/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 2635 by jfenwick, Thu Aug 27 04:54:41 2009 UTC revision 4800 by caltinay, Wed Mar 26 01:50:04 2014 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*****************************************************************************
3  *  *
4  * Copyright (c) 2003-2009 by University of Queensland  * Copyright (c) 2003-2014 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 2012-2013 by School of Earth Sciences
13    * Development from 2014 by Centre for Geoscience Computing (GeoComp)
14    *
15    *****************************************************************************/
16    
17    #include <pasowrap/PasoException.h>
18    #include <pasowrap/TransportProblemAdapter.h>
19  #include "MeshAdapter.h"  #include "MeshAdapter.h"
20  #include "escript/Data.h"  #include "escript/Data.h"
21  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
22    #include "esysUtils/blocktimer.h"
23    #include "esysUtils/EsysRandom.h"
24    
25    #include <boost/python/import.hpp>
26  #ifdef USE_NETCDF  #ifdef USE_NETCDF
27  #include <netcdfcpp.h>  #include <netcdfcpp.h>
28  #endif  #endif
 #ifdef PASO_MPI  
 #include <mpi.h>  
 #include "paso/Paso_MPI.h"  
 #endif  
 extern "C" {  
 #include "esysUtils/blocktimer.h"  
 }  
29    
30  using namespace std;  using namespace std;
31  using namespace escript;  using namespace paso;
32    
33  namespace finley {  namespace finley {
34    
 //  
35  // define the static constants  // define the static constants
36  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
37  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
# Line 48  const int MeshAdapter::ReducedContactEle Line 48  const int MeshAdapter::ReducedContactEle
48  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
49  const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;  const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
50    
51  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Mesh* finleyMesh)
52  {  {
53     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
54     //      // need to use a null_deleter as Finley_Mesh_free deletes the pointer
55     // need to use a null_deleter as Finley_Mesh_free deletes the pointer      // for us.
56     // for us.      m_finleyMesh.reset(finleyMesh, null_deleter());
    m_finleyMesh.reset(finleyMesh,null_deleter());  
57  }  }
58    
59  //  //
60  // The copy constructor should just increment the use count  // The copy constructor should just increment the use count
61  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in) :
62  m_finleyMesh(in.m_finleyMesh)      m_finleyMesh(in.m_finleyMesh)
63  {  {
64     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
65  }  }
66    
67  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
68  {  {
69     //      // I hope the case for the pointer being zero has been taken care of
70     // I hope the case for the pointer being zero has been taken care of.      if (m_finleyMesh.unique()) {
71     //  cout << "In MeshAdapter destructor." << endl;          delete m_finleyMesh.get();
72     if (m_finleyMesh.unique()) {      }
       Finley_Mesh_free(m_finleyMesh.get());  
    }  
73  }  }
74    
75  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
76  {  {
77     return m_finleyMesh.get()->MPIInfo->size;      return m_finleyMesh.get()->MPIInfo->size;
78  }  }
79    
80  int MeshAdapter::getMPIRank() const  int MeshAdapter::getMPIRank() const
81  {  {
82     return m_finleyMesh.get()->MPIInfo->rank;      return m_finleyMesh.get()->MPIInfo->rank;
83  }  }
84    
85  void MeshAdapter::MPIBarrier() const  void MeshAdapter::MPIBarrier() const
86  {  {
87  #ifdef PASO_MPI  #ifdef ESYS_MPI
88     MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);      MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
89  #endif  #endif
    return;  
90  }  }
91    
92  bool MeshAdapter::onMasterProcessor() const  bool MeshAdapter::onMasterProcessor() const
93  {  {
94     return m_finleyMesh.get()->MPIInfo->rank == 0;      return m_finleyMesh.get()->MPIInfo->rank == 0;
95  }  }
96    
97    #ifdef ESYS_MPI
98    MPI_Comm
99    #else
100    unsigned int
101    #endif
102    MeshAdapter::getMPIComm() const
103    {
104    #ifdef ESYS_MPI
105        return m_finleyMesh->MPIInfo->comm;
106    #else
107        return 0;
108    #endif
109    }
110    
111  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Mesh* MeshAdapter::getFinley_Mesh() const
112     return m_finleyMesh.get();  {
113        return m_finleyMesh.get();
114  }  }
115    
116  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
117  {  {
118     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;      m_finleyMesh.get()->write(fileName);
119     strcpy(fName,fileName.c_str());      checkFinleyError();
    Finley_Mesh_write(m_finleyMesh.get(),fName);  
    checkFinleyError();  
    TMPMEMFREE(fName);  
120  }  }
121    
122  void MeshAdapter::Print_Mesh_Info(const bool full) const  void MeshAdapter::Print_Mesh_Info(const bool full) const
123  {  {
124     Finley_PrintMesh_Info(m_finleyMesh.get(), full);      m_finleyMesh.get()->printInfo(full);
125  }  }
126    
127  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const string& fileName) const
128  {  {
129  #ifdef USE_NETCDF  #ifdef USE_NETCDF
130     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};      const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
131     NcVar *ids;      NcVar *ids;
132     int *int_ptr;      int *int_ptr;
133     Finley_Mesh *mesh = m_finleyMesh.get();      Mesh *mesh = m_finleyMesh.get();
134     Finley_TagMap* tag_map;      int num_Tags = 0;
135     int num_Tags = 0;      int mpi_size                         = mesh->MPIInfo->size;
136     int mpi_size             = mesh->MPIInfo->size;      int mpi_rank                         = mesh->MPIInfo->rank;
137     int mpi_rank             = mesh->MPIInfo->rank;      int numDim                           = mesh->Nodes->numDim;
138     int numDim               = mesh->Nodes->numDim;      int numNodes                         = mesh->Nodes->numNodes;
139     int numNodes             = mesh->Nodes->numNodes;      int num_Elements                     = mesh->Elements->numElements;
140     int num_Elements         = mesh->Elements->numElements;      int num_FaceElements                 = mesh->FaceElements->numElements;
141     int num_FaceElements         = mesh->FaceElements->numElements;      int num_ContactElements              = mesh->ContactElements->numElements;
142     int num_ContactElements      = mesh->ContactElements->numElements;      int num_Points                       = mesh->Points->numElements;
143     int num_Points           = mesh->Points->numElements;      int num_Elements_numNodes            = mesh->Elements->numNodes;
144     int num_Elements_numNodes        = mesh->Elements->numNodes;      int num_FaceElements_numNodes        = mesh->FaceElements->numNodes;
145     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;      int num_ContactElements_numNodes     = mesh->ContactElements->numNodes;
146     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;  #ifdef ESYS_MPI
147  #ifdef PASO_MPI      MPI_Status status;
    MPI_Status status;  
148  #endif  #endif
149    
150  /* Incoming token indicates it's my turn to write */  /* Incoming token indicates it's my turn to write */
151  #ifdef PASO_MPI  #ifdef ESYS_MPI
152     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);      if (mpi_rank>0) {
153            MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
154        }
155  #endif  #endif
156    
157     char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),      const std::string newFileName(esysUtils::appendRankToFileName(fileName,
158                                                       mpi_size, mpi_rank);                                                       mpi_size, mpi_rank));
159    
160     /* Figure out how much storage is required for tags */      // Figure out how much storage is required for tags
161     tag_map = mesh->TagMap;      num_Tags = mesh->tagMap.size();
162     num_Tags = 0;  
163     if (tag_map) {      // NetCDF error handler
164        while (tag_map) {      NcError err(NcError::verbose_nonfatal);
165           num_Tags++;      // Create the file.
166           tag_map=tag_map->next;      NcFile dataFile(newFileName.c_str(), NcFile::Replace);
167        }      string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
168     }      // check if writing was successful
169        if (!dataFile.is_valid())
170     // NetCDF error handler          throw FinleyAdapterException(msgPrefix+"Open file for output");
171     NcError err(NcError::verbose_nonfatal);  
172     // Create the file.      // Define dimensions (num_Elements and dim_Elements are identical,
173     NcFile dataFile(newFileName, NcFile::Replace);      // dim_Elements only appears if > 0)
174     // check if writing was successful      if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
175     if (!dataFile.is_valid())          throw FinleyAdapterException(msgPrefix+"add_dim(numNodes)");
176        throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);      if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
177            throw FinleyAdapterException(msgPrefix+"add_dim(numDim)");
178     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)      if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
179     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )          throw FinleyAdapterException(msgPrefix+"add_dim(mpi_size)");
180        throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);      if (num_Elements>0)
181     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
182        throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements)");
183     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )      if (num_FaceElements>0)
184        throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
185     if (num_Elements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements)");
186        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )      if (num_ContactElements>0)
187           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
188     if (num_FaceElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements)");
189        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )      if (num_Points>0)
190           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
191     if (num_ContactElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Points)");
192        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )      if (num_Elements>0)
193           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
194     if (num_Points>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements_Nodes)");
195        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )      if (num_FaceElements>0)
196           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
197     if (num_Elements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
198        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )      if (num_ContactElements>0)
199           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
200     if (num_FaceElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
201        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )      if (num_Tags>0)
202           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
203     if (num_ContactElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Tags)");
204        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )  
205           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);      // Attributes: MPI size, MPI rank, Name, order, reduced_order
206     if (num_Tags>0)      if (!dataFile.add_att("mpi_size", mpi_size))
207        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )          throw FinleyAdapterException(msgPrefix+"add_att(mpi_size)");
208           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);      if (!dataFile.add_att("mpi_rank", mpi_rank))
209            throw FinleyAdapterException(msgPrefix+"add_att(mpi_rank)");
210     // Attributes: MPI size, MPI rank, Name, order, reduced_order      if (!dataFile.add_att("Name",mesh->m_name.c_str()))
211     if (!dataFile.add_att("mpi_size", mpi_size) )          throw FinleyAdapterException(msgPrefix+"add_att(Name)");
212        throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("numDim",numDim))
213     if (!dataFile.add_att("mpi_rank", mpi_rank) )          throw FinleyAdapterException(msgPrefix+"add_att(order)");
214        throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("order",mesh->integrationOrder))
215     if (!dataFile.add_att("Name",mesh->Name) )          throw FinleyAdapterException(msgPrefix+"add_att(order)");
216        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder))
217     if (!dataFile.add_att("numDim",numDim) )          throw FinleyAdapterException(msgPrefix+"add_att(reduced_order)");
218        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("numNodes",numNodes))
219     if (!dataFile.add_att("order",mesh->order) )          throw FinleyAdapterException(msgPrefix+"add_att(numNodes)");
220        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Elements",num_Elements))
221     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements)");
222        throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_FaceElements",num_FaceElements))
223     if (!dataFile.add_att("numNodes",numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements)");
224        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_ContactElements",num_ContactElements))
225     if (!dataFile.add_att("num_Elements",num_Elements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements)");
226        throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Points",num_Points))
227     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Points)");
228        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes))
229     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements_numNodes)");
230        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
231     if (!dataFile.add_att("num_Points",num_Points) )          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements_numNodes)");
232        throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
233     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements_numNodes)");
234        throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
235     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(Elements_TypeId)");
236        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
237     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(FaceElements_TypeId)");
238        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
239     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(ContactElements_TypeId)");
240        throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
241     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(Points_TypeId)");
242        throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Tags", num_Tags) )
243     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Tags)");
244        throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);  
245     if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )      // // // // // Nodes // // // // //
246        throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);  
247     if (!dataFile.add_att("num_Tags", num_Tags) )      // Nodes nodeDistribution
248        throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);      if (! (ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
249            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_NodeDistribution)");
250     // // // // // Nodes // // // // //      int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
251        if (! (ids->put(int_ptr, mpi_size+1)) )
252     // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)          throw FinleyAdapterException(msgPrefix+"put(Nodes_NodeDistribution)");
253     if (numNodes>0) {  
254        // Nodes degreesOfFreedomDistribution
255        // Nodes Id      if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
256        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )          throw FinleyAdapterException(msgPrefix+"add_var(Nodes_DofDistribution)");
257           throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);      int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
258        int_ptr = &mesh->Nodes->Id[0];      if (! (ids->put(int_ptr, mpi_size+1)) )
259        if (! (ids->put(int_ptr, numNodes)) )          throw FinleyAdapterException(msgPrefix+"put(Nodes_DofDistribution)");
260           throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);  
261        // Only write nodes if non-empty because NetCDF doesn't like empty arrays
262        // Nodes Tag      // (it treats them as NC_UNLIMITED)
263        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )      if (numNodes>0) {
264           throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);          // Nodes Id
265        int_ptr = &mesh->Nodes->Tag[0];          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
266        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Id)");
267           throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->Id[0];
268            if (! (ids->put(int_ptr, numNodes)) )
269        // Nodes gDOF              throw FinleyAdapterException(msgPrefix+"put(Nodes_Id)");
270        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )  
271           throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);          // Nodes Tag
272        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
