/[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 4428 by caltinay, Thu May 30 06:39:10 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 53  const int MeshAdapter::ReducedContactEle Line 48  const int MeshAdapter::ReducedContactEle
48    
49  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_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;          Finley_Mesh_free(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  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  bool MeshAdapter::onMasterProcessor() const
91     return m_finleyMesh.get();  {
92        return m_finleyMesh.get()->MPIInfo->rank == 0;
93  }  }
94    
95  void MeshAdapter::write(const std::string& fileName) const  #ifdef ESYS_MPI
96    MPI_Comm
97    #else
98    unsigned int
99    #endif
100    MeshAdapter::getMPIComm() const
101  {  {
102     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;  #ifdef ESYS_MPI
103     strcpy(fName,fileName.c_str());      return m_finleyMesh->MPIInfo->comm;
104     Finley_Mesh_write(m_finleyMesh.get(),fName);  #else
105     checkFinleyError();      return 0;
106     TMPMEMFREE(fName);  #endif
107  }  }
108    
109  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  Finley_Mesh* MeshAdapter::getFinley_Mesh() const
110  {  {
111     Finley_PrintMesh_Info(m_finleyMesh.get(), full);      return m_finleyMesh.get();
112  }  }
113    
114  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
115    {
116        Finley_Mesh_write(m_finleyMesh.get(), fileName.c_str());
117        checkFinleyError();
118    }
119    
120    void MeshAdapter::Print_Mesh_Info(const bool full) const
121    {
122        Finley_PrintMesh_Info(m_finleyMesh.get(), full);
123    }
124    
125    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();      Finley_Mesh *mesh = m_finleyMesh.get();
132     Finley_TagMap* tag_map;      Finley_TagMap* tag_map;
133     int num_Tags = 0;      int num_Tags = 0;
134     int mpi_size             = mesh->MPIInfo->size;      int mpi_size                         = mesh->MPIInfo->size;
135     int mpi_rank             = mesh->MPIInfo->rank;      int mpi_rank                         = mesh->MPIInfo->rank;
136     int numDim               = mesh->Nodes->numDim;      int numDim                           = mesh->Nodes->numDim;
137     int numNodes             = mesh->Nodes->numNodes;      int numNodes                         = mesh->Nodes->numNodes;
138     int num_Elements         = mesh->Elements->numElements;      int num_Elements                     = mesh->Elements->numElements;
139     int num_FaceElements         = mesh->FaceElements->numElements;      int num_FaceElements                 = mesh->FaceElements->numElements;
140     int num_ContactElements      = mesh->ContactElements->numElements;      int num_ContactElements              = mesh->ContactElements->numElements;
141     int num_Points           = mesh->Points->numElements;      int num_Points                       = mesh->Points->numElements;
142     int num_Elements_numNodes        = mesh->Elements->numNodes;      int num_Elements_numNodes            = mesh->Elements->numNodes;
143     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;      int num_FaceElements_numNodes        = mesh->FaceElements->numNodes;
144     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;      int num_ContactElements_numNodes     = mesh->ContactElements->numNodes;
145  #ifdef PASO_MPI  #ifdef ESYS_MPI
146     MPI_Status status;      MPI_Status status;
147  #endif  #endif
148    
149  /* Incoming token indicates it's my turn to write */  /* Incoming token indicates it's my turn to write */
150  #ifdef PASO_MPI  #ifdef ESYS_MPI
151     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);      if (mpi_rank>0) {
152            MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
153        }
154  #endif  #endif
155    
156     char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),      char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
157                                                       mpi_size, mpi_rank);                                                       mpi_size, mpi_rank);
158    
159     /* Figure out how much storage is required for tags */      // Figure out how much storage is required for tags
160     tag_map = mesh->TagMap;      tag_map = mesh->TagMap;
161     num_Tags = 0;      num_Tags = 0;
162     if (tag_map) {      while (tag_map) {
163        while (tag_map) {          num_Tags++;
164           num_Tags++;          tag_map=tag_map->next;
165           tag_map=tag_map->next;      }
166        }  
167     }      // NetCDF error handler
168        NcError err(NcError::verbose_nonfatal);
169     // NetCDF error handler      // Create the file.
170     NcError err(NcError::verbose_nonfatal);      NcFile dataFile(newFileName, NcFile::Replace);
171     // Create the file.      string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
172     NcFile dataFile(newFileName, NcFile::Replace);      // check if writing was successful
173     // check if writing was successful      if (!dataFile.is_valid())
174     if (!dataFile.is_valid())          throw FinleyAdapterException(msgPrefix+"Open file for output");
175        throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);  
176        // Define dimensions (num_Elements and dim_Elements are identical,
177     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)      // dim_Elements only appears if > 0)
178     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )      if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
179        throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_dim(numNodes)");
180     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )      if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
181        throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_dim(numDim)");
182     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )      if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
183        throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_dim(mpi_size)");
184     if (num_Elements>0)      if (num_Elements>0)
185        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
186           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements)");
187     if (num_FaceElements>0)      if (num_FaceElements>0)
188        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
189           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements)");
190     if (num_ContactElements>0)      if (num_ContactElements>0)
191        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
192           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements)");
193     if (num_Points>0)      if (num_Points>0)
194        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
195           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Points)");
196     if (num_Elements>0)      if (num_Elements>0)
197        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
198           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements_Nodes)");
199     if (num_FaceElements>0)      if (num_FaceElements>0)
200        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
201           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
202     if (num_ContactElements>0)      if (num_ContactElements>0)
203        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
204           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
205     if (num_Tags>0)      if (num_Tags>0)
206        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
207           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Tags)");
208    
209     // Attributes: MPI size, MPI rank, Name, order, reduced_order      // Attributes: MPI size, MPI rank, Name, order, reduced_order
210     if (!dataFile.add_att("mpi_size", mpi_size) )      if (!dataFile.add_att("mpi_size", mpi_size) )
211        throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(mpi_size)");
212     if (!dataFile.add_att("mpi_rank", mpi_rank) )      if (!dataFile.add_att("mpi_rank", mpi_rank) )
213        throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(mpi_rank)");
214     if (!dataFile.add_att("Name",mesh->Name) )      if (!dataFile.add_att("Name",mesh->Name) )
215        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(Name)");
216     if (!dataFile.add_att("numDim",numDim) )      if (!dataFile.add_att("numDim",numDim) )
217        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(order)");
218     if (!dataFile.add_att("order",mesh->order) )      if (!dataFile.add_att("order",mesh->integrationOrder) )
219        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(order)");
220     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )      if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
221        throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(reduced_order)");
222     if (!dataFile.add_att("numNodes",numNodes) )      if (!dataFile.add_att("numNodes",numNodes) )
223        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(numNodes)");
224     if (!dataFile.add_att("num_Elements",num_Elements) )      if (!dataFile.add_att("num_Elements",num_Elements) )
225        throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements)");
226     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )      if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
227        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements)");
228     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )      if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
229        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements)");
230     if (!dataFile.add_att("num_Points",num_Points) )      if (!dataFile.add_att("num_Points",num_Points) )
231        throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_Points)");
232     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )      if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
233        throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements_numNodes)");
234     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )      if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
235        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements_numNodes)");
236     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )      if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
237        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements_numNodes)");
238     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )      if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
239        throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(Elements_TypeId)");
240     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )      if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
241        throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(FaceElements_TypeId)");
242     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )      if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
243        throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(ContactElements_TypeId)");
244     if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )      if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
245        throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(Points_TypeId)");
246     if (!dataFile.add_att("num_Tags", num_Tags) )      if (!dataFile.add_att("num_Tags", num_Tags) )
247        throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"add_att(num_Tags)");
248    
249     // // // // // Nodes // // // // //      // // // // // Nodes // // // // //
250    
251     // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)      // Nodes nodeDistribution
252     if (numNodes>0) {      if (! (ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
253            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_NodeDistribution)");
254        // Nodes Id      int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
255        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )      if (! (ids->put(int_ptr, mpi_size+1)) )
256           throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"put(Nodes_NodeDistribution)");
257        int_ptr = &mesh->Nodes->Id[0];  
258        if (! (ids->put(int_ptr, numNodes)) )      // Nodes degreesOfFreedomDistribution
259           throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);      if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
260            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_DofDistribution)");
261        // Nodes Tag      int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
262        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )      if (! (ids->put(int_ptr, mpi_size+1)) )
263           throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);          throw FinleyAdapterException(msgPrefix+"put(Nodes_DofDistribution)");
264        int_ptr = &mesh->Nodes->Tag[0];  
265        if (! (ids->put(int_ptr, numNodes)) )      // Only write nodes if non-empty because NetCDF doesn't like empty arrays
266           throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);      // (it treats them as NC_UNLIMITED)
267        if (numNodes>0) {
268        // Nodes gDOF          // Nodes Id
269        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
270           throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Id)");
271        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];          int_ptr = &mesh->Nodes->Id[0];
272        if (! (ids->put(int_ptr, numNodes)) )          if (! (ids->put(int_ptr, numNodes)) )
273           throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Nodes_Id)");
274    
275        // Nodes global node index          // Nodes Tag
276        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
277           throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Tag)");
278        int_ptr = &mesh->Nodes->globalNodesIndex[0];          int_ptr = &mesh->Nodes->Tag[0];
279        if (! (ids->put(int_ptr, numNodes)) )          if (! (ids->put(int_ptr, numNodes)) )
280           throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Nodes_Tag)");
281    
282        // Nodes grDof          // Nodes gDOF
283        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
284           throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gDOF)");
285        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
286        if (! (ids->put(int_ptr, numNodes)) )          if (! (ids->put(int_ptr, numNodes)) )
287           throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Nodes_gDOF)");
288    
289        // Nodes grNI          // Nodes global node index
290        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
291           throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gNI)");
292        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];          int_ptr = &mesh->Nodes->globalNodesIndex[0];
293        if (! (ids->put(int_ptr, numNodes)) )          if (! (ids->put(int_ptr, numNodes)) )
294           throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Nodes_gNI)");
295    
296        // Nodes Coordinates          // Nodes grDof
297        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
298           throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grDfI)");
299        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
300           throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, numNodes)) )
301                throw FinleyAdapterException(msgPrefix+"put(Nodes_grDfI)");
302        // Nodes degreesOfFreedomDistribution  
303        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )          // Nodes grNI
304           throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
305        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grNI)");
306        if (! (ids->put(int_ptr, mpi_size+1)) )          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
307           throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, numNodes)) )
308                throw FinleyAdapterException(msgPrefix+"put(Nodes_grNI)");
309        // Nodes nodeDistribution  
310        if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )          // Nodes Coordinates
311           throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
312        int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Coordinates)");
313        if (! (ids->put(int_ptr, mpi_size+1)) )          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
314           throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Nodes_Coordinates)");
315        }
316     }  
317        // // // // // Elements // // // // //
318     // // // // // Elements // // // // //      if (num_Elements>0) {
319            // Elements_Id
320     if (num_Elements>0) {          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
321                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Id)");
322        // Elements_Id          int_ptr = &mesh->Elements->Id[0];
323        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )          if (! (ids->put(int_ptr, num_Elements)) )
324           throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Elements_Id)");
325        int_ptr = &mesh->Elements->Id[0];  
326        if (! (ids->put(int_ptr, num_Elements)) )          // Elements_Tag
327           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
328                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Tag)");
329        // Elements_Tag          int_ptr = &mesh->Elements->Tag[0];
330        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )          if (! (ids->put(int_ptr, num_Elements)) )
331           throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Elements_Tag)");
332        int_ptr = &mesh->Elements->Tag[0];  
333        if (! (ids->put(int_ptr, num_Elements)) )          // Elements_Owner
334           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
335                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Owner)");
336        // Elements_Owner          int_ptr = &mesh->Elements->Owner[0];
337        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )          if (! (ids->put(int_ptr, num_Elements)) )
338           throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Elements_Owner)");
339        int_ptr = &mesh->Elements->Owner[0];  
340        if (! (ids->put(int_ptr, num_Elements)) )          // Elements_Color
341           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
342                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Color)");
343        // Elements_Color          int_ptr = &mesh->Elements->Color[0];
344        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )          if (! (ids->put(int_ptr, num_Elements)) )
345           throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Elements_Color)");
346        int_ptr = &mesh->Elements->Color[0];  
347        if (! (ids->put(int_ptr, num_Elements)) )          // Elements_Nodes
348           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
349                throw FinleyAdapterException(msgPrefix+"add_var(Elements_Nodes)");
350        // Elements_Nodes          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
351        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Nodes)");
352           throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);      }
353        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )  
354           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);      // // // // // Face_Elements // // // // //
355        if (num_FaceElements>0) {
356     }          // FaceElements_Id
