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

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

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

revision 1346 by ksteube, Wed Nov 14 22:48:12 2007 UTC revision 1877 by ksteube, Tue Oct 14 02:58:39 2008 UTC
# Line 1  Line 1 
1    
 /* $Id$ */  
   
2  /*******************************************************  /*******************************************************
3   *  *
4   *           Copyright 2003-2007 by ACceSS MNRF  * Copyright (c) 2003-2008 by University of Queensland
5   *       Copyright 2007 by University of Queensland  * Earth Systems Science Computational Center (ESSCC)
6   *  * http://www.uq.edu.au/esscc
7   *                http://esscc.uq.edu.au  *
8   *        Primary Business: Queensland, Australia  * Primary Business: Queensland, Australia
9   *  Licensed under the Open Software License version 3.0  * Licensed under the Open Software License version 3.0
10   *     http://www.opensource.org/licenses/osl-3.0.php  * http://www.opensource.org/licenses/osl-3.0.php
11   *  *
12   *******************************************************/  *******************************************************/
13    
14    
15  #include "MeshAdapter.h"  #include "MeshAdapter.h"
16  #include "escript/Data.h"  #include "escript/Data.h"
# Line 19  Line 18 
18  #ifdef USE_NETCDF  #ifdef USE_NETCDF
19  #include <netcdfcpp.h>  #include <netcdfcpp.h>
20  #endif  #endif
21    #ifdef PASO_MPI
22    #include <mpi.h>
23    #include "paso/Paso_MPI.h"
24    #endif
25  extern "C" {  extern "C" {
26  #include "escript/blocktimer.h"  #include "escript/blocktimer.h"
27  }  }
28  #include <vector>  #include <vector>
29    
30    #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH  256
31    
32  using namespace std;  using namespace std;
33  using namespace escript;  using namespace escript;
34    
# Line 48  const int MeshAdapter::ReducedContactEle Line 53  const int MeshAdapter::ReducedContactEle
53    
54  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
55  {  {
56    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
57    //     //
58    // need to use a null_deleter as Finley_Mesh_free deletes the pointer     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
59    // for us.     // for us.
60    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
61  }  }
62    
63  //  //
# Line 60  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 65  MeshAdapter::MeshAdapter(Finley_Mesh* fi
65  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
66  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
67  {  {
68    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
69  }  }
70    
71  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
72  {  {
73    //     //
74    // I hope the case for the pointer being zero has been taken care of.     // I hope the case for the pointer being zero has been taken care of.
75    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
76    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
77      Finley_Mesh_free(m_finleyMesh.get());        Finley_Mesh_free(m_finleyMesh.get());
78    }     }
79  }  }
80    
81  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
# Line 81  int MeshAdapter::getMPIRank() const Line 86  int MeshAdapter::getMPIRank() const
86  {  {
87     return m_finleyMesh.get()->MPIInfo->rank;     return m_finleyMesh.get()->MPIInfo->rank;
88  }  }
89    void MeshAdapter::MPIBarrier() const
90    {
91    #ifdef PASO_MPI
92       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
93    #endif
94       return;
95    }
96    bool MeshAdapter::onMasterProcessor() const
97    {
98       return m_finleyMesh.get()->MPIInfo->rank == 0;
99    }
100    
101    
102  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
# Line 89  Finley_Mesh* MeshAdapter::getFinley_Mesh Line 105  Finley_Mesh* MeshAdapter::getFinley_Mesh
105    
106  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
107  {  {
108    char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
109    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
110    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
111    checkFinleyError();     checkFinleyError();
112    TMPMEMFREE(fName);     TMPMEMFREE(fName);
113  }  }
114    
115  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  void MeshAdapter::Print_Mesh_Info(const bool full=false) const
116  {  {
117    Finley_PrintMesh_Info(m_finleyMesh.get(), full);     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
118  }  }
119    
120  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const std::string& fileName) const
121  {  {
122  #ifdef USE_NETCDF  #ifdef USE_NETCDF
123     const NcDim* ncdims[25]; /* ksteube how big should ncdims be? */     const NcDim* ncdims[12];
124     NcVar *ids, *data;     NcVar *ids;
125     int *int_ptr;     int *int_ptr;
126     Finley_Mesh *mesh = m_finleyMesh.get();     Finley_Mesh *mesh = m_finleyMesh.get();
127       Finley_TagMap* tag_map;
128       int num_Tags = 0;
129     int mpi_size             = mesh->MPIInfo->size;     int mpi_size             = mesh->MPIInfo->size;
130     int mpi_rank             = mesh->MPIInfo->rank;     int mpi_rank             = mesh->MPIInfo->rank;
131     int numDim               = mesh->Nodes->numDim;     int numDim               = mesh->Nodes->numDim;
# Line 119  void MeshAdapter::dump(const std::string Line 137  void MeshAdapter::dump(const std::string
137     int num_Elements_numNodes        = mesh->Elements->numNodes;     int num_Elements_numNodes        = mesh->Elements->numNodes;
138     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
139     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
140     char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank);  #ifdef PASO_MPI
141       MPI_Status status;
142    #endif
143    
144    /* Incoming token indicates it's my turn to write */
145    #ifdef PASO_MPI
146       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
147    #endif
148    
149       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
150                                                         mpi_size, mpi_rank);
151    
152       /* Figure out how much storage is required for tags */
153       tag_map = mesh->TagMap;
154       num_Tags = 0;
155       if (tag_map) {
156          while (tag_map) {
157             num_Tags++;
158             tag_map=tag_map->next;
159          }
160       }
161    
162     // NetCDF error handler     // NetCDF error handler
163     NcError err(NcError::verbose_nonfatal);     NcError err(NcError::verbose_nonfatal);
# Line 127  void MeshAdapter::dump(const std::string Line 165  void MeshAdapter::dump(const std::string
165     NcFile dataFile(newFileName, NcFile::Replace);     NcFile dataFile(newFileName, NcFile::Replace);
166     // check if writing was successful     // check if writing was successful
167     if (!dataFile.is_valid())     if (!dataFile.is_valid())
168          throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: opening of NetCDF file for output failed: " + *newFileName);
169    
170     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)     // Define dimensions (num_Elements and dim_Elements are identical, dim_Elements only appears if > 0)
171     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
172          throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending dimension numNodes to netCDF file failed: " + *newFileName);
173     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
174          throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending dimension numDim to netCDF file failed: " + *newFileName);
175     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )     if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
176          throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending dimension mpi_size to netCDF file failed: " + *newFileName);
177     if (num_Elements>0)     if (num_Elements>0)
178        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
179          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements to netCDF file failed: " + *newFileName);
180     if (num_FaceElements>0)     if (num_FaceElements>0)
181        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
182          throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements to netCDF file failed: " + *newFileName);
183     if (num_ContactElements>0)     if (num_ContactElements>0)
184        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
185          throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements to netCDF file failed: " + *newFileName);
186     if (num_Points>0)     if (num_Points>0)
187        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
188          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Points to netCDF file failed: " + *newFileName);
189     if (num_Elements>0)     if (num_Elements>0)
190        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
191          throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending dimension dim_Elements_Nodes to netCDF file failed: " + *newFileName);
192     if (num_FaceElements>0)     if (num_FaceElements>0)
193        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
194          throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending dimension dim_FaceElements_numNodes to netCDF file failed: " + *newFileName);
