break;              }
908     case(ReducedNodes):              break;
909     switch(target.getFunctionSpace().getTypeCode()) {          case ReducedNodes:
910     case(Nodes):              switch(target.getFunctionSpace().getTypeCode()) {
911     case(ReducedNodes):                  case Nodes:
912     case(DegreesOfFreedom):                  case ReducedNodes:
913     case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
914     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedDegreesOfFreedom:
915     break;                      Assemble_CopyNodalData(mesh->Nodes, target, in);
916     case(Elements):                      break;
917     case(ReducedElements):                  case Elements:
918     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case ReducedElements:
919     break;                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
920     case(FaceElements):                      break;
921     case(ReducedFaceElements):                  case FaceElements:
922     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ReducedFaceElements:
923     break;                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
924     case(Points):                      break;
925     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case Points:
926     break;                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
927     case(ContactElementsZero):                      break;
928     case(ReducedContactElementsZero):                  case ContactElementsZero:
929     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsZero:
930     break;                  case ContactElementsOne:
931     case(ContactElementsOne):                  case ReducedContactElementsOne:
932     case(ReducedContactElementsOne):                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
933     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
934     break;                  default:
935     default:                      stringstream temp;
936        stringstream temp;                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
937        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      throw FinleyAdapterException(temp.str());
938        throw FinleyAdapterException(temp.str());                      break;
939        break;              }
940     }              break;
941     break;          case Elements:
942     case(Elements):              if (target.getFunctionSpace().getTypeCode()==Elements) {
943     if (target.getFunctionSpace().getTypeCode()==Elements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
944        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
945     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_AverageElementData(mesh->Elements, target, in);
946        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);              } else {
947     } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
948        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");              }
949     }              break;
950     break;          case ReducedElements:
951     case(ReducedElements):              if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
952     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
953        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else {
954     } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
955        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");              }
956     }              break;
957     break;          case FaceElements:
958     case(FaceElements):              if (target.getFunctionSpace().getTypeCode()==FaceElements) {
959     if (target.getFunctionSpace().getTypeCode()==FaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
960        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
961     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_AverageElementData(mesh->FaceElements, target, in);
962        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);              } else {
963     } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
964        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");              }
965     }              break;
966     break;          case ReducedFaceElements:
967     case(ReducedFaceElements):              if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
968     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
969        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else {
970     } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
971        throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");              }
972     }              break;
973     break;          case Points:
974     case(Points):              if (target.getFunctionSpace().getTypeCode()==Points) {
975     if (target.getFunctionSpace().getTypeCode()==Points) {                  Assemble_CopyElementData(mesh->Points, target, in);
976        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);              } else {
977     } else {                  throw FinleyAdapterException("Error - No interpolation with data on points possible.");
978        throw FinleyAdapterException("Error - No interpolation with data on points possible.");              }
979     }              break;
980     break;          case ContactElementsZero:
981     case(ContactElementsZero):          case ContactElementsOne:
982     case(ContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
983     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
984        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
985     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_AverageElementData(mesh->ContactElements, target, in);
986        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);              } else {
987     } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
988        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");              }
989     }              break;
990     break;          case ReducedContactElementsZero:
991     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
992     case(ReducedContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
993     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
994        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else {
995     } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
996        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");              }
997     }              break;
998     break;          case DegreesOfFreedom:
999     case(DegreesOfFreedom):                    switch(target.getFunctionSpace().getTypeCode()) {
1000     switch(target.getFunctionSpace().getTypeCode()) {                  case ReducedDegreesOfFreedom:
1001     case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
1002     case(DegreesOfFreedom):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1003     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1004     break;  
1005                    case Nodes:
1006     case(Nodes):                  case ReducedNodes:
1007     case(ReducedNodes):                      if (getMPISize()>1) {
1008     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in);
1009        escript::Data temp=escript::Data(in);                          in2.expand();
1010        temp.expand();                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1011        escriptDataC _in2 = temp.getDataC();                      } else {
1012        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1013     } else {                      }
1014        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1015     }                  case Elements:
1016     break;                  case ReducedElements:
1017     case(Elements):                      if (getMPISize()>1) {
1018     case(ReducedElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1019     if (getMPISize()>1) {                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1020        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                      } else {
1021        escriptDataC _in2 = temp.getDataC();                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1022        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                      }
1023     } else {                      break;
1024        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case FaceElements:
1025     }                  case ReducedFaceElements:
1026     break;                      if (getMPISize()>1) {
1027     case(FaceElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1028     case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1029     if (getMPISize()>1) {                      } else {
1030        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1031        escriptDataC _in2 = temp.getDataC();                      }
1032        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1033                    case Points:
1034     } else {                      if (getMPISize()>1) {
1035        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                          //escript::Data in2=escript::Data(in, continuousFunction(*this) );
1036     }                      } else {
1037     break;                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1038     case(Points):                      }
1039     if (getMPISize()>1) {                      break;
1040        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  case ContactElementsZero:
1041        escriptDataC _in2 = temp.getDataC();                  case ContactElementsOne:
1042     } else {                  case ReducedContactElementsZero:
1043        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedContactElementsOne:
1044     }                      if (getMPISize()>1) {
1045     break;                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1046     case(ContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1047     case(ContactElementsOne):                      } else {
1048     case(ReducedContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1049     case(ReducedContactElementsOne):                      }
1050     if (getMPISize()>1) {                      break;
1051        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  default:
1052        escriptDataC _in2 = temp.getDataC();                      stringstream temp;
1053        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1054     } else {                      throw FinleyAdapterException(temp.str());
1055        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              }
1056     }              break;
1057     break;          case ReducedDegreesOfFreedom:
1058     default:              switch(target.getFunctionSpace().getTypeCode()) {
1059        stringstream temp;                  case Nodes:
1060        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1061        throw FinleyAdapterException(temp.str());                  case ReducedNodes:
1062        break;                      if (getMPISize()>1) {
1063     }                          escript::Data in2=escript::Data(in);
1064     break;                          in2.expand();
1065     case(ReducedDegreesOfFreedom):                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1066     switch(target.getFunctionSpace().getTypeCode()) {                      } else {
1067     case(Nodes):                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1068     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                      }
1069     break;                      break;
1070     case(ReducedNodes):                  case DegreesOfFreedom:
1071     if (getMPISize()>1) {                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1072        escript::Data temp=escript::Data(in);                      break;
1073        temp.expand();                  case ReducedDegreesOfFreedom:
1074        escriptDataC _in2 = temp.getDataC();                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1075        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                      break;
1076     } else {                  case Elements:
1077        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedElements:
1078     }                      if (getMPISize()>1) {
1079     break;                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1080     case(DegreesOfFreedom):                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1081     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                      } else {
1082     break;                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1083     case(ReducedDegreesOfFreedom):                      }
1084     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1085     break;                  case FaceElements:
1086     case(Elements):                  case ReducedFaceElements:
1087     case(ReducedElements):                      if (getMPISize()>1) {
1088     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1089        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1090        escriptDataC _in2 = temp.getDataC();                      } else {
1091        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1092     } else {                      }
1093        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