273        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Tag)");
274           throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->Tag[0];
275            if (! (ids->put(int_ptr, numNodes)) )
276        // Nodes global node index              throw FinleyAdapterException(msgPrefix+"put(Nodes_Tag)");
277        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )  
278           throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);          // Nodes gDOF
279        int_ptr = &mesh->Nodes->globalNodesIndex[0];          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
280        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gDOF)");
281           throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
282            if (! (ids->put(int_ptr, numNodes)) )
283        // Nodes grDof              throw FinleyAdapterException(msgPrefix+"put(Nodes_gDOF)");
284        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )  
285           throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);          // Nodes global node index
286        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
287        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gNI)");
288           throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalNodesIndex[0];
289            if (! (ids->put(int_ptr, numNodes)) )
290        // Nodes grNI              throw FinleyAdapterException(msgPrefix+"put(Nodes_gNI)");
291        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )  
292           throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);          // Nodes grDof
293        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
294        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grDfI)");
295           throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
296            if (! (ids->put(int_ptr, numNodes)) )
297        // Nodes Coordinates              throw FinleyAdapterException(msgPrefix+"put(Nodes_grDfI)");
298        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )  
299           throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);          // Nodes grNI
300        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
301           throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grNI)");
302            int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
303        // Nodes degreesOfFreedomDistribution          if (! (ids->put(int_ptr, numNodes)) )
304        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_grNI)");
305           throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);  
306        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];          // Nodes Coordinates
307        if (! (ids->put(int_ptr, mpi_size+1)) )          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
308           throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Coordinates)");
309            if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
310        // Nodes nodeDistribution              throw FinleyAdapterException(msgPrefix+"put(Nodes_Coordinates)");
311        if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )      }
312           throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);  
313        int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];      // // // // // Elements // // // // //
314        if (! (ids->put(int_ptr, mpi_size+1)) )      if (num_Elements>0) {
315           throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);          // Elements_Id
316            if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
317     }              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Id)");
318            int_ptr = &mesh->Elements->Id[0];
319     // // // // // Elements // // // // //          if (! (ids->put(int_ptr, num_Elements)) )
320                throw FinleyAdapterException(msgPrefix+"put(Elements_Id)");
321     if (num_Elements>0) {  
322            // Elements_Tag
323        // Elements_Id          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
324        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Tag)");
325           throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Tag[0];
326        int_ptr = &mesh->Elements->Id[0];          if (! (ids->put(int_ptr, num_Elements)) )
327        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Tag)");
328           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);  
329            // Elements_Owner
330        // Elements_Tag          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
331        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Owner)");
332           throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Owner[0];
333        int_ptr = &mesh->Elements->Tag[0];          if (! (ids->put(int_ptr, num_Elements)) )
334        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Owner)");
335           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);  
336            // Elements_Color
337        // Elements_Owner          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
338        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Color)");
339           throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Color[0];
340        int_ptr = &mesh->Elements->Owner[0];          if (! (ids->put(int_ptr, num_Elements)) )
341        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Color)");
342           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);  
343            // Elements_Nodes
344        // Elements_Color          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
345        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Nodes)");
346           throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
347        int_ptr = &mesh->Elements->Color[0];              throw FinleyAdapterException(msgPrefix+"put(Elements_Nodes)");
348        if (! (ids->put(int_ptr, num_Elements)) )      }
349           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);  
350        // // // // // Face_Elements // // // // //
351        // Elements_Nodes      if (num_FaceElements>0) {
352        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )          // FaceElements_Id
353           throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
354        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Id)");
355           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->FaceElements->Id[0];
356            if (! (ids->put(int_ptr, num_FaceElements)) )
357     }              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Id)");
358    
359     // // // // // Face_Elements // // // // //          // FaceElements_Tag
360            if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
361     if (num_FaceElements>0) {              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Tag)");
362            int_ptr = &mesh->FaceElements->Tag[0];
363        // FaceElements_Id          if (! (ids->put(int_ptr, num_FaceElements)) )
364        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Tag)");
365           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);  
366        int_ptr = &mesh->FaceElements->Id[0];          // FaceElements_Owner
367        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
368           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Owner)");
369            int_ptr = &mesh->FaceElements->Owner[0];
370        // FaceElements_Tag          if (! (ids->put(int_ptr, num_FaceElements)) )
371        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Owner)");
372           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);  
373        int_ptr = &mesh->FaceElements->Tag[0];          // FaceElements_Color
374        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
375           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Color)");
376            int_ptr = &mesh->FaceElements->Color[0];
377        // FaceElements_Owner          if (! (ids->put(int_ptr, num_FaceElements)) )
378        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Color)");
379           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);  
380        int_ptr = &mesh->FaceElements->Owner[0];          // FaceElements_Nodes
381        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
382           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Nodes)");
383            if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
384        // FaceElements_Color              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Nodes)");
385        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )      }
386           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);  
387        int_ptr = &mesh->FaceElements->Color[0];      // // // // // Contact_Elements // // // // //
388        if (! (ids->put(int_ptr, num_FaceElements)) )      if (num_ContactElements>0) {
389           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);  
390            // ContactElements_Id
391        // FaceElements_Nodes          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
392        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Id)");
393           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);          int_ptr = &mesh->ContactElements->Id[0];
394        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )          if (! (ids->put(int_ptr, num_ContactElements)) )
395           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Id)");
396    
397     }          // ContactElements_Tag
398            if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
399     // // // // // Contact_Elements // // // // //              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Tag)");
400            int_ptr = &mesh->ContactElements->Tag[0];
401     if (num_ContactElements>0) {          if (! (ids->put(int_ptr, num_ContactElements)) )
402                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Tag)");
403        // ContactElements_Id  
404        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )          // ContactElements_Owner
405           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
406        int_ptr = &mesh->ContactElements->Id[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Owner)");
407        if (! (ids->put(int_ptr, num_ContactElements)) )          int_ptr = &mesh->ContactElements->Owner[0];
408           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_ContactElements)) )
409                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Owner)");
410        // ContactElements_Tag  
411        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )          // ContactElements_Color
412           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
413        int_ptr = &mesh->ContactElements->Tag[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Color)");
414        if (! (ids->put(int_ptr, num_ContactElements)) )          int_ptr = &mesh->ContactElements->Color[0];
415           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_ContactElements)) )
416                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Color)");
417        // ContactElements_Owner  
418        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )          // ContactElements_Nodes
419           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
420        int_ptr = &mesh->ContactElements->Owner[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Nodes)");
421        if (! (ids->put(int_ptr, num_ContactElements)) )          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
422           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Nodes)");
423        }
424        // ContactElements_Color  
425        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )      // // // // // Points // // // // //
426           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);      if (num_Points>0) {
427        int_ptr = &mesh->ContactElements->Color[0];          // Points_Id
428        if (! (ids->put(int_ptr, num_ContactElements)) )          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
429           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Id)");
430            int_ptr = &mesh->Points->Id[0];
431        // ContactElements_Nodes          if (! (ids->put(int_ptr, num_Points)) )
432        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )              throw FinleyAdapterException(msgPrefix+"put(Points_Id)");
433           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);  
434        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )          // Points_Tag
435           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
436                throw FinleyAdapterException(msgPrefix+"add_var(Points_Tag)");
437     }          int_ptr = &mesh->Points->Tag[0];
438            if (! (ids->put(int_ptr, num_Points)) )
439     // // // // // Points // // // // //              throw FinleyAdapterException(msgPrefix+"put(Points_Tag)");
440    
441     if (num_Points>0) {          // Points_Owner
442            if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
443        fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");              throw FinleyAdapterException(msgPrefix+"add_var(Points_Owner)");
444            int_ptr = &mesh->Points->Owner[0];
445        // Points_Id          if (! (ids->put(int_ptr, num_Points)) )
446        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Owner)");
447           throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);  
448        int_ptr = &mesh->Points->Id[0];          // Points_Color
449        if (! (ids->put(int_ptr, num_Points)) )          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
450           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Color)");
451            int_ptr = &mesh->Points->Color[0];
452        // Points_Tag          if (! (ids->put(int_ptr, num_Points)) )
453        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Color)");
454           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);  
455        int_ptr = &mesh->Points->Tag[0];          // Points_Nodes
456        if (! (ids->put(int_ptr, num_Points)) )          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
457           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
458                throw FinleyAdapterException(msgPrefix+"add_var(Points_Nodes)");
459        // Points_Owner          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
460        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Nodes)");
461           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);      }
462        int_ptr = &mesh->Points->Owner[0];  
463        if (! (ids->put(int_ptr, num_Points)) )      // // // // // TagMap // // // // //
464           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);      if (num_Tags>0) {
465            // Temp storage to gather node IDs
466        // Points_Color          vector<int> Tags_keys;
467        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )  
468           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);          // Copy tag data into temp arrays
469        int_ptr = &mesh->Points->Color[0];          TagMap::const_iterator it;
470        if (! (ids->put(int_ptr, num_Points)) )          for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++) {
471           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);              Tags_keys.push_back(it->second);
472            }
473        // Points_Nodes  
474        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]          // Tags_keys
475        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )          if (! (ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
476           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Tags_keys)");
477        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )          int_ptr = &Tags_keys[0];
478           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_Tags)) )
479                throw FinleyAdapterException(msgPrefix+"put(Tags_keys)");
480     }  
481            // Tags_names_*
482     // // // // // TagMap // // // // //          // This is an array of strings, it should be stored as an array but
483            // instead I have hacked in one attribute per string because the NetCDF
484     if (num_Tags>0) {          // manual doesn't tell how to do an array of strings
485            int i = 0;
486        // Temp storage to gather node IDs          for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++, i++) {
487        int *Tags_keys = TMPMEMALLOC(num_Tags, int);              stringstream tagnamestream;
488        char name_temp[4096];              tagnamestream << "Tags_name_" << i;
489                const string tagname = tagnamestream.str();
490        /* Copy tag data into temp arrays */              if (!dataFile.add_att(tagname.c_str(), it->first.c_str()))
491        tag_map = mesh->TagMap;                  throw FinleyAdapterException(msgPrefix+"add_att(Tags_names_X)");
492        if (tag_map) {          }
493           int i = 0;      }
494           while (tag_map) {  
495              Tags_keys[i++] = tag_map->tag_key;      // Send token to next MPI process so he can take his turn
496              tag_map=tag_map->next;  #ifdef ESYS_MPI
497           }      if (mpi_rank<mpi_size-1) {
498        }          MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
499        }
       // Tags_keys  
       if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )  
          throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);  
       int_ptr = &Tags_keys[0];  
       if (! (ids->put(int_ptr, num_Tags)) )  
          throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);  
   