195     if (num_ContactElements>0)     if (num_ContactElements>0)
196        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
197          throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending dimension dim_ContactElements_numNodes to netCDF file failed: " + *newFileName);
198       if (num_Tags>0)
199          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
200             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
201    
202     // Attributes: MPI size, MPI rank, Name, order, reduced_order     // Attributes: MPI size, MPI rank, Name, order, reduced_order
203     if (!dataFile.add_att("mpi_size", mpi_size) )     if (!dataFile.add_att("mpi_size", mpi_size) )
204          throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending mpi_size to NetCDF file failed: " + *newFileName);
205     if (!dataFile.add_att("mpi_rank", mpi_rank) )     if (!dataFile.add_att("mpi_rank", mpi_rank) )
206          throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending mpi_rank to NetCDF file failed: " + *newFileName);
207     if (!dataFile.add_att("Name",mesh->Name) )     if (!dataFile.add_att("Name",mesh->Name) )
208          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
209     if (!dataFile.add_att("numDim",numDim) )     if (!dataFile.add_att("numDim",numDim) )
210          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
211     if (!dataFile.add_att("order",mesh->order) )     if (!dataFile.add_att("order",mesh->order) )
212          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
213     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
214          throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending reduced_order to NetCDF file failed: " + *newFileName);
215     if (!dataFile.add_att("numNodes",numNodes) )     if (!dataFile.add_att("numNodes",numNodes) )
216          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
217     if (!dataFile.add_att("num_Elements",num_Elements) )     if (!dataFile.add_att("num_Elements",num_Elements) )
218          throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending num_Elements to NetCDF file failed: " + *newFileName);
219     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
220          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements to NetCDF file failed: " + *newFileName);
221     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
222          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements to NetCDF file failed: " + *newFileName);
223     if (!dataFile.add_att("num_Points",num_Points) )     if (!dataFile.add_att("num_Points",num_Points) )
224          throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending num_Points to NetCDF file failed: " + *newFileName);
225     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
226          throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending num_Elements_numNodes to NetCDF file failed: " + *newFileName);
227     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
228          throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending num_FaceElements_numNodes to NetCDF file failed: " + *newFileName);
229     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
230          throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending num_ContactElements_numNodes to NetCDF file failed: " + *newFileName);
231       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
232          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
233       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
234          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
235       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
236          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
237       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
238          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
239       if (!dataFile.add_att("num_Tags", num_Tags) )
240          throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
241    
242     // // // // // Nodes // // // // //     // // // // // Nodes // // // // //
243    
244     // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)     // Only write nodes if non-empty because NetCDF doesn't like empty arrays (it treats them as NC_UNLIMITED)
245     if (numNodes>0) {     if (numNodes>0) {
246    
247     // Nodes Id        // Nodes Id
248     if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
249          throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Nodes_Id to netCDF file failed: " + *newFileName);
250     int_ptr = &mesh->Nodes->Id[0];        int_ptr = &mesh->Nodes->Id[0];
251     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
252          throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Nodes_Id to netCDF buffer failed: " + *newFileName);
253    
254     // Nodes Tag        // Nodes Tag
255     if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
256          throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Nodes_Tag to netCDF file failed: " + *newFileName);
257     int_ptr = &mesh->Nodes->Tag[0];        int_ptr = &mesh->Nodes->Tag[0];
258     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
259          throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Nodes_Tag to netCDF buffer failed: " + *newFileName);
260    
261     // Nodes gDOF        // Nodes gDOF
262     if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
263          throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Nodes_gDOF to netCDF file failed: " + *newFileName);
264     int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
265     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
266          throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Nodes_gDOF to netCDF buffer failed: " + *newFileName);
267    
268     // Nodes global node index        // Nodes global node index
269     if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
270          throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Nodes_gNI to netCDF file failed: " + *newFileName);
271     int_ptr = &mesh->Nodes->globalNodesIndex[0];        int_ptr = &mesh->Nodes->globalNodesIndex[0];
272     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
273          throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Nodes_gNI to netCDF buffer failed: " + *newFileName);
274    
275     // Nodes grDof        // Nodes grDof
276     if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
277          throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Nodes_grDfI to netCDF file failed: " + *newFileName);
278     int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
279     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
280          throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Nodes_grDfI to netCDF buffer failed: " + *newFileName);
281    
282     // Nodes grNI        // Nodes grNI
283     if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
284          throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Nodes_grNI to netCDF file failed: " + *newFileName);
285     int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
286     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
287          throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Nodes_grNI to netCDF buffer failed: " + *newFileName);
288    
289     // Nodes Coordinates        // Nodes Coordinates
290     if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
291          throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Nodes_Coordinates to netCDF file failed: " + *newFileName);
292     if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
293          throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Nodes_Coordinates to netCDF buffer failed: " + *newFileName);
294    
295     // Nodes degreesOfFreedomDistribution        // Nodes degreesOfFreedomDistribution
296     if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
297          throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Nodes_DofDistribution to netCDF file failed: " + *newFileName);
298     int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
299     if (! (ids->put(int_ptr, mpi_size+1)) )        if (! (ids->put(int_ptr, mpi_size+1)) )
300          throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Nodes_DofDistribution to netCDF buffer failed: " + *newFileName);
301    
302          // Nodes nodeDistribution
303          if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
304             throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
305          int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
306          if (! (ids->put(int_ptr, mpi_size+1)) )
307             throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
308    
309     }     }
310    
# Line 254  void MeshAdapter::dump(const std::string Line 312  void MeshAdapter::dump(const std::string
312    
313     if (num_Elements>0) {     if (num_Elements>0) {
314    
315       // Temp storage to gather node IDs        // Elements_Id
316       int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
317             throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
318       // Elements ReferenceElement->ElementTypeId        int_ptr = &mesh->Elements->Id[0];
319       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )        if (! (ids->put(int_ptr, num_Elements)) )