357            if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
358     // // // // // Face_Elements // // // // //              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Id)");
359            int_ptr = &mesh->FaceElements->Id[0];
360     if (num_FaceElements>0) {          if (! (ids->put(int_ptr, num_FaceElements)) )
361                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Id)");
362        // FaceElements_Id  
363        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )          // FaceElements_Tag
364           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
365        int_ptr = &mesh->FaceElements->Id[0];              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Tag)");
366        if (! (ids->put(int_ptr, num_FaceElements)) )          int_ptr = &mesh->FaceElements->Tag[0];
367           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_FaceElements)) )
368                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Tag)");
369        // FaceElements_Tag  
370        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )          // FaceElements_Owner
371           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
372        int_ptr = &mesh->FaceElements->Tag[0];              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Owner)");
373        if (! (ids->put(int_ptr, num_FaceElements)) )          int_ptr = &mesh->FaceElements->Owner[0];
374           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_FaceElements)) )
375                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Owner)");
376        // FaceElements_Owner  
377        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )          // FaceElements_Color
378           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
379        int_ptr = &mesh->FaceElements->Owner[0];              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Color)");
380        if (! (ids->put(int_ptr, num_FaceElements)) )          int_ptr = &mesh->FaceElements->Color[0];
381           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_FaceElements)) )
382                throw FinleyAdapterException(msgPrefix+"put(FaceElements_Color)");
383        // FaceElements_Color  
384        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )          // FaceElements_Nodes
385           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
386        int_ptr = &mesh->FaceElements->Color[0];              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Nodes)");
387        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
388           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Nodes)");
389        }
390        // FaceElements_Nodes  
391        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )      // // // // // Contact_Elements // // // // //
392           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);      if (num_ContactElements>0) {
393        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )  
394           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);          // ContactElements_Id
395            if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
396     }              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Id)");
397            int_ptr = &mesh->ContactElements->Id[0];
398     // // // // // Contact_Elements // // // // //          if (! (ids->put(int_ptr, num_ContactElements)) )
399                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Id)");
400     if (num_ContactElements>0) {  
401            // ContactElements_Tag
402        // ContactElements_Id          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
403        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Tag)");
404           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);          int_ptr = &mesh->ContactElements->Tag[0];
405        int_ptr = &mesh->ContactElements->Id[0];          if (! (ids->put(int_ptr, num_ContactElements)) )
406        if (! (ids->put(int_ptr, num_ContactElements)) )              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Tag)");
407           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);  
408            // ContactElements_Owner
409        // ContactElements_Tag          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
410        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Owner)");
411           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);          int_ptr = &mesh->ContactElements->Owner[0];
412        int_ptr = &mesh->ContactElements->Tag[0];          if (! (ids->put(int_ptr, num_ContactElements)) )
413        if (! (ids->put(int_ptr, num_ContactElements)) )              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Owner)");
414           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);  
415            // ContactElements_Color
416        // ContactElements_Owner          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
417        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Color)");
418           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);          int_ptr = &mesh->ContactElements->Color[0];
419        int_ptr = &mesh->ContactElements->Owner[0];          if (! (ids->put(int_ptr, num_ContactElements)) )
420        if (! (ids->put(int_ptr, num_ContactElements)) )              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Color)");
421           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);  
422            // ContactElements_Nodes
423        // ContactElements_Color          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
424        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Nodes)");
425           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
426        int_ptr = &mesh->ContactElements->Color[0];              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Nodes)");
427        if (! (ids->put(int_ptr, num_ContactElements)) )      }
428           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);  
429        // // // // // Points // // // // //
430        // ContactElements_Nodes      if (num_Points>0) {
431        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )          // Points_Id
432           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
433        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Points_Id)");
434           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Points->Id[0];
435            if (! (ids->put(int_ptr, num_Points)) )
436     }              throw FinleyAdapterException(msgPrefix+"put(Points_Id)");
437    
438     // // // // // Points // // // // //          // Points_Tag
439            if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
440     if (num_Points>0) {              throw FinleyAdapterException(msgPrefix+"add_var(Points_Tag)");
441            int_ptr = &mesh->Points->Tag[0];
442        fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");          if (! (ids->put(int_ptr, num_Points)) )
443                throw FinleyAdapterException(msgPrefix+"put(Points_Tag)");
444        // Points_Id  
445        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )          // Points_Owner
446           throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
447        int_ptr = &mesh->Points->Id[0];              throw FinleyAdapterException(msgPrefix+"add_var(Points_Owner)");
448        if (! (ids->put(int_ptr, num_Points)) )          int_ptr = &mesh->Points->Owner[0];
449           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_Points)) )
450                throw FinleyAdapterException(msgPrefix+"put(Points_Owner)");
451        // Points_Tag  
452        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )          // Points_Color
453           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
454        int_ptr = &mesh->Points->Tag[0];              throw FinleyAdapterException(msgPrefix+"add_var(Points_Color)");
455        if (! (ids->put(int_ptr, num_Points)) )          int_ptr = &mesh->Points->Color[0];
456           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_Points)) )
457                throw FinleyAdapterException(msgPrefix+"put(Points_Color)");
458        // Points_Owner  
459        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )          // Points_Nodes
460           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
461        int_ptr = &mesh->Points->Owner[0];          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
462        if (! (ids->put(int_ptr, num_Points)) )              throw FinleyAdapterException(msgPrefix+"add_var(Points_Nodes)");
463           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
464                throw FinleyAdapterException(msgPrefix+"put(Points_Nodes)");
465        // Points_Color      }
466        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )  
467           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);      // // // // // TagMap // // // // //
468        int_ptr = &mesh->Points->Color[0];      if (num_Tags>0) {
469        if (! (ids->put(int_ptr, num_Points)) )          // Temp storage to gather node IDs
470           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);          vector<int> Tags_keys;
471    
472        // Points_Nodes          // Copy tag data into temp arrays
473        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]          tag_map = mesh->TagMap;
474        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )          while (tag_map) {
475           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);              Tags_keys.push_back(tag_map->tag_key);
       if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )  
          throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);  
   
    }  
   
    // // // // // TagMap // // // // //  
   
    if (num_Tags>0) {  
   
       // Temp storage to gather node IDs  
       int *Tags_keys = TMPMEMALLOC(num_Tags, int);  
       char name_temp[4096];  
   
       /* Copy tag data into temp arrays */  
       tag_map = mesh->TagMap;  
       if (tag_map) {  
          int i = 0;  
          while (tag_map) {  
             Tags_keys[i++] = tag_map->tag_key;  
476              tag_map=tag_map->next;              tag_map=tag_map->next;
477           }          }
       }  
478    
479        // Tags_keys          // Tags_keys
480        if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )          if (! (ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
481           throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Tags_keys)");
482        int_ptr = &Tags_keys[0];          int_ptr = &Tags_keys[0];
483        if (! (ids->put(int_ptr, num_Tags)) )          if (! (ids->put(int_ptr, num_Tags)) )
484           throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(Tags_keys)");
485    
486        // Tags_names_*          // Tags_names_*
487        // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string          // This is an array of strings, it should be stored as an array but
488        // because the NetCDF manual doesn't tell how to do an array of strings          // instead I have hacked in one attribute per string because the NetCDF
489        tag_map = mesh->TagMap;          // manual doesn't tell how to do an array of strings
490        if (tag_map) {          tag_map = mesh->TagMap;
491           int i = 0;          int i = 0;
492           while (tag_map) {          while (tag_map) {
493              sprintf(name_temp, "Tags_name_%d", i);              stringstream tagnamestream;
494              if (!dataFile.add_att(name_temp, tag_map->name) )              tagnamestream << "Tags_name_" << i;
495                 throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);              const string tagname = tagnamestream.str();
496                if (!dataFile.add_att(tagname.c_str(), tag_map->name) )
497                    throw FinleyAdapterException(msgPrefix+"add_att(Tags_names_XX)");
498              tag_map=tag_map->next;              tag_map=tag_map->next;
499              i++;              i++;
500           }          }
501        }      }
   
       TMPMEMFREE(Tags_keys);  
   
    }  
502    
503  /* Send token to next MPI process so he can take his turn */      // Send token to next MPI process so he can take his turn
504  #ifdef PASO_MPI  #ifdef ESYS_MPI
505     if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);      if (mpi_rank<mpi_size-1) {
506            MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
507        }
508  #endif  #endif
509    
510     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
511    
512  #else  #else // USE_NETCDF
513     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.");
514  #endif  /* USE_NETCDF */  #endif // USE_NETCDF
515     checkFinleyError();      checkFinleyError();
516  }  }
517    
518  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
519  {  {
520     return "FinleyMesh";      return "FinleyMesh";
521  }  }
522    
523  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
524  {  {
525     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
526     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
527     if (loc==m_functionSpaceTypeNames.end()) {      if (loc==m_functionSpaceTypeNames.end()) {
528        return "Invalid function space type code.";          return "Invalid function space type code.";
529     } else {      } else {
530        return loc->second;          return loc->second;
531     }      }
532  }  }
533    
534  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
535  {  {
536     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
537     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
538     return (loc!=m_functionSpaceTypeNames.end());      return (loc!=m_functionSpaceTypeNames.end());
539  }  }
540    
541  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
542  {  {
543     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
544     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));                  DegreesOfFreedom,"Finley_DegreesOfFreedom"));
545     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
546     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));                  ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
547     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
548     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));                  Nodes,"Finley_Nodes"));
549     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
550     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));                  ReducedNodes,"Finley_Reduced_Nodes"));
551     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
552     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));                  Elements,"Finley_Elements"));
553     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
554     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));                  ReducedElements,"Finley_Reduced_Elements"));
555     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
556     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));                  FaceElements,"Finley_Face_Elements"));
557     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
558     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));                  ReducedFaceElements,"Finley_Reduced_Face_Elements"));
559     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
560     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));                  Points,"Finley_Points"));
561     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
562     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));                  ContactElementsZero,"Finley_Contact_Elements_0"));
563     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
564     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));                  ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
565     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
566     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));                  ContactElementsOne,"Finley_Contact_Elements_1"));
567     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
568     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));                  ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
569  }  }
570    
571  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
572  {  {
573     return Nodes;      return Nodes;
574  }  }
575    
576  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
577  {  {
578     return ReducedNodes;      return ReducedNodes;
579  }  }
580    
581  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
582  {  {
583     return Elements;      return Elements;
584  }  }
585    
586  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
587  {  {
588     return ReducedElements;      return ReducedElements;
589  }  }
590    
591  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
592  {  {
593     return FaceElements;      return FaceElements;
594  }  }
595    
596  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
597  {  {
598     return ReducedFaceElements;      return ReducedFaceElements;
599  }  }
600    
601  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
602  {  {
603     return ContactElementsZero;      return ContactElementsZero;
604  }  }
605    
606  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
607  {  {
608     return ReducedContactElementsZero;      return ReducedContactElementsZero;
609  }  }
610    
611  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
612  {  {
613     return ContactElementsOne;      return ContactElementsOne;
614  }  }
615    
616  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
617  {  {
618     return ReducedContactElementsOne;      return ReducedContactElementsOne;
619  }  }
620    
621  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
622  {  {
623     return DegreesOfFreedom;      return DegreesOfFreedom;
624  }  }
625    
626  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
627  {  {
628     return ReducedDegreesOfFreedom;      return ReducedDegreesOfFreedom;
629  }  }
630    
631  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
632  {  {
633     return Points;      return Points;
634  }  }
635    
636  //  //
# Line 635  int MeshAdapter::getDiracDeltaFunctionCo Line 638  int MeshAdapter::getDiracDeltaFunctionCo
638  //  //
639  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
640  {  {
641     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());      Finley_Mesh* mesh=m_finleyMesh.get();
642     checkFinleyError();      int numDim=Finley_Mesh_getDim(mesh);
643     return numDim;      checkFinleyError();
644        return numDim;
645  }  }
646    
647  //  //
# Line 645  int MeshAdapter::getDim() const Line 649  int MeshAdapter::getDim() const
649  //  //
650  int MeshAdapter::getNumDataPointsGlobal() const  int MeshAdapter::getNumDataPointsGlobal() const
651  {  {
652     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);      return m_finleyMesh.get()->Nodes->getGlobalNumNodes();
653  }  }
654    
655  //  //
# Line 654  int MeshAdapter::getNumDataPointsGlobal( Line 658  int MeshAdapter::getNumDataPointsGlobal(
658  //  //
659  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const
660  {  {
661     int numDataPointsPerSample=0;      int numDataPointsPerSample=0;
662     int numSamples=0;      int numSamples=0;
663     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
664     switch (functionSpaceCode) {      switch (functionSpaceCode) {
665     case(Nodes):          case Nodes:
666     numDataPointsPerSample=1;              numDataPointsPerSample=1;
667     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumNodes();