1094     }                  case Points:
1095     break;                      if (getMPISize()>1) {
1096     case(FaceElements):                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1097     case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->Points, in2, target);
1098     if (getMPISize()>1) {                      } else {
1099        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1100        escriptDataC _in2 = temp.getDataC();                      }
1101        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1102     } else {                  case ContactElementsZero:
1103        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ContactElementsOne:
1104     }                  case ReducedContactElementsZero:
1105     break;                  case ReducedContactElementsOne:
1106     case(Points):                      if (getMPISize()>1) {
1107     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1108        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1109        escriptDataC _in2 = temp.getDataC();                      } else {
1110        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1111     } else {                      }
1112        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      break;
1113     }                  default:
1114     break;                      stringstream temp;
1115     case(ContactElementsZero):                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1116     case(ContactElementsOne):                      throw FinleyAdapterException(temp.str());
1117     case(ReducedContactElementsZero):                      break;
1118     case(ReducedContactElementsOne):              }
1119     if (getMPISize()>1) {              break;
1120        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );          default:
1121        escriptDataC _in2 = temp.getDataC();              stringstream temp;
1122        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1123     } else {              throw FinleyAdapterException(temp.str());
1124        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              break;
1125     }      }
1126     break;      checkFinleyError();
    default:  
       stringstream temp;  
       temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1127  }  }
1128    
1129  //  //
1130  // copies the locations of sample points into x:  // copies the locations of sample points into x
1131  //  //
1132  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1133  {  {
1134     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1135     if (argDomain!=*this)      if (argDomain!=*this)
1136        throw FinleyAdapterException("Error - Illegal domain of data point locations");          throw FinleyAdapterException("Error - Illegal domain of data point locations");
1137     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1138     // in case of values node coordinates we can do the job directly:      // in case of appropriate function space we can do the job directly:
1139     if (arg.getFunctionSpace().getTypeCode()==Nodes) {      if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1140        escriptDataC _arg=arg.getDataC();          Assemble_NodeCoordinates(mesh->Nodes, arg);
1141        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);      } else {
1142     } else {          escript::Data tmp_data=Vector(0., continuousFunction(*this), true);
1143        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);          Assemble_NodeCoordinates(mesh->Nodes, tmp_data);
1144        escriptDataC _tmp_data=tmp_data.getDataC();          // this is then interpolated onto arg:
1145        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);          interpolateOnDomain(arg, tmp_data);
1146        // this is then interpolated onto arg:      }
1147        interpolateOnDomain(arg,tmp_data);      checkFinleyError();
    }  
    checkFinleyError();  
1148  }  }
1149    
1150  //  //
1151  // return the normal vectors at the location of data points as a Data object:  // return the normal vectors at the location of data points as a Data object
1152  //  //
1153  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1154  {  {
1155  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/      const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1156     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));      if (normalDomain!=*this)
1157     if (normalDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of normal locations");
1158        throw FinleyAdapterException("Error - Illegal domain of normal locations");      Mesh* mesh=m_finleyMesh.get();
1159     Finley_Mesh* mesh=m_finleyMesh.get();      switch(normal.getFunctionSpace().getTypeCode()) {
1160     escriptDataC _normal=normal.getDataC();          case Nodes:
1161     switch(normal.getFunctionSpace().getTypeCode()) {              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1162     case(Nodes):              break;
1163     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");          case ReducedNodes:
1164     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1165     case(ReducedNodes):              break;
1166     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");          case Elements:
1167     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1168     case(Elements):              break;
1169     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");          case ReducedElements:
1170     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1171     case(ReducedElements):              break;
1172     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");          case FaceElements:
1173     break;          case ReducedFaceElements:
1174     case (FaceElements):              Assemble_getNormal(mesh->Nodes, mesh->FaceElements, normal);
1175     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              break;
1176     break;          case Points:
1177     case (ReducedFaceElements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1178     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              break;
1179     break;          case ContactElementsOne:
1180     case(Points):          case ContactElementsZero:
1181     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");          case ReducedContactElementsOne:
1182     break;          case ReducedContactElementsZero:
1183     case (ContactElementsOne):              Assemble_getNormal(mesh->Nodes, mesh->ContactElements, normal);
1184     case (ContactElementsZero):              break;
1185     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);          case DegreesOfFreedom:
1186     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1187     case (ReducedContactElementsOne):              break;
1188     case (ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1189     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1190     break;              break;
1191     case(DegreesOfFreedom):          default:
1192     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");              stringstream temp;
1193     break;              temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1194     case(ReducedDegreesOfFreedom):              throw FinleyAdapterException(temp.str());
1195     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");              break;
1196     break;      }
1197     default:      checkFinleyError();
1198        stringstream temp;  }
1199        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();  
1200        throw FinleyAdapterException(temp.str());  //
1201        break;  // interpolates data to other domain
1202     }  //
1203     checkFinleyError();  void MeshAdapter::interpolateACross(escript::Data& target, const escript::Data& source) const
1204  }  {
1205        throw FinleyAdapterException("Error - Finley does not allow interpolation across domains.");
1206  //  }
1207  // interpolates data to other domain:  
1208  //  //
1209  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  // calculates the integral of a function defined on arg
1210  {  //
1211     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();  void MeshAdapter::setToIntegrals(vector<double>& integrals, const escript::Data& arg) const
1212     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());  {
1213     if (targetDomain!=this)      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1214        throw FinleyAdapterException("Error - Illegal domain of interpolation target");      if (argDomain!=*this)
1215            throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1216     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");  
1217  }      double blocktimer_start = blocktimer_time();
1218        Mesh* mesh=m_finleyMesh.get();
1219  //      switch(arg.getFunctionSpace().getTypeCode()) {
1220  // calculates the integral of a function defined of arg:          case Nodes:
1221  //              {
1222  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const                  escript::Data temp(arg, escript::function(*this));
1223  {                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1224     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));              }
1225     if (argDomain!=*this)              break;
1226        throw FinleyAdapterException("Error - Illegal domain of integration kernel");          case ReducedNodes:
1227                {
1228     double blocktimer_start = blocktimer_time();                  escript::Data temp(arg, escript::function(*this));
1229     Finley_Mesh* mesh=m_finleyMesh.get();                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1230     escriptDataC _temp;              }
1231     escript::Data temp;              break;
1232     escriptDataC _arg=arg.getDataC();          case Elements:
1233     switch(arg.getFunctionSpace().getTypeCode()) {          case ReducedElements:
1234     case(Nodes):              Assemble_integrate(mesh->Nodes, mesh->Elements, arg, &integrals[0]);
1235     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );              break;
1236     _temp=temp.getDataC();          case FaceElements:
1237     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);          case ReducedFaceElements:
1238     break;              Assemble_integrate(mesh->Nodes, mesh->FaceElements, arg, &integrals[0]);
1239     case(ReducedNodes):              break;
1240     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );          case Points:
1241     _temp=temp.getDataC();              throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1242     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);              break;
1243     break;          case ContactElementsZero:
1244     case(Elements):          case ReducedContactElementsZero:
1245     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case ContactElementsOne:
1246     break;          case ReducedContactElementsOne:
1247     case(ReducedElements):              Assemble_integrate(mesh->Nodes, mesh->ContactElements, arg, &integrals[0]);
1248     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);              break;
1249     break;          case DegreesOfFreedom:
1250     case(FaceElements):          case ReducedDegreesOfFreedom:
1251     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);              {
1252     break;                  escript::Data temp(arg, escript::function(*this));
1253     case(ReducedFaceElements):                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1254     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);              }
1255     break;              break;
1256     case(Points):          default:
1257     throw FinleyAdapterException("Error - Integral of data on points is not supported.");              stringstream temp;
1258     break;              temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1259     case(ContactElementsZero):              throw FinleyAdapterException(temp.str());
1260     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              break;
1261     break;      }
1262     case(ReducedContactElementsZero):      checkFinleyError();
1263     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);      blocktimer_increment("integrate()", blocktimer_start);
1264     break;  }
1265     case(ContactElementsOne):  
1266     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  //
1267     break;  // calculates the gradient of arg
1268     case(ReducedContactElementsOne):  //
1269     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  void MeshAdapter::setToGradient(escript::Data& grad, const escript::Data& arg) const
1270     break;  {
1271     case(DegreesOfFreedom):      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1272     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );      if (argDomain!=*this)
1273     _temp=temp.getDataC();          throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1274     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);      const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1275     break;      if (gradDomain!=*this)
1276     case(ReducedDegreesOfFreedom):          throw FinleyAdapterException("Error - Illegal domain of gradient");
1277     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );  