       // Tags_names_*  
       // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string  
       // because the NetCDF manual doesn't tell how to do an array of strings  
       tag_map = mesh->TagMap;  
       if (tag_map) {  
          int i = 0;  
          while (tag_map) {  
             sprintf(name_temp, "Tags_name_%d", i);  
             if (!dataFile.add_att(name_temp, tag_map->name) )  
                throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);  
             tag_map=tag_map->next;  
             i++;  
          }  
       }  
   
       TMPMEMFREE(Tags_keys);  
   
    }  
   
 /* Send token to next MPI process so he can take his turn */  
 #ifdef PASO_MPI  
    if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);  
500  #endif  #endif
501    
502     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
503    
504  #else  #else // USE_NETCDF
505     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");      setError(IO_ERROR, "MeshAdapter::dump: not configured with netCDF. Please contact your installation manager.");
506  #endif  /* USE_NETCDF */  #endif // USE_NETCDF
507     checkFinleyError();      checkFinleyError();
508  }  }
509    
510  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
511  {  {
512     return "FinleyMesh";      return "FinleyMesh";
513  }  }
514    
515  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
516  {  {
517     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
518     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
519     if (loc==m_functionSpaceTypeNames.end()) {      if (loc==m_functionSpaceTypeNames.end()) {
520        return "Invalid function space type code.";          return "Invalid function space type code.";
521     } else {      } else {
522        return loc->second;          return loc->second;
523     }      }
524  }  }
525    
526  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
527  {  {
528     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
529     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
530     return (loc!=m_functionSpaceTypeNames.end());      return (loc!=m_functionSpaceTypeNames.end());
531  }  }
532    
533  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
534  {  {
535     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
536     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));                  DegreesOfFreedom,"Finley_DegreesOfFreedom"));
537     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
538     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));                  ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
539     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
540     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));                  Nodes,"Finley_Nodes"));
541     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
542     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));                  ReducedNodes,"Finley_Reduced_Nodes"));
543     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
544     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));                  Elements,"Finley_Elements"));
545     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
546     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));                  ReducedElements,"Finley_Reduced_Elements"));
547     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
548     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));                  FaceElements,"Finley_Face_Elements"));
549     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
550     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));                  ReducedFaceElements,"Finley_Reduced_Face_Elements"));
551     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
552     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));                  Points,"Finley_Points"));
553     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
554     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));                  ContactElementsZero,"Finley_Contact_Elements_0"));
555     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
556     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));                  ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
557     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
558     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));                  ContactElementsOne,"Finley_Contact_Elements_1"));
559     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
560     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));                  ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
561  }  }
562    
563  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
564  {  {
565     return Nodes;      return Nodes;
566  }  }
567    
568  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
569  {  {
570     return ReducedNodes;      return ReducedNodes;
571  }  }
572    
573  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
574  {  {
575     return Elements;      return Elements;
576  }  }
577    
578  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
579  {  {
580     return ReducedElements;      return ReducedElements;
581  }  }
582    
583  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
584  {  {
585     return FaceElements;      return FaceElements;
586  }  }
587    
588  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
589  {  {
590     return ReducedFaceElements;      return ReducedFaceElements;
591  }  }
592    
593  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
594  {  {
595     return ContactElementsZero;      return ContactElementsZero;
596  }  }
597    
598  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
599  {  {
600     return ReducedContactElementsZero;      return ReducedContactElementsZero;
601  }  }
602    
603  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
604  {  {
605     return ContactElementsOne;      return ContactElementsOne;
606  }  }
607    
608  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
609  {  {
610     return ReducedContactElementsOne;      return ReducedContactElementsOne;
611  }  }
612    
613  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
614  {  {
615     return DegreesOfFreedom;      return DegreesOfFreedom;
616  }  }
617    
618  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
619  {  {
620     return ReducedDegreesOfFreedom;      return ReducedDegreesOfFreedom;
621  }  }
622    
623  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
624  {  {
625     return Points;      return Points;
626  }  }
627    
628  //  //
# Line 643  int MeshAdapter::getDiracDeltaFunctionCo Line 630  int MeshAdapter::getDiracDeltaFunctionCo
630  //  //
631  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
632  {  {
633     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
634     int numDim=Finley_Mesh_getDim(mesh);      return mesh->getDim();
    checkFinleyError();  
    return numDim;  
635  }  }
636    
637  //  //
# Line 654  int MeshAdapter::getDim() const Line 639  int MeshAdapter::getDim() const
639  //  //
640  int MeshAdapter::getNumDataPointsGlobal() const  int MeshAdapter::getNumDataPointsGlobal() const
641  {  {
642     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);      return m_finleyMesh.get()->Nodes->getGlobalNumNodes();
643  }  }
644    
645  //  //
# Line 663  int MeshAdapter::getNumDataPointsGlobal( Line 648  int MeshAdapter::getNumDataPointsGlobal(
648  //  //
649  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const  pair<int,int> MeshAdapter::getDataShape(int functionSpaceCode) const
650  {  {
651     int numDataPointsPerSample=0;      int numDataPointsPerSample=0;
652     int numSamples=0;      int numSamples=0;
653     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
654     switch (functionSpaceCode) {      switch (functionSpaceCode) {
655     case(Nodes):          case Nodes:
656     numDataPointsPerSample=1;              numDataPointsPerSample=1;
657     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumNodes();
658     break;              break;
659     case(ReducedNodes):          case ReducedNodes:
660     numDataPointsPerSample=1;              numDataPointsPerSample=1;
661     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);              numSamples=mesh->Nodes->getNumReducedNodes();
662     break;              break;
663     case(Elements):          case Elements:
664     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
665        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
666        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
667     }              }
668     break;              break;
669     case(ReducedElements):          case ReducedElements:
670     if (mesh->Elements!=NULL) {              if (mesh->Elements!=NULL) {
671        numSamples=mesh->Elements->numElements;                  numSamples=mesh->Elements->numElements;
672        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
673     }              }
674     break;              break;
675     case(FaceElements):          case FaceElements:
676     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
677        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
678        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
679     }              }
680     break;              break;
681     case(ReducedFaceElements):          case ReducedFaceElements:
682     if (mesh->FaceElements!=NULL) {              if (mesh->FaceElements!=NULL) {
683        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
684        numSamples=mesh->FaceElements->numElements;                  numSamples=mesh->FaceElements->numElements;
685     }              }
686     break;              break;
687     case(Points):          case Points:
688     if (mesh->Points!=NULL) {              if (mesh->Points!=NULL) {
689        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
690        numSamples=mesh->Points->numElements;                  numSamples=mesh->Points->numElements;
691     }              }
692     break;              break;
693     case(ContactElementsZero):          case ContactElementsZero:
694     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
695        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
696        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
697     }              }
698     break;              break;
699     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
700     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
701        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
702        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
703     }              }
704     break;              break;
705     case(ContactElementsOne):          case ContactElementsOne:
706     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
707        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
708        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
709     }              }
710     break;              break;
711     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
712     if (mesh->ContactElements!=NULL) {              if (mesh->ContactElements!=NULL) {
713        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;                  numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
714        numSamples=mesh->ContactElements->numElements;                  numSamples=mesh->ContactElements->numElements;
715     }              }
716     break;              break;
717     case(DegreesOfFreedom):          case DegreesOfFreedom:
718     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
719        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
720        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumDegreesOfFreedom();
721     }              }
722     break;              break;
723     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
724     if (mesh->Nodes!=NULL) {              if (mesh->Nodes!=NULL) {
725        numDataPointsPerSample=1;                  numDataPointsPerSample=1;
726        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);                  numSamples=mesh->Nodes->getNumReducedDegreesOfFreedom();
727     }              }
728     break;              break;
729     default:          default:
730        stringstream temp;              stringstream temp;
731        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();              temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
732        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
733        break;              break;
734     }      }
735     return pair<int,int>(numDataPointsPerSample,numSamples);      return pair<int,int>(numDataPointsPerSample,numSamples);
736  }  }
737    
738  //  //
739  // 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
740    // hand side:
741  //  //
742  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
743                                   SystemMatrixAdapter& mat, escript::Data& rhs,          escript::AbstractSystemMatrix& mat, escript::Data& rhs,
744                                   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,
745                                   const escript::Data& d, const escript::Data& y,          const escript::Data& D, const escript::Data& X, const escript::Data& Y,
746                                   const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d, const escript::Data& y,
747  {          const escript::Data& d_contact, const escript::Data& y_contact,
748     escriptDataC _rhs=rhs.getDataC();          const escript::Data& d_dirac, const escript::Data& y_dirac) const
749     escriptDataC _A  =A.getDataC();  {
750     escriptDataC _B=B.getDataC();      SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
751     escriptDataC _C=C.getDataC();      if (!smat)
752     escriptDataC _D=D.getDataC();          throw FinleyAdapterException("finley only supports Paso system matrices.");
753     escriptDataC _X=X.getDataC();  
754     escriptDataC _Y=Y.getDataC();      Mesh* mesh=m_finleyMesh.get();
755     escriptDataC _d=d.getDataC();      Paso_SystemMatrix* S = smat->getPaso_SystemMatrix();
756     escriptDataC _y=y.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, S, rhs, A, B, C, D, X, Y);
757     escriptDataC _d_contact=d_contact.getDataC();      checkFinleyError();
758     escriptDataC _y_contact=y_contact.getDataC();  
759    
760     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, S, rhs,
761                escript::Data(), escript::Data(), escript::Data(), d,
762     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );              escript::Data(), y);
763     checkFinleyError();      checkFinleyError();
764    
765     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );      Assemble_PDE(mesh->Nodes, mesh->ContactElements, S, rhs,
766     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), d_contact,
767                escript::Data(), y_contact);
768     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );      checkFinleyError();
769     checkFinleyError();  
770  }      Assemble_PDE(mesh->Nodes, mesh->Points, S, rhs, escript::Data(),
771                escript::Data(), escript::Data(), d_dirac, escript::Data(), y_dirac);
772  void  MeshAdapter::addPDEToLumpedSystem(      checkFinleyError();
773                                          escript::Data& mat,  }
774                                          const escript::Data& D,  
775                                          const escript::Data& d) const  void MeshAdapter::addPDEToLumpedSystem(escript::Data& mat,
776  {          const escript::Data& D, const escript::Data& d,
777     escriptDataC _mat=mat.getDataC();          const escript::Data& d_dirac, const bool useHRZ) const
778     escriptDataC _D=D.getDataC();  {
779     escriptDataC _d=d.getDataC();      Mesh* mesh=m_finleyMesh.get();
780        Assemble_LumpedSystem(mesh->Nodes, mesh->Elements, mat, D, useHRZ);
781     Finley_Mesh* mesh=m_finleyMesh.get();      checkFinleyError();
782    
783     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);      Assemble_LumpedSystem(mesh->Nodes, mesh->FaceElements, mat, d, useHRZ);
784     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);      checkFinleyError();
785    
786     checkFinleyError();      Assemble_LumpedSystem(mesh->Nodes, mesh->Points, mat, d_dirac, useHRZ);
787        checkFinleyError();
788  }  }
789    
   