320          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
321    
322       // Elements_Id        // Elements_Tag
323       if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
324          throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
325       int_ptr = &mesh->Elements->Id[0];        int_ptr = &mesh->Elements->Tag[0];
326       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
327          throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
328    
329       // Elements_Tag        // Elements_Owner
330       if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
331          throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
332       int_ptr = &mesh->Elements->Tag[0];        int_ptr = &mesh->Elements->Owner[0];
333       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
334          throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
335    
336       // Elements_Owner        // Elements_Color
337       if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
338          throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
339       int_ptr = &mesh->Elements->Owner[0];        int_ptr = &mesh->Elements->Color[0];
340       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
341          throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
342    
343       // Elements_Color        // Elements_Nodes
344       if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
345          throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
346       int_ptr = &mesh->Elements->Color[0];        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
347       if (! (ids->put(int_ptr, num_Elements)) )           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
         throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);  
   
      // Elements_Nodes  
      for (int i=0; i<num_Elements; i++)  
        for (int j=0; j<num_Elements_numNodes; j++)  
          Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]];  
      if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(Elements_Nodes);  
348    
349     }     }
350    
# Line 306  void MeshAdapter::dump(const std::string Line 352  void MeshAdapter::dump(const std::string
352    
353     if (num_FaceElements>0) {     if (num_FaceElements>0) {
354    
355       // Temp storage to gather node IDs        // FaceElements_Id
356       int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
357             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
358       // FaceElements ReferenceElement->ElementTypeId        int_ptr = &mesh->FaceElements->Id[0];
359       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )        if (! (ids->put(int_ptr, num_FaceElements)) )
360          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
361    
362       // FaceElements_Id        // FaceElements_Tag
363       if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
364          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
365       int_ptr = &mesh->FaceElements->Id[0];        int_ptr = &mesh->FaceElements->Tag[0];
366       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
367          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
368    
369       // FaceElements_Tag        // FaceElements_Owner
370       if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
371          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
372       int_ptr = &mesh->FaceElements->Tag[0];        int_ptr = &mesh->FaceElements->Owner[0];
373       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
374          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
375    
376       // FaceElements_Owner        // FaceElements_Color
377       if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
378          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
379       int_ptr = &mesh->FaceElements->Owner[0];        int_ptr = &mesh->FaceElements->Color[0];
380       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
381          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
382    
383       // FaceElements_Color        // FaceElements_Nodes
384       if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
385          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
386       int_ptr = &mesh->FaceElements->Color[0];        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
387       if (! (ids->put(int_ptr, num_FaceElements)) )           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
         throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);  
   
      // FaceElements_Nodes  
      for (int i=0; i<num_FaceElements; i++)  
        for (int j=0; j<num_FaceElements_numNodes; j++)  
          FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]];  
      if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(FaceElements_Nodes);  
388    
389     }     }
390    
# Line 358  void MeshAdapter::dump(const std::string Line 392  void MeshAdapter::dump(const std::string
392    
393     if (num_ContactElements>0) {     if (num_ContactElements>0) {
394    
395       // Temp storage to gather node IDs        // ContactElements_Id
396       int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
397             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
398       // ContactElements ReferenceElement->ElementTypeId        int_ptr = &mesh->ContactElements->Id[0];
399       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )        if (! (ids->put(int_ptr, num_ContactElements)) )
400          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
401    
402       // ContactElements_Id        // ContactElements_Tag
403       if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
404          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
405       int_ptr = &mesh->ContactElements->Id[0];        int_ptr = &mesh->ContactElements->Tag[0];
406       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
407          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
408    
409       // ContactElements_Tag        // ContactElements_Owner
410       if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
411          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
412       int_ptr = &mesh->ContactElements->Tag[0];        int_ptr = &mesh->ContactElements->Owner[0];
413       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
414          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
415    
416       // ContactElements_Owner        // ContactElements_Color
417       if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
418          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
419       int_ptr = &mesh->ContactElements->Owner[0];        int_ptr = &mesh->ContactElements->Color[0];
420       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
421          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
422    
423       // ContactElements_Color        // ContactElements_Nodes
424       if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
425          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
426       int_ptr = &mesh->ContactElements->Color[0];        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
427       if (! (ids->put(int_ptr, num_ContactElements)) )           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
         throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);  
   
      // ContactElements_Nodes  
      for (int i=0; i<num_ContactElements; i++)  
        for (int j=0; j<num_ContactElements_numNodes; j++)  
          ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]];  
      if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(ContactElements_Nodes);  
428    
429     }     }
430    
# Line 410  void MeshAdapter::dump(const std::string Line 432  void MeshAdapter::dump(const std::string
432    
433     if (num_Points>0) {     if (num_Points>0) {
434    
435       fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");        fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
   
      // Temp storage to gather node IDs  
      int *Points_Nodes = TMPMEMALLOC(num_Points,int);  
436    
437       // Points ReferenceElement->ElementTypeId        // Points_Id
438       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
439          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
440          int_ptr = &mesh->Points->Id[0];
441       // Points_Id        if (! (ids->put(int_ptr, num_Points)) )
442       if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
443          throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);  
444       int_ptr = &mesh->Points->Id[0];        // Points_Tag
445       if (! (ids->put(int_ptr, num_Points)) )        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
446          throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
447          int_ptr = &mesh->Points->Tag[0];
448       // Points_Tag        if (! (ids->put(int_ptr, num_Points)) )
449       if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
450          throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);  
451       int_ptr = &mesh->Points->Tag[0];        // Points_Owner
452       if (! (ids->put(int_ptr, num_Points)) )        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
453          throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