1278     _temp=temp.getDataC();      Mesh* mesh=m_finleyMesh.get();
1279     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);      escript::Data nodeData;
1280     break;      if (getMPISize()>1) {
1281     default:          if (arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom) {
1282        stringstream temp;              nodeData=escript::Data(arg, continuousFunction(*this));
1283        temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();          } else if(arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom) {
1284        throw FinleyAdapterException(temp.str());              nodeData=escript::Data(arg, reducedContinuousFunction(*this));
1285        break;          } else {
1286     }              nodeData = arg;
1287     checkFinleyError();          }
1288     blocktimer_increment("integrate()", blocktimer_start);      } else {
1289  }          nodeData = arg;
1290        }
1291  //      switch(grad.getFunctionSpace().getTypeCode()) {
1292  // calculates the gradient of arg:          case Nodes:
1293  //              throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1294  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const              break;
1295  {          case ReducedNodes:
1296     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));              throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1297     if (argDomain!=*this)              break;
1298        throw FinleyAdapterException("Error - Illegal domain of gradient argument");          case Elements:
1299     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));          case ReducedElements:
1300     if (gradDomain!=*this)              Assemble_gradient(mesh->Nodes, mesh->Elements, grad, nodeData);
1301        throw FinleyAdapterException("Error - Illegal domain of gradient");              break;
1302            case FaceElements:
1303     Finley_Mesh* mesh=m_finleyMesh.get();          case ReducedFaceElements:
1304     escriptDataC _grad=grad.getDataC();              Assemble_gradient(mesh->Nodes, mesh->FaceElements, grad, nodeData);
1305     escriptDataC nodeDataC;              break;
1306     escript::Data temp;          case Points:
1307     if (getMPISize()>1) {              throw FinleyAdapterException("Error - Gradient at points is not supported.");
1308        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {              break;
1309           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );          case ContactElementsZero:
1310           nodeDataC = temp.getDataC();          case ReducedContactElementsZero:
1311        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {          case ContactElementsOne:
1312           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );          case ReducedContactElementsOne:
1313           nodeDataC = temp.getDataC();              Assemble_gradient(mesh->Nodes, mesh->ContactElements, grad, nodeData);
1314        } else {              break;
1315           nodeDataC = arg.getDataC();          case DegreesOfFreedom:
1316        }              throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1317     } else {              break;
1318        nodeDataC = arg.getDataC();          case ReducedDegreesOfFreedom:
1319     }              throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1320     switch(grad.getFunctionSpace().getTypeCode()) {              break;
1321     case(Nodes):          default:
1322     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");              stringstream temp;
1323     break;              temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1324     case(ReducedNodes):              throw FinleyAdapterException(temp.str());
1325     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");              break;
1326     break;      }
1327     case(Elements):      checkFinleyError();
    Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);  
    break;  
    case(ReducedElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);  
    break;  
    case(FaceElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedFaceElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);  
    break;  
    case(Points):  
    throw FinleyAdapterException("Error - Gradient at points is not supported.");  
    break;  
    case(ContactElementsZero):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedContactElementsZero):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ContactElementsOne):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedContactElementsOne):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(DegreesOfFreedom):  
    throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");  
    break;  
    case(ReducedDegreesOfFreedom):  
    throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1328  }  }
1329    
1330  //  //
1331  // returns the size of elements:  // returns the size of elements
1332  //  //
1333  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1334  {  {
1335     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1336     escriptDataC tmp=size.getDataC();      switch(size.getFunctionSpace().getTypeCode()) {
1337     switch(size.getFunctionSpace().getTypeCode()) {          case Nodes:
1338     case(Nodes):              throw FinleyAdapterException("Error - Size of nodes is not supported.");
1339     throw FinleyAdapterException("Error - Size of nodes is not supported.");              break;
1340     break;          case ReducedNodes:
1341     case(ReducedNodes):              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1342     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");              break;
1343     break;          case Elements:
1344     case(Elements):          case ReducedElements:
1345     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);              Assemble_getSize(mesh->Nodes, mesh->Elements, size);
1346     break;              break;
1347     case(ReducedElements):          case FaceElements:
1348     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case ReducedFaceElements:
1349     break;              Assemble_getSize(mesh->Nodes, mesh->FaceElements, size);
1350     case(FaceElements):              break;
1351     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case Points:
1352     break;              throw FinleyAdapterException("Error - Size of point elements is not supported.");
1353     case(ReducedFaceElements):              break;
1354     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case ContactElementsZero:
1355     break;          case ContactElementsOne:
1356     case(Points):          case ReducedContactElementsZero:
1357     throw FinleyAdapterException("Error - Size of point elements is not supported.");          case ReducedContactElementsOne:
1358     break;              Assemble_getSize(mesh->Nodes,mesh->ContactElements,size);
1359     case(ContactElementsZero):              break;
1360     case(ContactElementsOne):          case DegreesOfFreedom:
1361     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1362     break;              break;
1363     case(ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1364     case(ReducedContactElementsOne):              throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1365     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              break;
1366     break;          default:
1367     case(DegreesOfFreedom):              stringstream temp;
1368     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");              temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1369     break;              throw FinleyAdapterException(temp.str());
1370     case(ReducedDegreesOfFreedom):              break;
1371     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");      }
1372     break;      checkFinleyError();
    default:  
       stringstream temp;  
       temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1373  }  }
1374    
1375  //  //
# Line 1448  void MeshAdapter::setToSize(escript::Dat Line 1377  void MeshAdapter::setToSize(escript::Dat
1377  //  //
1378  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1379  {  {
1380     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1381     escriptDataC tmp;      const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1382     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));      if (newDomain!=*this)
1383     if (newDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of new point locations");
1384        throw FinleyAdapterException("Error - Illegal domain of new point locations");      if (new_x.getFunctionSpace() == continuousFunction(*this)) {
1385     tmp = new_x.getDataC();          mesh->setCoordinates(new_x);
1386     Finley_Mesh_setCoordinates(mesh,&tmp);      } else {
1387     checkFinleyError();          throw FinleyAdapterException("As of escript version 3.3 SetX() only accepts ContinuousFunction arguments. Please interpolate.");
1388  }      }
1389        checkFinleyError();
1390  //  }
1391  // Helper for the save* methods. Extracts optional data variable names and the  
1392  // corresponding pointers from python dictionary. Caller must free arrays.  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1393  //  {
1394  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const      if (getMPISize() > 1) {
1395  {  #ifdef ESYS_MPI
1396     numData = boost::python::extract<int>(arg.attr("__len__")());          int myFirstNode=0, myLastNode=0, k=0;
1397     /* win32 refactor */          int* globalNodeIndex=0;
1398     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;          Mesh* mesh_p=m_finleyMesh.get();
1399     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;          /*
1400     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;           * this method is only used by saveDataCSV which would use the returned
1401             * values for reduced nodes wrongly so this case is disabled for now
1402     boost::python::list keys=arg.keys();          if (fs_code == FINLEY_REDUCED_NODES) {
1403     for (int i=0; i<numData; ++i) {              myFirstNode = NodeFile_getFirstReducedNode(mesh_p->Nodes);
1404        std::string n=boost::python::extract<std::string>(keys[i]);              myLastNode = NodeFile_getLastReducedNode(mesh_p->Nodes);
1405        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);              globalNodeIndex = NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1406        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)          } else
1407           throw FinleyAdapterException("Error: Data must be defined on same Domain");          */
1408        data[i] = d.getDataC();          if (fs_code == FINLEY_NODES) {
1409        dataPtr[i] = &(data[i]);              myFirstNode = mesh_p->Nodes->getFirstNode();
1410        names[i] = TMPMEMALLOC(n.length()+1, char);              myLastNode = mesh_p->Nodes->getLastNode();
1411        strcpy(names[i], n.c_str());              globalNodeIndex = mesh_p->Nodes->borrowGlobalNodesIndex();
1412     }          } else {
1413  }              throw FinleyAdapterException("Unsupported function space type for ownSample()");
1414            }
1415  //  
1416  // saves mesh and optionally data arrays in openDX format          k=globalNodeIndex[id];
1417  //          return ((myFirstNode <= k) && (k < myLastNode));
1418  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const  #endif
1419  {      }
1420     int num_data;      return true;
    char **names;  
    escriptDataC *data;  
    escriptDataC **ptr_data;  
   
    extractArgsFromDict(arg, num_data, names, data, ptr_data);  
    Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);  
    checkFinleyError();  
   
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0; i<num_data; i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
   
    return;  
 }  
   
 //  
 // saves mesh and optionally data arrays in VTK format  
 //  
 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  
 {  
    int num_data;  
    char **names;  
    escriptDataC *data;  
    escriptDataC **ptr_data;  
   
    extractArgsFromDict(arg, num_data, names, data, ptr_data);  
    Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);  
    checkFinleyError();  
   
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0; i<num_data; i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
1421  }  }
1422    
1423    
1424  //  //
1425  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1426  //  //
1427  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  escript::ASM_ptr MeshAdapter::newSystemMatrix(const int row_blocksize,
1428                                                   const int row_blocksize,                              const escript::FunctionSpace& row_functionspace,
1429                                                   const escript::FunctionSpace& row_functionspace,                              const int column_blocksize,
1430                                                   const int column_blocksize,                              const escript::FunctionSpace& column_functionspace,
1431                                                   const escript::FunctionSpace& column_functionspace,                              const int type) const
1432                                                   const int type) const  {
1433  {      // is the domain right?