668     break;              break;
669     case(ReducedNodes):          case ReducedNodes:
670     numDataPointsPerSample=1;              numDataPointsPerSample=1;
671     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumReducedNodes();
672     break;              break;
673     case(Elements):          case Elements:
674     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
675        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
676        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
677     }              }
678     break;              break;
679     case(ReducedElements):          case ReducedElements:
680     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
681        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
682        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
683     }              }
684     break;              break;
685     case(FaceElements):          case FaceElements:
686     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
687        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
688        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
689     }              }
690     break;              break;
691     case(ReducedFaceElements):          case ReducedFaceElements:
692     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
693        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
694        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
695     }              }
696     break;              break;
697     case(Points):          case Points:
698     if (mesh->Points!=NULL) {              if (mesh->Points!=NULL) {
699        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
700        numSamples=mesh->Points->numElements;                  numSamples=mesh->Points->numElements;
701     }              }
702     break;              break;
703     case(ContactElementsZero):          case ContactElementsZero:
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(ReducedContactElementsZero):          case ReducedContactElementsZero:
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(ContactElementsOne):          case ContactElementsOne:
716     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
717        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
718        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
719     }              }
720     break;              break;
721     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
722     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
723        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
724        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
725     }              }
726     break;              break;
727     case(DegreesOfFreedom):          case DegreesOfFreedom:
728     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
729        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
730        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumDegreesOfFreedom();
731     }              }
732     break;              break;
733     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
734     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
735        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
736        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumReducedDegreesOfFreedom();
737     }              }
738     break;              break;
739     default:          default:
740        stringstream temp;              stringstream temp;
741        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();              temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
742        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
743        break;              break;
744     }      }
745     return pair<int,int>(numDataPointsPerSample,numSamples);      return pair<int,int>(numDataPointsPerSample,numSamples);
746  }  }
747    
748  //  //
749  // 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
750    // hand side:
751  //  //
752  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
753                                   SystemMatrixAdapter& mat, escript::Data& rhs,          escript::AbstractSystemMatrix& mat, escript::Data& rhs,
754                                   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,
755                                   const escript::Data& d, const escript::Data& y,          const escript::Data& D, const escript::Data& X, const escript::Data& Y,
756                                   const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d, const escript::Data& y,
757  {          const escript::Data& d_contact, const escript::Data& y_contact,
758     escriptDataC _rhs=rhs.getDataC();          const escript::Data& d_dirac, const escript::Data& y_dirac) const
759     escriptDataC _A  =A.getDataC();  {
760     escriptDataC _B=B.getDataC();      SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
761     escriptDataC _C=C.getDataC();      if (!smat)
762     escriptDataC _D=D.getDataC();          throw FinleyAdapterException("finley only supports Paso system matrices.");
763     escriptDataC _X=X.getDataC();  
764     escriptDataC _Y=Y.getDataC();      escriptDataC _rhs=rhs.getDataC();
765     escriptDataC _d=d.getDataC();      escriptDataC _A  =A.getDataC();
766     escriptDataC _y=y.getDataC();      escriptDataC _B=B.getDataC();
767     escriptDataC _d_contact=d_contact.getDataC();      escriptDataC _C=C.getDataC();
768     escriptDataC _y_contact=y_contact.getDataC();      escriptDataC _D=D.getDataC();
769        escriptDataC _X=X.getDataC();
770     Finley_Mesh* mesh=m_finleyMesh.get();      escriptDataC _Y=Y.getDataC();
771        escriptDataC _d=d.getDataC();
772     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );      escriptDataC _y=y.getDataC();
773     checkFinleyError();      escriptDataC _d_contact=d_contact.getDataC();
774        escriptDataC _y_contact=y_contact.getDataC();
775     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );      escriptDataC _d_dirac=d_dirac.getDataC();
776     checkFinleyError();      escriptDataC _y_dirac=y_dirac.getDataC();
777    
778     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );      Finley_Mesh* mesh=m_finleyMesh.get();
779     checkFinleyError();      Paso_SystemMatrix* S = smat->getPaso_SystemMatrix();
780  }  
781        Finley_Assemble_PDE(mesh->Nodes, mesh->Elements, S, &_rhs, &_A, &_B, &_C,
782  void  MeshAdapter::addPDEToLumpedSystem(                          &_D, &_X, &_Y);
783                                          escript::Data& mat,      checkFinleyError();
784                                          const escript::Data& D,  
785                                          const escript::Data& d) const      Finley_Assemble_PDE(mesh->Nodes, mesh->FaceElements, S, &_rhs, 0, 0, 0,
786  {                          &_d, 0, &_y);
787     escriptDataC _mat=mat.getDataC();      checkFinleyError();
788     escriptDataC _D=D.getDataC();  
789     escriptDataC _d=d.getDataC();      Finley_Assemble_PDE(mesh->Nodes, mesh->ContactElements, S, &_rhs, 0, 0, 0,
790                &_d_contact, 0, &_y_contact);
791        checkFinleyError();
792    
793        Finley_Assemble_PDE(mesh->Nodes, mesh->Points, S, &_rhs, 0, 0, 0,
794                            &_d_dirac, 0, &_y_dirac );
795        checkFinleyError();
796    }
797    
798    void MeshAdapter::addPDEToLumpedSystem(escript::Data& mat,
799            const escript::Data& D, const escript::Data& d,
800            const escript::Data& d_dirac, const bool useHRZ) const
801    {
802        escriptDataC _mat=mat.getDataC();
803        escriptDataC _D=D.getDataC();
804        escriptDataC _d=d.getDataC();
805        escriptDataC _d_dirac=d_dirac.getDataC();
806    
807        Finley_Mesh* mesh=m_finleyMesh.get();
808    
809     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Assemble_LumpedSystem(mesh->Nodes, mesh->Elements, &_mat, &_D, useHRZ);
810        checkFinleyError();
811    
812     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);      Finley_Assemble_LumpedSystem(mesh->Nodes, mesh->FaceElements, &_mat, &_d, useHRZ);
813     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);      checkFinleyError();
814    
815     checkFinleyError();      Finley_Assemble_LumpedSystem(mesh->Nodes, mesh->Points, &_mat, &_d_dirac, useHRZ);
816        checkFinleyError();
817  }  }
818    
   
819  //  //
820  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
821  //  //
822  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,
823  {          const escript::Data& Y, const escript::Data& y,
824     Finley_Mesh* mesh=m_finleyMesh.get();          const escript::Data& y_contact, const escript::Data& y_dirac) const
825    {
826     escriptDataC _rhs=rhs.getDataC();      Finley_Mesh* mesh=m_finleyMesh.get();
827     escriptDataC _X=X.getDataC();  
828     escriptDataC _Y=Y.getDataC();      escriptDataC _rhs=rhs.getDataC();
829     escriptDataC _y=y.getDataC();      escriptDataC _X=X.getDataC();
830     escriptDataC _y_contact=y_contact.getDataC();      escriptDataC _Y=Y.getDataC();
831        escriptDataC _y=y.getDataC();
832        escriptDataC _y_contact=y_contact.getDataC();
833        escriptDataC _y_dirac=y_dirac.getDataC();
834    
835        Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y);
836        checkFinleyError();
837    
838     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );      Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y);
839     checkFinleyError();      checkFinleyError();
840    
841     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );      Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y_contact);
842     checkFinleyError();      checkFinleyError();
843    
844     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );      Finley_Assemble_PDE(mesh->Nodes,mesh->Points, 0, &_rhs, 0, 0, 0, 0, 0, &_y_dirac);
845     checkFinleyError();      checkFinleyError();
846  }  }
847    
848  //  //
849  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
850  //  //
851  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
852                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,          escript::AbstractTransportProblem& tp, escript::Data& source,
853                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,          const escript::Data& M, const escript::Data& A, const escript::Data& B,
854                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& C, const escript::Data& D, const escript::Data& X,
855                                             const escript::Data& d, const escript::Data& y,          const escript::Data& Y, const escript::Data& d, const escript::Data& y,
856                                             const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d_contact, const escript::Data& y_contact,
857  {          const escript::Data& d_dirac, const escript::Data& y_dirac) const
858     DataTypes::ShapeType shape;  {
859     source.expand();      TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
860     escriptDataC _source=source.getDataC();      if (!tpa)
861     escriptDataC _M=M.getDataC();          throw FinleyAdapterException("finley only supports Paso transport problems.");
862     escriptDataC _A=A.getDataC();  
863     escriptDataC _B=B.getDataC();      source.expand();
864     escriptDataC _C=C.getDataC();      escriptDataC _source=source.getDataC();
865     escriptDataC _D=D.getDataC();      escriptDataC _M=M.getDataC();
866     escriptDataC _X=X.getDataC();      escriptDataC _A=A.getDataC();
867     escriptDataC _Y=Y.getDataC();      escriptDataC _B=B.getDataC();
868     escriptDataC _d=d.getDataC();      escriptDataC _C=C.getDataC();
869     escriptDataC _y=y.getDataC();      escriptDataC _D=D.getDataC();
870     escriptDataC _d_contact=d_contact.getDataC();      escriptDataC _X=X.getDataC();
871     escriptDataC _y_contact=y_contact.getDataC();      escriptDataC _Y=Y.getDataC();
872        escriptDataC _d=d.getDataC();
873     Finley_Mesh* mesh=m_finleyMesh.get();      escriptDataC _y=y.getDataC();
874     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();      escriptDataC _d_contact=d_contact.getDataC();
875        escriptDataC _y_contact=y_contact.getDataC();
876     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );      escriptDataC _d_dirac=d_dirac.getDataC();
877     checkFinleyError();      escriptDataC _y_dirac=y_dirac.getDataC();
878    
879     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );      Finley_Mesh* mesh=m_finleyMesh.get();
880     checkFinleyError();      Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
881    
882     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );      Finley_Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->mass_matrix,
883     checkFinleyError();                          &_source, 0, 0, 0, &_M, 0, 0);
884        checkFinleyError();
885     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );  
886     checkFinleyError();      Finley_Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->transport_matrix,
887  }                          &_source, &_A, &_B, &_C, &_D, &_X, &_Y);
888        checkFinleyError();
889  //  
890  // interpolates data between different function spaces:      Finley_Assemble_PDE(mesh->Nodes, mesh->FaceElements, _tp->transport_matrix,
891  //                          &_source, 0, 0, 0, &_d, 0, &_y);
892  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const      checkFinleyError();
893  {  
894     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());      Finley_Assemble_PDE(mesh->Nodes, mesh->ContactElements,
895     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());                          _tp->transport_matrix, &_source, 0, 0, 0, &_d_contact, 0, &_y_contact);
896     if (inDomain!=*this)        checkFinleyError();
897        throw FinleyAdapterException("Error - Illegal domain of interpolant.");  
898     if (targetDomain!=*this)      Finley_Assemble_PDE(mesh->Nodes, mesh->Points, _tp->transport_matrix,
899        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");                          &_source, 0, 0, 0, &_d_dirac, 0, &_y_dirac);
900        checkFinleyError();
901     Finley_Mesh* mesh=m_finleyMesh.get();  }
902     escriptDataC _target=target.getDataC();  
903     escriptDataC _in=in.getDataC();  //
904     switch(in.getFunctionSpace().getTypeCode()) {  // interpolates data between different function spaces
905     case(Nodes):  //
906     switch(target.getFunctionSpace().getTypeCode()) {  void MeshAdapter::interpolateOnDomain(escript::Data& target, const escript::Data& in) const
907     case(Nodes):  {
908     case(ReducedNodes):      const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
909     case(DegreesOfFreedom):      const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
910     case(ReducedDegreesOfFreedom):      if (inDomain!=*this)
911     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);          throw FinleyAdapterException("Error - Illegal domain of interpolant.");
912     break;      if (targetDomain!=*this)
913     case(Elements):          throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
914     case(ReducedElements):  
915     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);      Finley_Mesh* mesh=m_finleyMesh.get();
916     break;      escriptDataC _target=target.getDataC();
917     case(FaceElements):      escriptDataC _in=in.getDataC();
918     case(ReducedFaceElements):      switch(in.getFunctionSpace().getTypeCode()) {
919     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);          case Nodes:
920     break;              switch(target.getFunctionSpace().getTypeCode()) {
921     case(Points):                  case Nodes:
922     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedNodes:
923     break;                  case DegreesOfFreedom:
924     case(ContactElementsZero):                  case ReducedDegreesOfFreedom:
925     case(ReducedContactElementsZero):                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
926     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
927     break;                  case Elements:
928     case(ContactElementsOne):                  case ReducedElements:
929     case(ReducedContactElementsOne):                      Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
930     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
931     break;                  case FaceElements:
932     default:                  case ReducedFaceElements:
933        stringstream temp;                      Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
934        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      break;
935        throw FinleyAdapterException(temp.str());                  case Points:
936        break;                      Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
937     }                      break;
938     break;                  case ContactElementsZero:
939     case(ReducedNodes):                  case ReducedContactElementsZero:
940     switch(target.getFunctionSpace().getTypeCode()) {                  case ContactElementsOne:
941     case(Nodes):                  case ReducedContactElementsOne:
942     case(ReducedNodes):                      Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
943     case(DegreesOfFreedom):                      break;
944     case(ReducedDegreesOfFreedom):                  default:
945     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      stringstream temp;
946     break;                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
947     case(Elements):                      throw FinleyAdapterException(temp.str());
948     case(ReducedElements):                      break;
949     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);              }
950     break;              break;
951     case(FaceElements):          case ReducedNodes:
952     case(ReducedFaceElements):              switch(target.getFunctionSpace().getTypeCode()) {
953     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case Nodes:
954     break;                  case ReducedNodes:
955     case(Points):                  case DegreesOfFreedom:
956     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedDegreesOfFreedom:
957     break;                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
958     case(ContactElementsZero):                      break;
959     case(ReducedContactElementsZero):                  case Elements:
960     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedElements:
961     break;                      Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
962     case(ContactElementsOne):                      break;
963     case(ReducedContactElementsOne):                  case FaceElements:
964     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedFaceElements:
965     break;                      Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
966     default:                      break;
967        stringstream temp;                  case Points:
968        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
969        throw FinleyAdapterException(temp.str());                      break;
970        break;                  case ContactElementsZero:
971     }                  case ReducedContactElementsZero:
972     break;                  case ContactElementsOne:
973     case(Elements):                  case ReducedContactElementsOne:
974     if (target.getFunctionSpace().getTypeCode()==Elements) {                      Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
975        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);                      break;