790  //  //
791  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
792  //  //
793  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,
794  {          const escript::Data& Y, const escript::Data& y,
795     Finley_Mesh* mesh=m_finleyMesh.get();          const escript::Data& y_contact, const escript::Data& y_dirac) const
796    {
797     escriptDataC _rhs=rhs.getDataC();      Mesh* mesh=m_finleyMesh.get();
798     escriptDataC _X=X.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, 0, rhs,
799     escriptDataC _Y=Y.getDataC();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
800     escriptDataC _y=y.getDataC();              X, Y);
801     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
802    
803     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );      Assemble_PDE(mesh->Nodes, mesh->FaceElements, 0, rhs,
804     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
805                escript::Data(), y);
806     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );      checkFinleyError();
807     checkFinleyError();  
808        Assemble_PDE(mesh->Nodes, mesh->ContactElements, 0, rhs,
809     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );              escript::Data(), escript::Data(), escript::Data(),
810     checkFinleyError();              escript::Data(), escript::Data(), y_contact);
811        checkFinleyError();
812    
813        Assemble_PDE(mesh->Nodes, mesh->Points, 0, rhs,
814                escript::Data(), escript::Data(), escript::Data(), escript::Data(),
815                escript::Data(), y_dirac);
816        checkFinleyError();
817  }  }
818    
819  //  //
820  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
821  //  //
822  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
823                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,          escript::AbstractTransportProblem& tp, escript::Data& source,
824                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,          const escript::Data& M, const escript::Data& A, const escript::Data& B,
825                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& C, const escript::Data& D, const escript::Data& X,
826                                             const escript::Data& d, const escript::Data& y,          const escript::Data& Y, const escript::Data& d, const escript::Data& y,
827                                             const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d_contact, const escript::Data& y_contact,
828  {          const escript::Data& d_dirac, const escript::Data& y_dirac) const
829     DataTypes::ShapeType shape;  {
830     source.expand();      TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
831     escriptDataC _source=source.getDataC();      if (!tpa)
832     escriptDataC _M=M.getDataC();          throw FinleyAdapterException("finley only supports Paso transport problems.");
833     escriptDataC _A=A.getDataC();  
834     escriptDataC _B=B.getDataC();      source.expand();
835     escriptDataC _C=C.getDataC();  
836     escriptDataC _D=D.getDataC();      Mesh* mesh=m_finleyMesh.get();
837     escriptDataC _X=X.getDataC();      Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
838     escriptDataC _Y=Y.getDataC();  
839     escriptDataC _d=d.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->mass_matrix, source,
840     escriptDataC _y=y.getDataC();                          escript::Data(), escript::Data(), escript::Data(),
841     escriptDataC _d_contact=d_contact.getDataC();                          M, escript::Data(), escript::Data());
842     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
843    
844     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->transport_matrix,
845     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();                          source, A, B, C, D, X, Y);
846        checkFinleyError();
847     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );  
848     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, _tp->transport_matrix,
849                            source, escript::Data(), escript::Data(),
850     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );                          escript::Data(), d, escript::Data(), y);
851     checkFinleyError();      checkFinleyError();
852    
853     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );      Assemble_PDE(mesh->Nodes, mesh->ContactElements,
854     checkFinleyError();                          _tp->transport_matrix, source, escript::Data(),
855                            escript::Data(), escript::Data(), d_contact,
856     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );                          escript::Data(), y_contact);
857     checkFinleyError();      checkFinleyError();
858  }  
859        Assemble_PDE(mesh->Nodes, mesh->Points, _tp->transport_matrix,
860  //                          source, escript::Data(), escript::Data(),
861  // interpolates data between different function spaces:                          escript::Data(), d_dirac, escript::Data(), y_dirac);
862  //      checkFinleyError();
863  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  }
864  {  
865     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));  //
866     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));  // interpolates data between different function spaces
867     if (inDomain!=*this)    //
868        throw FinleyAdapterException("Error - Illegal domain of interpolant.");  void MeshAdapter::interpolateOnDomain(escript::Data& target, const escript::Data& in) const
869     if (targetDomain!=*this)  {
870        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");      const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
871        const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
872     Finley_Mesh* mesh=m_finleyMesh.get();      if (inDomain!=*this)
873     escriptDataC _target=target.getDataC();          throw FinleyAdapterException("Error - Illegal domain of interpolant.");
874     escriptDataC _in=in.getDataC();      if (targetDomain!=*this)
875     switch(in.getFunctionSpace().getTypeCode()) {          throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
876     case(Nodes):  
877        switch(target.getFunctionSpace().getTypeCode()) {      Mesh* mesh=m_finleyMesh.get();
878        case(Nodes):      switch(in.getFunctionSpace().getTypeCode()) {
879        case(ReducedNodes):          case Nodes:
880        case(DegreesOfFreedom):              switch(target.getFunctionSpace().getTypeCode()) {
881        case(ReducedDegreesOfFreedom):                  case Nodes:
882        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedNodes:
883        break;                  case DegreesOfFreedom:
884        case(Elements):                  case ReducedDegreesOfFreedom:
885        case(ReducedElements):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
886        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
887        break;                  case Elements:
888        case(FaceElements):                  case ReducedElements:
889        case(ReducedFaceElements):                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in,target);
890        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      break;
891        break;                  case FaceElements:
892        case(Points):                  case ReducedFaceElements:
893        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
894        break;                      break;
895        case(ContactElementsZero):                  case Points:
896        case(ReducedContactElementsZero):                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
897        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
898        break;                  case ContactElementsZero:
899        case(ContactElementsOne):                  case ReducedContactElementsZero:
900        case(ReducedContactElementsOne):                  case ContactElementsOne:
901        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsOne:
902        break;                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
903        default:                      break;
904           stringstream temp;                  default:
905           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      stringstream temp;
906           throw FinleyAdapterException(temp.str());                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
907           break;                      throw FinleyAdapterException(temp.str());
908        }                      break;
909        break;              }
910     case(ReducedNodes):              break;
911        switch(target.getFunctionSpace().getTypeCode()) {          case ReducedNodes:
912        case(Nodes):              switch(target.getFunctionSpace().getTypeCode()) {
913        case(ReducedNodes):                  case Nodes:
914        case(DegreesOfFreedom):                  case ReducedNodes:
915        case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
916        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedDegreesOfFreedom:
917        break;                      Assemble_CopyNodalData(mesh->Nodes, target, in);
918        case(Elements):                      break;
919        case(ReducedElements):                  case Elements:
920        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case ReducedElements:
921        break;                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
922        case(FaceElements):                      break;
923        case(ReducedFaceElements):                  case FaceElements:
924        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ReducedFaceElements:
925        break;                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
926        case(Points):                      break;
927        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case Points:
928        break;                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
929        case(ContactElementsZero):                      break;
930        case(ReducedContactElementsZero):                  case ContactElementsZero:
931        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsZero:
932        break;                  case ContactElementsOne:
933        case(ContactElementsOne):                  case ReducedContactElementsOne:
934        case(ReducedContactElementsOne):                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
935        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
936        break;                  default:
937        default:                      stringstream temp;
938           stringstream temp;                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
939           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      throw FinleyAdapterException(temp.str());
940           throw FinleyAdapterException(temp.str());                      break;
941           break;              }
942        }              break;
943        break;          case Elements:
944     case(Elements):              if (target.getFunctionSpace().getTypeCode()==Elements) {
945        if (target.getFunctionSpace().getTypeCode()==Elements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
946           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
947        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_AverageElementData(mesh->Elements, target, in);
948           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);              } else {
949        } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
950           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");              }
951        }              break;
952        break;          case ReducedElements:
953     case(ReducedElements):              if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
954        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
955           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else {
956        } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
957           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");              }
958        }              break;
959        break;          case FaceElements:
960     case(FaceElements):              if (target.getFunctionSpace().getTypeCode()==FaceElements) {
961        if (target.getFunctionSpace().getTypeCode()==FaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
962           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
963        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_AverageElementData(mesh->FaceElements, target, in);
964           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);              } else {
965        } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
966           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");              }
967        }              break;
968        break;          case ReducedFaceElements:
969     case(ReducedFaceElements):              if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
970        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
971           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else {
972        } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
973           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");              }
974        }              break;
975        break;          case Points:
976     case(Points):              if (target.getFunctionSpace().getTypeCode()==Points) {
977        if (target.getFunctionSpace().getTypeCode()==Points) {                  Assemble_CopyElementData(mesh->Points, target, in);
978           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);              } else {
979        } else {                  throw FinleyAdapterException("Error - No interpolation with data on points possible.");
980           throw FinleyAdapterException("Error - No interpolation with data on points possible.");              }
981        }              break;
982        break;          case ContactElementsZero:
983     case(ContactElementsZero):          case ContactElementsOne:
984     case(ContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
985        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
986           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
987        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_AverageElementData(mesh->ContactElements, target, in);
988           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);              } else {
989        } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
990           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");              }
991        }              break;
992        break;          case ReducedContactElementsZero:
993     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
994     case(ReducedContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
995        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
996           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else {
997        } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
998           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");              }
999        }              break;
1000        break;          case DegreesOfFreedom:
1001     case(DegreesOfFreedom):                    switch(target.getFunctionSpace().getTypeCode()) {
1002        switch(target.getFunctionSpace().getTypeCode()) {                  case ReducedDegreesOfFreedom:
1003        case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
1004        case(DegreesOfFreedom):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1005        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1006        break;  
1007                      case Nodes:
1008        case(Nodes):                  case ReducedNodes:
1009        case(ReducedNodes):                      if (getMPISize()>1) {
1010        if (getMPISize()>1) {                          escript::Data in2=escript::Data(in);
1011           escript::Data temp=escript::Data(in);                          in2.expand();
1012           temp.expand();                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1013           escriptDataC _in2 = temp.getDataC();                      } else {
1014           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1015        } else {                      }
1016           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1017        }                  case Elements:
1018        break;                  case ReducedElements:
1019        case(Elements):                      if (getMPISize()>1) {
1020        case(ReducedElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1021        if (getMPISize()>1) {                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1022           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                      } else {
1023           escriptDataC _in2 = temp.getDataC();                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1024           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                      }
1025        } else {                      break;
1026           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case FaceElements:
1027        }                  case ReducedFaceElements:
1028        break;                      if (getMPISize()>1) {
1029        case(FaceElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1030        case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1031        if (getMPISize()>1) {                      } else {
1032           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1033           escriptDataC _in2 = temp.getDataC();                      }
1034           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1035                      case Points:
1036        } else {                      if (getMPISize()>1) {
1037           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                          //escript::Data in2=escript::Data(in, continuousFunction(*this) );
1038        }                      } else {
1039        break;                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1040        case(Points):                      }
1041        if (getMPISize()>1) {                      break;
1042           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  case ContactElementsZero:
1043           escriptDataC _in2 = temp.getDataC();                  case ContactElementsOne:
1044        } else {                  case ReducedContactElementsZero:
1045           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedContactElementsOne:
1046        }                      if (getMPISize()>1) {
1047        break;                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1048        case(ContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1049        case(ContactElementsOne):                      } else {
1050        case(ReducedContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1051        case(ReducedContactElementsOne):                      }
1052        if (getMPISize()>1) {                      break;
1053           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  default:
1054           escriptDataC _in2 = temp.getDataC();                      stringstream temp;
1055           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1056        } else {                      throw FinleyAdapterException(temp.str());
1057           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              }
1058        }              break;
1059        break;          case ReducedDegreesOfFreedom:
1060        default:              switch(target.getFunctionSpace().getTypeCode()) {
1061           stringstream temp;                  case Nodes:
1062           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1063           throw FinleyAdapterException(temp.str());                  case ReducedNodes:
1064           break;                      if (getMPISize()>1) {
1065        }                          escript::Data in2=escript::Data(in);
1066        break;                          in2.expand();
1067     case(ReducedDegreesOfFreedom):                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1068        switch(target.getFunctionSpace().getTypeCode()) {                      } else {
1069        case(Nodes):                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1070        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                      }
1071        break;                      break;
1072        case(ReducedNodes):                  case DegreesOfFreedom:
1073        if (getMPISize()>1) {                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1074           escript::Data temp=escript::Data(in);                      break;
1075           temp.expand();                  case ReducedDegreesOfFreedom:
1076           escriptDataC _in2 = temp.getDataC();                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1077           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                      break;
1078        } else {                  case Elements:
1079           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedElements:
1080        }                      if (getMPISize()>1) {
1081        break;                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1082        case(DegreesOfFreedom):                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1083        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                      } else {
1084        break;                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1085        case(ReducedDegreesOfFreedom):                      }
1086        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1087        break;                  case FaceElements:
1088        case(Elements):                  case ReducedFaceElements:
1089        case(ReducedElements):                      if (getMPISize()>1) {
1090        if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1091           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1092           escriptDataC _in2 = temp.getDataC();                      } else {
1093           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1094        } else {                      }
1095           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
1096        }                  case Points:
1097        break;                      if (getMPISize()>1) {
1098        case(FaceElements):                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1099        case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->Points, in2, target);
1100        if (getMPISize()>1) {                      } else {
1101           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1102           escriptDataC _in2 = temp.getDataC();                      }
1103           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1104        } else {                  case ContactElementsZero:
1105           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ContactElementsOne:
1106        }                  case ReducedContactElementsZero:
1107        break;                  case ReducedContactElementsOne:
1108        case(Points):                      if (getMPISize()>1) {
1109        if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1110           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1111           escriptDataC _in2 = temp.getDataC();                      } else {
1112           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1113        } else {                      }
1114           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      break;
1115        }                  default:
1116        break;                      stringstream temp;
1117        case(ContactElementsZero):                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1118        case(ContactElementsOne):                      throw FinleyAdapterException(temp.str());
1119        case(ReducedContactElementsZero):                      break;
1120        case(ReducedContactElementsOne):              }
1121        if (getMPISize()>1) {              break;
1122           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );          default:
1123           escriptDataC _in2 = temp.getDataC();              stringstream temp;
1124           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1125        } else {              throw FinleyAdapterException(temp.str());
1126           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              break;
1127        }      }
1128        break;      checkFinleyError();
       default:  
          stringstream temp;  
          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();  
          throw FinleyAdapterException(temp.str());  
          break;  
       }  
       break;  
    default:  
       stringstream temp;  
       temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1129  }  }
1130    
1131  //  //
1132  // copies the locations of sample points into x:  // copies the locations of sample points into x
1133  //  //
1134  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1135  {  {
1136     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1137     if (argDomain!=*this)      if (argDomain!=*this)
1138        throw FinleyAdapterException("Error - Illegal domain of data point locations");          throw FinleyAdapterException("Error - Illegal domain of data point locations");
1139     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1140     // in case of values node coordinates we can do the job directly:      // in case of appropriate function space we can do the job directly:
1141     if (arg.getFunctionSpace().getTypeCode()==Nodes) {      if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1142        escriptDataC _arg=arg.getDataC();          Assemble_NodeCoordinates(mesh->Nodes, arg);
1143        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);      } else {
1144     } else {          escript::Data tmp_data=Vector(0., continuousFunction(*this), true);
1145        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);          Assemble_NodeCoordinates(mesh->Nodes, tmp_data);
1146        escriptDataC _tmp_data=tmp_data.getDataC();          // this is then interpolated onto arg:
1147        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);          interpolateOnDomain(arg, tmp_data);
1148        // this is then interpolated onto arg:      }
1149        interpolateOnDomain(arg,tmp_data);      checkFinleyError();
    }  
    checkFinleyError();  
1150  }  }
1151    
1152  //  //
1153  // 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
1154  //  //
1155  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1156  {  {
1157  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/      const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1158     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));      if (normalDomain!=*this)
1159     if (normalDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of normal locations");
1160        throw FinleyAdapterException("Error - Illegal domain of normal locations");      Mesh* mesh=m_finleyMesh.get();
1161     Finley_Mesh* mesh=m_finleyMesh.get();      switch(normal.getFunctionSpace().getTypeCode()) {
1162     escriptDataC _normal=normal.getDataC();          case Nodes:
1163     switch(normal.getFunctionSpace().getTypeCode()) {              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1164     case(Nodes):              break;
1165     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");          case ReducedNodes:
1166     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1167     case(ReducedNodes):              break;
1168     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");          case Elements:
1169     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1170     case(Elements):              break;
1171     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");          case ReducedElements:
1172     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1173     case(ReducedElements):              break;
1174     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");          case FaceElements:
1175     break;          case ReducedFaceElements:
1176     case (FaceElements):              Assemble_getNormal(mesh->Nodes, mesh->FaceElements, normal);
1177     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              break;
1178     break;          case Points:
1179     case (ReducedFaceElements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1180     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              break;
1181     break;          case ContactElementsOne:
1182     case(Points):          case ContactElementsZero:
1183     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");          case ReducedContactElementsOne:
1184     break;          case ReducedContactElementsZero:
1185     case (ContactElementsOne):              Assemble_getNormal(mesh->Nodes, mesh->ContactElements, normal);
1186     case (ContactElementsZero):              break;
1187     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);          case DegreesOfFreedom:
1188     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1189     case (ReducedContactElementsOne):              break;
1190     case (ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1191     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1192     break;              break;
1193     case(DegreesOfFreedom):          default:
1194     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");              stringstream temp;
1195     break;              temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1196     case(ReducedDegreesOfFreedom):              throw FinleyAdapterException(temp.str());
1197     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");              break;
1198     break;      }
1199     default:      checkFinleyError();
       stringstream temp;  
       temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
 }  
   