1434     int reduceRowOrder=0;      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1435     int reduceColOrder=0;      if (row_domain!=*this)
1436     // is the domain right?          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1437     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1438     if (row_domain!=*this)      if (col_domain!=*this)
1439        throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");          throw FinleyAdapterException("Error - domain of column function space does not match the domain of matrix generator.");
1440     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));  
1441     if (col_domain!=*this)      int reduceRowOrder=0;
1442        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");      int reduceColOrder=0;
1443     // is the function space type right      // is the function space type right?
1444     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {      if (row_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1445        reduceRowOrder=0;          reduceRowOrder=1;
1446     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      } else if (row_functionspace.getTypeCode() != DegreesOfFreedom) {
1447        reduceRowOrder=1;          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1448     } else {      }
1449        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      if (column_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1450     }          reduceColOrder=1;
1451     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (column_functionspace.getTypeCode() != DegreesOfFreedom) {
1452        reduceColOrder=0;          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1453     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1454        reduceColOrder=1;  
1455     } else {      // generate matrix:
1456        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");      Paso_SystemMatrixPattern* fsystemMatrixPattern=
1457     }          getFinley_Mesh()->getPattern(reduceRowOrder, reduceColOrder);
1458     // generate matrix:      checkFinleyError();
1459        Paso_SystemMatrix* fsystemMatrix;
1460     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);      const int trilinos = 0;
1461     checkFinleyError();      if (trilinos) {
    Paso_SystemMatrix* fsystemMatrix;  
    int trilinos = 0;  
    if (trilinos) {  
1462  #ifdef TRILINOS  #ifdef TRILINOS
1463        /* Allocation Epetra_VrbMatrix here */          // FIXME: Allocation Epetra_VrbMatrix here...
1464  #endif  #endif
1465     }      } else {
1466     else {          fsystemMatrix=Paso_SystemMatrix_alloc(type, fsystemMatrixPattern,
1467        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);                  row_blocksize, column_blocksize, FALSE);
1468     }      }
1469     checkPasoError();      checkPasoError();
1470     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1471     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);      SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1472        return escript::ASM_ptr(sma);
1473  }  }
1474    
1475  //  //
1476  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1477  //  //
1478  TransportProblemAdapter MeshAdapter::newTransportProblem(  escript::ATP_ptr MeshAdapter::newTransportProblem(const int blocksize,
1479                                                           const double theta,          const escript::FunctionSpace& functionspace, const int type) const
1480                                                           const int blocksize,  {
1481                                                           const escript::FunctionSpace& functionspace,      // is the domain right?
1482                                                           const int type) const      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1483  {      if (domain!=*this)
1484     int reduceOrder=0;          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1485     // is the domain right?  
1486     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));      // is the function space type right?
1487     if (domain!=*this)      int reduceOrder=0;
1488        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");      if (functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1489     // is the function space type right          reduceOrder=1;
1490     if (functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (functionspace.getTypeCode() != DegreesOfFreedom) {
1491        reduceOrder=0;          throw FinleyAdapterException("Error - illegal function space type for transport problem.");
1492     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1493        reduceOrder=1;  
1494     } else {      // generate transport problem:
1495        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      Paso_SystemMatrixPattern* fsystemMatrixPattern=
1496     }          getFinley_Mesh()->getPattern(reduceOrder, reduceOrder);
1497     // generate matrix:      checkFinleyError();
1498        Paso_TransportProblem* transportProblem;
1499     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);      transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern, blocksize);
1500     checkFinleyError();      checkPasoError();
1501     Paso_FCTransportProblem* transportProblem;      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1502     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);      TransportProblemAdapter* tpa=new TransportProblemAdapter(
1503     checkPasoError();              transportProblem, blocksize, functionspace);
1504     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      return escript::ATP_ptr(tpa);
    return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);  
1505  }  }
1506    
1507  //  //
1508  // vtkObject MeshAdapter::createVtkObject() const  // returns true if data on functionSpaceCode is considered as being cell centered
 // TODO:  
 //  
   
1509  //  //
 // returns true if data at the atom_type is considered as being cell centered:  
1510  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1511  {  {
1512     switch(functionSpaceCode) {      switch(functionSpaceCode) {
1513     case(Nodes):          case Nodes:
1514     case(DegreesOfFreedom):          case DegreesOfFreedom:
1515     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1516     return false;              return false;
1517     break;          case Elements:
1518     case(Elements):          case FaceElements:
1519     case(FaceElements):          case Points:
1520     case(Points):          case ContactElementsZero:
1521     case(ContactElementsZero):          case ContactElementsOne:
1522     case(ContactElementsOne):          case ReducedElements:
1523     case(ReducedElements):          case ReducedFaceElements:
1524     case(ReducedFaceElements):          case ReducedContactElementsZero:
1525     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
1526     case(ReducedContactElementsOne):              return true;
1527     return true;          default:
1528     break;              stringstream temp;
1529     default:              temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1530        stringstream temp;              throw FinleyAdapterException(temp.str());
1531        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;              break;
1532        throw FinleyAdapterException(temp.str());      }
1533        break;      return false;
1534     }  }
1535     checkFinleyError();  
1536     return false;  bool
1537  }  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1538    {
1539  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const      /* The idea is to use equivalence classes. [Types which can be interpolated
1540  {         back and forth]:
1541     switch(functionSpaceType_source) {          class 1: DOF <-> Nodes
1542     case(Nodes):          class 2: ReducedDOF <-> ReducedNodes
1543     switch(functionSpaceType_target) {          class 3: Points
1544     case(Nodes):          class 4: Elements
1545     case(ReducedNodes):          class 5: ReducedElements
1546     case(ReducedDegreesOfFreedom):          class 6: FaceElements
1547     case(DegreesOfFreedom):          class 7: ReducedFaceElements
1548     case(Elements):          class 8: ContactElementZero <-> ContactElementOne
1549     case(ReducedElements):          class 9: ReducedContactElementZero <-> ReducedContactElementOne
1550     case(FaceElements):  
1551     case(ReducedFaceElements):      There is also a set of lines. Interpolation is possible down a line but
1552     case(Points):      not between lines.
