/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 2644 by jfenwick, Wed Sep 2 04:14:03 2009 UTC revision 4441 by caltinay, Fri Jun 7 02:23:49 2013 UTC
# Line 1  Line 1 
1    
2  /*******************************************************  /*****************************************************************************
3  *  *
4  * Copyright (c) 2003-2009 by University of Queensland  * Copyright (c) 2003-2013 by University of Queensland
5  * Earth Systems Science Computational Center (ESSCC)  * http://www.uq.edu.au
 * http://www.uq.edu.au/esscc  
6  *  *
7  * Primary Business: Queensland, Australia  * Primary Business: Queensland, Australia
8  * Licensed under the Open Software License version 3.0  * Licensed under the Open Software License version 3.0
9  * http://www.opensource.org/licenses/osl-3.0.php  * http://www.opensource.org/licenses/osl-3.0.php
10  *  *
11  *******************************************************/  * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12    * Development since 2012 by School of Earth Sciences
13    *
14    *****************************************************************************/
15    
16    #include <pasowrap/PasoException.h>
17    #include <pasowrap/TransportProblemAdapter.h>
18  #include "MeshAdapter.h"  #include "MeshAdapter.h"
19  #include "escript/Data.h"  #include "escript/Data.h"
20  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
21    #include "esysUtils/blocktimer.h"
22    
23    #include <boost/python/import.hpp>
24  #ifdef USE_NETCDF  #ifdef USE_NETCDF
25  #include <netcdfcpp.h>  #include <netcdfcpp.h>
26  #endif  #endif
 #ifdef PASO_MPI  
 #include <mpi.h>  
 #include "paso/Paso_MPI.h"  
 #endif  
 extern "C" {  
 #include "esysUtils/blocktimer.h"  
 }  
27    
28  using namespace std;  using namespace std;
29  using namespace escript;  using namespace paso;
30    
31  namespace finley {  namespace finley {
32    
 //  
33  // define the static constants  // define the static constants
34  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
35  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
# Line 50  const int MeshAdapter::ReducedContactEle Line 48  const int MeshAdapter::ReducedContactEle
48    
49  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
50  {  {
51     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
52     //      // need to use a null_deleter as Finley_Mesh_free deletes the pointer
53     // need to use a null_deleter as Finley_Mesh_free deletes the pointer      // for us.
54     // for us.      m_finleyMesh.reset(finleyMesh, null_deleter());
    m_finleyMesh.reset(finleyMesh,null_deleter());  
55  }  }
56    
57  //  //
58  // The copy constructor should just increment the use count  // The copy constructor should just increment the use count
59  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in) :
60  m_finleyMesh(in.m_finleyMesh)      m_finleyMesh(in.m_finleyMesh)
61  {  {
62     setFunctionSpaceTypeNames();      setFunctionSpaceTypeNames();
63  }  }
64    
65  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
66  {  {
67     //      // I hope the case for the pointer being zero has been taken care of
68     // I hope the case for the pointer being zero has been taken care of.      if (m_finleyMesh.unique()) {
69     //  cout << "In MeshAdapter destructor." << endl;          Finley_Mesh_free(m_finleyMesh.get());
70     if (m_finleyMesh.unique()) {      }
       Finley_Mesh_free(m_finleyMesh.get());  
    }  
71  }  }
72    
73  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
74  {  {
75     return m_finleyMesh.get()->MPIInfo->size;      return m_finleyMesh.get()->MPIInfo->size;
76  }  }
77    
78  int MeshAdapter::getMPIRank() const  int MeshAdapter::getMPIRank() const
79  {  {
80     return m_finleyMesh.get()->MPIInfo->rank;      return m_finleyMesh.get()->MPIInfo->rank;
81  }  }
82    
83  void MeshAdapter::MPIBarrier() const  void MeshAdapter::MPIBarrier() const
84  {  {
85  #ifdef PASO_MPI  #ifdef ESYS_MPI
86     MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);      MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
87  #endif  #endif
    return;  
88  }  }
89    
90  bool MeshAdapter::onMasterProcessor() const  bool MeshAdapter::onMasterProcessor() const
91  {  {
92     return m_finleyMesh.get()->MPIInfo->rank == 0;      return m_finleyMesh.get()->MPIInfo->rank == 0;
93  }  }
94    
95    #ifdef ESYS_MPI
96  #ifdef PASO_MPI  MPI_Comm
   MPI_Comm  
97  #else  #else
98    unsigned int  unsigned int
99  #endif  #endif
100  MeshAdapter::getMPIComm() const  MeshAdapter::getMPIComm() const
101  {  {
102  #ifdef PASO_MPI  #ifdef ESYS_MPI
103      return m_finleyMesh->MPIInfo->comm;      return m_finleyMesh->MPIInfo->comm;
104  #else  #else
105      return 0;      return 0;
106  #endif  #endif
107  }  }
108    
109    Finley_Mesh* MeshAdapter::getFinley_Mesh() const
110  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  {
111     return m_finleyMesh.get();      return m_finleyMesh.get();
112  }  }
113    
114  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
115  {  {
116     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;      Finley_Mesh_write(m_finleyMesh.get(), fileName.c_str());
117     strcpy(fName,fileName.c_str());      checkFinleyError();
    Finley_Mesh_write(m_finleyMesh.get(),fName);  
    checkFinleyError();  
    TMPMEMFREE(fName);  
118  }  }
119    
120  void MeshAdapter::Print_Mesh_Info(const bool full) const  void MeshAdapter::Print_Mesh_Info(const bool full) const
121  {  {
122     Finley_PrintMesh_Info(m_finleyMesh.get(), full);      Finley_PrintMesh_Info(m_finleyMesh.get(), full);
123  }  }
124    
125  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const string& fileName) const
126  {  {
127  #ifdef USE_NETCDF  #ifdef USE_NETCDF
128     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};      const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
129     NcVar *ids;      NcVar *ids;
130     int *int_ptr;      int *int_ptr;
131     Finley_Mesh *mesh = m_finleyMesh.get();      Finley_Mesh *mesh = m_finleyMesh.get();
132     Finley_TagMap* tag_map;      int num_Tags = 0;
133     int num_Tags = 0;      int mpi_size                         = mesh->MPIInfo->size;
134     int mpi_size             = mesh->MPIInfo->size;      int mpi_rank                         = mesh->MPIInfo->rank;
135     int mpi_rank             = mesh->MPIInfo->rank;      int numDim                           = mesh->Nodes->numDim;
136     int numDim               = mesh->Nodes->numDim;      int numNodes                         = mesh->Nodes->numNodes;
137     int numNodes             = mesh->Nodes->numNodes;      int num_Elements                     = mesh->Elements->numElements;
138     int num_Elements         = mesh->Elements->numElements;      int num_FaceElements                 = mesh->FaceElements->numElements;
139     int num_FaceElements         = mesh->FaceElements->numElements;      int num_ContactElements              = mesh->ContactElements->numElements;
140     int num_ContactElements      = mesh->ContactElements->numElements;      int num_Points                       = mesh->Points->numElements;
141     int num_Points           = mesh->Points->numElements;      int num_Elements_numNodes            = mesh->Elements->numNodes;
142     int num_Elements_numNodes        = mesh->Elements->numNodes;      int num_FaceElements_numNodes        = mesh->FaceElements->numNodes;
143     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;      int num_ContactElements_numNodes     = mesh->ContactElements->numNodes;
144     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;  #ifdef ESYS_MPI
145  #ifdef PASO_MPI      MPI_Status status;
    MPI_Status status;  
146  #endif  #endif
147    
148  /* Incoming token indicates it's my turn to write */  /* Incoming token indicates it's my turn to write */
149  #ifdef PASO_MPI  #ifdef ESYS_MPI
150     if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);      if (mpi_rank>0) {
151            MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
152        }
153  #endif  #endif
154    
155     char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),      char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
156                                                       mpi_size, mpi_rank);                                                       mpi_size, mpi_rank);
157    
158     /* Figure out how much storage is required for tags */      // Figure out how much storage is required for tags
159     tag_map = mesh->TagMap;      num_Tags = mesh->tagMap.size();
160     num_Tags = 0;  
161     if (tag_map) {      // NetCDF error handler
162        while (tag_map) {      NcError err(NcError::verbose_nonfatal);
163           num_Tags++;      // Create the file.
164           tag_map=tag_map->next;      NcFile dataFile(newFileName, NcFile::Replace);
165        }      string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
166     }      // check if writing was successful
167        if (!dataFile.is_valid())
168     // NetCDF error handler          throw FinleyAdapterException(msgPrefix+"Open file for output");
169     NcError err(NcError::verbose_nonfatal);  
170     // Create the file.      // Define dimensions (num_Elements and dim_Elements are identical,
171     NcFile dataFile(newFileName, NcFile::Replace);      // dim_Elements only appears if > 0)
172     // check if writing was successful      if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
173     if (!dataFile.is_valid())          throw FinleyAdapterException(msgPrefix+"add_dim(numNodes)");
174        throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);      if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
175            throw FinleyAdapterException(msgPrefix+"add_dim(numDim)");
176     // 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)) )
177     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )          throw FinleyAdapterException(msgPrefix+"add_dim(mpi_size)");
178        throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);      if (num_Elements>0)
179     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
180        throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements)");
181     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )      if (num_FaceElements>0)
182        throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
183     if (num_Elements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements)");
184        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )      if (num_ContactElements>0)
185           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
186     if (num_FaceElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements)");
187        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )      if (num_Points>0)
188           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
189     if (num_ContactElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Points)");
190        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )      if (num_Elements>0)
191           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)) )
192     if (num_Points>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Elements_Nodes)");
193        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )      if (num_FaceElements>0)
194           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)) )
195     if (num_Elements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
196        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )      if (num_ContactElements>0)
197           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)) )
198     if (num_FaceElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
199        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )      if (num_Tags>0)
200           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)) )
201     if (num_ContactElements>0)              throw FinleyAdapterException(msgPrefix+"add_dim(dim_Tags)");
202        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )  
203           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);      // Attributes: MPI size, MPI rank, Name, order, reduced_order
204     if (num_Tags>0)      if (!dataFile.add_att("mpi_size", mpi_size) )
205        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )          throw FinleyAdapterException(msgPrefix+"add_att(mpi_size)");
206           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);      if (!dataFile.add_att("mpi_rank", mpi_rank) )
207            throw FinleyAdapterException(msgPrefix+"add_att(mpi_rank)");
208     // Attributes: MPI size, MPI rank, Name, order, reduced_order      if (!dataFile.add_att("Name",mesh->Name) )
209     if (!dataFile.add_att("mpi_size", mpi_size) )          throw FinleyAdapterException(msgPrefix+"add_att(Name)");
210        throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("numDim",numDim) )
211     if (!dataFile.add_att("mpi_rank", mpi_rank) )          throw FinleyAdapterException(msgPrefix+"add_att(order)");
212        throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("order",mesh->integrationOrder) )
213     if (!dataFile.add_att("Name",mesh->Name) )          throw FinleyAdapterException(msgPrefix+"add_att(order)");
214        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
215     if (!dataFile.add_att("numDim",numDim) )          throw FinleyAdapterException(msgPrefix+"add_att(reduced_order)");
216        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("numNodes",numNodes) )
217     if (!dataFile.add_att("order",mesh->order) )          throw FinleyAdapterException(msgPrefix+"add_att(numNodes)");
218        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Elements",num_Elements) )
219     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements)");
220        throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
221     if (!dataFile.add_att("numNodes",numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements)");
222        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
223     if (!dataFile.add_att("num_Elements",num_Elements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements)");
224        throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Points",num_Points) )
225     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Points)");
226        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
227     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Elements_numNodes)");
228        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
229     if (!dataFile.add_att("num_Points",num_Points) )          throw FinleyAdapterException(msgPrefix+"add_att(num_FaceElements_numNodes)");
230        throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
231     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(num_ContactElements_numNodes)");
232        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) )
233     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(Elements_TypeId)");
234        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) )
235     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )          throw FinleyAdapterException(msgPrefix+"add_att(FaceElements_TypeId)");
236        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) )
237     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(ContactElements_TypeId)");
238        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) )
239     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(Points_TypeId)");
240        throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);      if (!dataFile.add_att("num_Tags", num_Tags) )
241     if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )          throw FinleyAdapterException(msgPrefix+"add_att(num_Tags)");
242        throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);  
243     if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )      // // // // // Nodes // // // // //
244        throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);  
245     if (!dataFile.add_att("num_Tags", num_Tags) )      // Nodes nodeDistribution
246        throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);      if (! (ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
247            throw FinleyAdapterException(msgPrefix+"add_var(Nodes_NodeDistribution)");
248     // // // // // Nodes // // // // //      int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
249        if (! (ids->put(int_ptr, mpi_size+1)) )
250     // 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)");
251     if (numNodes>0) {  
252        // Nodes degreesOfFreedomDistribution
253        // Nodes Id      if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
254        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )          throw FinleyAdapterException(msgPrefix+"add_var(Nodes_DofDistribution)");
255           throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);      int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
256        int_ptr = &mesh->Nodes->Id[0];      if (! (ids->put(int_ptr, mpi_size+1)) )
257        if (! (ids->put(int_ptr, numNodes)) )          throw FinleyAdapterException(msgPrefix+"put(Nodes_DofDistribution)");
258           throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);  
259        // Only write nodes if non-empty because NetCDF doesn't like empty arrays
260        // Nodes Tag      // (it treats them as NC_UNLIMITED)
261        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )      if (numNodes>0) {
262           throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);          // Nodes Id
263        int_ptr = &mesh->Nodes->Tag[0];          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
264        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Id)");
265           throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->Id[0];
266            if (! (ids->put(int_ptr, numNodes)) )
267        // Nodes gDOF              throw FinleyAdapterException(msgPrefix+"put(Nodes_Id)");
268        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )  
269           throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);          // Nodes Tag
270        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
271        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Tag)");
272           throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->Tag[0];
273            if (! (ids->put(int_ptr, numNodes)) )
274        // Nodes global node index              throw FinleyAdapterException(msgPrefix+"put(Nodes_Tag)");
275        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )  
276           throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);          // Nodes gDOF
277        int_ptr = &mesh->Nodes->globalNodesIndex[0];          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