454          int_ptr = &mesh->Points->Owner[0];
455       // Points_Owner        if (! (ids->put(int_ptr, num_Points)) )
456       if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
457          throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);  
458       int_ptr = &mesh->Points->Owner[0];        // Points_Color
459       if (! (ids->put(int_ptr, num_Points)) )        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
460          throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
461          int_ptr = &mesh->Points->Color[0];
462       // Points_Color        if (! (ids->put(int_ptr, num_Points)) )
463       if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
464          throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);  
465       int_ptr = &mesh->Points->Color[0];        // Points_Nodes
466       if (! (ids->put(int_ptr, num_Points)) )        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
467          throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
468             throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
469       // Points_Nodes        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
470       // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
      for (int i=0; i<num_Points; i++)  
        Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];  
      if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(Points_Nodes[0]), num_Points)) )  
         throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(Points_Nodes);  
471    
472     }     }
473    
474     // // // // // TagMap // // // // //     // // // // // TagMap // // // // //
475    
476       fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump does not save the TagMap yet\n\n\n");     if (num_Tags>0) {
477    
478          // Temp storage to gather node IDs
479          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
480          char name_temp[4096];
481    
482          /* Copy tag data into temp arrays */
483          tag_map = mesh->TagMap;
484          if (tag_map) {
485             int i = 0;
486             while (tag_map) {
487                Tags_keys[i++] = tag_map->tag_key;
488                tag_map=tag_map->next;
489             }
490          }
491    
492          // Tags_keys
493          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
494             throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
495          int_ptr = &Tags_keys[0];
496          if (! (ids->put(int_ptr, num_Tags)) )
497             throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
498    
499          // Tags_names_*
500          // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
501          // because the NetCDF manual doesn't tell how to do an array of strings
502          tag_map = mesh->TagMap;
503          if (tag_map) {
504             int i = 0;
505             while (tag_map) {
506                sprintf(name_temp, "Tags_name_%d", i);
507                if (!dataFile.add_att(name_temp, tag_map->name) )
508                   throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
509                tag_map=tag_map->next;
510                i++;
511             }
512          }
513    
514          TMPMEMFREE(Tags_keys);
515    
516       }
517    
518    /* Send token to next MPI process so he can take his turn */
519    #ifdef PASO_MPI
520       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
521    #endif
522    
523     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
524    
525  #else  #else
526     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.");
527  #endif  /* USE_NETCDF */  #endif  /* USE_NETCDF */
# Line 473  void MeshAdapter::dump(const std::string Line 530  void MeshAdapter::dump(const std::string
530    
531  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
532  {  {
533    return "FinleyMesh";     return "FinleyMesh";
534  }  }
535    
536  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
537  {  {
538    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
539    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
540    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
541      return "Invalid function space type code.";        return "Invalid function space type code.";
542    } else {     } else {
543      return loc->second;        return loc->second;
544    }     }
545  }  }
546    
547  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
548  {  {
549    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
550    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
551    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
552  }  }
553    
554  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
555  {  {
556    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
557      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
558    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
559      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
560    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
561      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
562    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
563      (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
564    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
565      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
566    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
567      (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
568    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
569      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
570    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
571      (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
572    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
573      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
574    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
575      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
576    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
577      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
578    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
579      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
580    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
581      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
582  }  }
583    
584  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
585  {  {
586    return Nodes;     return Nodes;
587  }  }
588  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
589  {  {
590    return ReducedNodes;     return ReducedNodes;
591  }  }
592    
593  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
594  {  {
595    return Elements;     return Elements;
596  }  }
597  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
598  {  {
599    return ReducedElements;     return ReducedElements;
600  }  }
601    
602  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
603  {  {
604    return FaceElements;     return FaceElements;
605  }  }
606  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
607  {  {
608    return ReducedFaceElements;     return ReducedFaceElements;
609  }  }
610    
611  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
612  {  {
613    return ContactElementsZero;     return ContactElementsZero;
614  }  }
615  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
616  {  {
617    return ReducedContactElementsZero;     return ReducedContactElementsZero;
618  }  }
619    
620  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
621  {  {
622    return ContactElementsOne;     return ContactElementsOne;
623  }  }
624  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
625  {  {
626    return ReducedContactElementsOne;     return ReducedContactElementsOne;
627  }  }
628    
629  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
630  {  {
631    return DegreesOfFreedom;     return DegreesOfFreedom;
632  }  }
633    
634  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
635  {  {
636    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
637  }  }
638    
639  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
640  {  {
641    return Points;     return Points;
642  }  }
643    
644  //  //
# Line 589  int MeshAdapter::getDiracDeltaFunctionCo Line 646  int MeshAdapter::getDiracDeltaFunctionCo
646  //  //
647  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
648  {  {
649    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());
650    checkFinleyError();     checkFinleyError();
651    return numDim;     return numDim;
652    }
653    
654    //
655    // Return the number of data points summed across all MPI processes
656    //
657    int MeshAdapter::getNumDataPointsGlobal() const
658    {
659       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
660  }  }
661    
662  //  //
# Line 604  pair<int,int> MeshAdapter::getDataShape( Line 669  pair<int,int> MeshAdapter::getDataShape(
669     int numSamples=0;     int numSamples=0;
670     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
671     switch (functionSpaceCode) {     switch (functionSpaceCode) {
672        case(Nodes):     case(Nodes):
673             numDataPointsPerSample=1;     numDataPointsPerSample=1;
674             numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
675             break;     break;
676        case(ReducedNodes):     case(ReducedNodes):