976     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  default:
977        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);                      stringstream temp;
978     } else {                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
979        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");                      throw FinleyAdapterException(temp.str());
980     }                      break;
981     break;              }
982     case(ReducedElements):              break;
983     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {          case Elements:
984        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              if (target.getFunctionSpace().getTypeCode()==Elements) {
985     } else {                  Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
986        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");              } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
987     }                  Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
988     break;              } else {
989     case(FaceElements):                  throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
990     if (target.getFunctionSpace().getTypeCode()==FaceElements) {              }
991        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              break;
992     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {          case ReducedElements:
993        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);              if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
994     } else {                  Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
995        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");              } else {
996     }                  throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
997     break;              }
998     case(ReducedFaceElements):              break;
999     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {          case FaceElements:
1000        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              if (target.getFunctionSpace().getTypeCode()==FaceElements) {
1001     } else {                  Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1002        throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");              } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1003     }                  Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
1004     break;              } else {
1005     case(Points):                  throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
1006     if (target.getFunctionSpace().getTypeCode()==Points) {              }
1007        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);              break;
1008     } else {          case ReducedFaceElements:
1009        throw FinleyAdapterException("Error - No interpolation with data on points possible.");              if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1010     }                  Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1011     break;              } else {
1012     case(ContactElementsZero):                  throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
1013     case(ContactElementsOne):              }
1014     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {              break;
1015        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);          case Points:
1016     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {              if (target.getFunctionSpace().getTypeCode()==Points) {
1017        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);                  Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1018     } else {              } else {
1019        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");                  throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1020     }              }
1021     break;              break;
1022     case(ReducedContactElementsZero):          case ContactElementsZero:
1023     case(ReducedContactElementsOne):          case ContactElementsOne:
1024     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {              if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1025        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);                  Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1026     } else {              } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1027        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");                  Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
1028     }              } else {
1029     break;                  throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1030     case(DegreesOfFreedom):                    }
1031     switch(target.getFunctionSpace().getTypeCode()) {              break;
1032     case(ReducedDegreesOfFreedom):          case ReducedContactElementsZero:
1033     case(DegreesOfFreedom):          case ReducedContactElementsOne:
1034     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);              if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1035     break;                  Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1036                } else {
1037     case(Nodes):                  throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1038     case(ReducedNodes):              }
1039     if (getMPISize()>1) {              break;
1040        escript::Data temp=escript::Data(in);          case DegreesOfFreedom:
1041        temp.expand();              switch(target.getFunctionSpace().getTypeCode()) {
1042        escriptDataC _in2 = temp.getDataC();                  case ReducedDegreesOfFreedom:
1043        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                  case DegreesOfFreedom:
1044     } else {                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1045        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1046     }  
1047     break;                  case Nodes:
1048     case(Elements):                  case ReducedNodes:
1049     case(ReducedElements):                      if (getMPISize()>1) {
1050     if (getMPISize()>1) {                          escript::Data temp=escript::Data(in);
1051        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          temp.expand();
1052        escriptDataC _in2 = temp.getDataC();                          escriptDataC _in2 = temp.getDataC();
1053        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1054     } else {                      } else {
1055        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1056     }                      }
1057     break;                      break;
1058     case(FaceElements):                  case Elements:
1059     case(ReducedFaceElements):                  case ReducedElements:
1060     if (getMPISize()>1) {                      if (getMPISize()>1) {
1061        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          escript::Data temp=escript::Data(in, continuousFunction(*this));
1062        escriptDataC _in2 = temp.getDataC();                          escriptDataC _in2 = temp.getDataC();
1063        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1064                        } else {
1065     } else {                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1066        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      }
1067     }                      break;
1068     break;                  case FaceElements:
1069     case(Points):                  case ReducedFaceElements:
1070     if (getMPISize()>1) {                      if (getMPISize()>1) {
1071        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          escript::Data temp=escript::Data(in, continuousFunction(*this));
1072        escriptDataC _in2 = temp.getDataC();                          escriptDataC _in2 = temp.getDataC();
1073     } else {                          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1074        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      } else {
1075     }                          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1076     break;                      }
1077     case(ContactElementsZero):                      break;
1078     case(ContactElementsOne):                  case Points:
1079     case(ReducedContactElementsZero):                      if (getMPISize()>1) {
1080     case(ReducedContactElementsOne):                          //escript::Data temp=escript::Data(in, continuousFunction(*this) );
1081     if (getMPISize()>1) {                          //escriptDataC _in2 = temp.getDataC();
1082        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                      } else {
1083        escriptDataC _in2 = temp.getDataC();                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1084        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);                      }
1085     } else {                      break;
1086        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ContactElementsZero:
1087     }                  case ContactElementsOne:
1088     break;                  case ReducedContactElementsZero:
1089     default:                  case ReducedContactElementsOne:
1090        stringstream temp;                      if (getMPISize()>1) {
1091        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                          escript::Data temp=escript::Data(in, continuousFunction(*this));
1092        throw FinleyAdapterException(temp.str());                          escriptDataC _in2 = temp.getDataC();
1093        break;                          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1094     }                      } else {
1095     break;                          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1096     case(ReducedDegreesOfFreedom):                      }
1097     switch(target.getFunctionSpace().getTypeCode()) {                      break;
1098     case(Nodes):                  default:
1099     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                      stringstream temp;
1100     break;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1101     case(ReducedNodes):                      throw FinleyAdapterException(temp.str());
1102     if (getMPISize()>1) {                      break;
1103        escript::Data temp=escript::Data(in);              }
1104        temp.expand();              break;
1105        escriptDataC _in2 = temp.getDataC();          case ReducedDegreesOfFreedom:
1106        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);              switch(target.getFunctionSpace().getTypeCode()) {
1107     } else {                  case Nodes:
1108        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1109     }                      break;
1110     break;                  case ReducedNodes:
1111     case(DegreesOfFreedom):                      if (getMPISize()>1) {
1112     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                          escript::Data temp=escript::Data(in);
1113     break;                          temp.expand();
1114     case(ReducedDegreesOfFreedom):                          escriptDataC _in2 = temp.getDataC();
1115     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1116     break;                      } else {
1117     case(Elements):                          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1118     case(ReducedElements):                      }
1119     if (getMPISize()>1) {                      break;
1120        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                  case DegreesOfFreedom:
1121        escriptDataC _in2 = temp.getDataC();                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1122        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                      break;
1123     } else {                  case ReducedDegreesOfFreedom:
1124        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1125     }                      break;
1126     break;                  case Elements:
1127     case(FaceElements):                  case ReducedElements:
1128     case(ReducedFaceElements):                      if (getMPISize()>1) {
1129     if (getMPISize()>1) {                          escript::Data temp=escript::Data(in, reducedContinuousFunction(*this) );
1130        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          escriptDataC _in2 = temp.getDataC();
1131        escriptDataC _in2 = temp.getDataC();                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1132        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      } else {
1133     } else {                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1134        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      }
1135     }                      break;
1136     break;                  case FaceElements:
1137     case(Points):                  case ReducedFaceElements:
1138     if (getMPISize()>1) {                      if (getMPISize()>1) {
1139        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          escript::Data temp=escript::Data(in, reducedContinuousFunction(*this) );
1140        escriptDataC _in2 = temp.getDataC();                          escriptDataC _in2 = temp.getDataC();
1141        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);                          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1142     } else {                      } else {
1143        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1144     }                      }
1145     break;                      break;
1146     case(ContactElementsZero):                  case Points:
1147     case(ContactElementsOne):                      if (getMPISize()>1) {
1148     case(ReducedContactElementsZero):                          escript::Data temp=escript::Data(in, reducedContinuousFunction(*this));
1149     case(ReducedContactElementsOne):                          escriptDataC _in2 = temp.getDataC();
1150     if (getMPISize()>1) {                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1151        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                      } else {
1152        escriptDataC _in2 = temp.getDataC();                          Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1153        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);                      }
1154     } else {                      break;
1155        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ContactElementsZero:
1156     }                  case ContactElementsOne:
1157     break;                  case ReducedContactElementsZero:
1158     default:                  case ReducedContactElementsOne:
1159        stringstream temp;                      if (getMPISize()>1) {
1160        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                          escript::Data temp=escript::Data(in, reducedContinuousFunction(*this));
1161        throw FinleyAdapterException(temp.str());                          escriptDataC _in2 = temp.getDataC();
1162        break;                          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1163     }                      } else {
1164     break;                          Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1165     default:                      }
1166        stringstream temp;                      break;
1167        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();                  default:
1168        throw FinleyAdapterException(temp.str());                      stringstream temp;
1169        break;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1170     }                      throw FinleyAdapterException(temp.str());
1171     checkFinleyError();                      break;
1172                }
1173                break;
1174            default:
1175                stringstream temp;
1176                temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1177                throw FinleyAdapterException(temp.str());
1178                break;
1179        }
1180        checkFinleyError();
1181  }  }
1182    
1183  //  //
1184  // copies the locations of sample points into x:  // copies the locations of sample points into x
1185  //  //
1186  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1187  {  {
1188     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1189     if (argDomain!=*this)      if (argDomain!=*this)
1190        throw FinleyAdapterException("Error - Illegal domain of data point locations");          throw FinleyAdapterException("Error - Illegal domain of data point locations");
1191     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1192     // in case of values node coordinates we can do the job directly:      // in case of appropriate function space we can do the job directly:
1193     if (arg.getFunctionSpace().getTypeCode()==Nodes) {      if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1194        escriptDataC _arg=arg.getDataC();          escriptDataC _arg=arg.getDataC();
1195        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);          Finley_Assemble_NodeCoordinates(mesh->Nodes, &_arg);
1196     } else {      } else {
1197        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);          escript::Data tmp_data=Vector(0., continuousFunction(*this), true);
1198        escriptDataC _tmp_data=tmp_data.getDataC();          escriptDataC _tmp_data=tmp_data.getDataC();
1199        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);          Finley_Assemble_NodeCoordinates(mesh->Nodes, &_tmp_data);
1200        // this is then interpolated onto arg:          // this is then interpolated onto arg:
1201        interpolateOnDomain(arg,tmp_data);          interpolateOnDomain(arg, tmp_data);
1202     }      }
1203     checkFinleyError();      checkFinleyError();
1204  }  }
1205    
1206  //  //
1207  // 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
1208  //  //
1209  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1210  {  {
1211     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());      const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1212     if (normalDomain!=*this)      if (normalDomain!=*this)
1213        throw FinleyAdapterException("Error - Illegal domain of normal locations");          throw FinleyAdapterException("Error - Illegal domain of normal locations");
1214     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1215     escriptDataC _normal=normal.getDataC();      escriptDataC _normal=normal.getDataC();
1216     switch(normal.getFunctionSpace().getTypeCode()) {      switch(normal.getFunctionSpace().getTypeCode()) {
1217     case(Nodes):          case Nodes:
1218     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1219     break;              break;
1220     case(ReducedNodes):          case ReducedNodes:
1221     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1222     break;              break;
1223     case(Elements):          case Elements:
1224     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1225     break;              break;
1226     case(ReducedElements):          case ReducedElements:
1227     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1228     break;              break;
1229     case (FaceElements):          case FaceElements:
1230     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);          case ReducedFaceElements:
1231     break;              Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1232     case (ReducedFaceElements):              break;
1233     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);          case Points:
1234     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1235     case(Points):              break;
1236     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");          case ContactElementsOne:
1237     break;          case ContactElementsZero:
1238     case (ContactElementsOne):          case ReducedContactElementsOne:
1239     case (ContactElementsZero):          case ReducedContactElementsZero:
1240     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1241     break;              break;
1242     case (ReducedContactElementsOne):          case DegreesOfFreedom:
1243     case (ReducedContactElementsZero):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1244     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              break;
1245     break;          case ReducedDegreesOfFreedom:
1246     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1247     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");              break;
1248     break;          default:
1249     case(ReducedDegreesOfFreedom):              stringstream temp;
1250     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");              temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1251     break;              throw FinleyAdapterException(temp.str());
1252     default:              break;
1253        stringstream temp;      }
1254        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();      checkFinleyError();
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1255  }  }
1256    
1257  //  //
1258  // interpolates data to other domain:  // interpolates data to other domain
1259  //  //
1260  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1261  {  {
1262     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());      escript::const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1263     if (targetDomain!=*this)      const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1264        throw FinleyAdapterException("Error - Illegal domain of interpolation target");      if (targetDomain!=this)
1265            throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1266     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");  
1267  }      throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1268    }
1269  //  
1270  // calculates the integral of a function defined of arg:  //
1271  //  // calculates the integral of a function defined on arg
1272  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  //
1273  {  void MeshAdapter::setToIntegrals(vector<double>& integrals, const escript::Data& arg) const
1274     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());  {
1275     if (argDomain!=*this)      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1276        throw FinleyAdapterException("Error - Illegal domain of integration kernel");      if (argDomain!=*this)
1277            throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1278     double blocktimer_start = blocktimer_time();  
1279     Finley_Mesh* mesh=m_finleyMesh.get();      double blocktimer_start = blocktimer_time();
1280     escriptDataC _temp;      Finley_Mesh* mesh=m_finleyMesh.get();
1281     escript::Data temp;      escriptDataC _temp;
1282     escriptDataC _arg=arg.getDataC();      escript::Data temp;
1283     switch(arg.getFunctionSpace().getTypeCode()) {      escriptDataC _arg=arg.getDataC();
1284     case(Nodes):      switch(arg.getFunctionSpace().getTypeCode()) {
1285     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );          case Nodes:
1286     _temp=temp.getDataC();              temp=escript::Data(arg, escript::function(*this));
1287     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);              _temp=temp.getDataC();
1288     break;              Finley_Assemble_integrate(mesh->Nodes, mesh->Elements, &_temp, &integrals[0]);
1289     case(ReducedNodes):              break;
1290     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );          case ReducedNodes:
1291     _temp=temp.getDataC();              temp=escript::Data( arg, escript::function(*this) );
1292     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);              _temp=temp.getDataC();
1293     break;              Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1294     case(Elements):              break;
1295     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case Elements:
1296     break;          case ReducedElements:
1297     case(ReducedElements):              Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1298     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);              break;
1299     break;          case FaceElements:
1300     case(FaceElements):          case ReducedFaceElements:
1301     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);              Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1302     break;              break;
1303     case(ReducedFaceElements):          case Points:
1304     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);              throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1305     break;              break;
1306     case(Points):          case ContactElementsZero:
1307     throw FinleyAdapterException("Error - Integral of data on points is not supported.");          case ReducedContactElementsZero:
1308     break;          case ContactElementsOne:
1309     case(ContactElementsZero):          case ReducedContactElementsOne:
1310     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1311     break;              break;
1312     case(ReducedContactElementsZero):          case DegreesOfFreedom:
1313     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);          case ReducedDegreesOfFreedom:
1314     break;              temp=escript::Data(arg, escript::function(*this));
1315     case(ContactElementsOne):              _temp=temp.getDataC();
1316     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1317     break;              break;
1318     case(ReducedContactElementsOne):          default:
1319     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              stringstream temp;
1320     break;              temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1321     case(DegreesOfFreedom):              throw FinleyAdapterException(temp.str());
1322     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );              break;
1323     _temp=temp.getDataC();      }
1324     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);      checkFinleyError();
1325     break;      blocktimer_increment("integrate()", blocktimer_start);
1326     case(ReducedDegreesOfFreedom):  }
1327     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );  
1328     _temp=temp.getDataC();  //
1329     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  // calculates the gradient of arg
1330     break;  //
1331     default:  void MeshAdapter::setToGradient(escript::Data& grad, const escript::Data& arg) const
1332        stringstream temp;  {
1333        temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1334        throw FinleyAdapterException(temp.str());      if (argDomain!=*this)
1335        break;          throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1336     }      const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1337     checkFinleyError();      if (gradDomain!=*this)
1338     blocktimer_increment("integrate()", blocktimer_start);          throw FinleyAdapterException("Error - Illegal domain of gradient");
1339  }  
1340        Finley_Mesh* mesh=m_finleyMesh.get();
1341  //      escriptDataC _grad=grad.getDataC();
1342  // calculates the gradient of arg:      escriptDataC nodeDataC;
1343  //      escript::Data temp;
1344  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const      if (getMPISize()>1) {
1345  {          if (arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom) {
1346     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());              temp=escript::Data(arg, continuousFunction(*this));
1347     if (argDomain!=*this)              nodeDataC = temp.getDataC();
1348        throw FinleyAdapterException("Error - Illegal domain of gradient argument");          } else if(arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom) {
1349     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());              temp=escript::Data(arg, reducedContinuousFunction(*this));
1350     if (gradDomain!=*this)              nodeDataC = temp.getDataC();
1351        throw FinleyAdapterException("Error - Illegal domain of gradient");          } else {
1352                nodeDataC = arg.getDataC();
1353     Finley_Mesh* mesh=m_finleyMesh.get();          }
1354     escriptDataC _grad=grad.getDataC();      } else {
1355     escriptDataC nodeDataC;          nodeDataC = arg.getDataC();
1356     escript::Data temp;      }
1357     if (getMPISize()>1) {      switch(grad.getFunctionSpace().getTypeCode()) {
1358        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {          case Nodes:
1359           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );              throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1360           nodeDataC = temp.getDataC();              break;
1361        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {          case ReducedNodes:
1362           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );              throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1363           nodeDataC = temp.getDataC();              break;
1364        } else {          case Elements:
1365           nodeDataC = arg.getDataC();          case ReducedElements:
1366        }              Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1367     } else {              break;
1368        nodeDataC = arg.getDataC();          case FaceElements:
1369     }          case ReducedFaceElements:
1370     switch(grad.getFunctionSpace().getTypeCode()) {              Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1371     case(Nodes):              break;
1372     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");          case Points:
1373     break;              throw FinleyAdapterException("Error - Gradient at points is not supported.");
1374     case(ReducedNodes):              break;
1375     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");          case ContactElementsZero:
1376     break;          case ReducedContactElementsZero:
1377     case(Elements):          case ContactElementsOne:
1378     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);          case ReducedContactElementsOne:
1379     break;              Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1380     case(ReducedElements):              break;
1381     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);          case DegreesOfFreedom:
1382     break;              throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1383     case(FaceElements):              break;
1384     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);          case ReducedDegreesOfFreedom:
1385     break;              throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1386     case(ReducedFaceElements):              break;
1387     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);          default:
1388     break;              stringstream temp;
1389     case(Points):              temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1390     throw FinleyAdapterException("Error - Gradient at points is not supported.");              throw FinleyAdapterException(temp.str());
1391     break;              break;
1392     case(ContactElementsZero):      }
1393     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);      checkFinleyError();
    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();  
1394  }  }
1395    
1396  //  //
1397  // returns the size of elements:  // returns the size of elements
1398  //  //
1399  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1400  {  {
1401     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1402     escriptDataC tmp=size.getDataC();      escriptDataC tmp=size.getDataC();
1403     switch(size.getFunctionSpace().getTypeCode()) {      switch(size.getFunctionSpace().getTypeCode()) {
1404     case(Nodes):          case Nodes:
1405     throw FinleyAdapterException("Error - Size of nodes is not supported.");              throw FinleyAdapterException("Error - Size of nodes is not supported.");
1406     break;              break;
1407     case(ReducedNodes):          case ReducedNodes:
1408     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1409     break;              break;
1410     case(Elements):          case Elements:
1411     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case ReducedElements:
1412     break;              Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1413     case(ReducedElements):              break;
1414     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case FaceElements:
1415     break;          case ReducedFaceElements:
1416     case(FaceElements):              Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1417     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);              break;
1418     break;          case Points:
1419     case(ReducedFaceElements):              throw FinleyAdapterException("Error - Size of point elements is not supported.");
1420     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);              break;
1421     break;          case ContactElementsZero:
1422     case(Points):          case ContactElementsOne:
1423     throw FinleyAdapterException("Error - Size of point elements is not supported.");          case ReducedContactElementsZero:
1424     break;          case ReducedContactElementsOne:
1425     case(ContactElementsZero):              Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1426     case(ContactElementsOne):              break;
1427     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);          case DegreesOfFreedom:
1428     break;              throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1429     case(ReducedContactElementsZero):              break;
1430     case(ReducedContactElementsOne):          case ReducedDegreesOfFreedom:
1431     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1432     break;              break;
1433     case(DegreesOfFreedom):          default:
1434     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");              stringstream temp;
1435     break;              temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1436     case(ReducedDegreesOfFreedom):              throw FinleyAdapterException(temp.str());
1437     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");              break;
1438     break;      }
1439     default:      checkFinleyError();
       stringstream temp;  
       temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1440  }  }
1441    
1442  // sets the location of nodes:  //
1443    // sets the location of nodes
1444    //
1445  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1446  {  {
1447     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1448     escriptDataC tmp;      const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1449     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());      if (newDomain!=*this)
1450     if (newDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of new point locations");
1451        throw FinleyAdapterException("Error - Illegal domain of new point locations");      if (new_x.getFunctionSpace() == continuousFunction(*this)) {
1452     tmp = new_x.getDataC();          Finley_Mesh_setCoordinates(mesh, new_x);
1453     Finley_Mesh_setCoordinates(mesh,&tmp);      } else {
1454     checkFinleyError();          throw FinleyAdapterException("As of escript version 3.3 SetX() only accepts ContinuousFunction arguments. Please interpolate.");
1455  }          //escript::Data new_x_inter=escript::Data(new_x, continuousFunction(*this));
1456            //Finley_Mesh_setCoordinates(mesh, new_x_inter);
1457  // saves a data array in openDX format:      }
1458  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const      checkFinleyError();
1459  {  }
1460     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;  
1461     const int num_data=boost::python::extract<int>(arg.attr("__len__")());  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1462     /* win32 refactor */  {
1463     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;      if (getMPISize() > 1) {
1464     for(int i=0;i<num_data;i++)  #ifdef ESYS_MPI
1465     {          index_t myFirstNode=0, myLastNode=0, k=0;
1466        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;          index_t* globalNodeIndex=0;
1467     }          Finley_Mesh* mesh_p=m_finleyMesh.get();
1468            /*
1469     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;           * this method is only used by saveDataCSV which would use the returned
1470     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;           * values for reduced nodes wrongly so this case is disabled for now
1471            if (fs_code == FINLEY_REDUCED_NODES) {
1472     boost::python::list keys=arg.keys();              myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1473     for (int i=0;i<num_data;++i) {              myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1474        std::string n=boost::python::extract<std::string>(keys[i]);              globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1475        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);          } else
1476        if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)          */
1477           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");          if (fs_code == FINLEY_NODES) {
1478        data[i]=d.getDataC();              myFirstNode = mesh_p->Nodes->getFirstNode();
1479        ptr_data[i]= &(data[i]);              myLastNode = mesh_p->Nodes->getLastNode();
1480        if (n.length()>MAX_namelength-1) {              globalNodeIndex = mesh_p->Nodes->borrowGlobalNodesIndex();
1481           strncpy(names[i],n.c_str(),MAX_namelength-1);          } else {
1482           names[i][MAX_namelength-1]='\0';              throw FinleyAdapterException("Unsupported function space type for ownSample()");
1483        } else {          }
1484           strcpy(names[i],n.c_str());  
1485        }          k=globalNodeIndex[id];
1486     }          return static_cast<bool>( (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 */  
1487  #endif  #endif
1488     }      }
1489     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);  
1490  }  }
1491  // creates a TransportProblemAdapter  
1492  TransportProblemAdapter MeshAdapter::newTransportProblem(  
1493                                                           const double theta,  //
1494                                                           const int blocksize,  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1495                                                           const escript::FunctionSpace& functionspace,  //
1496                                                           const int type) const  escript::ASM_ptr MeshAdapter::newSystemMatrix(const int row_blocksize,
1497  {                              const escript::FunctionSpace& row_functionspace,
1498     int reduceOrder=0;                              const int column_blocksize,
1499     // is the domain right?                              const escript::FunctionSpace& column_functionspace,
1500     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());                              const int type) const
1501     if (domain!=*this)  {
1502        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");      // is the domain right?