1553     case(ContactElementsZero):      class 1 and 2 belong to all lines so aren't considered.
1554     case(ReducedContactElementsZero):          line 0: class 3
1555     case(ContactElementsOne):          line 1: class 4,5
1556     case(ReducedContactElementsOne):          line 2: class 6,7
1557     return true;          line 3: class 8,9
1558     default:  
1559        stringstream temp;      For classes with multiple members (eg class 2) we have vars to record if
1560        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      there is at least one instance.
1561        throw FinleyAdapterException(temp.str());      e.g. hasnodes is true if we have at least one instance of Nodes.
1562     }      */
1563     break;      if (fs.empty())
1564     case(ReducedNodes):          return false;
1565     switch(functionSpaceType_target) {  
1566     case(ReducedNodes):      vector<int> hasclass(10);
1567     case(ReducedDegreesOfFreedom):      vector<int> hasline(4);    
1568     case(Elements):      bool hasnodes=false;
1569     case(ReducedElements):      bool hasrednodes=false;
1570     case(FaceElements):      bool hascez=false;
1571     case(ReducedFaceElements):      bool hasrcez=false;
1572     case(Points):      for (int i=0;i<fs.size();++i) {
1573     case(ContactElementsZero):          switch(fs[i]) {
1574     case(ReducedContactElementsZero):              case Nodes:
1575     case(ContactElementsOne):                  hasnodes=true; // fall through
1576     case(ReducedContactElementsOne):              case DegreesOfFreedom:
1577     return true;                  hasclass[1]=1;
1578     case(Nodes):                  break;
1579     case(DegreesOfFreedom):              case ReducedNodes:
1580     return false;                  hasrednodes=true; // fall through
1581     default:              case ReducedDegreesOfFreedom:
1582        stringstream temp;                  hasclass[2]=1;
1583        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                  break;
1584        throw FinleyAdapterException(temp.str());              case Points:
1585     }                  hasline[0]=1;
1586     break;                  hasclass[3]=1;
1587     case(Elements):                  break;
1588     if (functionSpaceType_target==Elements) {              case Elements:
1589        return true;                  hasclass[4]=1;
1590     } else if (functionSpaceType_target==ReducedElements) {                  hasline[1]=1;
1591        return true;                  break;
1592     } else {              case ReducedElements:
1593        return false;                  hasclass[5]=1;
1594     }                  hasline[1]=1;
1595     case(ReducedElements):                  break;
1596     if (functionSpaceType_target==ReducedElements) {              case FaceElements:
1597        return true;                  hasclass[6]=1;
1598     } else {                  hasline[2]=1;
1599        return false;                  break;
1600     }              case ReducedFaceElements:
1601     case(FaceElements):                  hasclass[7]=1;
1602     if (functionSpaceType_target==FaceElements) {                  hasline[2]=1;
1603        return true;                  break;
1604     } else if (functionSpaceType_target==ReducedFaceElements) {              case ContactElementsZero:
1605        return true;                  hascez=true; // fall through
1606     } else {              case ContactElementsOne:
1607        return false;                  hasclass[8]=1;
1608     }                  hasline[3]=1;
1609     case(ReducedFaceElements):                  break;
1610     if (functionSpaceType_target==ReducedFaceElements) {              case ReducedContactElementsZero:
1611        return true;                  hasrcez=true; // fall through
1612     } else {              case ReducedContactElementsOne:
1613        return false;                  hasclass[9]=1;
1614     }                  hasline[3]=1;
1615     case(Points):                  break;
1616     if (functionSpaceType_target==Points) {              default:
1617        return true;                  return false;
1618     } else {          }
1619        return false;      }
1620     }      int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1621     case(ContactElementsZero):  
1622     case(ContactElementsOne):      // fail if we have more than one leaf group
1623     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {      if (totlines>1)
1624        return true;          return false; // there are at least two branches we can't interpolate between
1625     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {      else if (totlines==1) {
1626        return true;          if (hasline[0]==1)              // we have points
1627     } else {              resultcode=Points;
1628        return false;          else if (hasline[1]==1) {
1629     }              if (hasclass[5]==1)
1630     case(ReducedContactElementsZero):                  resultcode=ReducedElements;
1631     case(ReducedContactElementsOne):              else
1632     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {                  resultcode=Elements;
1633        return true;          } else if (hasline[2]==1) {
1634     } else {              if (hasclass[7]==1)
1635        return false;                  resultcode=ReducedFaceElements;
1636     }              else
1637     case(DegreesOfFreedom):                  resultcode=FaceElements;
1638     switch(functionSpaceType_target) {          } else {   // so we must be in line3
1639     case(ReducedDegreesOfFreedom):              if (hasclass[9]==1) {
1640     case(DegreesOfFreedom):                  // need something from class 9
1641     case(Nodes):                  resultcode=(hasrcez ? ReducedContactElementsZero : ReducedContactElementsOne);
1642     case(ReducedNodes):              } else {
1643     case(Elements):                  // something from class 8
1644     case(ReducedElements):                  resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1645     case(Points):              }
1646     case(FaceElements):          }
1647     case(ReducedFaceElements):      } else { // totlines==0
1648     case(ContactElementsZero):          if (hasclass[2]==1) {
1649     case(ReducedContactElementsZero):              // something from class 2
1650     case(ContactElementsOne):              resultcode=(hasrednodes ? ReducedNodes : ReducedDegreesOfFreedom);
1651     case(ReducedContactElementsOne):          } else {
1652     return true;              // something from class 1
1653     default:              resultcode=(hasnodes ? Nodes : DegreesOfFreedom);
1654        stringstream temp;          }
1655        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      }
1656        throw FinleyAdapterException(temp.str());      return true;
1657     }  }
1658     break;  
1659     case(ReducedDegreesOfFreedom):  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,
1660     switch(functionSpaceType_target) {                                               int functionSpaceType_target) const
1661     case(ReducedDegreesOfFreedom):  {
1662     case(ReducedNodes):      switch(functionSpaceType_source) {
1663     case(Elements):          case Nodes:
1664     case(ReducedElements):              switch(functionSpaceType_target) {
1665     case(FaceElements):                  case Nodes:
1666     case(ReducedFaceElements):                  case ReducedNodes:
1667     case(Points):                  case ReducedDegreesOfFreedom:
1668     case(ContactElementsZero):                  case DegreesOfFreedom:
1669     case(ReducedContactElementsZero):                  case Elements:
1670     case(ContactElementsOne):                  case ReducedElements:
1671     case(ReducedContactElementsOne):                  case FaceElements:
1672     return true;                  case ReducedFaceElements:
1673     case(Nodes):                  case Points:
1674     case(DegreesOfFreedom):                  case ContactElementsZero:
1675     return false;                  case ReducedContactElementsZero:
1676     default:                  case ContactElementsOne:
1677        stringstream temp;                  case ReducedContactElementsOne:
1678        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      return true;
1679        throw FinleyAdapterException(temp.str());                  default:
1680     }                      stringstream temp;
1681     break;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1682     default:                      throw FinleyAdapterException(temp.str());
1683        stringstream temp;              }
1684        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;              break;
1685        throw FinleyAdapterException(temp.str());          case ReducedNodes:
1686        break;              switch(functionSpaceType_target) {
1687     }                  case ReducedNodes:
1688     checkFinleyError();                  case ReducedDegreesOfFreedom:
1689     return false;                  case Elements:
1690  }                  case ReducedElements:
1691                    case FaceElements:
1692  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const                  case ReducedFaceElements:
1693  {                  case Points:
1694     return false;                  case ContactElementsZero:
1695  }                  case ReducedContactElementsZero:
1696                    case ContactElementsOne:
1697  bool MeshAdapter::operator==(const AbstractDomain& other) const                  case ReducedContactElementsOne:
1698  {                      return true;
1699     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);                  case Nodes:
1700     if (temp!=0) {                  case DegreesOfFreedom:
1701        return (m_finleyMesh==temp->m_finleyMesh);                      return false;
1702     } else {                  default:
1703        return false;                      stringstream temp;
1704     }                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1705                        throw FinleyAdapterException(temp.str());
1706                }
1707                break;
1708            case Elements:
1709                if (functionSpaceType_target==Elements) {
1710                    return true;
1711                } else if (functionSpaceType_target==ReducedElements) {
1712                    return true;
1713                } else {
1714                    return false;
1715                }
1716            case ReducedElements:
1717                if (functionSpaceType_target==ReducedElements) {
1718                    return true;
1719                } else {
1720                    return false;
1721                }
1722            case FaceElements:
1723                if (functionSpaceType_target==FaceElements) {
1724                    return true;
1725                } else if (functionSpaceType_target==ReducedFaceElements) {
1726                    return true;
1727                } else {
1728                    return false;
1729                }
1730            case ReducedFaceElements:
1731                if (functionSpaceType_target==ReducedFaceElements) {
1732                    return true;
1733                } else {
1734                    return false;
1735                }
1736            case Points:
1737                if (functionSpaceType_target==Points) {
1738                    return true;
1739                } else {
1740                    return false;
1741                }
1742            case ContactElementsZero:
1743            case ContactElementsOne:
1744                if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1745                    return true;
1746                } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1747                    return true;
1748                } else {
1749                    return false;
1750                }
1751            case ReducedContactElementsZero:
1752            case ReducedContactElementsOne:
1753                if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1754                    return true;
1755                } else {
1756                    return false;
1757                }
1758            case DegreesOfFreedom:
1759                switch(functionSpaceType_target) {
1760                    case ReducedDegreesOfFreedom:
1761                    case DegreesOfFreedom:
1762                    case Nodes:
1763                    case ReducedNodes:
1764                    case Elements:
1765                    case ReducedElements:
1766                    case Points:
1767                    case FaceElements:
1768                    case ReducedFaceElements:
1769                    case ContactElementsZero:
1770                    case ReducedContactElementsZero:
1771                    case ContactElementsOne:
1772                    case ReducedContactElementsOne:
1773                        return true;
1774                    default:
1775                        stringstream temp;
1776                        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1777                        throw FinleyAdapterException(temp.str());
1778                }
1779                break;
1780            case ReducedDegreesOfFreedom:
1781                switch(functionSpaceType_target) {
1782                    case ReducedDegreesOfFreedom:
1783                    case ReducedNodes:
1784                    case Elements:
1785                    case ReducedElements:
1786                    case FaceElements:
1787                    case ReducedFaceElements:
1788                    case Points:
1789                    case ContactElementsZero:
1790                    case ReducedContactElementsZero:
1791                    case ContactElementsOne:
1792                    case ReducedContactElementsOne:
1793                        return true;
1794                    case Nodes:
1795                    case DegreesOfFreedom:
1796                        return false;
1797                    default:
1798                        stringstream temp;
1799                        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1800                        throw FinleyAdapterException(temp.str());
1801                }
1802                break;
1803            default:
1804                stringstream temp;
1805                temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1806                throw FinleyAdapterException(temp.str());
1807                break;
1808        }
1809        return false;
1810    }
1811    
1812    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
1813    {
1814        if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1815            return 1;
1816    
1817        if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1818            return -1;
1819    
1820        return 0;
1821    }
1822    
1823    bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,
1824            const escript::AbstractDomain& targetDomain,
1825            int functionSpaceType_target) const
1826    {
1827        return false;
1828    }
1829    
1830    bool MeshAdapter::operator==(const escript::AbstractDomain& other) const
1831    {
1832        const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1833        if (temp) {
1834            return (m_finleyMesh==temp->m_finleyMesh);
1835        } else {
1836            return false;
1837        }
1838  }  }
1839    
1840  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const escript::AbstractDomain& other) const
1841  {  {
1842     return !(operator==(other));      return !(operator==(other));
1843  }  }
1844    
1845  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1846  {  {
1847     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1848     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);      return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
1849     checkPasoError();                 package, symmetry, mesh->MPIInfo);
    return out;  
1850  }  }
1851    
1852  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
1853  {  {
1854     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1855     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);      return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
1856     checkPasoError();                  package, symmetry, mesh->MPIInfo);
    return out;  
1857  }  }
1858    
1859  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1860  {  {
1861     return continuousFunction(asAbstractContinuousDomain()).getX();      return continuousFunction(*this).getX();
1862  }  }
1863    
1864  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1865  {  {
1866     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();      return functionOnBoundary(*this).getNormal();
1867  }  }
1868    
1869  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1870  {  {
1871     return escript::function(asAbstractContinuousDomain()).getSize();      return escript::function(*this).getSize();
1872  }  }
1873    
1874  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1875  {  {
1876     int *out = NULL;      int *out = NULL;
1877     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1878     switch (functionSpaceType) {      switch (functionSpaceType) {
1879     case(Nodes):          case Nodes:
1880     out=mesh->Nodes->Id;              out=mesh->Nodes->Id;
1881     break;              break;
1882     case(ReducedNodes):          case ReducedNodes:
1883     out=mesh->Nodes->reducedNodesId;              out=mesh->Nodes->reducedNodesId;
1884     break;              break;
1885     case(Elements):          case Elements:
1886     out=mesh->Elements->Id;          case ReducedElements:
1887     break;              out=mesh->Elements->Id;
1888     case(ReducedElements):              break;
1889     out=mesh->Elements->Id;          case FaceElements:
1890     break;          case ReducedFaceElements:
1891     case(FaceElements):              out=mesh->FaceElements->Id;
1892     out=mesh->FaceElements->Id;              break;
1893     break;          case Points:
1894     case(ReducedFaceElements):              out=mesh->Points->Id;
1895     out=mesh->FaceElements->Id;              break;
1896     break;          case ContactElementsZero:
1897     case(Points):          case ReducedContactElementsZero:
1898     out=mesh->Points->Id;          case ContactElementsOne:
1899     break;          case ReducedContactElementsOne:
1900     case(ContactElementsZero):              out=mesh->ContactElements->Id;
1901     out=mesh->ContactElements->Id;              break;
1902     break;          case DegreesOfFreedom:
1903     case(ReducedContactElementsZero):              out=mesh->Nodes->degreesOfFreedomId;
1904     out=mesh->ContactElements->Id;              break;
1905     break;          case ReducedDegreesOfFreedom:
1906     case(ContactElementsOne):              out=mesh->Nodes->reducedDegreesOfFreedomId;
1907     out=mesh->ContactElements->Id;              break;
1908     break;          default:
1909     case(ReducedContactElementsOne):              stringstream temp;
1910     out=mesh->ContactElements->Id;              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1911     break;              throw FinleyAdapterException(temp.str());
1912     case(DegreesOfFreedom):              break;
1913     out=mesh->Nodes->degreesOfFreedomId;      }
1914     break;      return out;
    case(ReducedDegreesOfFreedom):  
    out=mesh->Nodes->reducedDegreesOfFreedomId;  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    return out;  