677             numDataPointsPerSample=1;     numDataPointsPerSample=1;
678             numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
679             break;     break;
680        case(Elements):     case(Elements):
681             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
682               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
683               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
684             }     }
685             break;     break;
686        case(ReducedElements):     case(ReducedElements):
687             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
688               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
689               numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
690             }     }
691             break;     break;
692        case(FaceElements):     case(FaceElements):
693             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
694                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
695                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
696             }     }
697             break;     break;
698        case(ReducedFaceElements):     case(ReducedFaceElements):
699             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
700                  numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
701                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
702             }     }
703             break;     break;
704        case(Points):     case(Points):
705             if (mesh->Points!=NULL) {     if (mesh->Points!=NULL) {
706               numDataPointsPerSample=1;        numDataPointsPerSample=1;
707               numSamples=mesh->Points->numElements;        numSamples=mesh->Points->numElements;
708             }     }
709             break;     break;
710        case(ContactElementsZero):     case(ContactElementsZero):
711             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
712               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
713               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
714             }     }
715             break;     break;
716        case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
717             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
718               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
719               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
720             }     }
721             break;     break;
722        case(ContactElementsOne):     case(ContactElementsOne):
723             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
724               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
725               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
726             }     }
727             break;     break;
728        case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
729             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
730               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
731               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
732             }     }
733             break;     break;
734        case(DegreesOfFreedom):     case(DegreesOfFreedom):
735             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
736               numDataPointsPerSample=1;        numDataPointsPerSample=1;
737               numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
738             }     }
739             break;     break;
740        case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
741             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
742               numDataPointsPerSample=1;        numDataPointsPerSample=1;
743               numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
744             }     }
745             break;     break;
746        default:     default:
747          stringstream temp;        stringstream temp;
748          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
749          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
750          break;        break;
751        }     }
752        return pair<int,int>(numDataPointsPerSample,numSamples);     return pair<int,int>(numDataPointsPerSample,numSamples);
753  }  }
754    
755  //  //
756  // 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 hand side:
757  //  //
758  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
759                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
760                       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,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
761                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
762                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
763  {  {
764     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
765     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
# Line 721  void MeshAdapter::addPDEToSystem( Line 786  void MeshAdapter::addPDEToSystem(
786  }  }
787    
788  void  MeshAdapter::addPDEToLumpedSystem(  void  MeshAdapter::addPDEToLumpedSystem(
789                       escript::Data& mat,                                          escript::Data& mat,
790                       const escript::Data& D,                                          const escript::Data& D,
791                       const escript::Data& d) const                                          const escript::Data& d) const
792  {  {
793     escriptDataC _mat=mat.getDataC();     escriptDataC _mat=mat.getDataC();
794     escriptDataC _D=D.getDataC();     escriptDataC _D=D.getDataC();
# Line 760  void MeshAdapter::addPDEToRHS( escript:: Line 825  void MeshAdapter::addPDEToRHS( escript::
825     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
826     checkFinleyError();     checkFinleyError();
827  }  }
828    //
829    // adds PDE of second order into a transport problem
830    //
831    void MeshAdapter::addPDEToTransportProblem(
832                                               TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
833                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
834                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
835                                               const escript::Data& d, const escript::Data& y,
836                                               const escript::Data& d_contact,const escript::Data& y_contact) const
837    {
838       DataTypes::ShapeType shape;
839       source.expand();
840       escriptDataC _source=source.getDataC();
841       escriptDataC _M=M.getDataC();
842       escriptDataC _A=A.getDataC();
843       escriptDataC _B=B.getDataC();
844       escriptDataC _C=C.getDataC();
845       escriptDataC _D=D.getDataC();
846       escriptDataC _X=X.getDataC();
847       escriptDataC _Y=Y.getDataC();
848       escriptDataC _d=d.getDataC();
849       escriptDataC _y=y.getDataC();
850       escriptDataC _d_contact=d_contact.getDataC();
851       escriptDataC _y_contact=y_contact.getDataC();
852    
853       Finley_Mesh* mesh=m_finleyMesh.get();
854       Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
855    
856       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
857       checkFinleyError();
858    
859       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
860       checkFinleyError();
861    
862       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
863       checkFinleyError();
864    
865       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
866       checkFinleyError();
867    }
868    
869  //  //
870  // interpolates data between different function spaces:  // interpolates data between different function spaces:
871  //  //
872  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
873  {  {
874    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
875    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
876    if (inDomain!=*this)       if (inDomain!=*this)  
877      throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
878    if (targetDomain!=*this)     if (targetDomain!=*this)
879      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
880    
881    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
882    escriptDataC _target=target.getDataC();     escriptDataC _target=target.getDataC();
883    escriptDataC _in=in.getDataC();     escriptDataC _in=in.getDataC();
884    switch(in.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
885       case(Nodes):     case(Nodes):
886          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
887             case(Nodes):     case(Nodes):
888             case(ReducedNodes):     case(ReducedNodes):
889             case(DegreesOfFreedom):     case(DegreesOfFreedom):
890             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
891                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
892                 break;     break;
893             case(Elements):     case(Elements):
894             case(ReducedElements):     case(ReducedElements):
895                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
896                 break;     break;
897             case(FaceElements):     case(FaceElements):
898             case(ReducedFaceElements):     case(ReducedFaceElements):
899                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