1503     // is the function space type right      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1504     if (functionspace.getTypeCode()==DegreesOfFreedom) {      if (row_domain!=*this)
1505        reduceOrder=0;          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1506     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1507        reduceOrder=1;      if (col_domain!=*this)
1508     } else {          throw FinleyAdapterException("Error - domain of column function space does not match the domain of matrix generator.");
1509        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");  
1510     }      int reduceRowOrder=0;
1511     // generate matrix:      int reduceColOrder=0;
1512        // is the function space type right?
1513     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);      if (row_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1514     checkFinleyError();          reduceRowOrder=1;
1515     Paso_FCTransportProblem* transportProblem;      } else if (row_functionspace.getTypeCode() != DegreesOfFreedom) {
1516     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1517     checkPasoError();      }
1518     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      if (column_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1519     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);          reduceColOrder=1;
1520        } else if (column_functionspace.getTypeCode() != DegreesOfFreedom) {
1521            throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1522        }
1523    
1524        // generate matrix:
1525        Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(
1526                getFinley_Mesh(), reduceRowOrder, reduceColOrder);
1527        checkFinleyError();
1528        Paso_SystemMatrix* fsystemMatrix;
1529        const int trilinos = 0;
1530        if (trilinos) {
1531    #ifdef TRILINOS
1532            // FIXME: Allocation Epetra_VrbMatrix here...
1533    #endif
1534        } else {
1535            fsystemMatrix=Paso_SystemMatrix_alloc(type, fsystemMatrixPattern,
1536                    row_blocksize, column_blocksize, FALSE);
1537        }
1538        checkPasoError();
1539        Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1540        SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1541        return escript::ASM_ptr(sma);
1542  }  }
1543    
1544  //  //
1545  // vtkObject MeshAdapter::createVtkObject() const  // creates a TransportProblemAdapter
 // TODO:  
1546  //  //
1547    escript::ATP_ptr MeshAdapter::newTransportProblem(const int blocksize,
1548            const escript::FunctionSpace& functionspace, const int type) const
1549    {
1550        // is the domain right?
1551        const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1552        if (domain!=*this)
1553            throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1554    
1555        // is the function space type right?
1556        int reduceOrder=0;
1557        if (functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1558            reduceOrder=1;
1559        } else if (functionspace.getTypeCode() != DegreesOfFreedom) {
1560            throw FinleyAdapterException("Error - illegal function space type for transport problem.");
1561        }
1562    
1563        // generate transport problem:
1564        Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(
1565                getFinley_Mesh(), reduceOrder, reduceOrder);
1566        checkFinleyError();
1567        Paso_TransportProblem* transportProblem;
1568        transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern, blocksize);
1569        checkPasoError();
1570        Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1571        TransportProblemAdapter* tpa=new TransportProblemAdapter(
1572                transportProblem, blocksize, functionspace);
1573        return escript::ATP_ptr(tpa);
1574    }
1575    
1576  //  //
1577  // 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
1578    //
1579  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1580  {  {
1581     switch(functionSpaceCode) {      switch(functionSpaceCode) {
1582     case(Nodes):          case Nodes:
1583     case(DegreesOfFreedom):          case DegreesOfFreedom:
1584     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1585     return false;              return false;
1586     break;          case Elements:
1587     case(Elements):          case FaceElements:
1588     case(FaceElements):          case Points:
1589     case(Points):          case ContactElementsZero:
1590     case(ContactElementsZero):          case ContactElementsOne:
1591     case(ContactElementsOne):          case ReducedElements:
1592     case(ReducedElements):          case ReducedFaceElements:
1593     case(ReducedFaceElements):          case ReducedContactElementsZero:
1594     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
1595     case(ReducedContactElementsOne):              return true;
1596     return true;          default:
1597     break;              stringstream temp;
1598     default:              temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1599        stringstream temp;              throw FinleyAdapterException(temp.str());
1600        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;              break;
1601        throw FinleyAdapterException(temp.str());      }
1602        break;      return false;
1603     }  }
1604     checkFinleyError();  
1605     return false;  bool
1606  }  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1607    {
1608  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const      /* The idea is to use equivalence classes. [Types which can be interpolated
1609  {         back and forth]:
1610     switch(functionSpaceType_source) {          class 1: DOF <-> Nodes
1611     case(Nodes):          class 2: ReducedDOF <-> ReducedNodes
1612     switch(functionSpaceType_target) {          class 3: Points
1613     case(Nodes):          class 4: Elements
1614     case(ReducedNodes):          class 5: ReducedElements
1615     case(ReducedDegreesOfFreedom):          class 6: FaceElements
1616     case(DegreesOfFreedom):          class 7: ReducedFaceElements
1617     case(Elements):          class 8: ContactElementZero <-> ContactElementOne
1618     case(ReducedElements):          class 9: ReducedContactElementZero <-> ReducedContactElementOne
1619     case(FaceElements):  
1620     case(ReducedFaceElements):      There is also a set of lines. Interpolation is possible down a line but
1621     case(Points):      not between lines.
1622     case(ContactElementsZero):      class 1 and 2 belong to all lines so aren't considered.
1623     case(ReducedContactElementsZero):          line 0: class 3
1624     case(ContactElementsOne):          line 1: class 4,5
1625     case(ReducedContactElementsOne):          line 2: class 6,7
1626     return true;          line 3: class 8,9
1627     default:  
1628        stringstream temp;      For classes with multiple members (eg class 2) we have vars to record if
1629        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      there is at least one instance.
1630        throw FinleyAdapterException(temp.str());      e.g. hasnodes is true if we have at least one instance of Nodes.
1631     }      */
1632     break;      if (fs.empty())
1633     case(ReducedNodes):          return false;
1634     switch(functionSpaceType_target) {  
1635     case(ReducedNodes):      vector<int> hasclass(10);
1636     case(ReducedDegreesOfFreedom):      vector<int> hasline(4);    
1637     case(Elements):      bool hasnodes=false;
1638     case(ReducedElements):      bool hasrednodes=false;
1639     case(FaceElements):      bool hascez=false;
1640     case(ReducedFaceElements):      bool hasrcez=false;
1641     case(Points):      for (int i=0;i<fs.size();++i) {
1642     case(ContactElementsZero):          switch(fs[i]) {
1643     case(ReducedContactElementsZero):              case Nodes:
1644     case(ContactElementsOne):                  hasnodes=true; // fall through
1645     case(ReducedContactElementsOne):              case DegreesOfFreedom:
1646     return true;                  hasclass[1]=1;
1647     case(Nodes):                  break;
1648     case(DegreesOfFreedom):              case ReducedNodes:
1649     return false;                  hasrednodes=true; // fall through
1650     default:              case ReducedDegreesOfFreedom:
1651        stringstream temp;                  hasclass[2]=1;
1652        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                  break;
1653        throw FinleyAdapterException(temp.str());              case Points:
1654     }                  hasline[0]=1;
1655     break;                  hasclass[3]=1;
1656     case(Elements):                  break;
1657     if (functionSpaceType_target==Elements) {              case Elements:
1658        return true;                  hasclass[4]=1;
1659     } else if (functionSpaceType_target==ReducedElements) {                  hasline[1]=1;
1660        return true;                  break;
1661     } else {              case ReducedElements:
1662        return false;                  hasclass[5]=1;
1663     }                  hasline[1]=1;
1664     case(ReducedElements):                  break;
1665     if (functionSpaceType_target==ReducedElements) {              case FaceElements:
1666        return true;                  hasclass[6]=1;
1667     } else {                  hasline[2]=1;
1668        return false;                  break;
1669     }              case ReducedFaceElements:
1670     case(FaceElements):                  hasclass[7]=1;
1671     if (functionSpaceType_target==FaceElements) {                  hasline[2]=1;
1672        return true;                  break;
1673     } else if (functionSpaceType_target==ReducedFaceElements) {              case ContactElementsZero:
1674        return true;                  hascez=true; // fall through
1675     } else {              case ContactElementsOne:
1676        return false;                  hasclass[8]=1;
1677     }                  hasline[3]=1;
1678     case(ReducedFaceElements):                  break;
1679     if (functionSpaceType_target==ReducedFaceElements) {              case ReducedContactElementsZero:
1680        return true;                  hasrcez=true; // fall through
1681     } else {              case ReducedContactElementsOne:
1682        return false;                  hasclass[9]=1;
1683     }                  hasline[3]=1;
1684     case(Points):                  break;
1685     if (functionSpaceType_target==Points) {              default:
1686        return true;                  return false;
1687     } else {          }
1688        return false;      }
1689     }      int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1690     case(ContactElementsZero):  
1691     case(ContactElementsOne):      // fail if we have more than one leaf group
1692     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {      if (totlines>1)
1693        return true;          return false; // there are at least two branches we can't interpolate between
1694     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {      else if (totlines==1) {
1695        return true;          if (hasline[0]==1)              // we have points
1696     } else {              resultcode=Points;
1697        return false;          else if (hasline[1]==1) {
1698     }              if (hasclass[5]==1)
1699     case(ReducedContactElementsZero):                  resultcode=ReducedElements;
1700     case(ReducedContactElementsOne):              else
1701     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {                  resultcode=Elements;
1702        return true;          } else if (hasline[2]==1) {
1703     } else {              if (hasclass[7]==1)
1704        return false;                  resultcode=ReducedFaceElements;
1705     }              else
1706     case(DegreesOfFreedom):                  resultcode=FaceElements;
1707     switch(functionSpaceType_target) {          } else {   // so we must be in line3
1708     case(ReducedDegreesOfFreedom):              if (hasclass[9]==1) {
1709     case(DegreesOfFreedom):                  // need something from class 9
1710     case(Nodes):                  resultcode=(hasrcez ? ReducedContactElementsZero : ReducedContactElementsOne);
1711     case(ReducedNodes):              } else {
1712     case(Elements):                  // something from class 8
1713     case(ReducedElements):                  resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1714     case(Points):              }
1715     case(FaceElements):          }
1716     case(ReducedFaceElements):      } else { // totlines==0
1717     case(ContactElementsZero):          if (hasclass[2]==1) {
1718     case(ReducedContactElementsZero):              // something from class 2
1719     case(ContactElementsOne):              resultcode=(hasrednodes ? ReducedNodes : ReducedDegreesOfFreedom);
1720     case(ReducedContactElementsOne):          } else {
1721     return true;              // something from class 1
1722     default:              resultcode=(hasnodes ? Nodes : DegreesOfFreedom);
1723        stringstream temp;          }
1724        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      }
1725        throw FinleyAdapterException(temp.str());      return true;
1726     }  }
1727     break;  
1728     case(ReducedDegreesOfFreedom):  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,
1729     switch(functionSpaceType_target) {                                               int functionSpaceType_target) const
1730     case(ReducedDegreesOfFreedom):  {
1731     case(ReducedNodes):      switch(functionSpaceType_source) {
1732     case(Elements):          case Nodes:
1733     case(ReducedElements):              switch(functionSpaceType_target) {
1734     case(FaceElements):                  case Nodes:
1735     case(ReducedFaceElements):                  case ReducedNodes:
1736     case(Points):                  case ReducedDegreesOfFreedom:
1737     case(ContactElementsZero):                  case DegreesOfFreedom:
1738     case(ReducedContactElementsZero):                  case Elements:
1739     case(ContactElementsOne):                  case ReducedElements:
1740     case(ReducedContactElementsOne):                  case FaceElements:
1741     return true;                  case ReducedFaceElements:
1742     case(Nodes):                  case Points:
1743     case(DegreesOfFreedom):                  case ContactElementsZero:
1744     return false;                  case ReducedContactElementsZero:
1745     default:                  case ContactElementsOne:
1746        stringstream temp;                  case ReducedContactElementsOne:
1747        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      return true;
1748        throw FinleyAdapterException(temp.str());                  default:
1749     }                      stringstream temp;
1750     break;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1751     default:                      throw FinleyAdapterException(temp.str());
1752        stringstream temp;              }
1753        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;              break;
1754        throw FinleyAdapterException(temp.str());          case ReducedNodes:
1755        break;              switch(functionSpaceType_target) {
1756     }                  case ReducedNodes:
1757     checkFinleyError();                  case ReducedDegreesOfFreedom:
1758     return false;                  case Elements:
1759  }                  case ReducedElements:
1760                    case FaceElements:
1761  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const                  case ReducedFaceElements:
1762  {                  case Points:
1763     return false;                  case ContactElementsZero:
1764  }                  case ReducedContactElementsZero:
1765                    case ContactElementsOne:
1766  bool MeshAdapter::operator==(const AbstractDomain& other) const                  case ReducedContactElementsOne:
1767  {                      return true;
1768     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);                  case Nodes:
1769     if (temp!=0) {                  case DegreesOfFreedom:
1770        return (m_finleyMesh==temp->m_finleyMesh);                      return false;
1771     } else {                  default:
1772        return false;                      stringstream temp;
1773     }                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1774                        throw FinleyAdapterException(temp.str());
1775                }
1776                break;
1777            case Elements:
1778                if (functionSpaceType_target==Elements) {
1779                    return true;
1780                } else if (functionSpaceType_target==ReducedElements) {
1781                    return true;
1782                } else {
1783                    return false;
1784                }
1785            case ReducedElements:
1786                if (functionSpaceType_target==ReducedElements) {
1787                    return true;
1788                } else {
1789                    return false;
1790                }
1791            case FaceElements:
1792                if (functionSpaceType_target==FaceElements) {
1793                    return true;
1794                } else if (functionSpaceType_target==ReducedFaceElements) {
1795                    return true;
1796                } else {
1797                    return false;
1798                }
1799            case ReducedFaceElements:
1800                if (functionSpaceType_target==ReducedFaceElements) {
1801                    return true;
1802                } else {
1803                    return false;
1804                }
1805            case Points:
1806                if (functionSpaceType_target==Points) {
1807                    return true;
1808                } else {
1809                    return false;
1810                }
1811            case ContactElementsZero:
1812            case ContactElementsOne:
1813                if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1814                    return true;
1815                } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1816                    return true;
1817                } else {
1818                    return false;
1819                }
1820            case ReducedContactElementsZero:
1821            case ReducedContactElementsOne:
1822                if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1823                    return true;
1824                } else {
1825                    return false;
1826                }
1827            case DegreesOfFreedom:
1828                switch(functionSpaceType_target) {
1829                    case ReducedDegreesOfFreedom:
1830                    case DegreesOfFreedom:
1831                    case Nodes:
1832                    case ReducedNodes:
1833                    case Elements:
1834                    case ReducedElements:
1835                    case Points:
1836                    case FaceElements:
1837                    case ReducedFaceElements:
1838                    case ContactElementsZero:
1839                    case ReducedContactElementsZero:
1840                    case ContactElementsOne:
1841                    case ReducedContactElementsOne:
1842                        return true;
1843                    default:
1844                        stringstream temp;
1845                        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1846                        throw FinleyAdapterException(temp.str());
1847                }
1848                break;
1849            case ReducedDegreesOfFreedom:
1850                switch(functionSpaceType_target) {
1851                    case ReducedDegreesOfFreedom:
1852                    case ReducedNodes:
1853                    case Elements:
1854                    case ReducedElements:
1855                    case FaceElements:
1856                    case ReducedFaceElements:
1857                    case Points:
1858                    case ContactElementsZero:
1859                    case ReducedContactElementsZero:
1860                    case ContactElementsOne:
1861                    case ReducedContactElementsOne:
1862                        return true;
1863                    case Nodes:
1864                    case DegreesOfFreedom:
1865                        return false;
1866                    default:
1867                        stringstream temp;
1868                        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1869                        throw FinleyAdapterException(temp.str());
1870                }
1871                break;
1872            default:
1873                stringstream temp;
1874                temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1875                throw FinleyAdapterException(temp.str());
1876                break;
1877        }
1878        return false;
1879    }
1880    
1881    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
1882    {
1883        if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1884            return 1;
1885    
1886        if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1887            return -1;
1888    
1889        return 0;
1890    }
1891    
1892    bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,
1893            const escript::AbstractDomain& targetDomain,
1894            int functionSpaceType_target) const
1895    {
1896        return false;
1897    }
1898    
1899    bool MeshAdapter::operator==(const escript::AbstractDomain& other) const
1900    {
1901        const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1902        if (temp) {
1903            return (m_finleyMesh==temp->m_finleyMesh);
1904        } else {
1905            return false;
1906        }
1907  }  }
1908    
1909  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const escript::AbstractDomain& other) const
1910  {  {
1911     return !(operator==(other));      return !(operator==(other));
1912  }  }
1913    
1914  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
1915  {  {
1916     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);      Finley_Mesh* mesh=m_finleyMesh.get();
1917     checkPasoError();      return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
1918     return out;                 package, symmetry, mesh->MPIInfo);
1919  }  }
1920    
1921  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
1922  {  {
1923     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);      Finley_Mesh* mesh=m_finleyMesh.get();
1924     checkPasoError();      return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
1925     return out;                  package, symmetry, mesh->MPIInfo);
1926  }  }
1927    
1928  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1929  {  {
1930     return continuousFunction(asAbstractContinuousDomain()).getX();      return continuousFunction(*this).getX();
1931  }  }
1932    
1933  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1934  {  {
1935     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();      return functionOnBoundary(*this).getNormal();
1936  }  }
1937    
1938  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1939  {  {
1940     return function(asAbstractContinuousDomain()).getSize();      return escript::function(*this).getSize();
1941  }  }
1942    
1943  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1944  {  {
1945     int *out = NULL;      int *out = NULL;
1946     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1947     switch (functionSpaceType) {      switch (functionSpaceType) {
1948     case(Nodes):          case Nodes:
1949     out=mesh->Nodes->Id;              out=mesh->Nodes->Id;
1950     break;              break;
1951     case(ReducedNodes):          case ReducedNodes:
1952     out=mesh->Nodes->reducedNodesId;              out=mesh->Nodes->reducedNodesId;
1953     break;              break;
1954     case(Elements):          case Elements:
1955     out=mesh->Elements->Id;          case ReducedElements:
1956     break;              out=mesh->Elements->Id;
1957     case(ReducedElements):              break;
1958     out=mesh->Elements->Id;          case FaceElements:
1959     break;          case ReducedFaceElements:
1960     case(FaceElements):              out=mesh->FaceElements->Id;
1961     out=mesh->FaceElements->Id;              break;
1962     break;          case Points:
1963     case(ReducedFaceElements):              out=mesh->Points->Id;
1964     out=mesh->FaceElements->Id;              break;
1965     break;          case ContactElementsZero:
1966     case(Points):          case ReducedContactElementsZero:
1967     out=mesh->Points->Id;          case ContactElementsOne:
1968     break;          case ReducedContactElementsOne:
1969     case(ContactElementsZero):              out=mesh->ContactElements->Id;
1970     out=mesh->ContactElements->Id;              break;
1971     break;          case DegreesOfFreedom:
1972     case(ReducedContactElementsZero):              out=mesh->Nodes->degreesOfFreedomId;
1973     out=mesh->ContactElements->Id;              break;
1974     break;          case ReducedDegreesOfFreedom:
1975     case(ContactElementsOne):              out=mesh->Nodes->reducedDegreesOfFreedomId;
1976     out=mesh->ContactElements->Id;              break;
1977     break;          default:
1978     case(ReducedContactElementsOne):              stringstream temp;
1979     out=mesh->ContactElements->Id;              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1980     break;              throw FinleyAdapterException(temp.str());
1981     case(DegreesOfFreedom):              break;
1982     out=mesh->Nodes->degreesOfFreedomId;      }
1983     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;  
1984  }  }
1985  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1986  {  {
1987     int out=0;      int out=0;
1988     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1989     switch (functionSpaceType) {      switch (functionSpaceType) {
1990     case(Nodes):          case Nodes:
1991     out=mesh->Nodes->Tag[sampleNo];              out=mesh->Nodes->Tag[sampleNo];
1992     break;              break;
1993     case(ReducedNodes):          case ReducedNodes:
1994     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");              throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1995     break;              break;
1996     case(Elements):          case Elements:
1997     out=mesh->Elements->Tag[sampleNo];          case ReducedElements:
1998     break;              out=mesh->Elements->Tag[sampleNo];
1999     case(ReducedElements):              break;
2000     out=mesh->Elements->Tag[sampleNo];          case FaceElements:
2001     break;          case ReducedFaceElements:
2002     case(FaceElements):              out=mesh->FaceElements->Tag[sampleNo];
2003     out=mesh->FaceElements->Tag[sampleNo];              break;
2004     break;          case Points:
2005     case(ReducedFaceElements):              out=mesh->Points->Tag[sampleNo];
2006     out=mesh->FaceElements->Tag[sampleNo];              break;
2007     break;          case ContactElementsZero:
2008     case(Points):          case ReducedContactElementsZero:
2009     out=mesh->Points->Tag[sampleNo];          case ContactElementsOne:
2010     break;          case ReducedContactElementsOne:
2011     case(ContactElementsZero):              out=mesh->ContactElements->Tag[sampleNo];
2012     out=mesh->ContactElements->Tag[sampleNo];              break;
2013     break;          case DegreesOfFreedom:
2014     case(ReducedContactElementsZero):              throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2015     out=mesh->ContactElements->Tag[sampleNo];              break;
2016     break;          case ReducedDegreesOfFreedom:
2017     case(ContactElementsOne):              throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2018     out=mesh->ContactElements->Tag[sampleNo];              break;
2019     break;          default:
2020     case(ReducedContactElementsOne):              stringstream temp;
2021     out=mesh->ContactElements->Tag[sampleNo];              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2022     break;              throw FinleyAdapterException(temp.str());
2023     case(DegreesOfFreedom):              break;
2024     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");      }
2025     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;  
2026  }  }
2027    
2028    
2029  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
2030  {  {
2031     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2032     escriptDataC tmp=mask.getDataC();      escriptDataC tmp=mask.getDataC();
2033     switch(functionSpaceType) {      switch(functionSpaceType) {
2034     case(Nodes):          case Nodes:
2035     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);              mesh->Nodes->setTags(newTag, mask);
2036     break;              break;
2037     case(ReducedNodes):          case ReducedNodes:
2038     throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2039     break;              break;
2040     case(DegreesOfFreedom):          case DegreesOfFreedom:
2041     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2042     break;              break;
2043     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
2044     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2045     break;              break;
2046     case(Elements):          case Elements:
2047     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case ReducedElements:
2048     break;              Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2049     case(ReducedElements):              break;