 //  
 // interpolates data to other domain:  
 //  
 void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  
 {  
    const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();  
    const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());  
    if (targetDomain!=this)  
       throw FinleyAdapterException("Error - Illegal domain of interpolation target");  
   
    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");  
 }  
   
 //  
 // calculates the integral of a function defined of arg:  
 //  
 void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  
 {  
    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));  
    if (argDomain!=*this)  
       throw FinleyAdapterException("Error - Illegal domain of integration kernel");  
   
    double blocktimer_start = blocktimer_time();  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    escriptDataC _temp;  
    escript::Data temp;  
    escriptDataC _arg=arg.getDataC();  
    switch(arg.getFunctionSpace().getTypeCode()) {  
    case(Nodes):  
    temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );  
    _temp=temp.getDataC();  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
    break;  
    case(ReducedNodes):  
    temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );  
    _temp=temp.getDataC();  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
    break;  
    case(Elements):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);  
    break;  
    case(ReducedElements):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);  
    break;  
    case(FaceElements):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);  
    break;  
    case(ReducedFaceElements):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);  
    break;  
    case(Points):  
    throw FinleyAdapterException("Error - Integral of data on points is not supported.");  
    break;  
    case(ContactElementsZero):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  
    break;  
    case(ReducedContactElementsZero):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  
    break;  
    case(ContactElementsOne):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  
    break;  
    case(ReducedContactElementsOne):  
    Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);  
    break;  
    case(DegreesOfFreedom):  
    temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );  
    _temp=temp.getDataC();  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
    break;  
    case(ReducedDegreesOfFreedom):  
    temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );  
    _temp=temp.getDataC();  
    Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
    blocktimer_increment("integrate()", blocktimer_start);  
 }  
   
 //  
 // calculates the gradient of arg:  
 //  
 void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  
 {  
    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));  
    if (argDomain!=*this)  
       throw FinleyAdapterException("Error - Illegal domain of gradient argument");  
    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));  
    if (gradDomain!=*this)  
       throw FinleyAdapterException("Error - Illegal domain of gradient");  
   
    Finley_Mesh* mesh=m_finleyMesh.get();  
    escriptDataC _grad=grad.getDataC();  
    escriptDataC nodeDataC;  
    escript::Data temp;  
    if (getMPISize()>1) {  
       if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {  
          temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );  
          nodeDataC = temp.getDataC();  
       } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {  
          temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );  
          nodeDataC = temp.getDataC();  
       } else {  
          nodeDataC = arg.getDataC();  
       }  
    } else {  
       nodeDataC = arg.getDataC();  
    }  
    switch(grad.getFunctionSpace().getTypeCode()) {  
    case(Nodes):  
    throw FinleyAdapterException("Error - Gradient at nodes is not supported.");  
    break;  
    case(ReducedNodes):  
    throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");  
    break;  
    case(Elements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);  
    break;  
    case(ReducedElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);  
    break;  
    case(FaceElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedFaceElements):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);  
    break;  
    case(Points):  
    throw FinleyAdapterException("Error - Gradient at points is not supported.");  
    break;  
    case(ContactElementsZero):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedContactElementsZero):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ContactElementsOne):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(ReducedContactElementsOne):  
    Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);  
    break;  
    case(DegreesOfFreedom):  
    throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");  
    break;  
    case(ReducedDegreesOfFreedom):  
    throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");  
    break;  
    default:  
       stringstream temp;  
       temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1200  }  }
1201    
1202  //  //
1203  // returns the size of elements:  // interpolates data to other domain
1204    //
1205    void MeshAdapter::interpolateACross(escript::Data& target, const escript::Data& source) const
1206    {
1207        throw FinleyAdapterException("Error - Finley does not allow interpolation across domains.");
1208    }
1209    
1210    //
1211    // calculates the integral of a function defined on arg
1212    //
1213    void MeshAdapter::setToIntegrals(vector<double>& integrals, const escript::Data& arg) const
1214    {
1215        const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1216        if (argDomain!=*this)
1217            throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1218    
1219        double blocktimer_start = blocktimer_time();
1220        Mesh* mesh=m_finleyMesh.get();
1221        switch(arg.getFunctionSpace().getTypeCode()) {
1222            case Nodes:
1223                {
1224                    escript::Data temp(arg, escript::function(*this));
1225                    Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1226                }
1227                break;
1228            case ReducedNodes:
1229                {
1230                    escript::Data temp(arg, escript::function(*this));
1231                    Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1232                }
1233                break;
1234            case Elements:
1235            case ReducedElements:
1236                Assemble_integrate(mesh->Nodes, mesh->Elements, arg, &integrals[0]);
1237                break;
1238            case FaceElements:
1239            case ReducedFaceElements:
1240                Assemble_integrate(mesh->Nodes, mesh->FaceElements, arg, &integrals[0]);
1241                break;
1242            case Points:
1243                throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1244                break;
1245            case ContactElementsZero:
1246            case ReducedContactElementsZero:
1247            case ContactElementsOne:
1248            case ReducedContactElementsOne:
1249                Assemble_integrate(mesh->Nodes, mesh->ContactElements, arg, &integrals[0]);
1250                break;
1251            case DegreesOfFreedom:
1252            case ReducedDegreesOfFreedom:
1253                {
1254                    escript::Data temp(arg, escript::function(*this));
1255                    Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1256                }
1257                break;
1258            default:
1259                stringstream temp;
1260                temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1261                throw FinleyAdapterException(temp.str());
1262                break;
1263        }
1264        checkFinleyError();
1265        blocktimer_increment("integrate()", blocktimer_start);
1266    }
1267    
1268    //
1269    // calculates the gradient of arg
1270    //
1271    void MeshAdapter::setToGradient(escript::Data& grad, const escript::Data& arg) const
1272    {
1273        const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1274        if (argDomain!=*this)
1275            throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1276        const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1277        if (gradDomain!=*this)
1278            throw FinleyAdapterException("Error - Illegal domain of gradient");
1279    
1280        Mesh* mesh=m_finleyMesh.get();
1281        escript::Data nodeData;
1282        if (getMPISize()>1) {
1283            if (arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom) {
1284                nodeData=escript::Data(arg, continuousFunction(*this));
1285            } else if(arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom) {
1286                nodeData=escript::Data(arg, reducedContinuousFunction(*this));
1287            } else {
1288                nodeData = arg;
1289            }
1290        } else {
1291            nodeData = arg;
1292        }
1293        switch(grad.getFunctionSpace().getTypeCode()) {
1294            case Nodes:
1295                throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1296                break;
1297            case ReducedNodes:
1298                throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1299                break;
1300            case Elements:
1301            case ReducedElements:
1302                Assemble_gradient(mesh->Nodes, mesh->Elements, grad, nodeData);
1303                break;
1304            case FaceElements:
1305            case ReducedFaceElements:
1306                Assemble_gradient(mesh->Nodes, mesh->FaceElements, grad, nodeData);
1307                break;
1308            case Points:
1309                throw FinleyAdapterException("Error - Gradient at points is not supported.");
1310                break;
1311            case ContactElementsZero:
1312            case ReducedContactElementsZero:
1313            case ContactElementsOne:
1314            case ReducedContactElementsOne:
1315                Assemble_gradient(mesh->Nodes, mesh->ContactElements, grad, nodeData);
1316                break;
1317            case DegreesOfFreedom:
1318                throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1319                break;
1320            case ReducedDegreesOfFreedom:
1321                throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1322                break;
1323            default:
1324                stringstream temp;
1325                temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1326                throw FinleyAdapterException(temp.str());
1327                break;
1328        }
1329        checkFinleyError();
1330    }
1331    
1332    //
1333    // returns the size of elements
1334  //  //
1335  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1336  {  {
1337     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1338     escriptDataC tmp=size.getDataC();      switch(size.getFunctionSpace().getTypeCode()) {
1339     switch(size.getFunctionSpace().getTypeCode()) {          case Nodes:
1340     case(Nodes):              throw FinleyAdapterException("Error - Size of nodes is not supported.");
1341     throw FinleyAdapterException("Error - Size of nodes is not supported.");              break;
1342     break;          case ReducedNodes:
1343     case(ReducedNodes):              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1344     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");              break;
1345     break;          case Elements:
1346     case(Elements):          case ReducedElements:
1347     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);              Assemble_getSize(mesh->Nodes, mesh->Elements, size);
1348     break;              break;
1349     case(ReducedElements):          case FaceElements:
1350     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case ReducedFaceElements:
1351     break;              Assemble_getSize(mesh->Nodes, mesh->FaceElements, size);
1352     case(FaceElements):              break;
1353     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case Points:
1354     break;              throw FinleyAdapterException("Error - Size of point elements is not supported.");
1355     case(ReducedFaceElements):              break;
1356     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case ContactElementsZero:
1357     break;          case ContactElementsOne:
1358     case(Points):          case ReducedContactElementsZero:
1359     throw FinleyAdapterException("Error - Size of point elements is not supported.");          case ReducedContactElementsOne:
1360     break;              Assemble_getSize(mesh->Nodes,mesh->ContactElements,size);
1361     case(ContactElementsZero):              break;
1362     case(ContactElementsOne):          case DegreesOfFreedom:
1363     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1364     break;              break;
1365     case(ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1366     case(ReducedContactElementsOne):              throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1367     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              break;
1368     break;          default:
1369     case(DegreesOfFreedom):              stringstream temp;
1370     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");              temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1371     break;              throw FinleyAdapterException(temp.str());
1372     case(ReducedDegreesOfFreedom):              break;
1373     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");      }
1374     break;      checkFinleyError();
    default:  
       stringstream temp;  
       temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();  
       throw FinleyAdapterException(temp.str());  
       break;  
    }  
    checkFinleyError();  
1375  }  }
1376    
1377  //  //
# Line 1448  void MeshAdapter::setToSize(escript::Dat Line 1379  void MeshAdapter::setToSize(escript::Dat
1379  //  //
1380  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1381  {  {
1382     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1383     escriptDataC tmp;      const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1384     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));      if (newDomain!=*this)
1385     if (newDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of new point locations");
1386        throw FinleyAdapterException("Error - Illegal domain of new point locations");      if (new_x.getFunctionSpace() == continuousFunction(*this)) {
1387     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {          mesh->setCoordinates(new_x);
1388         tmp = new_x.getDataC();      } else {
1389         Finley_Mesh_setCoordinates(mesh,&tmp);          throw FinleyAdapterException("As of escript version 3.3 SetX() only accepts ContinuousFunction arguments. Please interpolate.");
1390     } else {      }
1391         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );      checkFinleyError();
1392         tmp = new_x_inter.getDataC();  }
1393         Finley_Mesh_setCoordinates(mesh,&tmp);  
1394     }  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1395     checkFinleyError();  {
1396  }      if (getMPISize() > 1) {
1397    #ifdef ESYS_MPI
1398  //          int myFirstNode=0, myLastNode=0, k=0;
1399  // Helper for the save* methods. Extracts optional data variable names and the          int* globalNodeIndex=0;
1400  // corresponding pointers from python dictionary. Caller must free arrays.          Mesh* mesh_p=m_finleyMesh.get();
1401  //          /*
1402  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const           * this method is only used by saveDataCSV which would use the returned
1403  {           * values for reduced nodes wrongly so this case is disabled for now
1404     numData = boost::python::extract<int>(arg.attr("__len__")());          if (fs_code == FINLEY_REDUCED_NODES) {
1405     /* win32 refactor */              myFirstNode = NodeFile_getFirstReducedNode(mesh_p->Nodes);
1406     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;              myLastNode = NodeFile_getLastReducedNode(mesh_p->Nodes);
1407     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;              globalNodeIndex = NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1408     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;          } else
1409            */
1410     boost::python::list keys=arg.keys();          if (fs_code == FINLEY_NODES) {
1411     for (int i=0; i<numData; ++i) {              myFirstNode = mesh_p->Nodes->getFirstNode();
1412        std::string n=boost::python::extract<std::string>(keys[i]);              myLastNode = mesh_p->Nodes->getLastNode();
1413        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);              globalNodeIndex = mesh_p->Nodes->borrowGlobalNodesIndex();
1414        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)          } else {
1415           throw FinleyAdapterException("Error: Data must be defined on same Domain");              throw FinleyAdapterException("Unsupported function space type for ownSample()");
1416        data[i] = d.getDataC();          }
1417        dataPtr[i] = &(data[i]);  
1418        names[i] = TMPMEMALLOC(n.length()+1, char);          k=globalNodeIndex[id];
1419        strcpy(names[i], n.c_str());          return ((myFirstNode <= k) && (k < myLastNode));
1420     }  #endif
1421  }      }
1422        return true;
 //  
 // saves mesh and optionally data arrays in openDX format  
 //  
 void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const  
 {  
    int num_data;  
    char **names;  
    escriptDataC *data;  
    escriptDataC **ptr_data;  
   
    extractArgsFromDict(arg, num_data, names, data, ptr_data);  
    Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);  
    checkFinleyError();  
   