278        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gDOF)");
279           throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
280            if (! (ids->put(int_ptr, numNodes)) )
281        // Nodes grDof              throw FinleyAdapterException(msgPrefix+"put(Nodes_gDOF)");
282        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )  
283           throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);          // Nodes global node index
284        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
285        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_gNI)");
286           throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalNodesIndex[0];
287            if (! (ids->put(int_ptr, numNodes)) )
288        // Nodes grNI              throw FinleyAdapterException(msgPrefix+"put(Nodes_gNI)");
289        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )  
290           throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);          // Nodes grDof
291        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
292        if (! (ids->put(int_ptr, numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grDfI)");
293           throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
294            if (! (ids->put(int_ptr, numNodes)) )
295        // Nodes Coordinates              throw FinleyAdapterException(msgPrefix+"put(Nodes_grDfI)");
296        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )  
297           throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);          // Nodes grNI
298        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
299           throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_grNI)");
300            int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
301        // Nodes degreesOfFreedomDistribution          if (! (ids->put(int_ptr, numNodes)) )
302        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )              throw FinleyAdapterException(msgPrefix+"put(Nodes_grNI)");
303           throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);  
304        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];          // Nodes Coordinates
305        if (! (ids->put(int_ptr, mpi_size+1)) )          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
306           throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Nodes_Coordinates)");
307            if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
308        // Nodes nodeDistribution              throw FinleyAdapterException(msgPrefix+"put(Nodes_Coordinates)");
309        if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )      }
310           throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);  
311        int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];      // // // // // Elements // // // // //
312        if (! (ids->put(int_ptr, mpi_size+1)) )      if (num_Elements>0) {
313           throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);          // Elements_Id
314            if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
315     }              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Id)");
316            int_ptr = &mesh->Elements->Id[0];
317     // // // // // Elements // // // // //          if (! (ids->put(int_ptr, num_Elements)) )
318                throw FinleyAdapterException(msgPrefix+"put(Elements_Id)");
319     if (num_Elements>0) {  
320            // Elements_Tag
321        // Elements_Id          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
322        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Tag)");
323           throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Tag[0];
324        int_ptr = &mesh->Elements->Id[0];          if (! (ids->put(int_ptr, num_Elements)) )
325        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Tag)");
326           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);  
327            // Elements_Owner
328        // Elements_Tag          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
329        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Owner)");
330           throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Owner[0];
331        int_ptr = &mesh->Elements->Tag[0];          if (! (ids->put(int_ptr, num_Elements)) )
332        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Owner)");
333           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);  
334            // Elements_Color
335        // Elements_Owner          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
336        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Color)");
337           throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);          int_ptr = &mesh->Elements->Color[0];
338        int_ptr = &mesh->Elements->Owner[0];          if (! (ids->put(int_ptr, num_Elements)) )
339        if (! (ids->put(int_ptr, num_Elements)) )              throw FinleyAdapterException(msgPrefix+"put(Elements_Color)");
340           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);  
341            // Elements_Nodes
342        // Elements_Color          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
343        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )              throw FinleyAdapterException(msgPrefix+"add_var(Elements_Nodes)");
344           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)) )
345        int_ptr = &mesh->Elements->Color[0];              throw FinleyAdapterException(msgPrefix+"put(Elements_Nodes)");
346        if (! (ids->put(int_ptr, num_Elements)) )      }
347           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);  
348        // // // // // Face_Elements // // // // //
349        // Elements_Nodes      if (num_FaceElements>0) {
350        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )          // FaceElements_Id
351           throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
352        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Id)");
353           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);          int_ptr = &mesh->FaceElements->Id[0];
354            if (! (ids->put(int_ptr, num_FaceElements)) )
355     }              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Id)");
356    
357     // // // // // Face_Elements // // // // //          // FaceElements_Tag
358            if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
359     if (num_FaceElements>0) {              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Tag)");
360            int_ptr = &mesh->FaceElements->Tag[0];
361        // FaceElements_Id          if (! (ids->put(int_ptr, num_FaceElements)) )
362        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Tag)");
363           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);  
364        int_ptr = &mesh->FaceElements->Id[0];          // FaceElements_Owner
365        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
366           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Owner)");
367            int_ptr = &mesh->FaceElements->Owner[0];
368        // FaceElements_Tag          if (! (ids->put(int_ptr, num_FaceElements)) )
369        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Owner)");
370           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);  
371        int_ptr = &mesh->FaceElements->Tag[0];          // FaceElements_Color
372        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
373           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Color)");
374            int_ptr = &mesh->FaceElements->Color[0];
375        // FaceElements_Owner          if (! (ids->put(int_ptr, num_FaceElements)) )
376        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Color)");
377           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);  
378        int_ptr = &mesh->FaceElements->Owner[0];          // FaceElements_Nodes
379        if (! (ids->put(int_ptr, num_FaceElements)) )          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
380           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(FaceElements_Nodes)");
381            if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
382        // FaceElements_Color              throw FinleyAdapterException(msgPrefix+"put(FaceElements_Nodes)");
383        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )      }
384           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);  
385        int_ptr = &mesh->FaceElements->Color[0];      // // // // // Contact_Elements // // // // //
386        if (! (ids->put(int_ptr, num_FaceElements)) )      if (num_ContactElements>0) {
387           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);  
388            // ContactElements_Id
389        // FaceElements_Nodes          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
390        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Id)");
391           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);          int_ptr = &mesh->ContactElements->Id[0];
392        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )          if (! (ids->put(int_ptr, num_ContactElements)) )
393           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Id)");
394    
395     }          // ContactElements_Tag
396            if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
397     // // // // // Contact_Elements // // // // //              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Tag)");
398            int_ptr = &mesh->ContactElements->Tag[0];
399     if (num_ContactElements>0) {          if (! (ids->put(int_ptr, num_ContactElements)) )
400                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Tag)");
401        // ContactElements_Id  
402        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )          // ContactElements_Owner
403           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
404        int_ptr = &mesh->ContactElements->Id[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Owner)");
405        if (! (ids->put(int_ptr, num_ContactElements)) )          int_ptr = &mesh->ContactElements->Owner[0];
406           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_ContactElements)) )
407                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Owner)");
408        // ContactElements_Tag  
409        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )          // ContactElements_Color
410           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
411        int_ptr = &mesh->ContactElements->Tag[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Color)");
412        if (! (ids->put(int_ptr, num_ContactElements)) )          int_ptr = &mesh->ContactElements->Color[0];
413           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_ContactElements)) )
414                throw FinleyAdapterException(msgPrefix+"put(ContactElements_Color)");
415        // ContactElements_Owner  
416        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )          // ContactElements_Nodes
417           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]) ) )
418        int_ptr = &mesh->ContactElements->Owner[0];              throw FinleyAdapterException(msgPrefix+"add_var(ContactElements_Nodes)");
419        if (! (ids->put(int_ptr, num_ContactElements)) )          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
420           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"put(ContactElements_Nodes)");
421        }
422        // ContactElements_Color  
423        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )      // // // // // Points // // // // //
424           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);      if (num_Points>0) {
425        int_ptr = &mesh->ContactElements->Color[0];          // Points_Id
426        if (! (ids->put(int_ptr, num_ContactElements)) )          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
427           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Id)");
428            int_ptr = &mesh->Points->Id[0];
429        // ContactElements_Nodes          if (! (ids->put(int_ptr, num_Points)) )
430        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )              throw FinleyAdapterException(msgPrefix+"put(Points_Id)");
431           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);  
432        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )          // Points_Tag
433           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
434                throw FinleyAdapterException(msgPrefix+"add_var(Points_Tag)");
435     }          int_ptr = &mesh->Points->Tag[0];
436            if (! (ids->put(int_ptr, num_Points)) )
437     // // // // // Points // // // // //              throw FinleyAdapterException(msgPrefix+"put(Points_Tag)");
438    
439     if (num_Points>0) {          // Points_Owner
440            if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
441        fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");              throw FinleyAdapterException(msgPrefix+"add_var(Points_Owner)");
442            int_ptr = &mesh->Points->Owner[0];
443        // Points_Id          if (! (ids->put(int_ptr, num_Points)) )
444        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Owner)");
445           throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);  
446        int_ptr = &mesh->Points->Id[0];          // Points_Color
447        if (! (ids->put(int_ptr, num_Points)) )          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
448           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Points_Color)");
449            int_ptr = &mesh->Points->Color[0];
450        // Points_Tag          if (! (ids->put(int_ptr, num_Points)) )
451        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Color)");
452           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);  
453        int_ptr = &mesh->Points->Tag[0];          // Points_Nodes
454        if (! (ids->put(int_ptr, num_Points)) )          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
455           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
456                throw FinleyAdapterException(msgPrefix+"add_var(Points_Nodes)");
457        // Points_Owner          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
458        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )              throw FinleyAdapterException(msgPrefix+"put(Points_Nodes)");
459           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);      }
460        int_ptr = &mesh->Points->Owner[0];  
461        if (! (ids->put(int_ptr, num_Points)) )      // // // // // TagMap // // // // //
462           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);      if (num_Tags>0) {
463            // Temp storage to gather node IDs
464        // Points_Color          vector<int> Tags_keys;
465        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )  
466           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);          // Copy tag data into temp arrays
467        int_ptr = &mesh->Points->Color[0];          TagMap::const_iterator it;
468        if (! (ids->put(int_ptr, num_Points)) )          for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++) {
469           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);              Tags_keys.push_back(it->second);
470            }
471        // Points_Nodes  
472        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]          // Tags_keys
473        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )          if (! (ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
474           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);              throw FinleyAdapterException(msgPrefix+"add_var(Tags_keys)");
475        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )          int_ptr = &Tags_keys[0];
476           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);          if (! (ids->put(int_ptr, num_Tags)) )
477                throw FinleyAdapterException(msgPrefix+"put(Tags_keys)");
478     }  
479            // Tags_names_*
480     // // // // // TagMap // // // // //          // This is an array of strings, it should be stored as an array but
481            // instead I have hacked in one attribute per string because the NetCDF
482     if (num_Tags>0) {          // manual doesn't tell how to do an array of strings
483            int i = 0;
484        // Temp storage to gather node IDs          for (it=mesh->tagMap.begin(); it!=mesh->tagMap.end(); it++, i++) {
485        int *Tags_keys = TMPMEMALLOC(num_Tags, int);              stringstream tagnamestream;
486        char name_temp[4096];              tagnamestream << "Tags_name_" << i;
487                const string tagname = tagnamestream.str();
488        /* Copy tag data into temp arrays */              if (!dataFile.add_att(tagname.c_str(), it->first.c_str()))
489        tag_map = mesh->TagMap;                  throw FinleyAdapterException(msgPrefix+"add_att(Tags_names_X)");
490        if (tag_map) {          }
491           int i = 0;      }
492           while (tag_map) {  
493              Tags_keys[i++] = tag_map->tag_key;      // Send token to next MPI process so he can take his turn
494              tag_map=tag_map->next;  #ifdef ESYS_MPI
495           }      if (mpi_rank<mpi_size-1) {
496        }          MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
497        }
       // Tags_keys  
       if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )  
          throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);  
       int_ptr = &Tags_keys[0];  
       if (! (ids->put(int_ptr, num_Tags)) )  
          throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);  
   
       // Tags_names_*  
       // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string  
       // because the NetCDF manual doesn't tell how to do an array of strings  
       tag_map = mesh->TagMap;  
       if (tag_map) {  
          int i = 0;  
          while (tag_map) {  
             sprintf(name_temp, "Tags_name_%d", i);  
             if (!dataFile.add_att(name_temp, tag_map->name) )  
                throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);  
             tag_map=tag_map->next;  
             i++;  
          }  
       }  
   
       TMPMEMFREE(Tags_keys);  
   
    }  
   
 /* Send token to next MPI process so he can take his turn */  
 #ifdef PASO_MPI  
    if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);  
498  #endif  #endif
499    
500     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
501    
502  #else  #else // USE_NETCDF
503     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");      Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with netCDF. Please contact your installation manager.");