900                 break;     break;
901             case(Points):     case(Points):
902                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
903                 break;     break;
904             case(ContactElementsZero):     case(ContactElementsZero):
905             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
906                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
907                 break;     break;
908             case(ContactElementsOne):     case(ContactElementsOne):
909             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
910                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
911                 break;     break;
912             default:     default:
913                 stringstream temp;        stringstream temp;
914                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
915                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
916                 break;        break;
917          }     }
918          break;     break;
919       case(ReducedNodes):     case(ReducedNodes):
920          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
921             case(Nodes):     case(Nodes):
922             case(ReducedNodes):     case(ReducedNodes):
923             case(DegreesOfFreedom):     case(DegreesOfFreedom):
924             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
925                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
926                 break;     break;
927             case(Elements):     case(Elements):
928             case(ReducedElements):     case(ReducedElements):
929                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
930                 break;     break;
931             case(FaceElements):     case(FaceElements):
932             case(ReducedFaceElements):     case(ReducedFaceElements):
933                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
934                 break;     break;
935             case(Points):     case(Points):
936                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
937                 break;     break;
938             case(ContactElementsZero):     case(ContactElementsZero):
939             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
940                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
941                 break;     break;
942             case(ContactElementsOne):     case(ContactElementsOne):
943             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
944                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
945                 break;     break;
946             default:     default:
947                 stringstream temp;        stringstream temp;
948                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
949                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
950                 break;        break;
951          }     }
952          break;     break;
953       case(Elements):     case(Elements):
954          if (target.getFunctionSpace().getTypeCode()==Elements) {     if (target.getFunctionSpace().getTypeCode()==Elements) {
955             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
956          } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
957             Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
958          } else {     } else {
959             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
960          }     }
961          break;     break;
962       case(ReducedElements):     case(ReducedElements):
963          if (target.getFunctionSpace().getTypeCode()==ReducedElements) {     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
964             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
965          } else {     } else {
966             throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");        throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
967          }     }
968          break;     break;
969       case(FaceElements):     case(FaceElements):
970          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
971             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
972          } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
973             Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
974          } else {     } else {
975             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
976         }     }
977         break;     break;
978       case(ReducedFaceElements):     case(ReducedFaceElements):
979          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
980             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
981          } else {     } else {
982             throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");        throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
983         }     }
984         break;     break;
985       case(Points):     case(Points):
986          if (target.getFunctionSpace().getTypeCode()==Points) {     if (target.getFunctionSpace().getTypeCode()==Points) {
987             Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
988          } else {     } else {
989             throw FinleyAdapterException("Error - No interpolation with data on points possible.");        throw FinleyAdapterException("Error - No interpolation with data on points possible.");
990          }     }
991          break;     break;
992       case(ContactElementsZero):     case(ContactElementsZero):
993       case(ContactElementsOne):     case(ContactElementsOne):
994          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
995             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
996          } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
997             Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
998          } else {     } else {
999             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1000             break;     }
1001          }     break;
1002          break;     case(ReducedContactElementsZero):
1003       case(ReducedContactElementsZero):     case(ReducedContactElementsOne):
1004       case(ReducedContactElementsOne):     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1005          if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1006             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);     } else {
1007          } else {        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1008             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");     }
1009             break;     break;
1010          }     case(DegreesOfFreedom):      
1011          break;     switch(target.getFunctionSpace().getTypeCode()) {
1012       case(DegreesOfFreedom):           case(ReducedDegreesOfFreedom):
1013          switch(target.getFunctionSpace().getTypeCode()) {     case(DegreesOfFreedom):
1014             case(ReducedDegreesOfFreedom):     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1015             case(DegreesOfFreedom):     break;
1016                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);  
1017                break;     case(Nodes):
1018       case(ReducedNodes):
1019             case(Nodes):     if (getMPISize()>1) {
1020             case(ReducedNodes):        escript::Data temp=escript::Data(in);
1021                if (getMPISize()>1) {        temp.expand();
1022                    escript::Data temp=escript::Data(in);        escriptDataC _in2 = temp.getDataC();
1023                    temp.expand();        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1024                    escriptDataC _in2 = temp.getDataC();     } else {
1025                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1026                } else {     }
1027                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     break;
1028                }     case(Elements):
1029                break;     case(ReducedElements):
1030             case(Elements):     if (getMPISize()>1) {
1031             case(ReducedElements):        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1032                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1033                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1034                   escriptDataC _in2 = temp.getDataC();     } else {
1035                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1036                } else {     }
1037                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     break;
1038                }     case(FaceElements):
1039                break;     case(ReducedFaceElements):
1040             case(FaceElements):     if (getMPISize()>1) {
1041             case(ReducedFaceElements):        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1042                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1043                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1044                   escriptDataC _in2 = temp.getDataC();  
1045                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);     } else {
1046          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1047                } else {     }
1048                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     break;
1049                }     case(Points):
