/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 1859 by gross, Wed Oct 8 03:03:37 2008 UTC revision 4496 by caltinay, Mon Jul 15 06:53:44 2013 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 "escript/blocktimer.h"  
 }  
 #include <vector>  
   
 #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH  256  
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 51  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
84    {
85    #ifdef ESYS_MPI
86        MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
87    #endif
88    }
89    
90    bool MeshAdapter::onMasterProcessor() const
91    {
92        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];      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.");      Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with netCDF. Please contact your installation manager.");
504  #endif  /* USE_NETCDF */  #endif // USE_NETCDF
505     checkFinleyError();      checkFinleyError();
506  }  }
507    
508  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
509  {  {
510     return "FinleyMesh";      return "FinleyMesh";
511  }  }
512    
513  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
514  {  {
515     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
516     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
517     if (loc==m_functionSpaceTypeNames.end()) {      if (loc==m_functionSpaceTypeNames.end()) {
518        return "Invalid function space type code.";          return "Invalid function space type code.";
519     } else {      } else {
520        return loc->second;          return loc->second;
521     }      }
522  }  }
523    
524  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
525  {  {
526     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
527     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
528     return (loc!=m_functionSpaceTypeNames.end());      return (loc!=m_functionSpaceTypeNames.end());
529  }  }
530    
531  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
532  {  {
533     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
534     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));                  DegreesOfFreedom,"Finley_DegreesOfFreedom"));
535     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
536     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));                  ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
537     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
538     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));                  Nodes,"Finley_Nodes"));
539     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
540     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));                  ReducedNodes,"Finley_Reduced_Nodes"));
541     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
542     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));                  Elements,"Finley_Elements"));
543     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
544     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));                  ReducedElements,"Finley_Reduced_Elements"));
545     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
546     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));                  FaceElements,"Finley_Face_Elements"));
547     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
548     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));                  ReducedFaceElements,"Finley_Reduced_Face_Elements"));
549     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
550     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));                  Points,"Finley_Points"));
551     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
552     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));                  ContactElementsZero,"Finley_Contact_Elements_0"));
553     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
554     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));                  ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
555     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
556     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));                  ContactElementsOne,"Finley_Contact_Elements_1"));
557     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
558     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));                  ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
559  }  }
560    
561  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
562  {  {
563     return Nodes;      return Nodes;
564  }  }
565    
566  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
567  {  {
568     return ReducedNodes;      return ReducedNodes;
569  }  }
570    
571  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
572  {  {
573     return Elements;      return Elements;
574  }  }
575    
576  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
577  {  {
578     return ReducedElements;      return ReducedElements;
579  }  }
580    
581  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
582  {  {
583     return FaceElements;      return FaceElements;
584  }  }
585    
586  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
587  {  {
588     return ReducedFaceElements;      return ReducedFaceElements;
589  }  }
590    
591  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
592  {  {
593     return ContactElementsZero;      return ContactElementsZero;
594  }  }
595    
596  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
597  {  {
598     return ReducedContactElementsZero;      return ReducedContactElementsZero;
599  }  }
600    
601  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
602  {  {
603     return ContactElementsOne;      return ContactElementsOne;
604  }  }
605    
606  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
607  {  {
608     return ReducedContactElementsOne;      return ReducedContactElementsOne;
609  }  }
610    
611  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
612  {  {
613     return DegreesOfFreedom;      return DegreesOfFreedom;
614  }  }
615    
616  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
617  {  {
618     return ReducedDegreesOfFreedom;      return ReducedDegreesOfFreedom;
619  }  }
620    
621  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
622  {  {
623     return Points;      return Points;
624  }  }
625    
626  //  //
# Line 635  int MeshAdapter::getDiracDeltaFunctionCo Line 628  int MeshAdapter::getDiracDeltaFunctionCo
628  //  //
629  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
630  {  {
631     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());      Mesh* mesh=m_finleyMesh.get();
632     checkFinleyError();      return mesh->getDim();
    return numDim;  
633  }  }
634    
635  //  //
# Line 645  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 654  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        Assemble_PDE(mesh->Nodes, mesh->FaceElements, S, rhs,
758     Finley_Mesh* mesh=m_finleyMesh.get();              escript::Data(), escript::Data(), escript::Data(), d,
759                escript::Data(), y);
760     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );      checkFinleyError();
761     checkFinleyError();  
762        Assemble_PDE(mesh->Nodes, mesh->ContactElements, S, rhs,
763     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );              escript::Data(), escript::Data(), escript::Data(), d_contact,
764     checkFinleyError();              escript::Data(), y_contact);
765        checkFinleyError();
766     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );  
767     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->Points, S, rhs, escript::Data(),
768  }              escript::Data(), escript::Data(), d_dirac, escript::Data(), y_dirac);
769        checkFinleyError();
770  void  MeshAdapter::addPDEToLumpedSystem(  }
771                                          escript::Data& mat,  
772                                          const escript::Data& D,  void MeshAdapter::addPDEToLumpedSystem(escript::Data& mat,
773                                          const escript::Data& d) const          const escript::Data& D, const escript::Data& d,
774  {          const escript::Data& d_dirac, const bool useHRZ) const
775     escriptDataC _mat=mat.getDataC();  {
776     escriptDataC _D=D.getDataC();      Mesh* mesh=m_finleyMesh.get();
777     escriptDataC _d=d.getDataC();      Assemble_LumpedSystem(mesh->Nodes, mesh->Elements, mat, D, useHRZ);
778        checkFinleyError();
    Finley_Mesh* mesh=m_finleyMesh.get();  
779    
780     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);      Assemble_LumpedSystem(mesh->Nodes, mesh->FaceElements, mat, d, useHRZ);
781     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);      checkFinleyError();
782    
783     checkFinleyError();      Assemble_LumpedSystem(mesh->Nodes, mesh->Points, mat, d_dirac, useHRZ);
784        checkFinleyError();
785  }  }
786    
   
787  //  //
788  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
789  //  //
790  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,
791  {          const escript::Data& Y, const escript::Data& y,
792     Finley_Mesh* mesh=m_finleyMesh.get();          const escript::Data& y_contact, const escript::Data& y_dirac) const
793    {
794     escriptDataC _rhs=rhs.getDataC();      Mesh* mesh=m_finleyMesh.get();
795     escriptDataC _X=X.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, 0, rhs,
796     escriptDataC _Y=Y.getDataC();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
797     escriptDataC _y=y.getDataC();              X, Y);
798     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
799    
800     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );      Assemble_PDE(mesh->Nodes, mesh->FaceElements, 0, rhs,
801     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
802                escript::Data(), y);
803     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );      checkFinleyError();
804     checkFinleyError();  
805        Assemble_PDE(mesh->Nodes, mesh->ContactElements, 0, rhs,
806     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );              escript::Data(), escript::Data(), escript::Data(),
807     checkFinleyError();              escript::Data(), escript::Data(), y_contact);
808        checkFinleyError();
809    
810        Assemble_PDE(mesh->Nodes, mesh->Points, 0, rhs,
811                escript::Data(), escript::Data(), escript::Data(), escript::Data(),
812                escript::Data(), y_dirac);
813        checkFinleyError();
814  }  }
815    
816  //  //
817  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
818  //  //
819  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
820                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,          escript::AbstractTransportProblem& tp, escript::Data& source,
821                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,          const escript::Data& M, const escript::Data& A, const escript::Data& B,
822                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& C, const escript::Data& D, const escript::Data& X,
823                                             const escript::Data& d, const escript::Data& y,          const escript::Data& Y, const escript::Data& d, const escript::Data& y,
824                                             const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d_contact, const escript::Data& y_contact,
825  {          const escript::Data& d_dirac, const escript::Data& y_dirac) const
826     DataTypes::ShapeType shape;  {
827     source.expand();      TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
828     escriptDataC _source=source.getDataC();      if (!tpa)
829     escriptDataC _M=M.getDataC();          throw FinleyAdapterException("finley only supports Paso transport problems.");
830     escriptDataC _A=A.getDataC();  
831     escriptDataC _B=B.getDataC();      source.expand();
832     escriptDataC _C=C.getDataC();  
833     escriptDataC _D=D.getDataC();      Mesh* mesh=m_finleyMesh.get();
834     escriptDataC _X=X.getDataC();      Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
835     escriptDataC _Y=Y.getDataC();  
836     escriptDataC _d=d.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->mass_matrix, source,
837     escriptDataC _y=y.getDataC();                          escript::Data(), escript::Data(), escript::Data(),
838     escriptDataC _d_contact=d_contact.getDataC();                          M, escript::Data(), escript::Data());
839     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
840    
841     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->transport_matrix,
842     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();                          source, A, B, C, D, X, Y);
843        checkFinleyError();
844     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );  
845     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, _tp->transport_matrix,
846                            source, escript::Data(), escript::Data(),
847     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );                          escript::Data(), d, escript::Data(), y);
848     checkFinleyError();      checkFinleyError();
849    
850     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );      Assemble_PDE(mesh->Nodes, mesh->ContactElements,
851     checkFinleyError();                          _tp->transport_matrix, source, escript::Data(),
852                            escript::Data(), escript::Data(), d_contact,
853     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );                          escript::Data(), y_contact);
854     checkFinleyError();      checkFinleyError();
855  }  
856        Assemble_PDE(mesh->Nodes, mesh->Points, _tp->transport_matrix,
857  //                          source, escript::Data(), escript::Data(),
858  // interpolates data between different function spaces:                          escript::Data(), d_dirac, escript::Data(), y_dirac);
859  //      checkFinleyError();
860  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  }