2050     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case FaceElements:
2051     break;          case ReducedFaceElements:
2052     case(FaceElements):              Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2053     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);              break;
2054     break;          case Points:
2055     case(ReducedFaceElements):              Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2056     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);              break;
2057     break;          case ContactElementsZero:
2058     case(Points):          case ReducedContactElementsZero:
2059     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);          case ContactElementsOne:
2060     break;          case ReducedContactElementsOne:
2061     case(ContactElementsZero):              Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2062     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              break;
2063     break;          default:
2064     case(ReducedContactElementsZero):              stringstream temp;
2065     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2066     break;              throw FinleyAdapterException(temp.str());
2067     case(ContactElementsOne):      }
2068     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);      checkFinleyError();
2069     break;  }
2070     case(ReducedContactElementsOne):  
2071     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  void MeshAdapter::setTagMap(const string& name, int tag)
2072     break;  {
2073     default:      Finley_Mesh* mesh=m_finleyMesh.get();
2074        stringstream temp;      Finley_Mesh_addTagMap(mesh, name.c_str(), tag);
2075        temp << "Error - Finley does not know anything about function space type " << functionSpaceType;      checkFinleyError();
2076        throw FinleyAdapterException(temp.str());  }
2077     }  
2078     checkFinleyError();  int MeshAdapter::getTag(const string& name) const
2079     return;  {
2080  }      Finley_Mesh* mesh=m_finleyMesh.get();
2081        int tag = Finley_Mesh_getTag(mesh, name.c_str());
2082  void MeshAdapter::setTagMap(const std::string& name,  int tag)      checkFinleyError();
2083  {      return tag;
2084     Finley_Mesh* mesh=m_finleyMesh.get();  }
2085     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);  
2086     checkPasoError();  bool MeshAdapter::isValidTagName(const string& name) const
2087     // throwStandardException("MeshAdapter::set TagMap is not implemented.");  {
2088  }      Finley_Mesh* mesh=m_finleyMesh.get();
2089        return Finley_Mesh_isValidTagName(mesh, name.c_str());
2090  int MeshAdapter::getTag(const std::string& name) const  }
2091  {  
2092     Finley_Mesh* mesh=m_finleyMesh.get();  string MeshAdapter::showTagNames() const
2093     int tag=0;  {
2094     tag=Finley_Mesh_getTag(mesh, name.c_str());      stringstream temp;
2095     checkPasoError();      Finley_Mesh* mesh=m_finleyMesh.get();
2096     // throwStandardException("MeshAdapter::getTag is not implemented.");      Finley_TagMap* tag_map=mesh->TagMap;
2097     return tag;      while (tag_map) {
2098  }          temp << tag_map->name;
2099            tag_map=tag_map->next;
2100  bool MeshAdapter::isValidTagName(const std::string& name) const          if (tag_map) temp << ", ";
2101  {      }
2102     Finley_Mesh* mesh=m_finleyMesh.get();      return temp.str();
    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();  
2103  }  }
2104    
2105  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2106  {  {
2107    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2108    dim_t numTags=0;      switch(functionSpaceCode) {
2109    switch(functionSpaceCode) {          case Nodes:
2110     case(Nodes):              return mesh->Nodes->tagsInUse.size();
2111            numTags=mesh->Nodes->numTagsInUse;          case ReducedNodes:
2112            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2113     case(ReducedNodes):          case DegreesOfFreedom:
2114            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2115            break;          case ReducedDegreesOfFreedom:
2116     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2117            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2118            break;          case ReducedElements:
2119     case(ReducedDegreesOfFreedom):              return mesh->Elements->tagsInUse.size();
2120            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2121            break;          case ReducedFaceElements:
2122     case(Elements):              return mesh->FaceElements->tagsInUse.size();
2123     case(ReducedElements):          case Points:
2124            numTags=mesh->Elements->numTagsInUse;              return mesh->Points->tagsInUse.size();
2125            break;          case ContactElementsZero:
2126     case(FaceElements):          case ReducedContactElementsZero:
2127     case(ReducedFaceElements):          case ContactElementsOne:
2128            numTags=mesh->FaceElements->numTagsInUse;          case ReducedContactElementsOne:
2129            break;              return mesh->ContactElements->tagsInUse.size();
2130     case(Points):          default:
2131            numTags=mesh->Points->numTagsInUse;              stringstream ss;
2132            break;              ss << "Finley does not know anything about function space type "
2133     case(ContactElementsZero):                   << functionSpaceCode;
2134     case(ReducedContactElementsZero):              throw FinleyAdapterException(ss.str());
2135     case(ContactElementsOne):      }
2136     case(ReducedContactElementsOne):      return 0;
2137            numTags=mesh->ContactElements->numTagsInUse;  }
2138            break;  
2139     default:  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2140        stringstream temp;  {
2141        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;      Finley_Mesh* mesh=m_finleyMesh.get();
2142        throw FinleyAdapterException(temp.str());      switch(functionSpaceCode) {
2143    }          case Nodes:
2144    return numTags;              return &mesh->Nodes->tagsInUse[0];
2145  }          case ReducedNodes:
2146  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2147  {          case DegreesOfFreedom:
2148    Finley_Mesh* mesh=m_finleyMesh.get();              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2149    index_t* tags=NULL;          case ReducedDegreesOfFreedom:
2150    switch(functionSpaceCode) {              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2151     case(Nodes):          case Elements:
2152            tags=mesh->Nodes->tagsInUse;          case ReducedElements:
2153            break;              return &mesh->Elements->tagsInUse[0];
2154     case(ReducedNodes):          case FaceElements:
2155            throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case ReducedFaceElements:
2156            break;              return &mesh->FaceElements->tagsInUse[0];
2157     case(DegreesOfFreedom):          case Points:
2158            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              return &mesh->Points->tagsInUse[0];
2159            break;          case ContactElementsZero:
2160     case(ReducedDegreesOfFreedom):          case ReducedContactElementsZero:
2161            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case ContactElementsOne:
2162            break;          case ReducedContactElementsOne:
2163     case(Elements):              return &mesh->ContactElements->tagsInUse[0];
2164     case(ReducedElements):          default:
2165            tags=mesh->Elements->tagsInUse;              stringstream temp;
2166            break;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2167     case(FaceElements):              throw FinleyAdapterException(temp.str());
2168     case(ReducedFaceElements):      }
2169            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;  
2170  }  }
2171    
2172    
2173  bool MeshAdapter::canTag(int functionSpaceCode) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2174  {  {
2175    switch(functionSpaceCode) {      switch(functionSpaceCode) {
2176     case(Nodes):          case Nodes:
2177     case(Elements):          case Elements:
2178     case(ReducedElements):          case ReducedElements:
2179     case(FaceElements):          case FaceElements:
2180     case(ReducedFaceElements):          case ReducedFaceElements:
2181     case(Points):          case Points:
2182     case(ContactElementsZero):          case ContactElementsZero:
2183     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
2184     case(ContactElementsOne):          case ContactElementsOne:
2185     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
2186            return true;              return true;
2187     case(ReducedNodes):          default:
2188     case(DegreesOfFreedom):              return false;
2189     case(ReducedDegreesOfFreedom):      }
2190        return false;  }
2191     default:  
2192      return false;  escript::AbstractDomain::StatusType MeshAdapter::getStatus() const
2193    }  {
2194        Finley_Mesh* mesh=m_finleyMesh.get();
2195        return Finley_Mesh_getStatus(mesh);
2196    }
2197    
2198    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2199    {
2200        Finley_Mesh* mesh=m_finleyMesh.get();
2201        int order =-1;
2202        switch(functionSpaceCode) {
2203            case Nodes:
2204            case DegreesOfFreedom:
2205                order=mesh->approximationOrder;
2206                break;
2207            case ReducedNodes:
2208            case ReducedDegreesOfFreedom:
2209                order=mesh->reducedApproximationOrder;
2210                break;
2211            case Elements:
2212            case FaceElements:
2213            case Points:
2214            case ContactElementsZero:
2215            case ContactElementsOne:
2216                order=mesh->integrationOrder;
2217                break;
2218            case ReducedElements:
2219            case ReducedFaceElements:
2220            case ReducedContactElementsZero:
2221            case ReducedContactElementsOne:
2222                order=mesh->reducedIntegrationOrder;
2223                break;
2224            default:
2225                stringstream temp;
2226                temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2227                throw FinleyAdapterException(temp.str());
2228        }
2229        return order;
2230    }
2231    
2232    bool MeshAdapter::supportsContactElements() const
2233    {
2234        return true;
2235    }
2236    
2237    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id,
2238            index_t order, index_t reducedOrder)
2239    {
2240        m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2241    }
2242    
2243    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2244    {
2245        Finley_ReferenceElementSet_dealloc(m_refSet);
2246    }
2247    
2248    void MeshAdapter::addDiracPoints(const vector<double>& points,
2249                                     const vector<int>& tags) const
2250    {
2251        // points will be flattened
2252        const int dim = getDim();
2253        int numPoints=points.size()/dim;
2254        int numTags=tags.size();
2255        Finley_Mesh* mesh=m_finleyMesh.get();
2256    
2257        if ( points.size() % dim != 0 ) {
2258            throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2259        }
2260    
2261        if ((numTags > 0) && (numPoints != numTags))
2262            throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2263    
2264        Finley_Mesh_addPoints(mesh, numPoints, &points[0], &tags[0]);
2265        checkFinleyError();
2266    }
2267    
2268    // void MeshAdapter::addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2269    // {
2270    //       const int dim = getDim();
2271    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2272    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2273    //       Finley_Mesh* mesh=m_finleyMesh.get();
2274    //
2275    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2276    //       throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2277    //
2278    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2279    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2280    //
2281    //       for (int i=0;i<numPoints;++i) {
2282    //         int tag_id=-1;
2283    //         int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2284    //         if  ( numComps !=   dim ) {
2285    //                stringstream temp;
2286    //                temp << "Error - illegal number of components " << numComps << " for point " << i;
2287    //                throw FinleyAdapterException(temp.str());
2288    //         }
2289    //         points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2290    //         if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2291    //         if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2292    //
2293    //         if ( numTags > 0) {
2294    //                boost::python::extract<string> ex_str(tags[i]);
2295    //                if  ( ex_str.check() ) {
2296    //                    tag_id=getTag( ex_str());
2297    //                } else {
2298    //                     boost::python::extract<int> ex_int(tags[i]);
2299    //                     if ( ex_int.check() ) {
2300    //                         tag_id=ex_int();
2301    //                     } else {
2302    //                          stringstream temp;
2303    //                          temp << "Error - unable to extract tag for point " << i;
2304    //                          throw FinleyAdapterException(temp.str());
2305    //                    }
2306    //                }
2307    //         }
2308    //            tags_ptr[i]=tag_id;
2309    //       }
2310    //
2311    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2312    //       checkPasoError();
2313    //
2314    //       TMPMEMFREE(points_ptr);
2315    //       TMPMEMFREE(tags_ptr);
2316    // }
2317    
2318    /*
2319    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2320    {
2321        boost::python::list points =  boost::python::list();
2322        boost::python::list tags =  boost::python::list();
2323        points.append(point);
2324        tags.append(tag);
2325        addDiracPoints(points, tags);
2326    }
2327    */
2328    
2329    /*
2330    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const string& tag) const
2331    {
2332        boost::python::list points =   boost::python::list();
2333        boost::python::list tags =   boost::python::list();
2334        points.append(point);
2335        tags.append(tag);
2336        addDiracPoints(points, tags);
2337  }  }
2338    */
   
2339  }  // end of namespace  }  // end of namespace
2340    

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