504  #endif  /* USE_NETCDF */  #endif // USE_NETCDF
505     checkFinleyError();      checkFinleyError();
506  }  }
507    
508  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
509  {  {
510     return "FinleyMesh";      return "FinleyMesh";
511  }  }
512    
513  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
514  {  {
515     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
516     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
517     if (loc==m_functionSpaceTypeNames.end()) {      if (loc==m_functionSpaceTypeNames.end()) {
518        return "Invalid function space type code.";          return "Invalid function space type code.";
519     } else {      } else {
520        return loc->second;          return loc->second;
521     }      }
522  }  }
523    
524  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
525  {  {
526     FunctionSpaceNamesMapType::iterator loc;      FunctionSpaceNamesMapType::iterator loc;
527     loc=m_functionSpaceTypeNames.find(functionSpaceType);      loc=m_functionSpaceTypeNames.find(functionSpaceType);
528     return (loc!=m_functionSpaceTypeNames.end());      return (loc!=m_functionSpaceTypeNames.end());
529  }  }
530    
531  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
532  {  {
533     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
534     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));                  DegreesOfFreedom,"Finley_DegreesOfFreedom"));
535     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
536     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));                  ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
537     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
538     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));                  Nodes,"Finley_Nodes"));
539     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
540     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));                  ReducedNodes,"Finley_Reduced_Nodes"));
541     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
542     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));                  Elements,"Finley_Elements"));
543     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
544     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));                  ReducedElements,"Finley_Reduced_Elements"));
545     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
546     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));                  FaceElements,"Finley_Face_Elements"));
547     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
548     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));                  ReducedFaceElements,"Finley_Reduced_Face_Elements"));
549     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
550     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));                  Points,"Finley_Points"));
551     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
552     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));                  ContactElementsZero,"Finley_Contact_Elements_0"));
553     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
554     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));                  ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
555     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
556     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));                  ContactElementsOne,"Finley_Contact_Elements_1"));
557     m_functionSpaceTypeNames.insert      m_functionSpaceTypeNames.insert(FunctionSpaceNamesMapType::value_type(
558     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));                  ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
559  }  }
560    
561  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
562  {  {
563     return Nodes;      return Nodes;
564  }  }
565    
566  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
567  {  {
568     return ReducedNodes;      return ReducedNodes;
569  }  }
570    
571  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
572  {  {
573     return Elements;      return Elements;
574  }  }
575    
576  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
577  {  {
578     return ReducedElements;      return ReducedElements;
579  }  }
580    
581  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
582  {  {
583     return FaceElements;      return FaceElements;
584  }  }
585    
586  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
587  {  {
588     return ReducedFaceElements;      return ReducedFaceElements;
589  }  }
590    
591  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
592  {  {
593     return ContactElementsZero;      return ContactElementsZero;
594  }  }
595    
596  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
597  {  {
598     return ReducedContactElementsZero;      return ReducedContactElementsZero;
599  }  }
600    
601  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
602  {  {
603     return ContactElementsOne;      return ContactElementsOne;
604  }  }
605    
606  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
607  {  {
608     return ReducedContactElementsOne;      return ReducedContactElementsOne;
609  }  }
610    
611  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
612  {  {
613     return DegreesOfFreedom;      return DegreesOfFreedom;
614  }  }
615    
616  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
617  {  {
618     return ReducedDegreesOfFreedom;      return ReducedDegreesOfFreedom;
619  }  }
620    
621  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
622  {  {
623     return Points;      return Points;
624  }  }
625    
626  //  //
# Line 658  int MeshAdapter::getDiracDeltaFunctionCo Line 628  int MeshAdapter::getDiracDeltaFunctionCo
628  //  //
629  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
630  {  {
631     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
632     int numDim=Finley_Mesh_getDim(mesh);      int numDim=Finley_Mesh_getDim(mesh);
633     checkFinleyError();      checkFinleyError();
634     return numDim;      return numDim;
635  }  }
636    
637  //  //
# Line 669  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 678  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();      Finley_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();      Finley_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        Assemble_PDE(mesh->Nodes, mesh->FaceElements, S, rhs,
760     Finley_Mesh* mesh=m_finleyMesh.get();              escript::Data(), escript::Data(), escript::Data(), d,
761                escript::Data(), y);
762     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );      checkFinleyError();
763     checkFinleyError();  
764        Assemble_PDE(mesh->Nodes, mesh->ContactElements, S, rhs,
765     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );              escript::Data(), escript::Data(), escript::Data(), d_contact,
766     checkFinleyError();              escript::Data(), y_contact);
767        checkFinleyError();
768     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );  
769     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->Points, S, rhs, escript::Data(),
770  }              escript::Data(), escript::Data(), d_dirac, escript::Data(), y_dirac);
771        checkFinleyError();
772  void  MeshAdapter::addPDEToLumpedSystem(  }
773                                          escript::Data& mat,  
774                                          const escript::Data& D,  void MeshAdapter::addPDEToLumpedSystem(escript::Data& mat,
775                                          const escript::Data& d) const          const escript::Data& D, const escript::Data& d,
776  {          const escript::Data& d_dirac, const bool useHRZ) const
777     escriptDataC _mat=mat.getDataC();  {
778     escriptDataC _D=D.getDataC();      Finley_Mesh* mesh=m_finleyMesh.get();
779     escriptDataC _d=d.getDataC();      Assemble_LumpedSystem(mesh->Nodes, mesh->Elements, mat, D, useHRZ);
780        checkFinleyError();
    Finley_Mesh* mesh=m_finleyMesh.get();  
781    
782     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);      Assemble_LumpedSystem(mesh->Nodes, mesh->FaceElements, mat, d, useHRZ);
783     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);      checkFinleyError();
784    
785     checkFinleyError();      Assemble_LumpedSystem(mesh->Nodes, mesh->Points, mat, d_dirac, useHRZ);
786        checkFinleyError();
787  }  }
788    
   
789  //  //
790  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
791  //  //
792  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,
793  {          const escript::Data& Y, const escript::Data& y,
794     Finley_Mesh* mesh=m_finleyMesh.get();          const escript::Data& y_contact, const escript::Data& y_dirac) const
795    {
796     escriptDataC _rhs=rhs.getDataC();      Finley_Mesh* mesh=m_finleyMesh.get();
797     escriptDataC _X=X.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, 0, rhs,
798     escriptDataC _Y=Y.getDataC();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
799     escriptDataC _y=y.getDataC();              X, Y);
800     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
801    
802     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );      Assemble_PDE(mesh->Nodes, mesh->FaceElements, 0, rhs,
803     checkFinleyError();              escript::Data(), escript::Data(), escript::Data(), escript::Data(),
804                escript::Data(), y);
805     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );      checkFinleyError();
806     checkFinleyError();  
807        Assemble_PDE(mesh->Nodes, mesh->ContactElements, 0, rhs,
808     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );              escript::Data(), escript::Data(), escript::Data(),
809     checkFinleyError();              escript::Data(), escript::Data(), y_contact);
810        checkFinleyError();
811    
812        Assemble_PDE(mesh->Nodes, mesh->Points, 0, rhs,
813                escript::Data(), escript::Data(), escript::Data(), escript::Data(),
814                escript::Data(), y_dirac);
815        checkFinleyError();
816  }  }
817    
818  //  //
819  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
820  //  //
821  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
822                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,          escript::AbstractTransportProblem& tp, escript::Data& source,
823                                             const escript::Data& A, const escript::Data& B, const escript::Data& C,          const escript::Data& M, const escript::Data& A, const escript::Data& B,
824                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,          const escript::Data& C, const escript::Data& D, const escript::Data& X,
825                                             const escript::Data& d, const escript::Data& y,          const escript::Data& Y, const escript::Data& d, const escript::Data& y,
826                                             const escript::Data& d_contact,const escript::Data& y_contact) const          const escript::Data& d_contact, const escript::Data& y_contact,
827  {          const escript::Data& d_dirac, const escript::Data& y_dirac) const
828     DataTypes::ShapeType shape;  {
829     source.expand();      TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
830     escriptDataC _source=source.getDataC();      if (!tpa)
831     escriptDataC _M=M.getDataC();          throw FinleyAdapterException("finley only supports Paso transport problems.");
832     escriptDataC _A=A.getDataC();  
833     escriptDataC _B=B.getDataC();      source.expand();
834     escriptDataC _C=C.getDataC();  
835     escriptDataC _D=D.getDataC();      Finley_Mesh* mesh=m_finleyMesh.get();
836     escriptDataC _X=X.getDataC();      Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
837     escriptDataC _Y=Y.getDataC();  
838     escriptDataC _d=d.getDataC();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->mass_matrix, source,
839     escriptDataC _y=y.getDataC();                          escript::Data(), escript::Data(), escript::Data(),
840     escriptDataC _d_contact=d_contact.getDataC();                          M, escript::Data(), escript::Data());
841     escriptDataC _y_contact=y_contact.getDataC();      checkFinleyError();
842    
843     Finley_Mesh* mesh=m_finleyMesh.get();      Assemble_PDE(mesh->Nodes, mesh->Elements, _tp->transport_matrix,
844     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();                          source, A, B, C, D, X, Y);
845        checkFinleyError();
846     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );  
847     checkFinleyError();      Assemble_PDE(mesh->Nodes, mesh->FaceElements, _tp->transport_matrix,
848                            source, escript::Data(), escript::Data(),
849     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );                          escript::Data(), d, escript::Data(), y);
850     checkFinleyError();      checkFinleyError();
851    
852     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );      Assemble_PDE(mesh->Nodes, mesh->ContactElements,
853     checkFinleyError();                          _tp->transport_matrix, source, escript::Data(),
854                            escript::Data(), escript::Data(), d_contact,
855     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );                          escript::Data(), y_contact);
856     checkFinleyError();      checkFinleyError();
857  }  
858        Assemble_PDE(mesh->Nodes, mesh->Points, _tp->transport_matrix,
859  //                          source, escript::Data(), escript::Data(),
860  // interpolates data between different function spaces:                          escript::Data(), d_dirac, escript::Data(), y_dirac);
861  //      checkFinleyError();
862  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  }
863  {  
864     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));  //
865     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));  // interpolates data between different function spaces
866     if (inDomain!=*this)    //
867        throw FinleyAdapterException("Error - Illegal domain of interpolant.");  void MeshAdapter::interpolateOnDomain(escript::Data& target, const escript::Data& in) const
868     if (targetDomain!=*this)  {
869        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");      const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
870        const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
871     Finley_Mesh* mesh=m_finleyMesh.get();      if (inDomain!=*this)
872     escriptDataC _target=target.getDataC();          throw FinleyAdapterException("Error - Illegal domain of interpolant.");
873     escriptDataC _in=in.getDataC();      if (targetDomain!=*this)
874     switch(in.getFunctionSpace().getTypeCode()) {          throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
875     case(Nodes):  
876        switch(target.getFunctionSpace().getTypeCode()) {      Finley_Mesh* mesh=m_finleyMesh.get();
877        case(Nodes):      switch(in.getFunctionSpace().getTypeCode()) {
878        case(ReducedNodes):          case Nodes:
879        case(DegreesOfFreedom):              switch(target.getFunctionSpace().getTypeCode()) {
880        case(ReducedDegreesOfFreedom):                  case Nodes:
881        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedNodes:
882        break;                  case DegreesOfFreedom:
883        case(Elements):                  case ReducedDegreesOfFreedom:
884        case(ReducedElements):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
885        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
886        break;                  case Elements:
887        case(FaceElements):                  case ReducedElements:
888        case(ReducedFaceElements):                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in,target);
889        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                      break;
890        break;                  case FaceElements:
891        case(Points):                  case ReducedFaceElements:
892        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
893        break;                      break;
894        case(ContactElementsZero):                  case Points:
895        case(ReducedContactElementsZero):                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
896        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
897        break;                  case ContactElementsZero:
898        case(ContactElementsOne):                  case ReducedContactElementsZero:
899        case(ReducedContactElementsOne):                  case ContactElementsOne:
900        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsOne:
901        break;                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
902        default:                      break;
903           stringstream temp;                  default:
904           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      stringstream temp;
905           throw FinleyAdapterException(temp.str());                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
906           break;                      throw FinleyAdapterException(temp.str());
907        }                      break;
908        break;              }
909     case(ReducedNodes):              break;
910        switch(target.getFunctionSpace().getTypeCode()) {          case ReducedNodes:
911        case(Nodes):              switch(target.getFunctionSpace().getTypeCode()) {
912        case(ReducedNodes):                  case Nodes:
913        case(DegreesOfFreedom):                  case ReducedNodes:
914        case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
915        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedDegreesOfFreedom:
916        break;                      Assemble_CopyNodalData(mesh->Nodes, target, in);
917        case(Elements):                      break;
918        case(ReducedElements):                  case Elements:
919        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case ReducedElements:
920        break;                      Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
921        case(FaceElements):                      break;
922        case(ReducedFaceElements):                  case FaceElements:
923        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ReducedFaceElements:
924        break;                      Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
925        case(Points):                      break;
926        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case Points:
927        break;                      Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
928        case(ContactElementsZero):                      break;
929        case(ReducedContactElementsZero):                  case ContactElementsZero:
930        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                  case ReducedContactElementsZero:
931        break;                  case ContactElementsOne:
932        case(ContactElementsOne):                  case ReducedContactElementsOne:
933        case(ReducedContactElementsOne):                      Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
934        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);                      break;
935        break;                  default:
936        default:                      stringstream temp;
937           stringstream temp;                      temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
938           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();                      throw FinleyAdapterException(temp.str());
939           throw FinleyAdapterException(temp.str());                      break;
940           break;              }
941        }              break;
942        break;          case Elements:
943     case(Elements):              if (target.getFunctionSpace().getTypeCode()==Elements) {
944        if (target.getFunctionSpace().getTypeCode()==Elements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
945           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
946        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_AverageElementData(mesh->Elements, target, in);
947           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);              } else {
948        } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
949           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");              }
950        }              break;
951        break;          case ReducedElements:
952     case(ReducedElements):              if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
953        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {                  Assemble_CopyElementData(mesh->Elements, target, in);
954           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);              } else {
955        } else {                  throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
956           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");              }
957        }              break;
958        break;          case FaceElements:
959     case(FaceElements):              if (target.getFunctionSpace().getTypeCode()==FaceElements) {
960        if (target.getFunctionSpace().getTypeCode()==FaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
961           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
962        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_AverageElementData(mesh->FaceElements, target, in);
963           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);              } else {
964        } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
965           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");              }
966        }              break;
967        break;          case ReducedFaceElements:
968     case(ReducedFaceElements):              if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
969        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {                  Assemble_CopyElementData(mesh->FaceElements, target, in);
970           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);              } else {
971        } else {                  throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
972           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");              }
973        }              break;
974        break;          case Points:
975     case(Points):              if (target.getFunctionSpace().getTypeCode()==Points) {
976        if (target.getFunctionSpace().getTypeCode()==Points) {                  Assemble_CopyElementData(mesh->Points, target, in);
977           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);              } else {
978        } else {                  throw FinleyAdapterException("Error - No interpolation with data on points possible.");
979           throw FinleyAdapterException("Error - No interpolation with data on points possible.");              }
980        }              break;
981        break;          case ContactElementsZero:
982     case(ContactElementsZero):          case ContactElementsOne:
983     case(ContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
984        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
985           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
986        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_AverageElementData(mesh->ContactElements, target, in);
987           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);              } else {
988        } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
989           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");              }
990        }              break;
991        break;          case ReducedContactElementsZero:
992     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
993     case(ReducedContactElementsOne):              if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
994        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {                  Assemble_CopyElementData(mesh->ContactElements, target, in);
995           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);              } else {
996        } else {                  throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
997           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");              }
998        }              break;
999        break;          case DegreesOfFreedom:
1000     case(DegreesOfFreedom):                    switch(target.getFunctionSpace().getTypeCode()) {
1001        switch(target.getFunctionSpace().getTypeCode()) {                  case ReducedDegreesOfFreedom:
1002        case(ReducedDegreesOfFreedom):                  case DegreesOfFreedom:
1003        case(DegreesOfFreedom):                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1004        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1005        break;  
1006                      case Nodes:
1007        case(Nodes):                  case ReducedNodes:
1008        case(ReducedNodes):                      if (getMPISize()>1) {
1009        if (getMPISize()>1) {                          escript::Data in2=escript::Data(in);
1010           escript::Data temp=escript::Data(in);                          in2.expand();
1011           temp.expand();                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1012           escriptDataC _in2 = temp.getDataC();                      } else {
1013           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1014        } else {                      }
1015           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1016        }                  case Elements:
1017        break;                  case ReducedElements:
1018        case(Elements):                      if (getMPISize()>1) {
1019        case(ReducedElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1020        if (getMPISize()>1) {                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1021           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                      } else {
1022           escriptDataC _in2 = temp.getDataC();                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1023           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                      }
1024        } else {                      break;
1025           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                  case FaceElements:
1026        }                  case ReducedFaceElements:
1027        break;                      if (getMPISize()>1) {
1028        case(FaceElements):                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1029        case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1030        if (getMPISize()>1) {                      } else {
1031           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1032           escriptDataC _in2 = temp.getDataC();                      }
1033           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1034                      case Points:
1035        } else {                      if (getMPISize()>1) {
1036           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                          //escript::Data in2=escript::Data(in, continuousFunction(*this) );
1037        }                      } else {
1038        break;                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1039        case(Points):                      }
1040        if (getMPISize()>1) {                      break;
1041           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  case ContactElementsZero:
1042           escriptDataC _in2 = temp.getDataC();                  case ContactElementsOne:
1043        } else {                  case ReducedContactElementsZero:
1044           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                  case ReducedContactElementsOne:
1045        }                      if (getMPISize()>1) {
1046        break;                          escript::Data in2=escript::Data(in, continuousFunction(*this));
1047        case(ContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1048        case(ContactElementsOne):                      } else {
1049        case(ReducedContactElementsZero):                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1050        case(ReducedContactElementsOne):                      }
1051        if (getMPISize()>1) {                      break;
1052           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );                  default:
1053           escriptDataC _in2 = temp.getDataC();                      stringstream temp;
1054           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();
1055        } else {                      throw FinleyAdapterException(temp.str());
1056           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              }
1057        }              break;
1058        break;          case ReducedDegreesOfFreedom:
1059        default:              switch(target.getFunctionSpace().getTypeCode()) {
1060           stringstream temp;                  case Nodes:
1061           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.");
1062           throw FinleyAdapterException(temp.str());                  case ReducedNodes:
1063           break;                      if (getMPISize()>1) {
1064        }                          escript::Data in2=escript::Data(in);
1065        break;                          in2.expand();
1066     case(ReducedDegreesOfFreedom):                          Assemble_CopyNodalData(mesh->Nodes, target, in2);
1067        switch(target.getFunctionSpace().getTypeCode()) {                      } else {
1068        case(Nodes):                          Assemble_CopyNodalData(mesh->Nodes, target, in);
1069        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");                      }
1070        break;                      break;
1071        case(ReducedNodes):                  case DegreesOfFreedom:
1072        if (getMPISize()>1) {                      throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1073           escript::Data temp=escript::Data(in);                      break;
1074           temp.expand();                  case ReducedDegreesOfFreedom:
1075           escriptDataC _in2 = temp.getDataC();                      Assemble_CopyNodalData(mesh->Nodes, target, in);
1076           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);                      break;
1077        } else {                  case Elements:
1078           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                  case ReducedElements:
1079        }                      if (getMPISize()>1) {
1080        break;                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1081        case(DegreesOfFreedom):                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in2, target);
1082        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");                      } else {
1083        break;                          Assemble_interpolate(mesh->Nodes, mesh->Elements, in, target);
1084        case(ReducedDegreesOfFreedom):                      }
1085        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);                      break;
1086        break;                  case FaceElements:
1087        case(Elements):                  case ReducedFaceElements:
1088        case(ReducedElements):                      if (getMPISize()>1) {
1089        if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this) );
1090           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in2, target);
1091           escriptDataC _in2 = temp.getDataC();                      } else {
1092           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->FaceElements, in, target);
1093        } else {                      }
1094           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);                      break;
1095        }                  case Points:
1096        break;                      if (getMPISize()>1) {
1097        case(FaceElements):                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1098        case(ReducedFaceElements):                          Assemble_interpolate(mesh->Nodes, mesh->Points, in2, target);
1099        if (getMPISize()>1) {                      } else {
1100           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->Points, in, target);
1101           escriptDataC _in2 = temp.getDataC();                      }
1102           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);                      break;
1103        } else {                  case ContactElementsZero:
1104           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);                  case ContactElementsOne:
1105        }                  case ReducedContactElementsZero:
1106        break;                  case ReducedContactElementsOne:
1107        case(Points):                      if (getMPISize()>1) {
1108        if (getMPISize()>1) {                          escript::Data in2=escript::Data(in, reducedContinuousFunction(*this));
1109           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in2, target);
1110           escriptDataC _in2 = temp.getDataC();                      } else {
1111           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);                          Assemble_interpolate(mesh->Nodes, mesh->ContactElements, in, target);
1112        } else {                      }
1113           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);                      break;
1114        }                  default:
1115        break;                      stringstream temp;
1116        case(ContactElementsZero):                      temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1117        case(ContactElementsOne):                      throw FinleyAdapterException(temp.str());
1118        case(ReducedContactElementsZero):                      break;
1119        case(ReducedContactElementsOne):              }
1120        if (getMPISize()>1) {              break;
1121           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );          default:
1122           escriptDataC _in2 = temp.getDataC();              stringstream temp;
1123           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();
1124        } else {              throw FinleyAdapterException(temp.str());
1125           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);              break;
1126        }      }
1127        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();  
1128  }  }
1129    
1130  //  //
1131  // copies the locations of sample points into x:  // copies the locations of sample points into x
1132  //  //
1133  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1134  {  {
1135     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1136     if (argDomain!=*this)      if (argDomain!=*this)
1137        throw FinleyAdapterException("Error - Illegal domain of data point locations");          throw FinleyAdapterException("Error - Illegal domain of data point locations");
1138     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1139     // in case of values node coordinates we can do the job directly:      // in case of appropriate function space we can do the job directly:
1140     if (arg.getFunctionSpace().getTypeCode()==Nodes) {      if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1141        escriptDataC _arg=arg.getDataC();          Assemble_NodeCoordinates(mesh->Nodes, arg);
1142        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);      } else {
1143     } else {          escript::Data tmp_data=Vector(0., continuousFunction(*this), true);
1144        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);          Assemble_NodeCoordinates(mesh->Nodes, tmp_data);
1145        escriptDataC _tmp_data=tmp_data.getDataC();          // this is then interpolated onto arg:
1146        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);          interpolateOnDomain(arg, tmp_data);
1147        // this is then interpolated onto arg:      }
1148        interpolateOnDomain(arg,tmp_data);      checkFinleyError();
    }  
    checkFinleyError();  
1149  }  }
1150    
1151  //  //
1152  // 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
1153  //  //
1154  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1155  {  {
1156  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/      const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1157     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));      if (normalDomain!=*this)
1158     if (normalDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of normal locations");
1159        throw FinleyAdapterException("Error - Illegal domain of normal locations");      Finley_Mesh* mesh=m_finleyMesh.get();
1160     Finley_Mesh* mesh=m_finleyMesh.get();      switch(normal.getFunctionSpace().getTypeCode()) {
1161     escriptDataC _normal=normal.getDataC();          case Nodes:
1162     switch(normal.getFunctionSpace().getTypeCode()) {              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1163     case(Nodes):              break;
1164     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");          case ReducedNodes:
1165     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1166     case(ReducedNodes):              break;