861  {  
862     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());  //
863     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());  // interpolates data between different function spaces
864     if (inDomain!=*this)    //
865        throw FinleyAdapterException("Error - Illegal domain of interpolant.");  void MeshAdapter::interpolateOnDomain(escript::Data& target, const escript::Data& in) const
866     if (targetDomain!=*this)  {
867        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");      const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
868        const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
869     Finley_Mesh* mesh=m_finleyMesh.get();      if (inDomain!=*this)
870     escriptDataC _target=target.getDataC();          throw FinleyAdapterException("Error - Illegal domain of interpolant.");
871     escriptDataC _in=in.getDataC();      if (targetDomain!=*this)
872     switch(in.getFunctionSpace().getTypeCode()) {          throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
873     case(Nodes):  
874     switch(target.getFunctionSpace().getTypeCode()) {      Mesh* mesh=m_finleyMesh.get();
875     case(Nodes):      switch(in.getFunctionSpace().getTypeCode()) {
876     case(ReducedNodes):          case Nodes:
877     case(DegreesOfFreedom):              switch(target.getFunctionSpace().getTypeCode()) {
878     case(ReducedDegreesOfFreedom):                  case Nodes:
879     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedNodes:
880     break;                  case DegreesOfFreedom:
881     case(Elements):                  case ReducedDegreesOfFreedom:
882     case(ReducedElements):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
883     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
884     break;                  case Elements:
885     case(FaceElements):                  case ReducedElements:
886     case(ReducedFaceElements):                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in,target);
887     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      break;
888     break;                  case FaceElements:
889     case(Points):                  case ReducedFaceElements:
890     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
891     break;                      break;
892     case(ContactElementsZero):                  case Points:
893     case(ReducedContactElementsZero):                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
894     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
895     break;                  case ContactElementsZero:
896     case(ContactElementsOne):                  case ReducedContactElementsZero:
897     case(ReducedContactElementsOne):                  case ContactElementsOne:
898     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsOne:
899     break;                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
900     default:                      break;
901        stringstream temp;                  default:
902        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      stringstream temp;
903        throw FinleyAdapterException(temp.str());                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
904        break;                      throw FinleyAdapterException(temp.str());
905     }                      break;
906     break;              }
907     case(ReducedNodes):              break;
908     switch(target.getFunctionSpace().getTypeCode()) {          case ReducedNodes:
909     case(Nodes):              switch(target.getFunctionSpace().getTypeCode()) {
910     case(ReducedNodes):                  case Nodes:
911     case(DegreesOfFreedom):                  case ReducedNodes:
912     case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
913     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedDegreesOfFreedom:
914     break;                      Assemble_CopyNodalData(mesh->Nodes, target, in);
915     case(Elements):                      break;
916     case(ReducedElements):                  case Elements:
917     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case ReducedElements:
918     break;                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
919     case(FaceElements):                      break;
920     case(ReducedFaceElements):                  case FaceElements:
921     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ReducedFaceElements:
922     break;                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
923     case(Points):                      break;
924     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case Points:
925     break;                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
926     case(ContactElementsZero):                      break;
927     case(ReducedContactElementsZero):                  case ContactElementsZero:
928     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsZero:
929     break;                  case ContactElementsOne:
930     case(ContactElementsOne):                  case ReducedContactElementsOne:
931     case(ReducedContactElementsOne):                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
932     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
933     break;                  default:
934     default:                      stringstream temp;
935        stringstream temp;                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
936        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      throw FinleyAdapterException(temp.str());
937        throw FinleyAdapterException(temp.str());                      break;
938        break;              }
939     }              break;
940     break;          case Elements:
941     case(Elements):              if (target.getFunctionSpace().getTypeCode()==Elements) {
942     if (target.getFunctionSpace().getTypeCode()==Elements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
943        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
944     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_AverageElementData(mesh->Elements, target, in);
945        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);              } else {
946     } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
947        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");              }
948     }              break;
949     break;          case ReducedElements:
950     case(ReducedElements):              if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
951     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
952        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else {
953     } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
954        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");              }
955     }              break;
956     break;          case FaceElements:
957     case(FaceElements):              if (target.getFunctionSpace().getTypeCode()==FaceElements) {
958     if (target.getFunctionSpace().getTypeCode()==FaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
959        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
960     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_AverageElementData(mesh->FaceElements, target, in);
961        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);              } else {
962     } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
963        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");              }
964     }              break;
965     break;          case ReducedFaceElements:
966     case(ReducedFaceElements):              if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
967     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
968        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else {
969     } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
970        throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");              }
971     }              break;
972     break;          case Points:
973     case(Points):              if (target.getFunctionSpace().getTypeCode()==Points) {
974     if (target.getFunctionSpace().getTypeCode()==Points) {                  Assemble_CopyElementData(mesh->Points, target, in);
975        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);              } else {
976     } else {                  throw FinleyAdapterException("Error - No interpolation with data on points possible.");
977        throw FinleyAdapterException("Error - No interpolation with data on points possible.");              }
978     }              break;
979     break;          case ContactElementsZero:
980     case(ContactElementsZero):          case ContactElementsOne:
981     case(ContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
982     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
983        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
984     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_AverageElementData(mesh->ContactElements, target, in);
985        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);              } else {
986     } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
987        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");              }
988     }              break;
989     break;          case ReducedContactElementsZero:
990     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
991     case(ReducedContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
992     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
993        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else {
994     } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
995        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");              }
996     }              break;
997     break;          case DegreesOfFreedom:
998     case(DegreesOfFreedom):                    switch(target.getFunctionSpace().getTypeCode()) {
999     switch(target.getFunctionSpace().getTypeCode()) {                  case ReducedDegreesOfFreedom:
1000     case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
1001     case(DegreesOfFreedom):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1002     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1003     break;  
1004                    case Nodes:
1005     case(Nodes):                  case ReducedNodes:
1006     case(ReducedNodes):                      if (getMPISize()>1) {
1007     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in);
1008        escript::Data temp=escript::Data(in);                          in2.expand();
1009        temp.expand();                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1010        escriptDataC _in2 = temp.getDataC();                      } else {
1011        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1012     } else {                      }
1013        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1014     }                  case Elements:
1015     break;                  case ReducedElements:
1016     case(Elements):                      if (getMPISize()>1) {
1017     case(ReducedElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1018     if (getMPISize()>1) {                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1019        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                      } else {
1020        escriptDataC _in2 = temp.getDataC();                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1021        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                      }
1022     } else {                      break;
1023        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case FaceElements:
1024     }                  case ReducedFaceElements:
1025     break;                      if (getMPISize()>1) {
1026     case(FaceElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1027     case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1028     if (getMPISize()>1) {                      } else {
1029        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1030        escriptDataC _in2 = temp.getDataC();                      }
1031        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1032                    case Points:
1033     } else {                      if (getMPISize()>1) {
1034        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                          //escript::Data in2=escript::Data(in, continuousFunction(*this) );
1035     }                      } else {
1036     break;                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1037     case(Points):                      }
1038     if (getMPISize()>1) {                      break;
1039        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  case ContactElementsZero:
1040        escriptDataC _in2 = temp.getDataC();                  case ContactElementsOne:
1041     } else {                  case ReducedContactElementsZero:
1042        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedContactElementsOne:
1043     }                      if (getMPISize()>1) {
1044     break;                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1045     case(ContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1046     case(ContactElementsOne):                      } else {
1047     case(ReducedContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1048     case(ReducedContactElementsOne):                      }
1049     if (getMPISize()>1) {                      break;
1050        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  default:
1051        escriptDataC _in2 = temp.getDataC();                      stringstream temp;
1052        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();
1053     } else {                      throw FinleyAdapterException(temp.str());
1054        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              }
1055     }              break;
1056     break;          case ReducedDegreesOfFreedom:
1057     default:              switch(target.getFunctionSpace().getTypeCode()) {