1050                break;     if (getMPISize()>1) {
1051             case(Points):        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1052                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1053                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );     } else {
1054                   escriptDataC _in2 = temp.getDataC();        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1055                } else {     }
1056                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     break;
1057                }     case(ContactElementsZero):
1058                break;     case(ContactElementsOne):
1059             case(ContactElementsZero):     case(ReducedContactElementsZero):
1060             case(ContactElementsOne):     case(ReducedContactElementsOne):
1061             case(ReducedContactElementsZero):     if (getMPISize()>1) {
1062             case(ReducedContactElementsOne):        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1063                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1064                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1065                   escriptDataC _in2 = temp.getDataC();     } else {
1066                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1067                } else {     }
1068                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     break;
1069                }     default:
1070               break;        stringstream temp;
1071             default:        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1072               stringstream temp;        throw FinleyAdapterException(temp.str());
1073               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        break;
1074               throw FinleyAdapterException(temp.str());     }
1075               break;     break;
1076          }     case(ReducedDegreesOfFreedom):
1077          break;     switch(target.getFunctionSpace().getTypeCode()) {
1078       case(ReducedDegreesOfFreedom):     case(Nodes):
1079         switch(target.getFunctionSpace().getTypeCode()) {     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1080            case(Nodes):     break;
1081               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");     case(ReducedNodes):
1082               break;     if (getMPISize()>1) {
1083            case(ReducedNodes):        escript::Data temp=escript::Data(in);
1084                if (getMPISize()>1) {        temp.expand();
1085                    escript::Data temp=escript::Data(in);        escriptDataC _in2 = temp.getDataC();
1086                    temp.expand();        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1087                    escriptDataC _in2 = temp.getDataC();     } else {
1088                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1089                } else {     }
1090                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     break;
1091                }     case(DegreesOfFreedom):
1092                break;     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1093            case(DegreesOfFreedom):     break;
1094               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ReducedDegreesOfFreedom):
1095               break;     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1096            case(ReducedDegreesOfFreedom):     break;
1097               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     case(Elements):
1098               break;     case(ReducedElements):
1099            case(Elements):     if (getMPISize()>1) {
1100            case(ReducedElements):        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1101                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1102                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1103                   escriptDataC _in2 = temp.getDataC();     } else {
1104                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1105                } else {     }
1106                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     break;
1107               }     case(FaceElements):
1108               break;     case(ReducedFaceElements):
1109            case(FaceElements):     if (getMPISize()>1) {
1110            case(ReducedFaceElements):        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1111                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1112                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1113                   escriptDataC _in2 = temp.getDataC();     } else {
1114                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1115                } else {     }
1116                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     break;
1117                }     case(Points):
1118               break;     if (getMPISize()>1) {
1119            case(Points):        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1120                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1121                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1122                   escriptDataC _in2 = temp.getDataC();     } else {
1123                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1124                } else {     }
1125                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     break;
1126               }     case(ContactElementsZero):
1127               break;     case(ContactElementsOne):
1128            case(ContactElementsZero):     case(ReducedContactElementsZero):
1129            case(ContactElementsOne):     case(ReducedContactElementsOne):
1130            case(ReducedContactElementsZero):     if (getMPISize()>1) {
1131            case(ReducedContactElementsOne):        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1132                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1133                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1134                   escriptDataC _in2 = temp.getDataC();     } else {
1135                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1136                } else {     }
1137                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     break;
1138               }     default:
1139               break;        stringstream temp;
1140            default:        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1141               stringstream temp;        throw FinleyAdapterException(temp.str());
1142               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        break;
1143               throw FinleyAdapterException(temp.str());     }
1144               break;     break;
1145         }     default:
1146         break;        stringstream temp;
1147       default:        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1148          stringstream temp;        throw FinleyAdapterException(temp.str());
1149          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        break;
1150          throw FinleyAdapterException(temp.str());     }
1151          break;     checkFinleyError();
   }  
   checkFinleyError();  
1152  }  }
1153    
1154  //  //
# Line 1053  void MeshAdapter::interpolateOnDomain(es Line 1156  void MeshAdapter::interpolateOnDomain(es
1156  //  //
1157  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1158  {  {
1159    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1160    if (argDomain!=*this)     if (argDomain!=*this)
1161       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1162    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1163    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1164    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1165       escriptDataC _arg=arg.getDataC();        escriptDataC _arg=arg.getDataC();
1166       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1167    } else {     } else {
1168       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1169       escriptDataC _tmp_data=tmp_data.getDataC();        escriptDataC _tmp_data=tmp_data.getDataC();
1170       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1171       // this is then interpolated onto arg:        // this is then interpolated onto arg:
1172       interpolateOnDomain(arg,tmp_data);        interpolateOnDomain(arg,tmp_data);
1173    }     }
1174    checkFinleyError();     checkFinleyError();
1175  }  }
1176    
1177  //  //
# Line 1076  void MeshAdapter::setToX(escript::Data& Line 1179  void MeshAdapter::setToX(escript::Data&
1179  //  //
1180  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1181  {  {
1182    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1183    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1184       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1185    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1186    escriptDataC _normal=normal.getDataC();     Finley_Mesh* mesh=m_finleyMesh.get();
1187    switch(normal.getFunctionSpace().getTypeCode()) {     escriptDataC _normal=normal.getDataC();
1188      case(Nodes):     switch(normal.getFunctionSpace().getTypeCode()) {
1189        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     case(Nodes):
1190        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1191      case(ReducedNodes):     break;
1192        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");     case(ReducedNodes):