1167     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");          case Elements:
1168     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1169     case(Elements):              break;
1170     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");          case ReducedElements:
1171     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1172     case(ReducedElements):              break;
1173     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");          case FaceElements:
1174     break;          case ReducedFaceElements:
1175     case (FaceElements):              Assemble_setNormal(mesh->Nodes, mesh->FaceElements, normal);
1176     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              break;
1177     break;          case Points:
1178     case (ReducedFaceElements):              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1179     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);              break;
1180     break;          case ContactElementsOne:
1181     case(Points):          case ContactElementsZero:
1182     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");          case ReducedContactElementsOne:
1183     break;          case ReducedContactElementsZero:
1184     case (ContactElementsOne):              Assemble_setNormal(mesh->Nodes, mesh->ContactElements, normal);
1185     case (ContactElementsZero):              break;
1186     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);          case DegreesOfFreedom:
1187     break;              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1188     case (ReducedContactElementsOne):              break;
1189     case (ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1190     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);              throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1191     break;              break;
1192     case(DegreesOfFreedom):          default:
1193     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");              stringstream temp;
1194     break;              temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1195     case(ReducedDegreesOfFreedom):              throw FinleyAdapterException(temp.str());
1196     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");              break;
1197     break;      }
1198     default:      checkFinleyError();
1199        stringstream temp;  }
1200        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();  
1201        throw FinleyAdapterException(temp.str());  //
1202        break;  // interpolates data to other domain
1203     }  //
1204     checkFinleyError();  void MeshAdapter::interpolateACross(escript::Data& target, const escript::Data& source) const
1205  }  {
1206        throw FinleyAdapterException("Error - Finley does not allow interpolation across domains.");
1207  //  }
1208  // interpolates data to other domain:  
1209  //  //
1210  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  // calculates the integral of a function defined on arg
1211  {  //
1212     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();  void MeshAdapter::setToIntegrals(vector<double>& integrals, const escript::Data& arg) const
1213     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());  {
1214     if (targetDomain!=this)      const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1215        throw FinleyAdapterException("Error - Illegal domain of interpolation target");      if (argDomain!=*this)
1216            throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1217     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");  
1218  }      double blocktimer_start = blocktimer_time();
1219        Finley_Mesh* mesh=m_finleyMesh.get();
1220  //      switch(arg.getFunctionSpace().getTypeCode()) {
1221  // calculates the integral of a function defined of arg:          case Nodes:
1222  //              {
1223  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const                  escript::Data temp(arg, escript::function(*this));
1224  {                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1225     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));              }
1226     if (argDomain!=*this)              break;
1227        throw FinleyAdapterException("Error - Illegal domain of integration kernel");          case ReducedNodes:
1228                {
1229     double blocktimer_start = blocktimer_time();                  escript::Data temp(arg, escript::function(*this));
1230     Finley_Mesh* mesh=m_finleyMesh.get();                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1231     escriptDataC _temp;              }
1232     escript::Data temp;              break;
1233     escriptDataC _arg=arg.getDataC();          case Elements:
1234     switch(arg.getFunctionSpace().getTypeCode()) {          case ReducedElements:
1235     case(Nodes):              Assemble_integrate(mesh->Nodes, mesh->Elements, arg, &integrals[0]);
1236     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );              break;
1237     _temp=temp.getDataC();          case FaceElements:
1238     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);          case ReducedFaceElements:
1239     break;              Assemble_integrate(mesh->Nodes, mesh->FaceElements, arg, &integrals[0]);
1240     case(ReducedNodes):              break;
1241     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );          case Points:
1242     _temp=temp.getDataC();              throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1243     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);              break;
1244     break;          case ContactElementsZero:
1245     case(Elements):          case ReducedContactElementsZero:
1246     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);          case ContactElementsOne:
1247     break;          case ReducedContactElementsOne:
1248     case(ReducedElements):              Assemble_integrate(mesh->Nodes, mesh->ContactElements, arg, &integrals[0]);
1249     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);              break;
1250     break;          case DegreesOfFreedom:
1251     case(FaceElements):          case ReducedDegreesOfFreedom:
1252     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);              {
1253     break;                  escript::Data temp(arg, escript::function(*this));
1254     case(ReducedFaceElements):                  Assemble_integrate(mesh->Nodes, mesh->Elements, temp, &integrals[0]);
1255     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);              }
1256     break;              break;
1257     case(Points):          default:
1258     throw FinleyAdapterException("Error - Integral of data on points is not supported.");              stringstream temp;
1259     break;              temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1260     case(ContactElementsZero):              throw FinleyAdapterException(temp.str());
1261     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);              break;
1262     break;      }
1263     case(ReducedContactElementsZero):      checkFinleyError();
1264     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);      blocktimer_increment("integrate()", blocktimer_start);
    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();  
1265  }  }
1266    
1267  //  //
1268  // returns the size of elements:  // calculates the gradient of arg
1269    //
1270    void MeshAdapter::setToGradient(escript::Data& grad, const escript::Data& arg) const
1271    {
1272        const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1273        if (argDomain!=*this)
1274            throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1275        const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1276        if (gradDomain!=*this)
1277            throw FinleyAdapterException("Error - Illegal domain of gradient");
1278    
1279        Finley_Mesh* mesh=m_finleyMesh.get();
1280        escript::Data nodeData;
1281        if (getMPISize()>1) {
1282            if (arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom) {
1283                nodeData=escript::Data(arg, continuousFunction(*this));
1284            } else if(arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom) {
1285                nodeData=escript::Data(arg, reducedContinuousFunction(*this));
1286            } else {
1287                nodeData = arg;
1288            }
1289        } else {
1290            nodeData = arg;
1291        }
1292        switch(grad.getFunctionSpace().getTypeCode()) {
1293            case Nodes:
1294                throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1295                break;
1296            case ReducedNodes:
1297                throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1298                break;
1299            case Elements:
1300            case ReducedElements:
1301                Assemble_gradient(mesh->Nodes, mesh->Elements, grad, nodeData);
1302                break;
1303            case FaceElements:
1304            case ReducedFaceElements:
1305                Assemble_gradient(mesh->Nodes, mesh->FaceElements, grad, nodeData);
1306                break;
1307            case Points:
1308                throw FinleyAdapterException("Error - Gradient at points is not supported.");
1309                break;
1310            case ContactElementsZero:
1311            case ReducedContactElementsZero:
1312            case ContactElementsOne:
1313            case ReducedContactElementsOne:
1314                Assemble_gradient(mesh->Nodes, mesh->ContactElements, grad, nodeData);
1315                break;
1316            case DegreesOfFreedom:
1317                throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1318                break;
1319            case ReducedDegreesOfFreedom:
1320                throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1321                break;
1322            default:
1323                stringstream temp;
1324                temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1325                throw FinleyAdapterException(temp.str());
1326                break;
1327        }
1328        checkFinleyError();
1329    }
1330    
1331    //
1332    // returns the size of elements
1333  //  //
1334  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1335  {  {
1336     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1337     escriptDataC tmp=size.getDataC();      switch(size.getFunctionSpace().getTypeCode()) {
1338     switch(size.getFunctionSpace().getTypeCode()) {          case Nodes:
1339     case(Nodes):              throw FinleyAdapterException("Error - Size of nodes is not supported.");
1340     throw FinleyAdapterException("Error - Size of nodes is not supported.");              break;
1341     break;          case ReducedNodes:
1342     case(ReducedNodes):              throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1343     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");              break;
1344     break;          case Elements:
1345     case(Elements):          case ReducedElements:
1346     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);              Assemble_getSize(mesh->Nodes, mesh->Elements, size);
1347     break;              break;
1348     case(ReducedElements):          case FaceElements:
1349     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);          case ReducedFaceElements:
1350     break;              Assemble_getSize(mesh->Nodes, mesh->FaceElements, size);
1351     case(FaceElements):              break;
1352     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case Points:
1353     break;              throw FinleyAdapterException("Error - Size of point elements is not supported.");
1354     case(ReducedFaceElements):              break;
1355     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);          case ContactElementsZero:
1356     break;          case ContactElementsOne:
1357     case(Points):          case ReducedContactElementsZero:
1358     throw FinleyAdapterException("Error - Size of point elements is not supported.");          case ReducedContactElementsOne:
1359     break;              Assemble_getSize(mesh->Nodes,mesh->ContactElements,size);
1360     case(ContactElementsZero):              break;
1361     case(ContactElementsOne):          case DegreesOfFreedom:
1362     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1363     break;              break;
1364     case(ReducedContactElementsZero):          case ReducedDegreesOfFreedom:
1365     case(ReducedContactElementsOne):              throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1366     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);              break;
1367     break;          default:
1368     case(DegreesOfFreedom):              stringstream temp;
1369     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();
1370     break;              throw FinleyAdapterException(temp.str());
1371     case(ReducedDegreesOfFreedom):              break;
1372     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");      }
1373     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();  
1374  }  }
1375    
1376  //  //
# Line 1463  void MeshAdapter::setToSize(escript::Dat Line 1378  void MeshAdapter::setToSize(escript::Dat
1378  //  //
1379  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1380  {  {
1381     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1382     escriptDataC tmp;      const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1383     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));      if (newDomain!=*this)
1384     if (newDomain!=*this)          throw FinleyAdapterException("Error - Illegal domain of new point locations");
1385        throw FinleyAdapterException("Error - Illegal domain of new point locations");      if (new_x.getFunctionSpace() == continuousFunction(*this)) {
1386     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {          Finley_Mesh_setCoordinates(mesh, new_x);
1387         tmp = new_x.getDataC();      } else {
1388         Finley_Mesh_setCoordinates(mesh,&tmp);          throw FinleyAdapterException("As of escript version 3.3 SetX() only accepts ContinuousFunction arguments. Please interpolate.");
1389     } else {      }
1390         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );      checkFinleyError();
        tmp = new_x_inter.getDataC();  
        Finley_Mesh_setCoordinates(mesh,&tmp);  
    }  
    checkFinleyError();  
 }  
   
 //  
 // Helper for the save* methods. Extracts optional data variable names and the  
 // corresponding pointers from python dictionary. Caller must free arrays.  
 //  
 void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const  
 {  
    numData = boost::python::extract<int>(arg.attr("__len__")());  
    /* win32 refactor */  
    names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;  
    data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;  
    dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;  
   
    boost::python::list keys=arg.keys();  
    for (int i=0; i<numData; ++i) {  
       std::string n=boost::python::extract<std::string>(keys[i]);  
       escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
       if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)  
          throw FinleyAdapterException("Error: Data must be defined on same Domain");  
       data[i] = d.getDataC();  
       dataPtr[i] = &(data[i]);  
       names[i] = TMPMEMALLOC(n.length()+1, char);  
       strcpy(names[i], n.c_str());  
    }  
 }  
   
 //  
 // 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);  
1391  }  }
1392    
1393  bool MeshAdapter::ownSample(int fs_code, index_t id) const  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1394  {  {
1395  #ifdef PASO_MPI      if (getMPISize() > 1) {
1396      index_t myFirstNode=0, myLastNode=0, k=0;  #ifdef ESYS_MPI
1397      index_t* globalNodeIndex=0;          int myFirstNode=0, myLastNode=0, k=0;
1398      Finley_Mesh* mesh_p=m_finleyMesh.get();          int* globalNodeIndex=0;
1399      if (fs_code == FINLEY_REDUCED_NODES)          Finley_Mesh* mesh_p=m_finleyMesh.get();
1400      {          /*
1401      myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);           * this method is only used by saveDataCSV which would use the returned
1402      myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);           * values for reduced nodes wrongly so this case is disabled for now
1403      globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);          if (fs_code == FINLEY_REDUCED_NODES) {
1404      }              myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1405      else              myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1406      {              globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1407      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);          } else
1408      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);          */
1409      globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);          if (fs_code == FINLEY_NODES) {
1410      }              myFirstNode = mesh_p->Nodes->getFirstNode();
1411      k=globalNodeIndex[id];              myLastNode = mesh_p->Nodes->getLastNode();
1412      return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );              globalNodeIndex = mesh_p->Nodes->borrowGlobalNodesIndex();
1413            } else {
1414                throw FinleyAdapterException("Unsupported function space type for ownSample()");
1415            }
1416    
1417            k=globalNodeIndex[id];
1418            return ((myFirstNode <= k) && (k < myLastNode));
1419  #endif  #endif
1420        }
1421      return true;      return true;
1422  }  }
1423    
1424    
   
1425  //  //
1426  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1427  //  //
1428  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  escript::ASM_ptr MeshAdapter::newSystemMatrix(const int row_blocksize,
1429                                                   const int row_blocksize,                              const escript::FunctionSpace& row_functionspace,
1430                                                   const escript::FunctionSpace& row_functionspace,                              const int column_blocksize,
1431                                                   const int column_blocksize,                              const escript::FunctionSpace& column_functionspace,
1432                                                   const escript::FunctionSpace& column_functionspace,                              const int type) const
1433                                                   const int type) const  {
1434  {      // is the domain right?