1058        stringstream temp;                  case Nodes:
1059        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.");
1060        throw FinleyAdapterException(temp.str());                  case ReducedNodes:
1061        break;                      if (getMPISize()>1) {
1062     }                          escript::Data in2=escript::Data(in);
1063     break;                          in2.expand();
1064     case(ReducedDegreesOfFreedom):                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1065     switch(target.getFunctionSpace().getTypeCode()) {                      } else {
1066     case(Nodes):                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1067     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                      }
1068     break;                      break;
1069     case(ReducedNodes):                  case DegreesOfFreedom:
1070     if (getMPISize()>1) {                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1071        escript::Data temp=escript::Data(in);                      break;
1072        temp.expand();                  case ReducedDegreesOfFreedom:
1073        escriptDataC _in2 = temp.getDataC();                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1074        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                      break;
1075     } else {                  case Elements:
1076        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedElements:
1077     }                      if (getMPISize()>1) {
1078     break;                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1079     case(DegreesOfFreedom):                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1080     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                      } else {
1081     break;                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1082     case(ReducedDegreesOfFreedom):                      }
1083     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1084     break;                  case FaceElements:
1085     case(Elements):                  case ReducedFaceElements:
1086     case(ReducedElements):                      if (getMPISize()>1) {
1087     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1088        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1089        escriptDataC _in2 = temp.getDataC();                      } else {
1090        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1091     } else {                      }
1092        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
1093     }                  case Points:
1094     break;                      if (getMPISize()>1) {
1095     case(FaceElements):                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1096     case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->Points, in2, target);
1097     if (getMPISize()>1) {                      } else {
1098        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1099        escriptDataC _in2 = temp.getDataC();                      }
1100        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1101     } else {                  case ContactElementsZero:
1102        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ContactElementsOne:
1103     }                  case ReducedContactElementsZero:
1104     break;                  case ReducedContactElementsOne:
1105     case(Points):                      if (getMPISize()>1) {
1106     if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1107        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1108        escriptDataC _in2 = temp.getDataC();                      } else {
1109        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1110     } else {                      }
1111        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      break;
1112     }                  default:
1113     break;                      stringstream temp;
1114     case(ContactElementsZero):                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1115     case(ContactElementsOne):                      throw FinleyAdapterException(temp.str());
1116     case(ReducedContactElementsZero):                      break;
1117     case(ReducedContactElementsOne):              }
1118     if (getMPISize()>1) {              break;
1119        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );          default:
1120        escriptDataC _in2 = temp.getDataC();              stringstream temp;
1121        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();
1122     } else {              throw FinleyAdapterException(temp.str());
1123        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              break;
1124     }      }
1125     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();  
1126  }  }
1127    
1128  //  //
1129  // copies the locations of sample points into x:  // copies the locations of sample points into x
1130  //  //
1131  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1132  {  {
1133     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1134     if (argDomain!=*this)      if (argDomain!=*this)
1135        throw FinleyAdapterException("Error - Illegal domain of data point locations");          throw FinleyAdapterException("Error - Illegal domain of data point locations");
1136     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1137     // in case of values node coordinates we can do the job directly:      // in case of appropriate function space we can do the job directly:
1138     if (arg.getFunctionSpace().getTypeCode()==Nodes) {      if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1139        escriptDataC _arg=arg.getDataC();          Assemble_NodeCoordinates(mesh->Nodes, arg);
1140        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);      } else {
1141     } else {          escript::Data tmp_data=Vector(0., continuousFunction(*this), true);
1142        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);          Assemble_NodeCoordinates(mesh->Nodes, tmp_data);
1143        escriptDataC _tmp_data=tmp_data.getDataC();          // this is then interpolated onto arg:
1144        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);          interpolateOnDomain(arg, tmp_data);
1145        // this is then interpolated onto arg:      }
1146        interpolateOnDomain(arg,tmp_data);      checkFinleyError();
    }  
    checkFinleyError();  
1147  }  }
1148    
1149  //  //
1150  // 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
1151  //  //
1152  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1153  {  {
1154     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());      const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1155     if (normalDomain!=*this)      if (normalDomain!=*this)
1156        throw FinleyAdapterException("Error - Illegal domain of normal locations");          throw FinleyAdapterException("Error - Illegal domain of normal locations");
1157     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1158     escriptDataC _normal=normal.getDataC();      switch(normal.getFunctionSpace().getTypeCode()) {
1159     switch(normal.getFunctionSpace().getTypeCode()) {          case Nodes:
1160     case(Nodes):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1161     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");              break;
1162     break;          case ReducedNodes:
1163     case(ReducedNodes):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1164     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");              break;
1165     break;          case Elements:
1166     case(Elements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1167     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");              break;
1168     break;          case ReducedElements:
1169     case(ReducedElements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1170     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");              break;
1171     break;          case FaceElements:
1172     case (FaceElements):          case ReducedFaceElements:
1173     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              Assemble_getNormal(mesh->Nodes, mesh->FaceElements, normal);
1174     break;              break;
1175     case (ReducedFaceElements):          case Points:
1176     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1177     break;              break;
1178     case(Points):          case ContactElementsOne:
1179     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");          case ContactElementsZero:
1180     break;          case ReducedContactElementsOne:
1181     case (ContactElementsOne):          case ReducedContactElementsZero:
1182     case (ContactElementsZero):              Assemble_getNormal(mesh->Nodes, mesh->ContactElements, normal);
1183     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              break;
1184     break;          case DegreesOfFreedom:
1185     case (ReducedContactElementsOne):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1186     case (ReducedContactElementsZero):              break;
1187     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);          case ReducedDegreesOfFreedom:
1188     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1189     case(DegreesOfFreedom):              break;
1190     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");          default:
1191     break;              stringstream temp;
1192     case(ReducedDegreesOfFreedom):              temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1193     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");              throw FinleyAdapterException(temp.str());
1194     break;              break;
1195     default:      }
1196        stringstream temp;      checkFinleyError();
1197        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();  }
1198        throw FinleyAdapterException(temp.str());  
1199        break;  //
1200     }  // interpolates data to other domain
1201     checkFinleyError();  //
1202  }  void MeshAdapter::interpolateACross(escript::Data& target, const escript::Data& source) const
1203    {
1204  //      throw FinleyAdapterException("Error - Finley does not allow interpolation across domains.");
1205  // interpolates data to other domain:  }
1206  //  
1207  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  //
1208  {  // calculates the integral of a function defined on arg
1209     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());  //
1210     if (targetDomain!=*this)  void MeshAdapter::setToIntegrals(vector<double>& integrals, const escript::Data& arg) const
1211        throw FinleyAdapterException("Error - Illegal domain of interpolation target");  {
1212        const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1213     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");      if (argDomain!=*this)
1214  }          throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1215    
1216  //      double blocktimer_start = blocktimer_time();
1217  // calculates the integral of a function defined of arg:      Mesh* mesh=m_finleyMesh.get();
1218  //      switch(arg.getFunctionSpace().getTypeCode()) {
1219  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const          case Nodes:
1220  {              {
1221     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());                  escript::Data temp(arg, escript::function(*this));
1222     if (argDomain!=*this)                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1223        throw FinleyAdapterException("Error - Illegal domain of integration kernel");              }
1224                break;
1225     double blocktimer_start = blocktimer_time();          case ReducedNodes:
1226     Finley_Mesh* mesh=m_finleyMesh.get();              {
1227     escriptDataC _temp;                  escript::Data temp(arg, escript::function(*this));
1228     escript::Data temp;                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1229     escriptDataC _arg=arg.getDataC();              }
1230     switch(arg.getFunctionSpace().getTypeCode()) {              break;
1231     case(Nodes):          case Elements:
1232     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );          case ReducedElements:
1233     _temp=temp.getDataC();              Assemble_integrate(mesh->Nodes, mesh->Elements, arg, &integrals[0]);
1234     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);              break;
1235     break;          case FaceElements:
1236     case(ReducedNodes):          case ReducedFaceElements:
1237     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );              Assemble_integrate(mesh->Nodes, mesh->FaceElements, arg, &integrals[0]);
1238     _temp=temp.getDataC();              break;
1239     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);          case Points:
1240     break;              throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1241     case(Elements):              break;
1242     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case ContactElementsZero:
1243     break;          case ReducedContactElementsZero:
1244     case(ReducedElements):          case ContactElementsOne:
1245     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case ReducedContactElementsOne:
1246     break;              Assemble_integrate(mesh->Nodes, mesh->ContactElements, arg, &integrals[0]);
1247     case(FaceElements):              break;
1248     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);          case DegreesOfFreedom:
1249     break;          case ReducedDegreesOfFreedom:
1250     case(ReducedFaceElements):              {
1251     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);                  escript::Data temp(arg, escript::function(*this));
1252     break;                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1253     case(Points):              }
1254     throw FinleyAdapterException("Error - Integral of data on points is not supported.");              break;
1255     break;          default:
1256     case(ContactElementsZero):              stringstream temp;