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0; i<num_data; i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
   
    return;  
 }  
   
 //  
 // saves mesh and optionally data arrays in VTK format  
 //  
 void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg,  const std::string& metadata, const std::string& metadata_schema) const  
 {  
    int num_data;  
    char **names;  
    escriptDataC *data;  
    escriptDataC **ptr_data;  
   
    extractArgsFromDict(arg, num_data, names, data, ptr_data);  
    Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data, metadata.c_str(), metadata_schema.c_str());  
    checkFinleyError();  
   
    /* win32 refactor */  
    TMPMEMFREE(data);  
    TMPMEMFREE(ptr_data);  
    for(int i=0; i<num_data; i++)  
    {  
       TMPMEMFREE(names[i]);  
    }  
    TMPMEMFREE(names);  
1423  }  }
1424    
1425    
1426  //  //
1427  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1428  //  //
1429  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  escript::ASM_ptr MeshAdapter::newSystemMatrix(const int row_blocksize,
1430                                                   const int row_blocksize,                              const escript::FunctionSpace& row_functionspace,
1431                                                   const escript::FunctionSpace& row_functionspace,                              const int column_blocksize,
1432                                                   const int column_blocksize,                              const escript::FunctionSpace& column_functionspace,
1433                                                   const escript::FunctionSpace& column_functionspace,                              const int type) const
1434                                                   const int type) const  {
1435  {      // is the domain right?
1436     int reduceRowOrder=0;      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1437     int reduceColOrder=0;      if (row_domain!=*this)
1438     // is the domain right?          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1439     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1440     if (row_domain!=*this)      if (col_domain!=*this)
1441        throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");          throw FinleyAdapterException("Error - domain of column function space does not match the domain of matrix generator.");
1442     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));  
1443     if (col_domain!=*this)      int reduceRowOrder=0;
1444        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");      int reduceColOrder=0;
1445     // is the function space type right      // is the function space type right?
1446     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {      if (row_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1447        reduceRowOrder=0;          reduceRowOrder=1;
1448     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      } else if (row_functionspace.getTypeCode() != DegreesOfFreedom) {
1449        reduceRowOrder=1;          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1450     } else {      }
1451        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      if (column_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1452     }          reduceColOrder=1;
1453     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (column_functionspace.getTypeCode() != DegreesOfFreedom) {
1454        reduceColOrder=0;          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1455     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1456        reduceColOrder=1;  
1457     } else {      // generate matrix:
1458        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");      paso::SystemMatrixPattern* fsystemMatrixPattern=
1459     }          getFinley_Mesh()->getPattern(reduceRowOrder, reduceColOrder);
1460     // generate matrix:      checkFinleyError();
1461        Paso_SystemMatrix* fsystemMatrix;
1462     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);      const int trilinos = 0;
1463     checkFinleyError();      if (trilinos) {
    Paso_SystemMatrix* fsystemMatrix;  
    int trilinos = 0;  
    if (trilinos) {  
1464  #ifdef TRILINOS  #ifdef TRILINOS
1465        /* Allocation Epetra_VrbMatrix here */          // FIXME: Allocation Epetra_VrbMatrix here...
1466  #endif  #endif
1467     }      } else {
1468     else {          fsystemMatrix=Paso_SystemMatrix_alloc(type, fsystemMatrixPattern,
1469        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);                  row_blocksize, column_blocksize, FALSE);
1470     }      }
1471     checkPasoError();      checkPasoError();
1472     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      paso::SystemMatrixPattern_free(fsystemMatrixPattern);
1473     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);      SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1474        return escript::ASM_ptr(sma);
1475  }  }
1476    
1477  //  //
1478  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1479  //  //
1480  TransportProblemAdapter MeshAdapter::newTransportProblem(  escript::ATP_ptr MeshAdapter::newTransportProblem(const int blocksize,
1481                                                           const double theta,          const escript::FunctionSpace& functionspace, const int type) const
1482                                                           const int blocksize,  {
1483                                                           const escript::FunctionSpace& functionspace,      // is the domain right?
1484                                                           const int type) const      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1485  {      if (domain!=*this)
1486     int reduceOrder=0;          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1487     // is the domain right?  
1488     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));      // is the function space type right?
1489     if (domain!=*this)      int reduceOrder=0;
1490        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");      if (functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1491     // is the function space type right          reduceOrder=1;
1492     if (functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (functionspace.getTypeCode() != DegreesOfFreedom) {
1493        reduceOrder=0;          throw FinleyAdapterException("Error - illegal function space type for transport problem.");
1494     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1495        reduceOrder=1;  
1496     } else {      // generate transport problem:
1497        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      paso::SystemMatrixPattern* fsystemMatrixPattern=
1498     }          getFinley_Mesh()->getPattern(reduceOrder, reduceOrder);
1499     // generate matrix:      checkFinleyError();
1500        Paso_TransportProblem* transportProblem;
1501     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);      transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern, blocksize);
1502     checkFinleyError();      checkPasoError();
1503     Paso_FCTransportProblem* transportProblem;      paso::SystemMatrixPattern_free(fsystemMatrixPattern);
1504     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);      TransportProblemAdapter* tpa=new TransportProblemAdapter(
1505     checkPasoError();              transportProblem, blocksize, functionspace);
1506     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      return escript::ATP_ptr(tpa);
    return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);  
1507  }  }
1508    
1509  //  //
1510  // vtkObject MeshAdapter::createVtkObject() const  // returns true if data on functionSpaceCode is considered as being cell centered
 // TODO:  
 //  
   