1915  }  }
1916  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1917  {  {
1918     int out=0;      int out=0;
1919     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1920     switch (functionSpaceType) {      switch (functionSpaceType) {
1921     case(Nodes):          case Nodes:
1922     out=mesh->Nodes->Tag[sampleNo];              out=mesh->Nodes->Tag[sampleNo];
1923     break;              break;
1924     case(ReducedNodes):          case ReducedNodes:
1925     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");              throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1926     break;              break;
1927     case(Elements):          case Elements:
1928     out=mesh->Elements->Tag[sampleNo];          case ReducedElements:
1929     break;              out=mesh->Elements->Tag[sampleNo];
1930     case(ReducedElements):              break;
1931     out=mesh->Elements->Tag[sampleNo];          case FaceElements:
1932     break;          case ReducedFaceElements:
1933     case(FaceElements):              out=mesh->FaceElements->Tag[sampleNo];
1934     out=mesh->FaceElements->Tag[sampleNo];              break;
1935     break;          case Points:
1936     case(ReducedFaceElements):              out=mesh->Points->Tag[sampleNo];
1937     out=mesh->FaceElements->Tag[sampleNo];              break;
1938     break;          case ContactElementsZero:
1939     case(Points):          case ReducedContactElementsZero:
1940     out=mesh->Points->Tag[sampleNo];          case ContactElementsOne:
1941     break;          case ReducedContactElementsOne:
1942     case(ContactElementsZero):              out=mesh->ContactElements->Tag[sampleNo];
1943     out=mesh->ContactElements->Tag[sampleNo];              break;
1944     break;          case DegreesOfFreedom:
1945     case(ReducedContactElementsZero):              throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1946     out=mesh->ContactElements->Tag[sampleNo];              break;
1947     break;          case ReducedDegreesOfFreedom:
1948     case(ContactElementsOne):              throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1949     out=mesh->ContactElements->Tag[sampleNo];              break;
1950     break;          default:
1951     case(ReducedContactElementsOne):              stringstream temp;
1952     out=mesh->ContactElements->Tag[sampleNo];              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1953     break;              throw FinleyAdapterException(temp.str());
1954     case(DegreesOfFreedom):              break;
1955     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");      }
1956     break;      return out;
    case(ReducedDegreesOfFreedom):  
    throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    return out;  
1957  }  }
1958    
1959    
1960  void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const  void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
1961  {  {
1962     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1963     escriptDataC tmp=mask.getDataC();      switch(functionSpaceType) {
1964     switch(functionSpaceType) {          case Nodes:
1965     case(Nodes):              mesh->Nodes->setTags(newTag, mask);
1966     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);              break;
1967     break;          case ReducedNodes:
1968     case(ReducedNodes):              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1969     throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case DegreesOfFreedom:
1970     break;              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1971     case(DegreesOfFreedom):          case ReducedDegreesOfFreedom:
1972     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1973     break;          case Elements:
1974     case(ReducedDegreesOfFreedom):          case ReducedElements:
1975     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");              mesh->Elements->setTags(newTag, mask);
1976     break;              break;
1977     case(Elements):          case FaceElements:
1978     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case ReducedFaceElements:
1979     break;              mesh->FaceElements->setTags(newTag, mask);
1980     case(ReducedElements):              break;
1981     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case Points:
1982     break;              mesh->Points->setTags(newTag, mask);
1983     case(FaceElements):              break;
1984     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ContactElementsZero:
1985     break;          case ReducedContactElementsZero:
1986     case(ReducedFaceElements):          case ContactElementsOne:
1987     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ReducedContactElementsOne:
1988     break;              mesh->ContactElements->setTags(newTag, mask);
1989     case(Points):              break;
1990     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);          default:
1991     break;              stringstream temp;
1992     case(ContactElementsZero):              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
1993     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              throw FinleyAdapterException(temp.str());
1994     break;      }
1995     case(ReducedContactElementsZero):      checkFinleyError();
1996     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  }
1997     break;  
1998     case(ContactElementsOne):  void MeshAdapter::setTagMap(const string& name, int tag)
1999     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  {
2000     break;      Mesh* mesh=m_finleyMesh.get();
2001     case(ReducedContactElementsOne):      mesh->addTagMap(name.c_str(), tag);
2002     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);      checkFinleyError();
2003     break;  }
2004     default:  
2005        stringstream temp;  int MeshAdapter::getTag(const string& name) const
2006        temp << "Error - Finley does not know anything about function space type " << functionSpaceType;  {
2007        throw FinleyAdapterException(temp.str());      Mesh* mesh=m_finleyMesh.get();
2008     }      int tag = mesh->getTag(name.c_str());
2009     checkFinleyError();      checkFinleyError();
2010     return;      return tag;
2011  }  }
2012    
2013  void MeshAdapter::setTagMap(const std::string& name,  int tag)  bool MeshAdapter::isValidTagName(const string& name) const
2014  {  {
2015     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2016     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);      return mesh->isValidTagName(name.c_str());
2017     checkPasoError();  }
2018     // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
2019  }  string MeshAdapter::showTagNames() const
2020    {
2021  int MeshAdapter::getTag(const std::string& name) const      stringstream temp;
2022  {      Mesh* mesh=m_finleyMesh.get();
2023     Finley_Mesh* mesh=m_finleyMesh.get();      TagMap::const_iterator it = mesh->tagMap.begin();
2024     int tag=0;      while (it != mesh->tagMap.end()) {
2025     tag=Finley_Mesh_getTag(mesh, name.c_str());          temp << it->first;
2026     checkPasoError();          ++it;
2027     // throwStandardException("MeshAdapter::getTag is not implemented.");          if (it != mesh->tagMap.end())
2028     return tag;              temp << ", ";
2029  }      }
2030        return temp.str();
 bool MeshAdapter::isValidTagName(const std::string& name) const  
 {  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    return Finley_Mesh_isValidTagName(mesh,name.c_str());  
 }  
   
 std::string MeshAdapter::showTagNames() const  
 {  
    stringstream temp;  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    Finley_TagMap* tag_map=mesh->TagMap;  
    while (tag_map) {  
       temp << tag_map->name;  
       tag_map=tag_map->next;  
       if (tag_map) temp << ", ";  
    }  
    return temp.str();  
2031  }  }
2032    
2033  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2034  {  {
2035    Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2036    dim_t numTags=0;      switch(functionSpaceCode) {
2037    switch(functionSpaceCode) {          case Nodes:
2038     case(Nodes):              return mesh->Nodes->tagsInUse.size();
2039            numTags=mesh->Nodes->numTagsInUse;          case ReducedNodes:
2040            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2041     case(ReducedNodes):          case DegreesOfFreedom:
2042            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2043            break;          case ReducedDegreesOfFreedom:
2044     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2045            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2046            break;          case ReducedElements:
2047     case(ReducedDegreesOfFreedom):              return mesh->Elements->tagsInUse.size();
2048            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2049            break;          case ReducedFaceElements:
2050     case(Elements):              return mesh->FaceElements->tagsInUse.size();
2051     case(ReducedElements):          case Points:
2052            numTags=mesh->Elements->numTagsInUse;              return mesh->Points->tagsInUse.size();
2053            break;          case ContactElementsZero:
2054     case(FaceElements):          case ReducedContactElementsZero:
2055     case(ReducedFaceElements):          case ContactElementsOne:
2056            numTags=mesh->FaceElements->numTagsInUse;          case ReducedContactElementsOne:
2057            break;              return mesh->ContactElements->tagsInUse.size();
2058     case(Points):          default:
2059            numTags=mesh->Points->numTagsInUse;              stringstream ss;