1257     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1258     break;              throw FinleyAdapterException(temp.str());
1259     case(ReducedContactElementsZero):              break;
1260     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);      }
1261     break;      checkFinleyError();
1262     case(ContactElementsOne):      blocktimer_increment("integrate()", blocktimer_start);
1263     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  }
1264     break;  
1265     case(ReducedContactElementsOne):  //
1266     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  // calculates the gradient of arg
1267     break;  //
1268     case(DegreesOfFreedom):  void MeshAdapter::setToGradient(escript::Data& grad, const escript::Data& arg) const
1269     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );  {
1270     _temp=temp.getDataC();      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1271     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);      if (argDomain!=*this)
1272     break;          throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1273     case(ReducedDegreesOfFreedom):      const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1274     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );      if (gradDomain!=*this)
1275     _temp=temp.getDataC();          throw FinleyAdapterException("Error - Illegal domain of gradient");
1276     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
1277     break;      Mesh* mesh=m_finleyMesh.get();
1278     default:      escript::Data nodeData;
1279        stringstream temp;      if (getMPISize()>1) {
1280        temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();          if (arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom) {
1281        throw FinleyAdapterException(temp.str());              nodeData=escript::Data(arg, continuousFunction(*this));
1282        break;          } else if(arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom) {
1283     }              nodeData=escript::Data(arg, reducedContinuousFunction(*this));
1284     checkFinleyError();          } else {
1285     blocktimer_increment("integrate()", blocktimer_start);              nodeData = arg;
1286  }          }
1287        } else {
1288  //          nodeData = arg;
1289  // calculates the gradient of arg:      }
1290  //      switch(grad.getFunctionSpace().getTypeCode()) {
1291  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const          case Nodes:
1292  {              throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1293     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());              break;
1294     if (argDomain!=*this)          case ReducedNodes:
1295        throw FinleyAdapterException("Error - Illegal domain of gradient argument");              throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1296     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());              break;
1297     if (gradDomain!=*this)          case Elements:
1298        throw FinleyAdapterException("Error - Illegal domain of gradient");          case ReducedElements:
1299                Assemble_gradient(mesh->Nodes, mesh->Elements, grad, nodeData);
1300     Finley_Mesh* mesh=m_finleyMesh.get();              break;
1301     escriptDataC _grad=grad.getDataC();          case FaceElements:
1302     escriptDataC nodeDataC;          case ReducedFaceElements:
1303     escript::Data temp;              Assemble_gradient(mesh->Nodes, mesh->FaceElements, grad, nodeData);
1304     if (getMPISize()>1) {              break;
1305        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {          case Points:
1306           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );              throw FinleyAdapterException("Error - Gradient at points is not supported.");
1307           nodeDataC = temp.getDataC();              break;
1308        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {          case ContactElementsZero:
1309           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );          case ReducedContactElementsZero:
1310           nodeDataC = temp.getDataC();          case ContactElementsOne:
1311        } else {          case ReducedContactElementsOne:
1312           nodeDataC = arg.getDataC();              Assemble_gradient(mesh->Nodes, mesh->ContactElements, grad, nodeData);
1313        }              break;
1314     } else {          case DegreesOfFreedom:
1315        nodeDataC = arg.getDataC();              throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1316     }              break;
1317     switch(grad.getFunctionSpace().getTypeCode()) {          case ReducedDegreesOfFreedom:
1318     case(Nodes):              throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1319     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");              break;
1320     break;          default:
1321     case(ReducedNodes):              stringstream temp;
1322     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");              temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1323     break;              throw FinleyAdapterException(temp.str());
1324     case(Elements):              break;
1325     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);      }
1326     break;      checkFinleyError();
    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();  
1327  }  }
1328    
1329  //  //
1330  // returns the size of elements:  // returns the size of elements
1331  //  //
1332  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1333  {  {
1334     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1335     escriptDataC tmp=size.getDataC();      switch(size.getFunctionSpace().getTypeCode()) {
1336     switch(size.getFunctionSpace().getTypeCode()) {          case Nodes:
1337     case(Nodes):              throw FinleyAdapterException("Error - Size of nodes is not supported.");
1338     throw FinleyAdapterException("Error - Size of nodes is not supported.");              break;
1339     break;          case ReducedNodes:
1340     case(ReducedNodes):              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1341     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");              break;
1342     break;          case Elements:
1343     case(Elements):          case ReducedElements:
1344     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);              Assemble_getSize(mesh->Nodes, mesh->Elements, size);
1345     break;              break;
1346     case(ReducedElements):          case FaceElements:
1347     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case ReducedFaceElements:
1348     break;              Assemble_getSize(mesh->Nodes, mesh->FaceElements, size);
1349     case(FaceElements):              break;
1350     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case Points:
1351     break;              throw FinleyAdapterException("Error - Size of point elements is not supported.");
1352     case(ReducedFaceElements):              break;
1353     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case ContactElementsZero:
1354     break;          case ContactElementsOne:
1355     case(Points):          case ReducedContactElementsZero:
1356     throw FinleyAdapterException("Error - Size of point elements is not supported.");          case ReducedContactElementsOne:
1357     break;              Assemble_getSize(mesh->Nodes,mesh->ContactElements,size);
1358     case(ContactElementsZero):              break;
1359     case(ContactElementsOne):          case DegreesOfFreedom:
1360     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1361     break;              break;
1362     case(ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1363     case(ReducedContactElementsOne):              throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1364     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              break;
1365     break;          default:
1366     case(DegreesOfFreedom):              stringstream temp;
1367     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();
1368     break;              throw FinleyAdapterException(temp.str());
1369     case(ReducedDegreesOfFreedom):              break;
1370     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");      }
1371     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();  
1372  }  }
1373    
1374  // sets the location of nodes:  //
1375    // sets the location of nodes
1376    //
1377  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1378  {  {
1379     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1380     escriptDataC tmp;      const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1381     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());      if (newDomain!=*this)
1382     if (newDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of new point locations");
1383        throw FinleyAdapterException("Error - Illegal domain of new point locations");      if (new_x.getFunctionSpace() == continuousFunction(*this)) {
1384     tmp = new_x.getDataC();          mesh->setCoordinates(new_x);
1385     Finley_Mesh_setCoordinates(mesh,&tmp);      } else {
1386     checkFinleyError();          throw FinleyAdapterException("As of escript version 3.3 SetX() only accepts ContinuousFunction arguments. Please interpolate.");
1387  }      }
1388        checkFinleyError();
1389  // saves a data array in openDX format:  }
1390  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const  
1391  {  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1392     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;  {
1393     const int num_data=boost::python::extract<int>(arg.attr("__len__")());      if (getMPISize() > 1) {
1394     /* win32 refactor */  #ifdef ESYS_MPI
1395     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;          int myFirstNode=0, myLastNode=0, k=0;
1396     for(int i=0;i<num_data;i++)          int* globalNodeIndex=0;
1397     {          Mesh* mesh_p=m_finleyMesh.get();
1398        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;          /*
1399     }           * this method is only used by saveDataCSV which would use the returned
1400             * values for reduced nodes wrongly so this case is disabled for now
1401     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;          if (fs_code == FINLEY_REDUCED_NODES) {
1402     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;              myFirstNode = NodeFile_getFirstReducedNode(mesh_p->Nodes);
1403                myLastNode = NodeFile_getLastReducedNode(mesh_p->Nodes);
1404     boost::python::list keys=arg.keys();              globalNodeIndex = NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1405     for (int i=0;i<num_data;++i) {          } else
1406        std::string n=boost::python::extract<std::string>(keys[i]);          */
1407        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);          if (fs_code == FINLEY_NODES) {
1408        if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)              myFirstNode = mesh_p->Nodes->getFirstNode();
1409           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");              myLastNode = mesh_p->Nodes->getLastNode();
1410        data[i]=d.getDataC();              globalNodeIndex = mesh_p->Nodes->borrowGlobalNodesIndex();
1411        ptr_data[i]= &(data[i]);          } else {
1412        if (n.length()>MAX_namelength-1) {              throw FinleyAdapterException("Unsupported function space type for ownSample()");
1413           strncpy(names[i],n.c_str(),MAX_namelength-1);          }
1414           names[i][MAX_namelength-1]='\0';  
1415        } else {          k=globalNodeIndex[id];
1416           strcpy(names[i],n.c_str());          return ((myFirstNode <= k) && (k < myLastNode));
       }  
    }  
    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 a data array in openVTK format:  
 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  
 {  
    unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;  
    const int num_data=boost::python::extract<int>(arg.attr("__len__")());  
    /* win32 refactor */  
    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  
    for(int i=0;i<num_data;i++)  
    {  
       names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
    }  
   
    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  
    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
    boost::python::list keys=arg.keys();  
    for (int i=0;i<num_data;++i) {  
       std::string n=boost::python::extract<std::string>(keys[i]);  
       escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
       if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
          throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
       data[i]=d.getDataC();  
       ptr_data[i]=&(data[i]);  
       if (n.length()>MAX_namelength-1) {  
          strncpy(names[i],n.c_str(),MAX_namelength-1);  
          names[i][MAX_namelength-1]='\0';  
       } else {  
          strcpy(names[i],n.c_str());  
       }  
    }  
    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);  
   
    return;  
 }  
                                                                                                                                                                       
                                                                                                                                                                       
 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  
 SystemMatrixAdapter MeshAdapter::newSystemMatrix(  
                                                  const int row_blocksize,  
                                                  const escript::FunctionSpace& row_functionspace,  
                                                  const int column_blocksize,  
                                                  const escript::FunctionSpace& column_functionspace,  
                                                  const int type) const  
 {  
    int reduceRowOrder=0;  
    int reduceColOrder=0;  
    // is the domain right?  