1511  //  //
 // returns true if data at the atom_type is considered as being cell centered:  
1512  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1513  {  {
1514     switch(functionSpaceCode) {      switch(functionSpaceCode) {
1515     case(Nodes):          case Nodes:
1516     case(DegreesOfFreedom):          case DegreesOfFreedom:
1517     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1518     return false;              return false;
1519     break;          case Elements:
1520     case(Elements):          case FaceElements:
1521     case(FaceElements):          case Points:
1522     case(Points):          case ContactElementsZero:
1523     case(ContactElementsZero):          case ContactElementsOne:
1524     case(ContactElementsOne):          case ReducedElements:
1525     case(ReducedElements):          case ReducedFaceElements:
1526     case(ReducedFaceElements):          case ReducedContactElementsZero:
1527     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
1528     case(ReducedContactElementsOne):              return true;
1529     return true;          default:
1530     break;              stringstream temp;
1531     default:              temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1532        stringstream temp;              throw FinleyAdapterException(temp.str());
1533        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;              break;
1534        throw FinleyAdapterException(temp.str());      }
1535        break;      return false;
    }  
    checkFinleyError();  
    return false;  
1536  }  }
1537    
1538  bool  bool
1539  MeshAdapter::commonFunctionSpace(const std::vector<int>& fs, int& resultcode) const  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1540  {  {
1541     /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]      /* The idea is to use equivalence classes. [Types which can be interpolated
1542      class 1: DOF <-> Nodes         back and forth]:
1543      class 2: ReducedDOF <-> ReducedNodes          class 1: DOF <-> Nodes
1544      class 3: Points          class 2: ReducedDOF <-> ReducedNodes
1545      class 4: Elements          class 3: Points
1546      class 5: ReducedElements          class 4: Elements
1547      class 6: FaceElements          class 5: ReducedElements
1548      class 7: ReducedFaceElements          class 6: FaceElements
1549      class 8: ContactElementZero <-> ContactElementOne          class 7: ReducedFaceElements
1550      class 9: ReducedContactElementZero <-> ReducedContactElementOne          class 8: ContactElementZero <-> ContactElementOne
1551            class 9: ReducedContactElementZero <-> ReducedContactElementOne
1552     There is also a set of lines. Interpolation is possible down a line but not between lines.  
1553     class 1 and 2 belong to all lines so aren't considered.      There is also a set of lines. Interpolation is possible down a line but
1554      line 0: class 3      not between lines.
1555      line 1: class 4,5      class 1 and 2 belong to all lines so aren't considered.
1556      line 2: class 6,7          line 0: class 3
1557      line 3: class 8,9          line 1: class 4,5
1558            line 2: class 6,7
1559     For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.          line 3: class 8,9
1560     eg hasnodes is true if we have at least one instance of Nodes.  
1561     */      For classes with multiple members (eg class 2) we have vars to record if
1562      if (fs.size()==0)      there is at least one instance.
1563      {      e.g. hasnodes is true if we have at least one instance of Nodes.
1564      return false;      */
1565      }      if (fs.empty())
1566      std::vector<int> hasclass(10);          return false;
1567      std::vector<int> hasline(4);      
1568        vector<int> hasclass(10);
1569        vector<int> hasline(4);    
1570      bool hasnodes=false;      bool hasnodes=false;
1571      bool hasrednodes=false;      bool hasrednodes=false;
1572      bool hascez=false;      bool hascez=false;
1573      bool hasrcez=false;      bool hasrcez=false;
1574      for (int i=0;i<fs.size();++i)      for (int i=0;i<fs.size();++i) {
1575      {          switch(fs[i]) {
1576      switch(fs[i])              case Nodes:
1577      {                  hasnodes=true; // fall through
1578      case(Nodes):   hasnodes=true;   // no break is deliberate              case DegreesOfFreedom:
1579      case(DegreesOfFreedom):                  hasclass[1]=1;
1580          hasclass[1]=1;                  break;
1581          break;              case ReducedNodes:
1582      case(ReducedNodes):    hasrednodes=true;    // no break is deliberate                  hasrednodes=true; // fall through
1583      case(ReducedDegreesOfFreedom):              case ReducedDegreesOfFreedom:
1584          hasclass[2]=1;                  hasclass[2]=1;
1585          break;                  break;
1586      case(Points):              case Points:
1587          hasline[0]=1;                  hasline[0]=1;
1588          hasclass[3]=1;                  hasclass[3]=1;
1589          break;                  break;
1590      case(Elements):              case Elements:
1591          hasclass[4]=1;                  hasclass[4]=1;
1592          hasline[1]=1;                  hasline[1]=1;
1593          break;                  break;
1594      case(ReducedElements):              case ReducedElements:
1595          hasclass[5]=1;                  hasclass[5]=1;
1596          hasline[1]=1;                  hasline[1]=1;
1597          break;                  break;
1598      case(FaceElements):              case FaceElements:
1599          hasclass[6]=1;                  hasclass[6]=1;
1600          hasline[2]=1;                  hasline[2]=1;
1601          break;                  break;
1602      case(ReducedFaceElements):              case ReducedFaceElements:
1603          hasclass[7]=1;                  hasclass[7]=1;
1604          hasline[2]=1;                  hasline[2]=1;
1605          break;                  break;
1606      case(ContactElementsZero):  hascez=true;    // no break is deliberate              case ContactElementsZero:
1607      case(ContactElementsOne):                  hascez=true; // fall through
1608          hasclass[8]=1;              case ContactElementsOne:
1609          hasline[3]=1;                  hasclass[8]=1;
1610          break;                  hasline[3]=1;
1611      case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate                  break;
1612      case(ReducedContactElementsOne):              case ReducedContactElementsZero:
1613          hasclass[9]=1;                  hasrcez=true; // fall through
1614          hasline[3]=1;              case ReducedContactElementsOne:
1615          break;                  hasclass[9]=1;
1616      default:                  hasline[3]=1;
1617          return false;                  break;
1618      }              default:
1619                    return false;
1620            }
1621      }      }
1622      int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];      int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
     // fail if we have more than one leaf group  
1623    
1624        // fail if we have more than one leaf group
1625      if (totlines>1)      if (totlines>1)
1626      {          return false; // there are at least two branches we can't interpolate between
1627      return false;   // there are at least two branches we can't interpolate between      else if (totlines==1) {
1628      }          if (hasline[0]==1)              // we have points
1629      else if (totlines==1)              resultcode=Points;
1630      {          else if (hasline[1]==1) {
1631      if (hasline[0]==1)      // we have points              if (hasclass[5]==1)
1632      {                  resultcode=ReducedElements;
1633          resultcode=Points;              else
1634      }                  resultcode=Elements;
1635      else if (hasline[1]==1)          } else if (hasline[2]==1) {
1636      {              if (hasclass[7]==1)
1637          if (hasclass[5]==1)                  resultcode=ReducedFaceElements;
1638          {              else
1639          resultcode=ReducedElements;                  resultcode=FaceElements;
1640          }          } else {   // so we must be in line3
1641          else              if (hasclass[9]==1) {
1642          {                  // need something from class 9
1643          resultcode=Elements;                  resultcode=(hasrcez ? ReducedContactElementsZero : ReducedContactElementsOne);
1644          }              } else {
1645      }                  // something from class 8
1646      else if (hasline[2]==1)                  resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1647      {              }
1648          if (hasclass[7]==ReducedFaceElements)          }
1649          {      } else { // totlines==0
1650          resultcode=ReducedFaceElements;          if (hasclass[2]==1) {
1651          }              // something from class 2
1652          else              resultcode=(hasrednodes ? ReducedNodes : ReducedDegreesOfFreedom);
1653          {          } else {
1654          resultcode=FaceElements;              // something from class 1
1655          }              resultcode=(hasnodes ? Nodes : DegreesOfFreedom);
1656      }          }
     else    // so we must be in line3  
     {  
         if (hasclass[9]==1)  
         {  
         // need something from class 9  
         resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);  
         }  
         else  
         {  
         // something from class 8  
         resultcode=(hascez?ContactElementsZero:ContactElementsOne);  
         }  
     }  
     }  
     else    // totlines==0  
     {  
     if (hasclass[2]==1)  
     {  
         // something from class 2  
         resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);  
     }  
     else  
     {   // something from class 1  
         resultcode=(hasnodes?Nodes:DegreesOfFreedom);  
     }  
1657      }      }
1658      return true;      return true;
1659  }  }
1660    
1661  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,
1662                                                 int functionSpaceType_target) const
1663  {  {
1664     switch(functionSpaceType_source) {      switch(functionSpaceType_source) {
1665     case(Nodes):          case Nodes:
1666      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1667      case(Nodes):                  case Nodes:
1668      case(ReducedNodes):                  case ReducedNodes:
1669      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1670      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1671      case(Elements):                  case Elements:
1672      case(ReducedElements):                  case ReducedElements:
1673      case(FaceElements):                  case FaceElements:
1674      case(ReducedFaceElements):                  case ReducedFaceElements:
1675      case(Points):                  case Points:
1676      case(ContactElementsZero):                  case ContactElementsZero:
1677      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1678      case(ContactElementsOne):                  case ContactElementsOne:
1679      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1680      return true;                      return true;
1681      default:                  default:
1682            stringstream temp;                      stringstream temp;
1683            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1684            throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1685     }              }
1686     break;              break;
1687     case(ReducedNodes):          case ReducedNodes:
1688      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1689      case(ReducedNodes):                  case ReducedNodes:
1690      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1691      case(Elements):                  case Elements:
1692      case(ReducedElements):                  case ReducedElements:
1693      case(FaceElements):                  case FaceElements:
1694      case(ReducedFaceElements):                  case ReducedFaceElements:
1695      case(Points):                  case Points:
1696      case(ContactElementsZero):                  case ContactElementsZero:
1697      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1698      case(ContactElementsOne):                  case ContactElementsOne:
1699      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1700      return true;                      return true;
1701      case(Nodes):                  case Nodes:
1702      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1703      return false;                      return false;
1704      default:                  default:
1705          stringstream temp;                      stringstream temp;
1706          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1707          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1708     }              }
1709     break;              break;
1710     case(Elements):          case Elements:
1711      if (functionSpaceType_target==Elements) {              if (functionSpaceType_target==Elements) {
1712        return true;                  return true;
1713      } else if (functionSpaceType_target==ReducedElements) {              } else if (functionSpaceType_target==ReducedElements) {
1714        return true;                  return true;
1715          } else {              } else {
1716            return false;                  return false;
1717          }              }
1718     case(ReducedElements):          case ReducedElements:
1719      if (functionSpaceType_target==ReducedElements) {              if (functionSpaceType_target==ReducedElements) {
1720        return true;                  return true;
1721      } else {              } else {
1722            return false;                  return false;
1723      }              }
1724     case(FaceElements):          case FaceElements:
1725      if (functionSpaceType_target==FaceElements) {              if (functionSpaceType_target==FaceElements) {
1726              return true;                  return true;
1727      } else if (functionSpaceType_target==ReducedFaceElements) {              } else if (functionSpaceType_target==ReducedFaceElements) {
1728              return true;                  return true;
1729      } else {              } else {
1730              return false;                  return false;
1731      }              }
1732     case(ReducedFaceElements):          case ReducedFaceElements:
1733      if (functionSpaceType_target==ReducedFaceElements) {              if (functionSpaceType_target==ReducedFaceElements) {
1734              return true;                  return true;
1735      } else {              } else {
1736          return false;                  return false;
1737      }              }
1738     case(Points):          case Points:
1739      if (functionSpaceType_target==Points) {              if (functionSpaceType_target==Points) {
1740              return true;                  return true;
1741      } else {              } else {
1742              return false;                  return false;
1743      }              }
1744     case(ContactElementsZero):          case ContactElementsZero:
1745     case(ContactElementsOne):          case ContactElementsOne:
1746      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {              if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1747              return true;                  return true;
1748      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {              } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1749              return true;                  return true;
1750      } else {              } else {
1751              return false;                  return false;
1752      }              }
1753     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
1754     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
1755      if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {              if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1756              return true;                  return true;
1757      } else {              } else {
1758              return false;                  return false;
1759      }              }
1760     case(DegreesOfFreedom):          case DegreesOfFreedom:
1761      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1762      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1763      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1764      case(Nodes):                  case Nodes:
1765      case(ReducedNodes):                  case ReducedNodes:
1766      case(Elements):                  case Elements:
1767      case(ReducedElements):                  case ReducedElements:
1768      case(Points):                  case Points:
1769      case(FaceElements):                  case FaceElements:
1770      case(ReducedFaceElements):                  case ReducedFaceElements:
1771      case(ContactElementsZero):                  case ContactElementsZero:
1772      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1773      case(ContactElementsOne):                  case ContactElementsOne:
1774      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1775      return true;                      return true;
1776      default:                  default:
1777          stringstream temp;                      stringstream temp;
1778          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1779          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1780      }              }
1781      break;              break;
1782     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1783     switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1784      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1785      case(ReducedNodes):                  case ReducedNodes:
1786      case(Elements):                  case Elements:
1787      case(ReducedElements):                  case ReducedElements:
1788      case(FaceElements):                  case FaceElements:
1789      case(ReducedFaceElements):                  case ReducedFaceElements:
1790      case(Points):                  case Points:
1791      case(ContactElementsZero):                  case ContactElementsZero:
1792      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1793      case(ContactElementsOne):                  case ContactElementsOne:
1794      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1795      return true;                      return true;
1796      case(Nodes):                  case Nodes:
1797      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1798      return false;                      return false;
1799      default:                  default:
1800          stringstream temp;                      stringstream temp;
1801          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1802          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1803      }              }
1804      break;              break;
1805     default:          default:
1806        stringstream temp;              stringstream temp;
1807        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1808        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
1809        break;              break;
1810     }      }
1811     checkFinleyError();      return false;
1812     return false;  }
1813  }  
1814    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
1815  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const  {
1816  {      if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1817     return false;          return 1;
1818  }  
1819        if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1820  bool MeshAdapter::operator==(const AbstractDomain& other) const          return -1;
1821  {  
1822     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);      return 0;
1823     if (temp!=0) {  }
1824        return (m_finleyMesh==temp->m_finleyMesh);  
1825     } else {  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,
1826        return false;          const escript::AbstractDomain& targetDomain,
1827     }          int functionSpaceType_target) const
1828    {
1829        return false;
1830    }
1831    
1832    bool MeshAdapter::operator==(const escript::AbstractDomain& other) const
1833    {
1834        const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1835        if (temp) {
1836            return (m_finleyMesh==temp->m_finleyMesh);
1837        } else {
1838            return false;
1839        }
1840  }  }
1841    
1842  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const escript::AbstractDomain& other) const
1843  {  {
1844     return !(operator==(other));      return !(operator==(other));
1845  }  }
1846    
1847  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
1848  {  {
1849     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1850     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);      return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
1851     checkPasoError();                 package, symmetry, mesh->MPIInfo);
    return out;  
1852  }  }
1853    
1854  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
1855  {  {
1856     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1857     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);      return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
1858     checkPasoError();                  package, symmetry, mesh->MPIInfo);
    return out;  
1859  }  }
1860    
1861  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1862  {  {
1863     return continuousFunction(asAbstractContinuousDomain()).getX();      return continuousFunction(*this).getX();
1864  }  }
1865    
1866  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1867  {  {
1868     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();      return functionOnBoundary(*this).getNormal();
1869  }  }
1870    
1871  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1872  {  {
1873     return escript::function(asAbstractContinuousDomain()).getSize();      return escript::function(*this).getSize();
1874  }  }
1875    
1876  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1877  {  {
1878     int *out = NULL;      int *out = NULL;
1879     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1880     switch (functionSpaceType) {      switch (functionSpaceType) {
1881     case(Nodes):          case Nodes:
1882     out=mesh->Nodes->Id;              out=mesh->Nodes->Id;
1883     break;              break;
1884     case(ReducedNodes):          case ReducedNodes:
1885     out=mesh->Nodes->reducedNodesId;              out=mesh->Nodes->reducedNodesId;
1886     break;              break;
1887     case(Elements):          case Elements:
1888     out=mesh->Elements->Id;          case ReducedElements:
1889     break;              out=mesh->Elements->Id;
1890     case(ReducedElements):              break;
1891     out=mesh->Elements->Id;          case FaceElements:
1892     break;          case ReducedFaceElements:
1893     case(FaceElements):              out=mesh->FaceElements->Id;
1894     out=mesh->FaceElements->Id;              break;
1895     break;          case Points:
1896     case(ReducedFaceElements):              out=mesh->Points->Id;
1897     out=mesh->FaceElements->Id;              break;
1898     break;          case ContactElementsZero:
1899     case(Points):          case ReducedContactElementsZero:
1900     out=mesh->Points->Id;          case ContactElementsOne:
1901     break;          case ReducedContactElementsOne:
1902     case(ContactElementsZero):              out=mesh->ContactElements->Id;
1903     out=mesh->ContactElements->Id;              break;
1904     break;          case DegreesOfFreedom:
1905     case(ReducedContactElementsZero):              out=mesh->Nodes->degreesOfFreedomId;
1906     out=mesh->ContactElements->Id;              break;
1907     break;          case ReducedDegreesOfFreedom:
1908     case(ContactElementsOne):              out=mesh->Nodes->reducedDegreesOfFreedomId;
1909     out=mesh->ContactElements->Id;              break;
1910     break;          default:
1911     case(ReducedContactElementsOne):              stringstream temp;
1912     out=mesh->ContactElements->Id;              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1913     break;              throw FinleyAdapterException(temp.str());
1914     case(DegreesOfFreedom):              break;
1915     out=mesh->Nodes->degreesOfFreedomId;      }
1916     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;  
1917  }  }
1918  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1919  {  {
1920     int out=0;      int out=0;
1921     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1922     switch (functionSpaceType) {      switch (functionSpaceType) {
1923     case(Nodes):          case Nodes:
1924     out=mesh->Nodes->Tag[sampleNo];              out=mesh->Nodes->Tag[sampleNo];
1925     break;              break;
1926     case(ReducedNodes):          case ReducedNodes:
1927     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");              throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1928     break;              break;
1929     case(Elements):          case Elements:
1930     out=mesh->Elements->Tag[sampleNo];          case ReducedElements:
1931     break;              out=mesh->Elements->Tag[sampleNo];
1932     case(ReducedElements):              break;
1933     out=mesh->Elements->Tag[sampleNo];          case FaceElements:
1934     break;          case ReducedFaceElements:
1935     case(FaceElements):              out=mesh->FaceElements->Tag[sampleNo];
1936     out=mesh->FaceElements->Tag[sampleNo];              break;
1937     break;          case Points:
1938     case(ReducedFaceElements):              out=mesh->Points->Tag[sampleNo];
1939     out=mesh->FaceElements->Tag[sampleNo];              break;
1940     break;          case ContactElementsZero:
1941     case(Points):          case ReducedContactElementsZero:
1942     out=mesh->Points->Tag[sampleNo];          case ContactElementsOne:
1943     break;          case ReducedContactElementsOne:
1944     case(ContactElementsZero):              out=mesh->ContactElements->Tag[sampleNo];
1945     out=mesh->ContactElements->Tag[sampleNo];              break;
1946     break;          case DegreesOfFreedom:
1947     case(ReducedContactElementsZero):              throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1948     out=mesh->ContactElements->Tag[sampleNo];              break;
1949     break;          case ReducedDegreesOfFreedom:
1950     case(ContactElementsOne):              throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1951     out=mesh->ContactElements->Tag[sampleNo];              break;
1952     break;          default:
1953     case(ReducedContactElementsOne):              stringstream temp;
1954     out=mesh->ContactElements->Tag[sampleNo];              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1955     break;              throw FinleyAdapterException(temp.str());
1956     case(DegreesOfFreedom):              break;
1957     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");      }
1958     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;  
1959  }  }
1960    
1961    
1962  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
1963  {  {
1964     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
1965     escriptDataC tmp=mask.getDataC();      switch(functionSpaceType) {
1966     switch(functionSpaceType) {          case Nodes:
1967     case(Nodes):              mesh->Nodes->setTags(newTag, mask);
1968     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);              break;
1969     break;          case ReducedNodes:
1970     case(ReducedNodes):              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1971     throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case DegreesOfFreedom:
1972     break;              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1973     case(DegreesOfFreedom):          case ReducedDegreesOfFreedom:
1974     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1975     break;          case Elements:
1976     case(ReducedDegreesOfFreedom):          case ReducedElements:
1977     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");              mesh->Elements->setTags(newTag, mask);
1978     break;              break;
1979     case(Elements):          case FaceElements:
1980     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case ReducedFaceElements:
1981     break;              mesh->FaceElements->setTags(newTag, mask);
1982     case(ReducedElements):              break;
1983     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case Points:
1984     break;              mesh->Points->setTags(newTag, mask);
1985     case(FaceElements):              break;
1986     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ContactElementsZero:
1987     break;          case ReducedContactElementsZero:
1988     case(ReducedFaceElements):          case ContactElementsOne:
1989     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ReducedContactElementsOne:
1990     break;              mesh->ContactElements->setTags(newTag, mask);
1991     case(Points):              break;
1992     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);          default:
1993     break;              stringstream temp;
1994     case(ContactElementsZero):              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
1995     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              throw FinleyAdapterException(temp.str());
1996     break;      }
1997     case(ReducedContactElementsZero):      checkFinleyError();
1998     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  }
1999     break;  
2000     case(ContactElementsOne):  void MeshAdapter::setTagMap(const string& name, int tag)
2001     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  {
2002     break;      Mesh* mesh=m_finleyMesh.get();
2003     case(ReducedContactElementsOne):      mesh->addTagMap(name.c_str(), tag);
2004     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);      checkFinleyError();
2005     break;  }
2006     default:  
2007        stringstream temp;  int MeshAdapter::getTag(const string& name) const
2008        temp << "Error - Finley does not know anything about function space type " << functionSpaceType;  {
2009        throw FinleyAdapterException(temp.str());      Mesh* mesh=m_finleyMesh.get();
2010     }      int tag = mesh->getTag(name.c_str());
2011     checkFinleyError();      checkFinleyError();
2012     return;      return tag;
2013  }  }
2014    
2015  void MeshAdapter::setTagMap(const std::string& name,  int tag)  bool MeshAdapter::isValidTagName(const string& name) const
2016  {  {
2017     Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2018     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);      return mesh->isValidTagName(name.c_str());
2019     checkPasoError();  }
2020     // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
2021  }  string MeshAdapter::showTagNames() const
2022    {
2023  int MeshAdapter::getTag(const std::string& name) const      stringstream temp;
2024  {      Mesh* mesh=m_finleyMesh.get();
2025     Finley_Mesh* mesh=m_finleyMesh.get();      TagMap::const_iterator it = mesh->tagMap.begin();
2026     int tag=0;      while (it != mesh->tagMap.end()) {
2027     tag=Finley_Mesh_getTag(mesh, name.c_str());          temp << it->first;
2028     checkPasoError();          ++it;
2029     // throwStandardException("MeshAdapter::getTag is not implemented.");          if (it != mesh->tagMap.end())
2030     return tag;              temp << ", ";
2031  }      }
2032        return temp.str();
 bool MeshAdapter::isValidTagName(const std::string& name) const  
 {  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    return Finley_Mesh_isValidTagName(mesh,name.c_str());  
 }  
   