1435     int reduceRowOrder=0;      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1436     int reduceColOrder=0;      if (row_domain!=*this)
1437     // is the domain right?          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1438     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1439     if (row_domain!=*this)      if (col_domain!=*this)
1440        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.");
1441     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));  
1442     if (col_domain!=*this)      int reduceRowOrder=0;
1443        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");      int reduceColOrder=0;
1444     // is the function space type right      // is the function space type right?
1445     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {      if (row_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1446        reduceRowOrder=0;          reduceRowOrder=1;
1447     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      } else if (row_functionspace.getTypeCode() != DegreesOfFreedom) {
1448        reduceRowOrder=1;          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1449     } else {      }
1450        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      if (column_functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1451     }          reduceColOrder=1;
1452     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (column_functionspace.getTypeCode() != DegreesOfFreedom) {
1453        reduceColOrder=0;          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1454     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1455        reduceColOrder=1;  
1456     } else {      // generate matrix:
1457        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(
1458     }              getFinley_Mesh(), reduceRowOrder, reduceColOrder);
1459     // generate matrix:      checkFinleyError();
1460        Paso_SystemMatrix* fsystemMatrix;
1461     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);      const int trilinos = 0;
1462     checkFinleyError();      if (trilinos) {
    Paso_SystemMatrix* fsystemMatrix;  
    int trilinos = 0;  
    if (trilinos) {  
1463  #ifdef TRILINOS  #ifdef TRILINOS
1464        /* Allocation Epetra_VrbMatrix here */          // FIXME: Allocation Epetra_VrbMatrix here...
1465  #endif  #endif
1466     }      } else {
1467     else {          fsystemMatrix=Paso_SystemMatrix_alloc(type, fsystemMatrixPattern,
1468        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);                  row_blocksize, column_blocksize, FALSE);
1469     }      }
1470     checkPasoError();      checkPasoError();
1471     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1472     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);      SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1473        return escript::ASM_ptr(sma);
1474  }  }
1475    
1476  //  //
1477  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1478  //  //
1479  TransportProblemAdapter MeshAdapter::newTransportProblem(  escript::ATP_ptr MeshAdapter::newTransportProblem(const int blocksize,
1480                                                           const double theta,          const escript::FunctionSpace& functionspace, const int type) const
1481                                                           const int blocksize,  {
1482                                                           const escript::FunctionSpace& functionspace,      // is the domain right?
1483                                                           const int type) const      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1484  {      if (domain!=*this)
1485     int reduceOrder=0;          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1486     // is the domain right?  
1487     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));      // is the function space type right?
1488     if (domain!=*this)      int reduceOrder=0;
1489        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");      if (functionspace.getTypeCode() == ReducedDegreesOfFreedom) {
1490     // is the function space type right          reduceOrder=1;
1491     if (functionspace.getTypeCode()==DegreesOfFreedom) {      } else if (functionspace.getTypeCode() != DegreesOfFreedom) {
1492        reduceOrder=0;          throw FinleyAdapterException("Error - illegal function space type for transport problem.");
1493     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      }
1494        reduceOrder=1;  
1495     } else {      // generate transport problem:
1496        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(
1497     }              getFinley_Mesh(), reduceOrder, reduceOrder);
1498     // generate matrix:      checkFinleyError();
1499        Paso_TransportProblem* transportProblem;
1500     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);      transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern, blocksize);
1501     checkFinleyError();      checkPasoError();
1502     Paso_FCTransportProblem* transportProblem;      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1503     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);      TransportProblemAdapter* tpa=new TransportProblemAdapter(
1504     checkPasoError();              transportProblem, blocksize, functionspace);
1505     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);      return escript::ATP_ptr(tpa);
    return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);  
1506  }  }
1507    
1508  //  //
1509  // vtkObject MeshAdapter::createVtkObject() const  // returns true if data on functionSpaceCode is considered as being cell centered
 // TODO:  
 //  
   
1510  //  //
 // returns true if data at the atom_type is considered as being cell centered:  
1511  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1512  {  {
1513     switch(functionSpaceCode) {      switch(functionSpaceCode) {
1514     case(Nodes):          case Nodes:
1515     case(DegreesOfFreedom):          case DegreesOfFreedom:
1516     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1517     return false;              return false;
1518     break;          case Elements:
1519     case(Elements):          case FaceElements:
1520     case(FaceElements):          case Points:
1521     case(Points):          case ContactElementsZero:
1522     case(ContactElementsZero):          case ContactElementsOne:
1523     case(ContactElementsOne):          case ReducedElements:
1524     case(ReducedElements):          case ReducedFaceElements:
1525     case(ReducedFaceElements):          case ReducedContactElementsZero:
1526     case(ReducedContactElementsZero):          case ReducedContactElementsOne:
1527     case(ReducedContactElementsOne):              return true;
1528     return true;          default:
1529     break;              stringstream temp;
1530     default:              temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1531        stringstream temp;              throw FinleyAdapterException(temp.str());
1532        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;              break;
1533        throw FinleyAdapterException(temp.str());      }
1534        break;      return false;
    }  
    checkFinleyError();  
    return false;  
1535  }  }
1536    
1537  bool  bool
1538  MeshAdapter::commonFunctionSpace(const std::vector<int>& fs, int& resultcode) const  MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1539  {  {
1540     /* 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
1541      class 1: DOF <-> Nodes         back and forth]:
1542      class 2: ReducedDOF <-> ReducedNodes          class 1: DOF <-> Nodes
1543      class 3: Points          class 2: ReducedDOF <-> ReducedNodes
1544      class 4: Elements          class 3: Points
1545      class 5: ReducedElements          class 4: Elements
1546      class 6: FaceElements          class 5: ReducedElements
1547      class 7: ReducedFaceElements          class 6: FaceElements
1548      class 8: ContactElementZero <-> ContactElementOne          class 7: ReducedFaceElements
1549      class 9: ReducedContactElementZero <-> ReducedContactElementOne          class 8: ContactElementZero <-> ContactElementOne
1550            class 9: ReducedContactElementZero <-> ReducedContactElementOne
1551     There is also a set of lines. Interpolation is possible down a line but not between lines.  
1552     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
1553      line 0: class 3      not between lines.
1554      line 1: class 4,5      class 1 and 2 belong to all lines so aren't considered.
1555      line 2: class 6,7          line 0: class 3
1556      line 3: class 8,9          line 1: class 4,5
1557            line 2: class 6,7
1558     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
1559     eg hasnodes is true if we have at least one instance of Nodes.  
1560     */      For classes with multiple members (eg class 2) we have vars to record if
1561      if (fs.size()==0)      there is at least one instance.
1562      {      e.g. hasnodes is true if we have at least one instance of Nodes.
1563      return false;      */
1564      }      if (fs.empty())
1565      std::vector<int> hasclass(10);          return false;
1566      std::vector<int> hasline(4);      
1567        vector<int> hasclass(10);
1568        vector<int> hasline(4);    
1569      bool hasnodes=false;      bool hasnodes=false;
1570      bool hasrednodes=false;      bool hasrednodes=false;
1571      bool hascez=false;      bool hascez=false;
1572      bool hasrcez=false;      bool hasrcez=false;
1573      for (int i=0;i<fs.size();++i)      for (int i=0;i<fs.size();++i) {
1574      {          switch(fs[i]) {
1575      switch(fs[i])              case Nodes:
1576      {                  hasnodes=true; // fall through
1577      case(Nodes):   hasnodes=true;   // no break is deliberate              case DegreesOfFreedom:
1578      case(DegreesOfFreedom):                  hasclass[1]=1;
1579          hasclass[1]=1;                  break;
1580          break;              case ReducedNodes:
1581      case(ReducedNodes):    hasrednodes=true;    // no break is deliberate                  hasrednodes=true; // fall through
1582      case(ReducedDegreesOfFreedom):              case ReducedDegreesOfFreedom:
1583          hasclass[2]=1;                  hasclass[2]=1;
1584          break;                  break;
1585      case(Points):              case Points:
1586          hasline[0]=1;                  hasline[0]=1;
1587          hasclass[3]=1;                  hasclass[3]=1;
1588          break;                  break;
1589      case(Elements):              case Elements:
1590          hasclass[4]=1;                  hasclass[4]=1;
1591          hasline[1]=1;                  hasline[1]=1;
1592          break;                  break;
1593      case(ReducedElements):              case ReducedElements:
1594          hasclass[5]=1;                  hasclass[5]=1;
1595          hasline[1]=1;                  hasline[1]=1;
1596          break;                  break;
1597      case(FaceElements):              case FaceElements:
1598          hasclass[6]=1;                  hasclass[6]=1;
1599          hasline[2]=1;                  hasline[2]=1;
1600          break;                  break;
1601      case(ReducedFaceElements):              case ReducedFaceElements:
1602          hasclass[7]=1;                  hasclass[7]=1;
1603          hasline[2]=1;                  hasline[2]=1;
1604          break;                  break;
1605      case(ContactElementsZero):  hascez=true;    // no break is deliberate              case ContactElementsZero:
1606      case(ContactElementsOne):                  hascez=true; // fall through
1607          hasclass[8]=1;              case ContactElementsOne:
1608          hasline[3]=1;                  hasclass[8]=1;
1609          break;                  hasline[3]=1;
1610      case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate                  break;
1611      case(ReducedContactElementsOne):              case ReducedContactElementsZero:
1612          hasclass[9]=1;                  hasrcez=true; // fall through
1613          hasline[3]=1;              case ReducedContactElementsOne:
1614          break;                  hasclass[9]=1;
1615      default:                  hasline[3]=1;
1616          return false;                  break;
1617      }              default:
1618                    return false;
1619            }
1620      }      }
1621      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  
1622    
1623        // fail if we have more than one leaf group
1624      if (totlines>1)      if (totlines>1)
1625      {          return false; // there are at least two branches we can't interpolate between
1626      return false;   // there are at least two branches we can't interpolate between      else if (totlines==1) {
1627      }          if (hasline[0]==1)              // we have points
1628      else if (totlines==1)              resultcode=Points;
1629      {          else if (hasline[1]==1) {
1630      if (hasline[0]==1)      // we have points              if (hasclass[5]==1)
1631      {                  resultcode=ReducedElements;
1632          resultcode=Points;              else
1633      }                  resultcode=Elements;
1634      else if (hasline[1]==1)          } else if (hasline[2]==1) {
1635      {              if (hasclass[7]==1)
1636          if (hasclass[5]==1)                  resultcode=ReducedFaceElements;
1637          {              else
1638          resultcode=ReducedElements;                  resultcode=FaceElements;
1639          }          } else {   // so we must be in line3
1640          else              if (hasclass[9]==1) {
1641          {                  // need something from class 9
1642          resultcode=Elements;                  resultcode=(hasrcez ? ReducedContactElementsZero : ReducedContactElementsOne);
1643          }              } else {
1644      }                  // something from class 8
1645      else if (hasline[2]==1)                  resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1646      {              }
1647          if (hasclass[7]==1)          }
1648          {      } else { // totlines==0
1649          resultcode=ReducedFaceElements;          if (hasclass[2]==1) {
1650          }              // something from class 2
1651          else              resultcode=(hasrednodes ? ReducedNodes : ReducedDegreesOfFreedom);
1652          {          } else {
1653          resultcode=FaceElements;              // something from class 1
1654          }              resultcode=(hasnodes ? Nodes : DegreesOfFreedom);
1655      }          }
     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);  
     }  
1656      }      }
1657      return true;      return true;
1658  }  }
1659    
1660  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,
1661                                                 int functionSpaceType_target) const
1662  {  {
1663     switch(functionSpaceType_source) {      switch(functionSpaceType_source) {
1664     case(Nodes):          case Nodes:
1665      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1666      case(Nodes):                  case Nodes:
1667      case(ReducedNodes):                  case ReducedNodes:
1668      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1669      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1670      case(Elements):                  case Elements:
1671      case(ReducedElements):                  case ReducedElements:
1672      case(FaceElements):                  case FaceElements:
1673      case(ReducedFaceElements):                  case ReducedFaceElements:
1674      case(Points):                  case Points:
1675      case(ContactElementsZero):                  case ContactElementsZero:
1676      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1677      case(ContactElementsOne):                  case ContactElementsOne:
1678      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1679      return true;                      return true;
1680      default:                  default:
1681            stringstream temp;                      stringstream temp;