    const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());  
    if (row_domain!=*this)  
       throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");  
    const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());  
    if (col_domain!=*this)  
       throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");  
    // is the function space type right  
    if (row_functionspace.getTypeCode()==DegreesOfFreedom) {  
       reduceRowOrder=0;  
    } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {  
       reduceRowOrder=1;  
    } else {  
       throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");  
    }  
    if (column_functionspace.getTypeCode()==DegreesOfFreedom) {  
       reduceColOrder=0;  
    } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {  
       reduceColOrder=1;  
    } else {  
       throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");  
    }  
    // generate matrix:  
   
    Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);  
    checkFinleyError();  
    Paso_SystemMatrix* fsystemMatrix;  
    int trilinos = 0;  
    if (trilinos) {  
 #ifdef TRILINOS  
       /* Allocation Epetra_VrbMatrix here */  
1417  #endif  #endif
1418     }      }
1419     else {      return true;
       fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);  
    }  
    checkPasoError();  
    Paso_SystemMatrixPattern_free(fsystemMatrixPattern);  
    return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  
1420  }  }
1421  // creates a TransportProblemAdapter  
1422  TransportProblemAdapter MeshAdapter::newTransportProblem(  
1423                                                           const double theta,  //
1424                                                           const int blocksize,  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1425                                                           const escript::FunctionSpace& functionspace,  //
1426                                                           const int type) const  escript::ASM_ptr MeshAdapter::newSystemMatrix(const int row_blocksize,
1427  {                              const escript::FunctionSpace& row_functionspace,
1428     int reduceOrder=0;                              const int column_blocksize,
1429     // is the domain right?                              const escript::FunctionSpace& column_functionspace,
1430     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());                              const int type) const
1431     if (domain!=*this)  {
1432        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");      // is the domain right?
1433     // is the function space type right      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1434     if (functionspace.getTypeCode()==DegreesOfFreedom) {      if (row_domain!=*this)
1435        reduceOrder=0;          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1436     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1437        reduceOrder=1;      if (col_domain!=*this)
1438     } else {          throw FinleyAdapterException("Error - domain of column function space does not match the domain of matrix generator.");
1439        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");  
1440     }      int reduceRowOrder=0;
1441     // generate matrix:      int reduceColOrder=0;
1442        // is the function space type right?
1443     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);      if (row_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1444     checkFinleyError();          reduceRowOrder=1;
1445     Paso_FCTransportProblem* transportProblem;      } else if (row_functionspace.getTypeCode() != DegreesOfFreedom) {
1446     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1447     checkPasoError();      }
1448     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      if (column_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1449     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);          reduceColOrder=1;
1450        } else if (column_functionspace.getTypeCode() != DegreesOfFreedom) {
1451            throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1452        }
1453    
1454        // generate matrix:
1455        Paso_SystemMatrixPattern* fsystemMatrixPattern=
1456            getFinley_Mesh()->getPattern(reduceRowOrder, reduceColOrder);
1457        checkFinleyError();
1458        Paso_SystemMatrix* fsystemMatrix;
1459        const int trilinos = 0;
1460        if (trilinos) {
1461    #ifdef TRILINOS
1462            // FIXME: Allocation Epetra_VrbMatrix here...
1463    #endif
1464        } else {
1465            fsystemMatrix=Paso_SystemMatrix_alloc(type, fsystemMatrixPattern,
1466                    row_blocksize, column_blocksize, FALSE);
1467        }
1468        checkPasoError();
1469        Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1470        SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1471        return escript::ASM_ptr(sma);
1472  }  }
1473    
1474  //  //
1475  // vtkObject MeshAdapter::createVtkObject() const  // creates a TransportProblemAdapter
 // TODO:  
1476  //  //
1477    escript::ATP_ptr MeshAdapter::newTransportProblem(const int blocksize,
1478            const escript::FunctionSpace& functionspace, const int type) const
1479    {
1480        // is the domain right?
1481        const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1482        if (domain!=*this)
1483            throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1484    
1485        // is the function space type right?
1486        int reduceOrder=0;
1487        if (functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1488            reduceOrder=1;
1489        } else if (functionspace.getTypeCode() != DegreesOfFreedom) {
1490            throw FinleyAdapterException("Error - illegal function space type for transport problem.");
1491        }
1492    
1493        // generate transport problem:
1494        Paso_SystemMatrixPattern* fsystemMatrixPattern=
1495            getFinley_Mesh()->getPattern(reduceOrder, reduceOrder);
1496        checkFinleyError();
1497        Paso_TransportProblem* transportProblem;
1498        transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern, blocksize);
1499        checkPasoError();
1500        Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1501        TransportProblemAdapter* tpa=new TransportProblemAdapter(
1502                transportProblem, blocksize, functionspace);
1503        return escript::ATP_ptr(tpa);
1504    }
1505    
1506  //  //
1507  // returns true if data at the atom_type is considered as being cell centered:  // returns true if data on functionSpaceCode is considered as being cell centered
1508    //
1509  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1510  {  {
1511     switch(functionSpaceCode) {      switch(functionSpaceCode) {
1512     case(Nodes):          case Nodes:
1513     case(DegreesOfFreedom):          case DegreesOfFreedom:
1514     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1515     return false;              return false;
1516     break;          case Elements:
1517     case(Elements):          case FaceElements:
1518     case(FaceElements):          case Points:
1519     case(Points):          case ContactElementsZero:
1520     case(ContactElementsZero):          case ContactElementsOne:
1521     case(ContactElementsOne):          case ReducedElements:
1522     case(ReducedElements):          case ReducedFaceElements:
1523     case(ReducedFaceElements):          case ReducedContactElementsZero:
1524     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
1525     case(ReducedContactElementsOne):              return true;
1526     return true;          default:
1527     break;              stringstream temp;
1528     default:              temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1529        stringstream temp;              throw FinleyAdapterException(temp.str());
1530        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;              break;
1531        throw FinleyAdapterException(temp.str());      }
1532        break;      return false;
1533     }  }
1534     checkFinleyError();  
1535     return false;  bool
1536  }  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1537    {
1538  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const      /* The idea is to use equivalence classes. [Types which can be interpolated
1539  {         back and forth]:
1540     switch(functionSpaceType_source) {          class 1: DOF <-> Nodes
1541     case(Nodes):          class 2: ReducedDOF <-> ReducedNodes
1542     switch(functionSpaceType_target) {          class 3: Points
1543     case(Nodes):          class 4: Elements
1544     case(ReducedNodes):          class 5: ReducedElements
1545     case(ReducedDegreesOfFreedom):          class 6: FaceElements
1546     case(DegreesOfFreedom):          class 7: ReducedFaceElements
1547     case(Elements):          class 8: ContactElementZero <-> ContactElementOne
1548     case(ReducedElements):          class 9: ReducedContactElementZero <-> ReducedContactElementOne
1549     case(FaceElements):  
1550     case(ReducedFaceElements):      There is also a set of lines. Interpolation is possible down a line but
1551     case(Points):      not between lines.
1552     case(ContactElementsZero):      class 1 and 2 belong to all lines so aren't considered.
1553     case(ReducedContactElementsZero):          line 0: class 3
1554     case(ContactElementsOne):          line 1: class 4,5
1555     case(ReducedContactElementsOne):          line 2: class 6,7
1556     return true;          line 3: class 8,9
1557     default:  
1558        stringstream temp;      For classes with multiple members (eg class 2) we have vars to record if
1559        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      there is at least one instance.
1560        throw FinleyAdapterException(temp.str());      e.g. hasnodes is true if we have at least one instance of Nodes.