 std::string MeshAdapter::showTagNames() const  
 {  
    stringstream temp;  
    Finley_Mesh* mesh=m_finleyMesh.get();  
    Finley_TagMap* tag_map=mesh->TagMap;  
    while (tag_map) {  
       temp << tag_map->name;  
       tag_map=tag_map->next;  
       if (tag_map) temp << ", ";  
    }  
    return temp.str();  
2033  }  }
2034    
2035  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2036  {  {
2037    Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2038    dim_t numTags=0;      switch(functionSpaceCode) {
2039    switch(functionSpaceCode) {          case Nodes:
2040     case(Nodes):              return mesh->Nodes->tagsInUse.size();
2041            numTags=mesh->Nodes->numTagsInUse;          case ReducedNodes:
2042            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2043     case(ReducedNodes):          case DegreesOfFreedom:
2044            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2045            break;          case ReducedDegreesOfFreedom:
2046     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2047            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2048            break;          case ReducedElements:
2049     case(ReducedDegreesOfFreedom):              return mesh->Elements->tagsInUse.size();
2050            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2051            break;          case ReducedFaceElements:
2052     case(Elements):              return mesh->FaceElements->tagsInUse.size();
2053     case(ReducedElements):          case Points:
2054            numTags=mesh->Elements->numTagsInUse;              return mesh->Points->tagsInUse.size();
2055            break;          case ContactElementsZero:
2056     case(FaceElements):          case ReducedContactElementsZero:
2057     case(ReducedFaceElements):          case ContactElementsOne:
2058            numTags=mesh->FaceElements->numTagsInUse;          case ReducedContactElementsOne:
2059            break;              return mesh->ContactElements->tagsInUse.size();
2060     case(Points):          default:
2061            numTags=mesh->Points->numTagsInUse;              stringstream ss;
2062            break;              ss << "Finley does not know anything about function space type "
2063     case(ContactElementsZero):                   << functionSpaceCode;
2064     case(ReducedContactElementsZero):              throw FinleyAdapterException(ss.str());
2065     case(ContactElementsOne):      }
2066     case(ReducedContactElementsOne):      return 0;
           numTags=mesh->ContactElements->numTagsInUse;  
           break;  
    default:  
       stringstream temp;  
       temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;  
       throw FinleyAdapterException(temp.str());  
   }  
   return numTags;  
2067  }  }
2068    
2069  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2070  {  {
2071    Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2072    index_t* tags=NULL;      switch(functionSpaceCode) {
2073    switch(functionSpaceCode) {          case Nodes:
2074     case(Nodes):              return &mesh->Nodes->tagsInUse[0];
2075            tags=mesh->Nodes->tagsInUse;          case ReducedNodes:
2076            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2077     case(ReducedNodes):          case DegreesOfFreedom:
2078            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2079            break;          case ReducedDegreesOfFreedom:
2080     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2081            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2082            break;          case ReducedElements:
2083     case(ReducedDegreesOfFreedom):              return &mesh->Elements->tagsInUse[0];
2084            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2085            break;          case ReducedFaceElements:
2086     case(Elements):              return &mesh->FaceElements->tagsInUse[0];
2087     case(ReducedElements):          case Points:
2088            tags=mesh->Elements->tagsInUse;              return &mesh->Points->tagsInUse[0];
2089            break;          case ContactElementsZero:
2090     case(FaceElements):          case ReducedContactElementsZero:
2091     case(ReducedFaceElements):          case ContactElementsOne:
2092            tags=mesh->FaceElements->tagsInUse;          case ReducedContactElementsOne:
2093            break;              return &mesh->ContactElements->tagsInUse[0];
2094     case(Points):          default:
2095            tags=mesh->Points->tagsInUse;              stringstream temp;
2096            break;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2097     case(ContactElementsZero):              throw FinleyAdapterException(temp.str());
2098     case(ReducedContactElementsZero):      }
2099     case(ContactElementsOne):      return NULL;
    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;  
2100  }  }
2101    
2102    
2103  bool MeshAdapter::canTag(int functionSpaceCode) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2104  {  {
2105    switch(functionSpaceCode) {      switch(functionSpaceCode) {
2106     case(Nodes):          case Nodes:
2107     case(Elements):          case Elements:
2108     case(ReducedElements):          case ReducedElements:
2109     case(FaceElements):          case FaceElements:
2110     case(ReducedFaceElements):          case ReducedFaceElements:
2111     case(Points):          case Points:
2112     case(ContactElementsZero):          case ContactElementsZero:
2113     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
2114     case(ContactElementsOne):          case ContactElementsOne:
2115     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
2116            return true;              return true;
2117     case(ReducedNodes):          default:
2118     case(DegreesOfFreedom):              return false;
2119     case(ReducedDegreesOfFreedom):      }
       return false;  
    default:  
     return false;  
   }  
2120  }  }
2121    
2122  AbstractDomain::StatusType MeshAdapter::getStatus() const  escript::AbstractDomain::StatusType MeshAdapter::getStatus() const
2123  {  {
2124    Finley_Mesh* mesh=m_finleyMesh.get();      Mesh* mesh=m_finleyMesh.get();
2125    return Finley_Mesh_getStatus(mesh);      return mesh->getStatus();
2126    }
2127    
2128    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2129    {
2130        Mesh* mesh=m_finleyMesh.get();
2131        int order =-1;
2132        switch(functionSpaceCode) {
2133            case Nodes:
2134            case DegreesOfFreedom:
2135                order=mesh->approximationOrder;
2136                break;
2137            case ReducedNodes:
2138            case ReducedDegreesOfFreedom:
2139                order=mesh->reducedApproximationOrder;
2140                break;
2141            case Elements:
2142            case FaceElements:
2143            case Points:
2144            case ContactElementsZero:
2145            case ContactElementsOne:
2146                order=mesh->integrationOrder;
2147                break;
2148            case ReducedElements:
2149            case ReducedFaceElements:
2150            case ReducedContactElementsZero:
2151            case ReducedContactElementsOne:
2152                order=mesh->reducedIntegrationOrder;
2153                break;
2154            default:
2155                stringstream temp;
2156                temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2157                throw FinleyAdapterException(temp.str());
2158        }
2159        return order;
2160  }  }
2161    
2162    bool MeshAdapter::supportsContactElements() const
2163    {
2164        return true;
2165    }
2166    
2167    escript::Data MeshAdapter::randomFill(const escript::DataTypes::ShapeType& shape,
2168           const escript::FunctionSpace& what, long seed, const boost::python::tuple& filter) const
2169    {
2170        escript::Data towipe(0, shape, what, true);
2171        // since we just made this object, no sharing is possible and we don't need to check for
2172        // exlusive write
2173        escript::DataTypes::ValueType& dv=towipe.getExpandedVectorReference();
2174        const size_t dvsize=dv.size();
2175        esysUtils::randomFillArray(seed, &(dv[0]), dvsize);
2176        return towipe;  
2177    }
2178    
2179    
2180    void MeshAdapter::addDiracPoints(const vector<double>& points,
2181                                     const vector<int>& tags) const
2182    {
2183        // points will be flattened
2184        const int dim = getDim();
2185        int numPoints=points.size()/dim;
2186        int numTags=tags.size();
2187        Mesh* mesh=m_finleyMesh.get();
2188    
2189        if ( points.size() % dim != 0 ) {
2190            throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2191        }
2192    
2193        if ((numTags > 0) && (numPoints != numTags))
2194            throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2195    
2196        mesh->addPoints(numPoints, &points[0], &tags[0]);
2197        checkFinleyError();
2198    }
2199    
2200    // void MeshAdapter::addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2201    // {
2202    //       const int dim = getDim();
2203    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2204    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2205    //       Mesh* mesh=m_finleyMesh.get();
2206    //
2207    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2208    //       throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2209    //
2210    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2211    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2212    //
2213    //       for (int i=0;i<numPoints;++i) {
2214    //         int tag_id=-1;
2215    //         int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2216    //         if  ( numComps !=   dim ) {
2217    //                stringstream temp;
2218    //                temp << "Error - illegal number of components " << numComps << " for point " << i;
2219    //                throw FinleyAdapterException(temp.str());
2220    //         }
2221    //         points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2222    //         if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2223    //         if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2224    //
2225    //         if ( numTags > 0) {
2226    //                boost::python::extract<string> ex_str(tags[i]);
2227    //                if  ( ex_str.check() ) {
2228    //                    tag_id=getTag( ex_str());
2229    //                } else {
2230    //                     boost::python::extract<int> ex_int(tags[i]);
2231    //                     if ( ex_int.check() ) {
2232    //                         tag_id=ex_int();
2233    //                     } else {
2234    //                          stringstream temp;
2235    //                          temp << "Error - unable to extract tag for point " << i;
2236    //                          throw FinleyAdapterException(temp.str());
2237    //                    }
2238    //                }
2239    //         }
2240    //            tags_ptr[i]=tag_id;
2241    //       }
2242    //
2243    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2244    //       checkPasoError();
2245    //
2246    //       TMPMEMFREE(points_ptr);
2247    //       TMPMEMFREE(tags_ptr);
2248    // }
2249    
2250    /*
2251    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2252    {
2253        boost::python::list points =  boost::python::list();
2254        boost::python::list tags =  boost::python::list();
2255        points.append(point);
2256        tags.append(tag);
2257        addDiracPoints(points, tags);
2258    }
2259    */
2260    
2261    /*
2262    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const string& tag) const
2263    {
2264        boost::python::list points =   boost::python::list();
2265        boost::python::list tags =   boost::python::list();
2266        points.append(point);
2267        tags.append(tag);
2268        addDiracPoints(points, tags);
2269    }
2270    */
2271  }  // end of namespace  }  // end of namespace
2272    

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