1682            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;
1683            throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1684     }              }
1685     break;              break;
1686     case(ReducedNodes):          case ReducedNodes:
1687      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1688      case(ReducedNodes):                  case ReducedNodes:
1689      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1690      case(Elements):                  case Elements:
1691      case(ReducedElements):                  case ReducedElements:
1692      case(FaceElements):                  case FaceElements:
1693      case(ReducedFaceElements):                  case ReducedFaceElements:
1694      case(Points):                  case Points:
1695      case(ContactElementsZero):                  case ContactElementsZero:
1696      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1697      case(ContactElementsOne):                  case ContactElementsOne:
1698      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1699      return true;                      return true;
1700      case(Nodes):                  case Nodes:
1701      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1702      return false;                      return false;
1703      default:                  default:
1704          stringstream temp;                      stringstream temp;
1705          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;
1706          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1707     }              }
1708     break;              break;
1709     case(Elements):          case Elements:
1710      if (functionSpaceType_target==Elements) {              if (functionSpaceType_target==Elements) {
1711        return true;                  return true;
1712      } else if (functionSpaceType_target==ReducedElements) {              } else if (functionSpaceType_target==ReducedElements) {
1713        return true;                  return true;
1714          } else {              } else {
1715            return false;                  return false;
1716          }              }
1717     case(ReducedElements):          case ReducedElements:
1718      if (functionSpaceType_target==ReducedElements) {              if (functionSpaceType_target==ReducedElements) {
1719        return true;                  return true;
1720      } else {              } else {
1721            return false;                  return false;
1722      }              }
1723     case(FaceElements):          case FaceElements:
1724      if (functionSpaceType_target==FaceElements) {              if (functionSpaceType_target==FaceElements) {
1725              return true;                  return true;
1726      } else if (functionSpaceType_target==ReducedFaceElements) {              } else if (functionSpaceType_target==ReducedFaceElements) {
1727              return true;                  return true;
1728      } else {              } else {
1729              return false;                  return false;
1730      }              }
1731     case(ReducedFaceElements):          case ReducedFaceElements:
1732      if (functionSpaceType_target==ReducedFaceElements) {              if (functionSpaceType_target==ReducedFaceElements) {
1733              return true;                  return true;
1734      } else {              } else {
1735          return false;                  return false;
1736      }              }
1737     case(Points):          case Points:
1738      if (functionSpaceType_target==Points) {              if (functionSpaceType_target==Points) {
1739              return true;                  return true;
1740      } else {              } else {
1741              return false;                  return false;
1742      }              }
1743     case(ContactElementsZero):          case ContactElementsZero:
1744     case(ContactElementsOne):          case ContactElementsOne:
1745      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {              if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1746              return true;                  return true;
1747      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {              } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1748              return true;                  return true;
1749      } else {              } else {
1750              return false;                  return false;
1751      }              }
1752     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
1753     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
1754      if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {              if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1755              return true;                  return true;
1756      } else {              } else {
1757              return false;                  return false;
1758      }              }
1759     case(DegreesOfFreedom):          case DegreesOfFreedom:
1760      switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1761      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1762      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1763      case(Nodes):                  case Nodes:
1764      case(ReducedNodes):                  case ReducedNodes:
1765      case(Elements):                  case Elements:
1766      case(ReducedElements):                  case ReducedElements:
1767      case(Points):                  case Points:
1768      case(FaceElements):                  case FaceElements:
1769      case(ReducedFaceElements):                  case ReducedFaceElements:
1770      case(ContactElementsZero):                  case ContactElementsZero:
1771      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1772      case(ContactElementsOne):                  case ContactElementsOne:
1773      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1774      return true;                      return true;
1775      default:                  default:
1776          stringstream temp;                      stringstream temp;
1777          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;
1778          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1779      }              }
1780      break;              break;
1781     case(ReducedDegreesOfFreedom):          case ReducedDegreesOfFreedom:
1782     switch(functionSpaceType_target) {              switch(functionSpaceType_target) {
1783      case(ReducedDegreesOfFreedom):                  case ReducedDegreesOfFreedom:
1784      case(ReducedNodes):                  case ReducedNodes:
1785      case(Elements):                  case Elements:
1786      case(ReducedElements):                  case ReducedElements:
1787      case(FaceElements):                  case FaceElements:
1788      case(ReducedFaceElements):                  case ReducedFaceElements:
1789      case(Points):                  case Points:
1790      case(ContactElementsZero):                  case ContactElementsZero:
1791      case(ReducedContactElementsZero):                  case ReducedContactElementsZero:
1792      case(ContactElementsOne):                  case ContactElementsOne:
1793      case(ReducedContactElementsOne):                  case ReducedContactElementsOne:
1794      return true;                      return true;
1795      case(Nodes):                  case Nodes:
1796      case(DegreesOfFreedom):                  case DegreesOfFreedom:
1797      return false;                      return false;
1798      default:                  default:
1799          stringstream temp;                      stringstream temp;
1800          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;
1801          throw FinleyAdapterException(temp.str());                      throw FinleyAdapterException(temp.str());
1802      }              }
1803      break;              break;
1804     default:          default:
1805        stringstream temp;              stringstream temp;
1806        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;
1807        throw FinleyAdapterException(temp.str());              throw FinleyAdapterException(temp.str());
1808        break;              break;
1809     }      }
1810     checkFinleyError();      return false;
1811     return false;  }
1812  }  
1813    signed char MeshAdapter::preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
1814  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const  {
1815  {      if (probeInterpolationOnDomain(functionSpaceType_source, functionSpaceType_target))
1816     return false;          return 1;
1817  }  
1818        if (probeInterpolationOnDomain(functionSpaceType_target, functionSpaceType_source))
1819  bool MeshAdapter::operator==(const AbstractDomain& other) const          return -1;
1820  {  
1821     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);      return 0;
    if (temp!=0) {  
       return (m_finleyMesh==temp->m_finleyMesh);  
    } else {  
       return false;  
    }  
1822  }  }
1823    
1824  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,
1825            const escript::AbstractDomain& targetDomain,
1826            int functionSpaceType_target) const
1827  {  {
1828     return !(operator==(other));      return false;
1829    }
1830    
1831    bool MeshAdapter::operator==(const escript::AbstractDomain& other) const
1832    {
1833        const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1834        if (temp) {
1835            return (m_finleyMesh==temp->m_finleyMesh);
1836        } else {
1837            return false;
1838        }
1839    }
1840    
1841    bool MeshAdapter::operator!=(const escript::AbstractDomain& other) const
1842    {
1843        return !(operator==(other));
1844  }  }
1845    
1846  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
1847  {  {
1848     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1849     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);      return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
1850     checkPasoError();                 package, symmetry, mesh->MPIInfo);
    return out;  
1851  }  }
1852    
1853  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
1854  {  {
1855     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1856     int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);      return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
1857     checkPasoError();                  package, symmetry, mesh->MPIInfo);
    return out;  
1858  }  }
1859    
1860  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1861  {  {
1862     return continuousFunction(asAbstractContinuousDomain()).getX();      return continuousFunction(*this).getX();
1863  }  }
1864    
1865  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1866  {  {
1867     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();      return functionOnBoundary(*this).getNormal();
1868  }  }
1869    
1870  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1871  {  {
1872     return escript::function(asAbstractContinuousDomain()).getSize();      return escript::function(*this).getSize();
1873  }  }
1874    
1875  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1876  {  {
1877     int *out = NULL;      int *out = NULL;
1878     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1879     switch (functionSpaceType) {      switch (functionSpaceType) {
1880     case(Nodes):          case Nodes:
1881     out=mesh->Nodes->Id;              out=mesh->Nodes->Id;
1882     break;              break;
1883     case(ReducedNodes):          case ReducedNodes:
1884     out=mesh->Nodes->reducedNodesId;              out=mesh->Nodes->reducedNodesId;
1885     break;              break;
1886     case(Elements):          case Elements:
1887     out=mesh->Elements->Id;          case ReducedElements:
1888     break;              out=mesh->Elements->Id;
1889     case(ReducedElements):              break;
1890     out=mesh->Elements->Id;          case FaceElements:
1891     break;          case ReducedFaceElements:
1892     case(FaceElements):              out=mesh->FaceElements->Id;
1893     out=mesh->FaceElements->Id;              break;
1894     break;          case Points:
1895     case(ReducedFaceElements):              out=mesh->Points->Id;
1896     out=mesh->FaceElements->Id;              break;
1897     break;          case ContactElementsZero:
1898     case(Points):          case ReducedContactElementsZero:
1899     out=mesh->Points->Id;          case ContactElementsOne:
1900     break;          case ReducedContactElementsOne:
1901     case(ContactElementsZero):              out=mesh->ContactElements->Id;
1902     out=mesh->ContactElements->Id;              break;
1903     break;          case DegreesOfFreedom:
1904     case(ReducedContactElementsZero):              out=mesh->Nodes->degreesOfFreedomId;
1905     out=mesh->ContactElements->Id;              break;
1906     break;          case ReducedDegreesOfFreedom:
1907     case(ContactElementsOne):              out=mesh->Nodes->reducedDegreesOfFreedomId;
1908     out=mesh->ContactElements->Id;              break;
1909     break;          default:
1910     case(ReducedContactElementsOne):              stringstream temp;
1911     out=mesh->ContactElements->Id;              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1912     break;              throw FinleyAdapterException(temp.str());
1913     case(DegreesOfFreedom):              break;
1914     out=mesh->Nodes->degreesOfFreedomId;      }
1915     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;  
1916  }  }
1917  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1918  {  {
1919     int out=0;      int out=0;
1920     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1921     switch (functionSpaceType) {      switch (functionSpaceType) {
1922     case(Nodes):          case Nodes:
1923     out=mesh->Nodes->Tag[sampleNo];              out=mesh->Nodes->Tag[sampleNo];
1924     break;              break;
1925     case(ReducedNodes):          case ReducedNodes:
1926     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");              throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1927     break;              break;
1928     case(Elements):          case Elements:
1929     out=mesh->Elements->Tag[sampleNo];          case ReducedElements:
1930     break;              out=mesh->Elements->Tag[sampleNo];
1931     case(ReducedElements):              break;
1932     out=mesh->Elements->Tag[sampleNo];          case FaceElements:
1933     break;          case ReducedFaceElements:
1934     case(FaceElements):              out=mesh->FaceElements->Tag[sampleNo];
1935     out=mesh->FaceElements->Tag[sampleNo];              break;
1936     break;          case Points:
1937     case(ReducedFaceElements):              out=mesh->Points->Tag[sampleNo];
1938     out=mesh->FaceElements->Tag[sampleNo];              break;
1939     break;          case ContactElementsZero:
1940     case(Points):          case ReducedContactElementsZero:
1941     out=mesh->Points->Tag[sampleNo];          case ContactElementsOne:
1942     break;          case ReducedContactElementsOne:
1943     case(ContactElementsZero):              out=mesh->ContactElements->Tag[sampleNo];
1944     out=mesh->ContactElements->Tag[sampleNo];              break;
1945     break;          case DegreesOfFreedom:
1946     case(ReducedContactElementsZero):              throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1947     out=mesh->ContactElements->Tag[sampleNo];              break;
1948     break;          case ReducedDegreesOfFreedom:
1949     case(ContactElementsOne):              throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1950     out=mesh->ContactElements->Tag[sampleNo];              break;
1951     break;          default:
1952     case(ReducedContactElementsOne):              stringstream temp;
1953     out=mesh->ContactElements->Tag[sampleNo];              temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1954     break;              throw FinleyAdapterException(temp.str());
1955     case(DegreesOfFreedom):              break;
1956     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");      }
1957     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;  
1958  }  }
1959    
1960    