1561     }      */
1562     break;      if (fs.empty())
1563     case(ReducedNodes):          return false;
1564     switch(functionSpaceType_target) {  
1565     case(ReducedNodes):      vector<int> hasclass(10);
1566     case(ReducedDegreesOfFreedom):      vector<int> hasline(4);    
1567     case(Elements):      bool hasnodes=false;
1568     case(ReducedElements):      bool hasrednodes=false;
1569     case(FaceElements):      bool hascez=false;
1570     case(ReducedFaceElements):      bool hasrcez=false;
1571     case(Points):      for (int i=0;i<fs.size();++i) {
1572     case(ContactElementsZero):          switch(fs[i]) {
1573     case(ReducedContactElementsZero):              case Nodes:
1574     case(ContactElementsOne):                  hasnodes=true; // fall through
1575     case(ReducedContactElementsOne):              case DegreesOfFreedom:
1576     return true;                  hasclass[1]=1;
1577     case(Nodes):                  break;
1578     case(DegreesOfFreedom):              case ReducedNodes:
1579     return false;                  hasrednodes=true; // fall through
1580     default:              case ReducedDegreesOfFreedom:
1581        stringstream temp;                  hasclass[2]=1;
1582        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                  break;
1583        throw FinleyAdapterException(temp.str());              case Points:
1584     }                  hasline[0]=1;
1585     break;                  hasclass[3]=1;
1586     case(Elements):                  break;
1587     if (functionSpaceType_target==Elements) {              case Elements:
1588        return true;                  hasclass[4]=1;
1589     } else if (functionSpaceType_target==ReducedElements) {                  hasline[1]=1;
1590        return true;                  break;
1591     } else {              case ReducedElements:
1592        return false;                  hasclass[5]=1;
1593     }                  hasline[1]=1;
1594     case(ReducedElements):                  break;
1595     if (functionSpaceType_target==ReducedElements) {              case FaceElements:
1596        return true;                  hasclass[6]=1;
1597     } else {                  hasline[2]=1;
1598        return false;                  break;
1599     }              case ReducedFaceElements:
1600     case(FaceElements):                  hasclass[7]=1;
1601     if (functionSpaceType_target==FaceElements) {                  hasline[2]=1;
1602        return true;                  break;
1603     } else if (functionSpaceType_target==ReducedFaceElements) {              case ContactElementsZero:
1604        return true;                  hascez=true; // fall through
1605     } else {              case ContactElementsOne:
1606        return false;                  hasclass[8]=1;
1607     }                  hasline[3]=1;
1608     case(ReducedFaceElements):                  break;
1609     if (functionSpaceType_target==ReducedFaceElements) {              case ReducedContactElementsZero:
1610        return true;                  hasrcez=true; // fall through
1611     } else {              case ReducedContactElementsOne:
1612        return false;                  hasclass[9]=1;
1613     }                  hasline[3]=1;
1614     case(Points):                  break;
1615     if (functionSpaceType_target==Points) {              default:
1616        return true;                  return false;
1617     } else {          }
1618        return false;      }
1619     }      int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1620     case(ContactElementsZero):  
1621     case(ContactElementsOne):      // fail if we have more than one leaf group
1622     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {      if (totlines>1)
1623        return true;          return false; // there are at least two branches we can't interpolate between
1624     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {      else if (totlines==1) {
1625        return true;          if (hasline[0]==1)              // we have points
1626     } else {              resultcode=Points;
1627        return false;          else if (hasline[1]==1) {
1628     }              if (hasclass[5]==1)
1629     case(ReducedContactElementsZero):                  resultcode=ReducedElements;
1630     case(ReducedContactElementsOne):              else
1631     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {                  resultcode=Elements;
1632        return true;          } else if (hasline[2]==1) {
1633     } else {              if (hasclass[7]==1)
1634        return false;                  resultcode=ReducedFaceElements;
1635     }              else
1636     case(DegreesOfFreedom):                  resultcode=FaceElements;
1637     switch(functionSpaceType_target) {          } else {   // so we must be in line3
1638     case(ReducedDegreesOfFreedom):              if (hasclass[9]==1) {
1639     case(DegreesOfFreedom):                  // need something from class 9
1640     case(Nodes):                  resultcode=(hasrcez ? ReducedContactElementsZero : ReducedContactElementsOne);
1641     case(ReducedNodes):              } else {
1642     case(Elements):                  // something from class 8
1643     case(ReducedElements):                  resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1644     case(Points):              }
1645     case(FaceElements):          }
1646     case(ReducedFaceElements):      } else { // totlines==0
1647     case(ContactElementsZero):          if (hasclass[2]==1) {
1648     case(ReducedContactElementsZero):              // something from class 2
1649     case(ContactElementsOne):              resultcode=(hasrednodes ? ReducedNodes : ReducedDegreesOfFreedom);
1650     case(ReducedContactElementsOne):          } else {
1651     return true;              // something from class 1
1652     default:              resultcode=(hasnodes ? Nodes : DegreesOfFreedom);
1653        stringstream temp;          }
1654        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      }
1655        throw FinleyAdapterException(temp.str());      return true;
1656     }  }
1657     break;  
1658     case(ReducedDegreesOfFreedom):  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,
1659     switch(functionSpaceType_target) {                                               int functionSpaceType_target) const
1660     case(ReducedDegreesOfFreedom):  {
1661     case(ReducedNodes):      switch(functionSpaceType_source) {
1662     case(Elements):          case Nodes:
1663     case(ReducedElements):              switch(functionSpaceType_target) {
1664     case(FaceElements):                  case Nodes:
1665     case(ReducedFaceElements):                  case ReducedNodes:
1666     case(Points):                  case ReducedDegreesOfFreedom:
1667     case(ContactElementsZero):                  case DegreesOfFreedom:
1668     case(ReducedContactElementsZero):                  case Elements:
1669     case(ContactElementsOne):                  case ReducedElements:
1670     case(ReducedContactElementsOne):                  case FaceElements:
1671     return true;                  case ReducedFaceElements:
1672     case(Nodes):                  case Points:
1673     case(DegreesOfFreedom):                  case ContactElementsZero:
1674     return false;                  case ReducedContactElementsZero:
1675     default:                  case ContactElementsOne:
1676        stringstream temp;                  case ReducedContactElementsOne:
1677        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      return true;
1678        throw FinleyAdapterException(temp.str());                  default:
1679     }                      stringstream temp;
1680     break;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1681     default:                      throw FinleyAdapterException(temp.str());
1682        stringstream temp;              }
1683        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;              break;
1684        throw FinleyAdapterException(temp.str());          case ReducedNodes:
1685        break;              switch(functionSpaceType_target) {
1686     }                  case ReducedNodes:
1687     checkFinleyError();                  case ReducedDegreesOfFreedom:
1688     return false;                  case Elements:
1689  }                  case ReducedElements:
1690                    case FaceElements:
1691  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const                  case ReducedFaceElements:
1692  {                  case Points:
1693     return false;                  case ContactElementsZero:
1694  }                  case ReducedContactElementsZero:
1695                    case ContactElementsOne:
1696  bool MeshAdapter::operator==(const AbstractDomain& other) const                  case ReducedContactElementsOne:
1697  {                      return true;
1698     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);                  case Nodes:
1699     if (temp!=0) {                  case DegreesOfFreedom:
1700        return (m_finleyMesh==temp->m_finleyMesh);                      return false;
1701     } else {                  default:
1702        return false;                      stringstream temp;
1703     }                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1704                        throw FinleyAdapterException(temp.str());
1705                }
1706                break;
1707            case Elements:
1708                if (functionSpaceType_target==Elements) {
1709                    return true;
1710                } else if (functionSpaceType_target==ReducedElements) {
1711                    return true;
1712                } else {
1713                    return false;
1714                }
1715            case ReducedElements:
1716                if (functionSpaceType_target==ReducedElements) {
1717                    return true;
1718                } else {
1719                    return false;
1720                }
1721            case FaceElements:
1722                if (functionSpaceType_target==FaceElements) {
1723                    return true;
1724                } else if (functionSpaceType_target==ReducedFaceElements) {
1725                    return true;
1726                } else {
1727                    return false;
1728                }
1729            case ReducedFaceElements:
1730                if (functionSpaceType_target==ReducedFaceElements) {
1731                    return true;
1732                } else {
1733                    return false;
1734                }
1735            case Points:
1736                if (functionSpaceType_target==Points) {
1737                    return true;
1738                } else {
1739                    return false;
1740                }
1741            case ContactElementsZero:
1742            case ContactElementsOne:
1743                if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1744                    return true;
1745                } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1746                    return true;
1747                } else {
1748                    return false;
1749                }
1750            case ReducedContactElementsZero:
1751            case ReducedContactElementsOne:
1752                if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1753                    return true;
1754                } else {
1755                    return false;
1756                }
1757            case DegreesOfFreedom:
1758                switch(functionSpaceType_target) {
1759                    case ReducedDegreesOfFreedom:
1760                    case DegreesOfFreedom:
1761                    case Nodes:
1762                    case ReducedNodes:
1763                    case Elements:
1764                    case ReducedElements:
1765                    case Points:
1766                    case FaceElements:
1767                    case ReducedFaceElements:
1768                    case ContactElementsZero:
1769                    case ReducedContactElementsZero:
1770                    case ContactElementsOne:
1771                    case ReducedContactElementsOne:
1772                        return true;
1773                    default:
1774                        stringstream temp;