2060            break;              ss << "Finley does not know anything about function space type "
2061     case(ContactElementsZero):                   << functionSpaceCode;
2062     case(ReducedContactElementsZero):              throw FinleyAdapterException(ss.str());
2063     case(ContactElementsOne):      }
2064     case(ReducedContactElementsOne):      return 0;
2065            numTags=mesh->ContactElements->numTagsInUse;  }
2066            break;  
2067     default:  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2068        stringstream temp;  {
2069        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;      Mesh* mesh=m_finleyMesh.get();
2070        throw FinleyAdapterException(temp.str());      switch(functionSpaceCode) {
2071    }          case Nodes:
2072    return numTags;              return &mesh->Nodes->tagsInUse[0];
2073  }          case ReducedNodes:
2074  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2075  {          case DegreesOfFreedom:
2076    Finley_Mesh* mesh=m_finleyMesh.get();              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2077    index_t* tags=NULL;          case ReducedDegreesOfFreedom:
2078    switch(functionSpaceCode) {              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2079     case(Nodes):          case Elements:
2080            tags=mesh->Nodes->tagsInUse;          case ReducedElements:
2081            break;              return &mesh->Elements->tagsInUse[0];
2082     case(ReducedNodes):          case FaceElements:
2083            throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case ReducedFaceElements:
2084            break;              return &mesh->FaceElements->tagsInUse[0];
2085     case(DegreesOfFreedom):          case Points:
2086            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              return &mesh->Points->tagsInUse[0];
2087            break;          case ContactElementsZero:
2088     case(ReducedDegreesOfFreedom):          case ReducedContactElementsZero:
2089            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case ContactElementsOne:
2090            break;          case ReducedContactElementsOne:
2091     case(Elements):              return &mesh->ContactElements->tagsInUse[0];
2092     case(ReducedElements):          default:
2093            tags=mesh->Elements->tagsInUse;              stringstream temp;
2094            break;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2095     case(FaceElements):              throw FinleyAdapterException(temp.str());
2096     case(ReducedFaceElements):      }
2097            tags=mesh->FaceElements->tagsInUse;      return NULL;
           break;  
    case(Points):  
           tags=mesh->Points->tagsInUse;  
           break;  
    case(ContactElementsZero):  
    case(ReducedContactElementsZero):  
    case(ContactElementsOne):  
    case(ReducedContactElementsOne):  
           tags=mesh->ContactElements->tagsInUse;  
           break;  
    default:  
       stringstream temp;  
       temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;  
       throw FinleyAdapterException(temp.str());  
   }  
   return tags;  
2098  }  }
2099    
2100    
2101  bool MeshAdapter::canTag(int functionSpaceCode) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2102  {  {
2103    switch(functionSpaceCode) {      switch(functionSpaceCode) {
2104     case(Nodes):          case Nodes:
2105     case(Elements):          case Elements:
2106     case(ReducedElements):          case ReducedElements:
2107     case(FaceElements):          case FaceElements:
2108     case(ReducedFaceElements):          case ReducedFaceElements:
2109     case(Points):          case Points:
2110     case(ContactElementsZero):          case ContactElementsZero:
2111     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
2112     case(ContactElementsOne):          case ContactElementsOne:
2113     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
2114            return true;              return true;
2115     case(ReducedNodes):          default:
2116     case(DegreesOfFreedom):              return false;
2117     case(ReducedDegreesOfFreedom):      }
2118        return false;  }
2119     default:  
2120      return false;  escript::AbstractDomain::StatusType MeshAdapter::getStatus() const
2121    }  {
2122        Mesh* mesh=m_finleyMesh.get();
2123        return mesh->getStatus();
2124    }
2125    
2126    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2127    {
2128        Mesh* mesh=m_finleyMesh.get();
2129        int order =-1;
2130        switch(functionSpaceCode) {
2131            case Nodes:
2132            case DegreesOfFreedom:
2133                order=mesh->approximationOrder;
2134                break;
2135            case ReducedNodes:
2136            case ReducedDegreesOfFreedom:
2137                order=mesh->reducedApproximationOrder;
2138                break;
2139            case Elements:
2140            case FaceElements:
2141            case Points:
2142            case ContactElementsZero:
2143            case ContactElementsOne:
2144                order=mesh->integrationOrder;
2145                break;
2146            case ReducedElements:
2147            case ReducedFaceElements:
2148            case ReducedContactElementsZero:
2149            case ReducedContactElementsOne:
2150                order=mesh->reducedIntegrationOrder;
2151                break;
2152            default:
2153                stringstream temp;
2154                temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2155                throw FinleyAdapterException(temp.str());
2156        }
2157        return order;
2158    }
2159    
2160    bool MeshAdapter::supportsContactElements() const
2161    {
2162        return true;
2163    }
2164    
2165    void MeshAdapter::addDiracPoints(const vector<double>& points,
2166                                     const vector<int>& tags) const
2167    {
2168        // points will be flattened
2169        const int dim = getDim();
2170        int numPoints=points.size()/dim;
2171        int numTags=tags.size();
2172        Mesh* mesh=m_finleyMesh.get();
2173    
2174        if ( points.size() % dim != 0 ) {
2175            throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2176        }
2177    
2178        if ((numTags > 0) && (numPoints != numTags))
2179            throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2180    
2181        mesh->addPoints(numPoints, &points[0], &tags[0]);
2182        checkFinleyError();
2183    }
2184    
2185    // void MeshAdapter::addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2186    // {
2187    //       const int dim = getDim();
2188    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2189    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2190    //       Mesh* mesh=m_finleyMesh.get();
2191    //
2192    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2193    //       throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2194    //
2195    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2196    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2197    //
2198    //       for (int i=0;i<numPoints;++i) {
2199    //         int tag_id=-1;
2200    //         int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2201    //         if  ( numComps !=   dim ) {
2202    //                stringstream temp;
2203    //                temp << "Error - illegal number of components " << numComps << " for point " << i;
2204    //                throw FinleyAdapterException(temp.str());
2205    //         }
2206    //         points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2207    //         if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2208    //         if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2209    //
2210    //         if ( numTags > 0) {
2211    //                boost::python::extract<string> ex_str(tags[i]);
2212    //                if  ( ex_str.check() ) {
2213    //                    tag_id=getTag( ex_str());
2214    //                } else {
2215    //                     boost::python::extract<int> ex_int(tags[i]);
2216    //                     if ( ex_int.check() ) {
2217    //                         tag_id=ex_int();
2218    //                     } else {
2219    //                          stringstream temp;
2220    //                          temp << "Error - unable to extract tag for point " << i;
2221    //                          throw FinleyAdapterException(temp.str());
2222    //                    }
2223    //                }
2224    //         }
2225    //            tags_ptr[i]=tag_id;
2226    //       }
2227    //
2228    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2229    //       checkPasoError();
2230    //
2231    //       TMPMEMFREE(points_ptr);
2232    //       TMPMEMFREE(tags_ptr);
2233    // }
2234    
2235    /*
2236    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2237    {
2238        boost::python::list points =  boost::python::list();
2239        boost::python::list tags =  boost::python::list();
2240        points.append(point);
2241        tags.append(tag);
2242        addDiracPoints(points, tags);
2243    }
2244    */
2245    
2246    /*
2247    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const string& tag) const
2248    {
2249        boost::python::list points =   boost::python::list();
2250        boost::python::list tags =   boost::python::list();
2251        points.append(point);
2252        tags.append(tag);
2253        addDiracPoints(points, tags);
2254  }  }
2255    */
   
2256  }  // end of namespace  }  // end of namespace
2257    

Legend:
Removed from v.2315  
changed lines
  Added in v.4612

  ViewVC Help
Powered by ViewVC 1.1.26