1961  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
1962  {  {
1963     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
1964     escriptDataC tmp=mask.getDataC();      switch(functionSpaceType) {
1965     switch(functionSpaceType) {          case Nodes:
1966     case(Nodes):              mesh->Nodes->setTags(newTag, mask);
1967     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);              break;
1968     break;          case ReducedNodes:
1969     case(ReducedNodes):              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1970     throw FinleyAdapterException("Error - ReducedNodes does not support tags");          case DegreesOfFreedom:
1971     break;              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1972     case(DegreesOfFreedom):          case ReducedDegreesOfFreedom:
1973     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1974     break;          case Elements:
1975     case(ReducedDegreesOfFreedom):          case ReducedElements:
1976     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");              mesh->Elements->setTags(newTag, mask);
1977     break;              break;
1978     case(Elements):          case FaceElements:
1979     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case ReducedFaceElements:
1980     break;              mesh->FaceElements->setTags(newTag, mask);
1981     case(ReducedElements):              break;
1982     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);          case Points:
1983     break;              mesh->Points->setTags(newTag, mask);
1984     case(FaceElements):              break;
1985     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ContactElementsZero:
1986     break;          case ReducedContactElementsZero:
1987     case(ReducedFaceElements):          case ContactElementsOne:
1988     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);          case ReducedContactElementsOne:
1989     break;              mesh->ContactElements->setTags(newTag, mask);
1990     case(Points):              break;
1991     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);          default:
1992     break;              stringstream temp;
1993     case(ContactElementsZero):              temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
1994     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);              throw FinleyAdapterException(temp.str());
1995     break;      }
1996     case(ReducedContactElementsZero):      checkFinleyError();
1997     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  }
1998     break;  
1999     case(ContactElementsOne):  void MeshAdapter::setTagMap(const string& name, int tag)
2000     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);  {
2001     break;      Finley_Mesh* mesh=m_finleyMesh.get();
2002     case(ReducedContactElementsOne):      Finley_Mesh_addTagMap(mesh, name.c_str(), tag);
2003     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);      checkFinleyError();
2004     break;  }
2005     default:  
2006        stringstream temp;  int MeshAdapter::getTag(const string& name) const
2007        temp << "Error - Finley does not know anything about function space type " << functionSpaceType;  {
2008        throw FinleyAdapterException(temp.str());      Finley_Mesh* mesh=m_finleyMesh.get();
2009     }      int tag = Finley_Mesh_getTag(mesh, name.c_str());
2010     checkFinleyError();      checkFinleyError();
2011     return;      return tag;
2012  }  }
2013    
2014  void MeshAdapter::setTagMap(const std::string& name,  int tag)  bool MeshAdapter::isValidTagName(const string& name) const
2015  {  {
2016     Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2017     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);      return Finley_Mesh_isValidTagName(mesh, name.c_str());
2018     checkPasoError();  }
2019     // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
2020  }  string MeshAdapter::showTagNames() const
2021    {
2022  int MeshAdapter::getTag(const std::string& name) const      stringstream temp;
2023  {      Finley_Mesh* mesh=m_finleyMesh.get();
2024     Finley_Mesh* mesh=m_finleyMesh.get();      TagMap::const_iterator it = mesh->tagMap.begin();
2025     int tag=0;      while (it != mesh->tagMap.end()) {
2026     tag=Finley_Mesh_getTag(mesh, name.c_str());          temp << it->first;
2027     checkPasoError();          ++it;
2028     // throwStandardException("MeshAdapter::getTag is not implemented.");          if (it != mesh->tagMap.end())
2029     return tag;              temp << ", ";
2030  }      }
2031        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();  
2032  }  }
2033    
2034  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2035  {  {
2036    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2037    dim_t numTags=0;      switch(functionSpaceCode) {
2038    switch(functionSpaceCode) {          case Nodes:
2039     case(Nodes):              return mesh->Nodes->tagsInUse.size();
2040            numTags=mesh->Nodes->numTagsInUse;          case ReducedNodes:
2041            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2042     case(ReducedNodes):          case DegreesOfFreedom:
2043            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2044            break;          case ReducedDegreesOfFreedom:
2045     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2046            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2047            break;          case ReducedElements:
2048     case(ReducedDegreesOfFreedom):              return mesh->Elements->tagsInUse.size();
2049            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2050            break;          case ReducedFaceElements:
2051     case(Elements):              return mesh->FaceElements->tagsInUse.size();
2052     case(ReducedElements):          case Points:
2053            numTags=mesh->Elements->numTagsInUse;              return mesh->Points->tagsInUse.size();
2054            break;          case ContactElementsZero:
2055     case(FaceElements):          case ReducedContactElementsZero:
2056     case(ReducedFaceElements):          case ContactElementsOne:
2057            numTags=mesh->FaceElements->numTagsInUse;          case ReducedContactElementsOne:
2058            break;              return mesh->ContactElements->tagsInUse.size();
2059     case(Points):          default:
2060            numTags=mesh->Points->numTagsInUse;              stringstream ss;
2061            break;              ss << "Finley does not know anything about function space type "
2062     case(ContactElementsZero):                   << functionSpaceCode;
2063     case(ReducedContactElementsZero):              throw FinleyAdapterException(ss.str());
2064     case(ContactElementsOne):      }
2065     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;  
2066  }  }
2067    
2068  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2069  {  {
2070    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2071    index_t* tags=NULL;      switch(functionSpaceCode) {
2072    switch(functionSpaceCode) {          case Nodes:
2073     case(Nodes):              return &mesh->Nodes->tagsInUse[0];
2074            tags=mesh->Nodes->tagsInUse;          case ReducedNodes:
2075            break;              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2076     case(ReducedNodes):          case DegreesOfFreedom:
2077            throw FinleyAdapterException("Error - ReducedNodes does not support tags");              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2078            break;          case ReducedDegreesOfFreedom:
2079     case(DegreesOfFreedom):              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2080            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");          case Elements:
2081            break;          case ReducedElements:
2082     case(ReducedDegreesOfFreedom):              return &mesh->Elements->tagsInUse[0];
2083            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");          case FaceElements:
2084            break;          case ReducedFaceElements:
2085     case(Elements):              return &mesh->FaceElements->tagsInUse[0];
2086     case(ReducedElements):          case Points:
2087            tags=mesh->Elements->tagsInUse;              return &mesh->Points->tagsInUse[0];
2088            break;          case ContactElementsZero:
2089     case(FaceElements):          case ReducedContactElementsZero:
2090     case(ReducedFaceElements):          case ContactElementsOne:
2091            tags=mesh->FaceElements->tagsInUse;          case ReducedContactElementsOne:
2092            break;              return &mesh->ContactElements->tagsInUse[0];
2093     case(Points):          default:
2094            tags=mesh->Points->tagsInUse;              stringstream temp;
2095            break;              temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2096     case(ContactElementsZero):              throw FinleyAdapterException(temp.str());
2097     case(ReducedContactElementsZero):      }
2098     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;  
2099  }  }
2100    
2101    
2102  bool MeshAdapter::canTag(int functionSpaceCode) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2103  {  {
2104    switch(functionSpaceCode) {      switch(functionSpaceCode) {
2105     case(Nodes):          case Nodes:
2106     case(Elements):          case Elements:
2107     case(ReducedElements):          case ReducedElements:
2108     case(FaceElements):          case FaceElements:
2109     case(ReducedFaceElements):          case ReducedFaceElements:
2110     case(Points):          case Points:
2111     case(ContactElementsZero):          case ContactElementsZero:
2112     case(ReducedContactElementsZero):          case ReducedContactElementsZero:
2113     case(ContactElementsOne):          case ContactElementsOne:
2114     case(ReducedContactElementsOne):          case ReducedContactElementsOne:
2115            return true;              return true;
2116     case(ReducedNodes):          default:
2117     case(DegreesOfFreedom):              return false;
2118     case(ReducedDegreesOfFreedom):      }
       return false;  
    default:  
     return false;  
   }  
2119  }  }
2120    
2121  AbstractDomain::StatusType MeshAdapter::getStatus() const  escript::AbstractDomain::StatusType MeshAdapter::getStatus() const
2122  {  {
2123    Finley_Mesh* mesh=m_finleyMesh.get();      Finley_Mesh* mesh=m_finleyMesh.get();
2124    return Finley_Mesh_getStatus(mesh);      return Finley_Mesh_getStatus(mesh);
2125  }  }
2126    
2127    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2128    {
2129        Finley_Mesh* mesh=m_finleyMesh.get();
2130        int order =-1;
2131        switch(functionSpaceCode) {
2132            case Nodes:
2133            case DegreesOfFreedom:
2134                order=mesh->approximationOrder;
2135                break;
2136            case ReducedNodes:
2137            case ReducedDegreesOfFreedom:
2138                order=mesh->reducedApproximationOrder;
2139                break;
2140            case Elements:
2141            case FaceElements:
2142            case Points:
2143            case ContactElementsZero:
2144            case ContactElementsOne:
2145                order=mesh->integrationOrder;
2146                break;
2147            case ReducedElements:
2148            case ReducedFaceElements:
2149            case ReducedContactElementsZero:
2150            case ReducedContactElementsOne:
2151                order=mesh->reducedIntegrationOrder;
2152                break;
2153            default:
2154                stringstream temp;
2155                temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2156                throw FinleyAdapterException(temp.str());
2157        }
2158        return order;
2159    }
2160    
2161    bool MeshAdapter::supportsContactElements() const
2162    {
2163        return true;
2164    }
2165    
2166    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id,
2167            index_t order, index_t reducedOrder)
2168    {
2169        m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2170    }
2171    
2172    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2173    {
2174        Finley_ReferenceElementSet_dealloc(m_refSet);
2175    }
2176    
2177    void MeshAdapter::addDiracPoints(const vector<double>& points,
2178                                     const vector<int>& tags) const
2179    {
2180        // points will be flattened
2181        const int dim = getDim();
2182        int numPoints=points.size()/dim;
2183        int numTags=tags.size();
2184        Finley_Mesh* mesh=m_finleyMesh.get();
2185    
2186        if ( points.size() % dim != 0 ) {
2187            throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2188        }
2189    
2190        if ((numTags > 0) && (numPoints != numTags))
2191            throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2192    
2193        Finley_Mesh_addPoints(mesh, numPoints, &points[0], &tags[0]);
2194        checkFinleyError();
2195    }
2196    
2197    // void MeshAdapter::addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2198    // {
2199    //       const int dim = getDim();
2200    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2201    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2202    //       Finley_Mesh* mesh=m_finleyMesh.get();
2203    //
2204    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2205    //       throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2206    //
2207    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2208    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2209    //
2210    //       for (int i=0;i<numPoints;++i) {
2211    //         int tag_id=-1;
2212    //         int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2213    //         if  ( numComps !=   dim ) {
2214    //                stringstream temp;
2215    //                temp << "Error - illegal number of components " << numComps << " for point " << i;
2216    //                throw FinleyAdapterException(temp.str());
2217    //         }
2218    //         points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2219    //         if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2220    //         if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2221    //
2222    //         if ( numTags > 0) {
2223    //                boost::python::extract<string> ex_str(tags[i]);
2224    //                if  ( ex_str.check() ) {
2225    //                    tag_id=getTag( ex_str());
2226    //                } else {
2227    //                     boost::python::extract<int> ex_int(tags[i]);
2228    //                     if ( ex_int.check() ) {
2229    //                         tag_id=ex_int();
2230    //                     } else {
2231    //                          stringstream temp;
2232    //                          temp << "Error - unable to extract tag for point " << i;
2233    //                          throw FinleyAdapterException(temp.str());
2234    //                    }
2235    //                }
2236    //         }
2237    //            tags_ptr[i]=tag_id;
2238    //       }
2239    //
2240    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2241    //       checkPasoError();
2242    //
2243    //       TMPMEMFREE(points_ptr);
2244    //       TMPMEMFREE(tags_ptr);
2245    // }
2246    
2247    /*
2248    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2249    {
2250        boost::python::list points =  boost::python::list();
2251        boost::python::list tags =  boost::python::list();
2252        points.append(point);
2253        tags.append(tag);
2254        addDiracPoints(points, tags);
2255    }
2256    */
2257    
2258    /*
2259    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const string& tag) const
2260    {
2261        boost::python::list points =   boost::python::list();
2262        boost::python::list tags =   boost::python::list();
2263        points.append(point);
2264        tags.append(tag);
2265        addDiracPoints(points, tags);
2266    }
2267    */
2268  }  // end of namespace  }  // end of namespace
2269    

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