1775                        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1776                        throw FinleyAdapterException(temp.str());
1777                }
1778                break;
1779            case ReducedDegreesOfFreedom:
1780                switch(functionSpaceType_target) {
1781                    case ReducedDegreesOfFreedom:
1782                    case ReducedNodes:
1783                    case Elements:
1784                    case ReducedElements:
1785                    case FaceElements:
1786                    case ReducedFaceElements:
1787                    case Points:
1788                    case ContactElementsZero:
1789                    case ReducedContactElementsZero:
1790                    case ContactElementsOne:
1791                    case ReducedContactElementsOne:
1792                        return true;
1793                    case Nodes:
1794                    case DegreesOfFreedom:
1795                        return false;
1796                    default:
1797                        stringstream temp;
1798                        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1799                        throw FinleyAdapterException(temp.str());
1800                }
1801                break;
1802            default:
1803                stringstream temp;
1804                temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1805                throw FinleyAdapterException(temp.str());
1806                break;
1807        }
1808        return false;
1809    }
1810    
1811    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
1812    {
1813        if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1814            return 1;
1815    
1816        if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1817            return -1;
1818    
1819        return 0;
1820    }
1821    
1822    bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,
1823            const escript::AbstractDomain& targetDomain,
1824            int functionSpaceType_target) const
1825    {
1826        return false;
1827    }
1828    
1829    bool MeshAdapter::operator==(const escript::AbstractDomain& other) const
1830    {
1831        const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1832        if (temp) {
1833            return (m_finleyMesh==temp->m_finleyMesh);
1834        } else {
1835            return false;
1836        }
1837  }  }
1838    
1839  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const escript::AbstractDomain& other) const
1840  {  {
1841     return !(operator==(other));      return !(operator==(other));
1842  }  }
1843    
1844  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
1845  {  {
1846     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);      Mesh* mesh=m_finleyMesh.get();
1847     checkPasoError();      return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
1848     return out;                 package, symmetry, mesh->MPIInfo);
1849  }  }
1850    
1851  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
1852  {  {
1853     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);      Mesh* mesh=m_finleyMesh.get();
1854     checkPasoError();      return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
1855     return out;                  package, symmetry, mesh->MPIInfo);
1856  }  }
1857    
1858  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1859  {  {
1860     return continuousFunction(asAbstractContinuousDomain()).getX();      return continuousFunction(*this).getX();
1861  }  }
1862    
1863  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1864  {  {
1865     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();      return functionOnBoundary(*this).getNormal();
1866  }  }
1867    
1868  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1869  {  {
1870     return function(asAbstractContinuousDomain()).getSize();      return escript::function(*this).getSize();
1871  }  }
1872    
1873  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1874  {  {
1875     int *out = NULL;      int *out = NULL;
1876     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1877     switch (functionSpaceType) {      switch (functionSpaceType) {
1878     case(Nodes):          case Nodes:
1879     out=mesh->Nodes->Id;              out=mesh->Nodes->Id;
1880     break;              break;
1881     case(ReducedNodes):          case ReducedNodes:
1882     out=mesh->Nodes->reducedNodesId;              out=mesh->Nodes->reducedNodesId;
1883     break;              break;
1884     case(Elements):          case Elements:
1885     out=mesh->Elements->Id;          case ReducedElements:
1886     break;              out=mesh->Elements->Id;
1887     case(ReducedElements):              break;
1888     out=mesh->Elements->Id;          case FaceElements:
1889     break;          case ReducedFaceElements:
1890     case(FaceElements):              out=mesh->FaceElements->Id;
1891     out=mesh->FaceElements->Id;              break;
1892     break;          case Points:
1893     case(ReducedFaceElements):              out=mesh->Points->Id;
1894     out=mesh->FaceElements->Id;              break;
1895     break;          case ContactElementsZero:
1896     case(Points):          case ReducedContactElementsZero:
1897     out=mesh->Points->Id;          case ContactElementsOne:
1898     break;          case ReducedContactElementsOne:
1899     case(ContactElementsZero):              out=mesh->ContactElements->Id;
1900     out=mesh->ContactElements->Id;              break;
1901     break;          case DegreesOfFreedom:
1902     case(ReducedContactElementsZero):              out=mesh->Nodes->degreesOfFreedomId;
1903     out=mesh->ContactElements->Id;              break;
1904     break;          case ReducedDegreesOfFreedom:
1905     case(ContactElementsOne):              out=mesh->Nodes->reducedDegreesOfFreedomId;
1906     out=mesh->ContactElements->Id;              break;
1907     break;          default:
1908     case(ReducedContactElementsOne):              stringstream temp;
1909     out=mesh->ContactElements->Id;              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1910     break;              throw FinleyAdapterException(temp.str());
1911     case(DegreesOfFreedom):              break;
1912     out=mesh->Nodes->degreesOfFreedomId;      }
1913     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;  
1914  }  }
1915  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1916  {  {
1917     int out=0;      int out=0;
1918     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1919     switch (functionSpaceType) {      switch (functionSpaceType) {
1920     case(Nodes):          case Nodes:
1921     out=mesh->Nodes->Tag[sampleNo];              out=mesh->Nodes->Tag[sampleNo];
1922     break;              break;
1923     case(ReducedNodes):          case ReducedNodes:
1924     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");              throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1925     break;              break;
1926     case(Elements):          case Elements:
1927     out=mesh->Elements->Tag[sampleNo];          case ReducedElements:
1928     break;              out=mesh->Elements->Tag[sampleNo];
1929     case(ReducedElements):              break;
1930     out=mesh->Elements->Tag[sampleNo];          case FaceElements:
1931     break;          case ReducedFaceElements:
1932     case(FaceElements):              out=mesh->FaceElements->Tag[sampleNo];
1933     out=mesh->FaceElements->Tag[sampleNo];              break;
1934     break;          case Points:
1935     case(ReducedFaceElements):              out=mesh->Points->Tag[sampleNo];
1936     out=mesh->FaceElements->Tag[sampleNo];              break;
1937     break;          case ContactElementsZero:
1938     case(Points):          case ReducedContactElementsZero:
1939     out=mesh->Points->Tag[sampleNo];          case ContactElementsOne:
1940     break;          case ReducedContactElementsOne:
1941     case(ContactElementsZero):              out=mesh->ContactElements->Tag[sampleNo];
1942     out=mesh->ContactElements->Tag[sampleNo];              break;
1943     break;          case DegreesOfFreedom:
1944     case(ReducedContactElementsZero):              throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1945     out=mesh->ContactElements->Tag[sampleNo];              break;
1946     break;          case ReducedDegreesOfFreedom:
1947     case(ContactElementsOne):              throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1948     out=mesh->ContactElements->Tag[sampleNo];              break;
1949     break;          default:
1950     case(ReducedContactElementsOne):              stringstream temp;
1951     out=mesh->ContactElements->Tag[sampleNo];              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1952     break;              throw FinleyAdapterException(temp.str());
1953     case(DegreesOfFreedom):              break;
1954     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");      }
1955     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;  
1956  }  }
1957    
1958    
1959  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
1960  {  {
1961     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1962     escriptDataC tmp=mask.getDataC();      switch(functionSpaceType) {
1963     switch(functionSpaceType) {          case Nodes:
1964     case(Nodes):              mesh->Nodes->setTags(newTag, mask);
1965     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);              break;
1966     break;          case ReducedNodes:
1967     case(ReducedNodes):              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1968     throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case DegreesOfFreedom:
1969     break;              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1970     case(DegreesOfFreedom):          case ReducedDegreesOfFreedom:
1971     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1972     break;          case Elements:
1973     case(ReducedDegreesOfFreedom):          case ReducedElements:
1974     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");              mesh->Elements->setTags(newTag, mask);
1975     break;              break;
1976     case(Elements):          case FaceElements:
1977     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case ReducedFaceElements:
1978     break;              mesh->FaceElements->setTags(newTag, mask);
1979     case(ReducedElements):              break;
1980     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case Points:
1981     break;              mesh->Points->setTags(newTag, mask);
1982     case(FaceElements):              break;
1983     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ContactElementsZero:
1984     break;          case ReducedContactElementsZero:
1985     case(ReducedFaceElements):          case ContactElementsOne:
1986     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ReducedContactElementsOne:
1987     break;              mesh->ContactElements->setTags(newTag, mask);
1988     case(Points):              break;
1989     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);          default:
1990     break;              stringstream temp;
1991     case(ContactElementsZero):              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
1992     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              throw FinleyAdapterException(temp.str());
1993     break;      }
1994     case(ReducedContactElementsZero):      checkFinleyError();
1995     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  }
1996     break;  
1997     case(ContactElementsOne):  void MeshAdapter::setTagMap(const string& name, int tag)
1998     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  {
1999     break;      Mesh* mesh=m_finleyMesh.get();
2000     case(ReducedContactElementsOne):      mesh->addTagMap(name.c_str(), tag);
2001     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);      checkFinleyError();
2002     break;  }
2003     default:  
2004        stringstream temp;  int MeshAdapter::getTag(const string& name) const
2005        temp << "Error - Finley does not know anything about function space type " << functionSpaceType;  {
2006        throw FinleyAdapterException(temp.str());      Mesh* mesh=m_finleyMesh.get();
2007     }      int tag = mesh->getTag(name.c_str());
2008     checkFinleyError();      checkFinleyError();
2009     return;      return tag;
2010  }  }
2011    
2012  void MeshAdapter::setTagMap(const std::string& name,  int tag)  bool MeshAdapter::isValidTagName(const string& name) const
2013  {  {
2014     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2015     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);      return mesh->isValidTagName(name.c_str());
2016     checkPasoError();  }
2017     // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
2018  }  string MeshAdapter::showTagNames() const
2019    {
2020  int MeshAdapter::getTag(const std::string& name) const      stringstream temp;
2021  {      Mesh* mesh=m_finleyMesh.get();
2022     Finley_Mesh* mesh=m_finleyMesh.get();      TagMap::const_iterator it = mesh->tagMap.begin();
2023     int tag=0;      while (it != mesh->tagMap.end()) {
2024     tag=Finley_Mesh_getTag(mesh, name.c_str());          temp << it->first;
2025     checkPasoError();          ++it;
2026     // throwStandardException("MeshAdapter::getTag is not implemented.");          if (it != mesh->tagMap.end())
2027     return tag;              temp << ", ";
2028  }      }
2029        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();  
2030  }  }
2031    
2032  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2033  {  {
2034    Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2035    dim_t numTags=0;      switch(functionSpaceCode) {
2036    switch(functionSpaceCode) {          case Nodes:
2037     case(Nodes):              return mesh->Nodes->tagsInUse.size();
2038            numTags=mesh->Nodes->numTagsInUse;          case ReducedNodes:
2039            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2040     case(ReducedNodes):          case DegreesOfFreedom:
2041            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2042            break;          case ReducedDegreesOfFreedom:
2043     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2044            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2045            break;          case ReducedElements:
2046     case(ReducedDegreesOfFreedom):              return mesh->Elements->tagsInUse.size();
2047            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2048            break;          case ReducedFaceElements:
2049     case(Elements):              return mesh->FaceElements->tagsInUse.size();
2050     case(ReducedElements):          case Points:
2051            numTags=mesh->Elements->numTagsInUse;              return mesh->Points->tagsInUse.size();
2052            break;          case ContactElementsZero:
2053     case(FaceElements):          case ReducedContactElementsZero:
2054     case(ReducedFaceElements):          case ContactElementsOne:
2055            numTags=mesh->FaceElements->numTagsInUse;          case ReducedContactElementsOne:
2056            break;              return mesh->ContactElements->tagsInUse.size();
2057     case(Points):          default:
2058            numTags=mesh->Points->numTagsInUse;              stringstream ss;
2059            break;              ss << "Finley does not know anything about function space type "
2060     case(ContactElementsZero):                   << functionSpaceCode;
2061     case(ReducedContactElementsZero):              throw FinleyAdapterException(ss.str());
2062     case(ContactElementsOne):      }
2063     case(ReducedContactElementsOne):      return 0;
2064            numTags=mesh->ContactElements->numTagsInUse;  }
2065            break;  
2066     default:  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2067        stringstream temp;  {
2068        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;      Mesh* mesh=m_finleyMesh.get();
2069        throw FinleyAdapterException(temp.str());      switch(functionSpaceCode) {
2070    }          case Nodes:
2071    return numTags;              return &mesh->Nodes->tagsInUse[0];
2072  }          case ReducedNodes:
2073  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2074  {          case DegreesOfFreedom:
2075    Finley_Mesh* mesh=m_finleyMesh.get();              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2076    index_t* tags=NULL;          case ReducedDegreesOfFreedom:
2077    switch(functionSpaceCode) {              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2078     case(Nodes):          case Elements:
2079            tags=mesh->Nodes->tagsInUse;          case ReducedElements:
2080            break;              return &mesh->Elements->tagsInUse[0];
2081     case(ReducedNodes):          case FaceElements:
2082            throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case ReducedFaceElements:
2083            break;              return &mesh->FaceElements->tagsInUse[0];
2084     case(DegreesOfFreedom):          case Points:
2085            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              return &mesh->Points->tagsInUse[0];
2086            break;          case ContactElementsZero:
2087     case(ReducedDegreesOfFreedom):          case ReducedContactElementsZero:
2088            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case ContactElementsOne:
2089            break;          case ReducedContactElementsOne:
2090     case(Elements):              return &mesh->ContactElements->tagsInUse[0];
2091     case(ReducedElements):          default:
2092            tags=mesh->Elements->tagsInUse;              stringstream temp;
2093            break;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2094     case(FaceElements):              throw FinleyAdapterException(temp.str());
2095     case(ReducedFaceElements):      }
2096            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;  
2097  }  }
2098    
2099    
2100  bool MeshAdapter::canTag(int functionSpaceCode) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2101  {  {
2102    switch(functionSpaceCode) {      switch(functionSpaceCode) {
2103     case(Nodes):          case Nodes:
2104     case(Elements):          case Elements:
2105     case(ReducedElements):          case ReducedElements:
2106     case(FaceElements):          case FaceElements:
2107     case(ReducedFaceElements):          case ReducedFaceElements:
2108     case(Points):          case Points:
2109     case(ContactElementsZero):          case ContactElementsZero:
2110     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
2111     case(ContactElementsOne):          case ContactElementsOne:
2112     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
2113            return true;              return true;
2114     case(ReducedNodes):          default:
2115     case(DegreesOfFreedom):              return false;
2116     case(ReducedDegreesOfFreedom):      }
2117        return false;  }
2118     default:  
2119      return false;  escript::AbstractDomain::StatusType MeshAdapter::getStatus() const
2120    }  {
2121        Mesh* mesh=m_finleyMesh.get();
2122        return mesh->getStatus();
2123    }
2124    
2125    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2126    {
2127        Mesh* mesh=m_finleyMesh.get();
2128        int order =-1;
2129        switch(functionSpaceCode) {
2130            case Nodes:
2131            case DegreesOfFreedom:
2132                order=mesh->approximationOrder;
2133                break;
2134            case ReducedNodes:
2135            case ReducedDegreesOfFreedom:
2136                order=mesh->reducedApproximationOrder;
2137                break;
2138            case Elements:
2139            case FaceElements:
2140            case Points:
2141            case ContactElementsZero:
2142            case ContactElementsOne:
2143                order=mesh->integrationOrder;
2144                break;
2145            case ReducedElements:
2146            case ReducedFaceElements:
2147            case ReducedContactElementsZero:
2148            case ReducedContactElementsOne:
2149                order=mesh->reducedIntegrationOrder;
2150                break;
2151            default:
2152                stringstream temp;
2153                temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2154                throw FinleyAdapterException(temp.str());
2155        }
2156        return order;
2157    }
2158    
2159    bool MeshAdapter::supportsContactElements() const
2160    {
2161        return true;
2162    }
2163    
2164    void MeshAdapter::addDiracPoints(const vector<double>& points,
2165                                     const vector<int>& tags) const
2166    {
2167        // points will be flattened
2168        const int dim = getDim();
2169        int numPoints=points.size()/dim;
2170        int numTags=tags.size();
2171        Mesh* mesh=m_finleyMesh.get();
2172    
2173        if ( points.size() % dim != 0 ) {
2174            throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2175        }
2176    
2177        if ((numTags > 0) && (numPoints != numTags))
2178            throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2179    
2180        mesh->addPoints(numPoints, &points[0], &tags[0]);
2181        checkFinleyError();
2182    }
2183    
2184    // void MeshAdapter::addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2185    // {
2186    //       const int dim = getDim();
2187    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2188    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2189    //       Mesh* mesh=m_finleyMesh.get();
2190    //
2191    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2192    //       throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2193    //
2194    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2195    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2196    //
2197    //       for (int i=0;i<numPoints;++i) {
2198    //         int tag_id=-1;
2199    //         int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2200    //         if  ( numComps !=   dim ) {
2201    //                stringstream temp;
2202    //                temp << "Error - illegal number of components " << numComps << " for point " << i;
2203    //                throw FinleyAdapterException(temp.str());
2204    //         }
2205    //         points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2206    //         if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2207    //         if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2208    //
2209    //         if ( numTags > 0) {
2210    //                boost::python::extract<string> ex_str(tags[i]);
2211    //                if  ( ex_str.check() ) {
2212    //                    tag_id=getTag( ex_str());
2213    //                } else {
2214    //                     boost::python::extract<int> ex_int(tags[i]);
2215    //                     if ( ex_int.check() ) {
2216    //                         tag_id=ex_int();
2217    //                     } else {
2218    //                          stringstream temp;
2219    //                          temp << "Error - unable to extract tag for point " << i;
2220    //                          throw FinleyAdapterException(temp.str());
2221    //                    }
2222    //                }
2223    //         }
2224    //            tags_ptr[i]=tag_id;
2225    //       }
2226    //
2227    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2228    //       checkPasoError();
2229    //
2230    //       TMPMEMFREE(points_ptr);
2231    //       TMPMEMFREE(tags_ptr);
2232    // }
2233    
2234    /*
2235    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2236    {
2237        boost::python::list points =  boost::python::list();
2238        boost::python::list tags =  boost::python::list();
2239        points.append(point);
2240        tags.append(tag);
2241        addDiracPoints(points, tags);
2242    }
2243    */
2244    
2245    /*
2246    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const string& tag) const
2247    {
2248        boost::python::list points =   boost::python::list();
2249        boost::python::list tags =   boost::python::list();
2250        points.append(point);
2251        tags.append(tag);
2252        addDiracPoints(points, tags);
2253  }  }
2254    */
   
2255  }  // end of namespace  }  // end of namespace
2256    

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