1193        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1194      case(Elements):     break;
1195        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     case(Elements):
1196        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1197      case(ReducedElements):     break;
1198        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");     case(ReducedElements):
1199        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1200      case (FaceElements):     break;
1201        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     case (FaceElements):
1202        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1203      case (ReducedFaceElements):     break;
1204        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     case (ReducedFaceElements):
1205        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1206      case(Points):     break;
1207        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     case(Points):
1208        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1209      case (ContactElementsOne):     break;
1210      case (ContactElementsZero):     case (ContactElementsOne):
1211        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     case (ContactElementsZero):
1212        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1213      case (ReducedContactElementsOne):     break;
1214      case (ReducedContactElementsZero):     case (ReducedContactElementsOne):
1215        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     case (ReducedContactElementsZero):
1216        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1217      case(DegreesOfFreedom):     break;
1218        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case(DegreesOfFreedom):
1219        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1220      case(ReducedDegreesOfFreedom):     break;
1221        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(ReducedDegreesOfFreedom):
1222        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1223      default:     break;
1224       default:
1225        stringstream temp;        stringstream temp;
1226        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();        temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1227        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1228        break;        break;
1229    }     }
1230    checkFinleyError();     checkFinleyError();
1231  }  }
1232    
1233  //  //
# Line 1131  void MeshAdapter::setToNormal(escript::D Line 1235  void MeshAdapter::setToNormal(escript::D
1235  //  //
1236  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1237  {  {
1238    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
1239    if (targetDomain!=*this)     if (targetDomain!=*this)
1240       throw FinleyAdapterException("Error - Illegal domain of interpolation target");        throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1241    
1242    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1243  }  }
1244    
1245  //  //
# Line 1143  void MeshAdapter::interpolateACross(escr Line 1247  void MeshAdapter::interpolateACross(escr
1247  //  //
1248  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1249  {  {
1250    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1251    if (argDomain!=*this)     if (argDomain!=*this)
1252       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1253    
1254    double blocktimer_start = blocktimer_time();     double blocktimer_start = blocktimer_time();
1255    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1256    escriptDataC _temp;     escriptDataC _temp;
1257    escript::Data temp;     escript::Data temp;
1258    escriptDataC _arg=arg.getDataC();     escriptDataC _arg=arg.getDataC();
1259    switch(arg.getFunctionSpace().getTypeCode()) {     switch(arg.getFunctionSpace().getTypeCode()) {
1260       case(Nodes):     case(Nodes):
1261          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1262          _temp=temp.getDataC();     _temp=temp.getDataC();
1263          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1264          break;     break;
1265       case(ReducedNodes):     case(ReducedNodes):
1266          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1267          _temp=temp.getDataC();     _temp=temp.getDataC();
1268          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1269          break;     break;
1270       case(Elements):     case(Elements):
1271          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1272          break;     break;
1273       case(ReducedElements):     case(ReducedElements):
1274          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1275          break;     break;
1276       case(FaceElements):     case(FaceElements):
1277          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1278          break;     break;
1279       case(ReducedFaceElements):     case(ReducedFaceElements):
1280          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1281          break;     break;
1282       case(Points):     case(Points):
1283          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1284          break;     break;
1285       case(ContactElementsZero):     case(ContactElementsZero):
1286          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1287          break;     break;
1288       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1289          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1290          break;     break;
1291       case(ContactElementsOne):     case(ContactElementsOne):
1292          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1293          break;     break;
1294       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1295          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1296          break;     break;
1297       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1298          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1299          _temp=temp.getDataC();     _temp=temp.getDataC();
1300          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1301          break;     break;
1302       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1303          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1304          _temp=temp.getDataC();     _temp=temp.getDataC();
1305          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1306          break;     break;
1307       default:     default:
1308          stringstream temp;        stringstream temp;
1309          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();        temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1310          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1311          break;        break;
1312    }     }
1313    checkFinleyError();     checkFinleyError();
1314    blocktimer_increment("integrate()", blocktimer_start);     blocktimer_increment("integrate()", blocktimer_start);
1315  }  }
1316    
1317  //  //
# Line 1215  void MeshAdapter::setToIntegrals(std::ve Line 1319  void MeshAdapter::setToIntegrals(std::ve
1319  //  //
1320  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1321  {  {
1322    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1323    if (argDomain!=*this)     if (argDomain!=*this)
1324      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1325    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1326    if (gradDomain!=*this)     if (gradDomain!=*this)
1327       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1328    
1329    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1330    escriptDataC _grad=grad.getDataC();     escriptDataC _grad=grad.getDataC();
1331    escriptDataC nodeDataC;     escriptDataC nodeDataC;
1332    escript::Data temp;     escript::Data temp;
1333    if (getMPISize()>1) {     if (getMPISize()>1) {
1334        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1335          temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1336          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1337        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1338          temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1339          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1340        } else {        } else {
1341          nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1342        }        }
1343    } else {     } else {
1344       nodeDataC = arg.getDataC();        nodeDataC = arg.getDataC();
1345    }     }
1346    switch(grad.getFunctionSpace().getTypeCode()) {     switch(grad.getFunctionSpace().getTypeCode()) {
1347         case(Nodes):     case(Nodes):
1348            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1349            break;     break;
1350         case(ReducedNodes):     case(ReducedNodes):
1351            throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1352            break;     break;
1353         case(Elements):     case(Elements):
1354            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1355            break;     break;
1356         case(ReducedElements):     case(ReducedElements):
1357            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1358            break;     break;
1359         case(FaceElements):     case(FaceElements):
1360            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1361            break;     break;
1362         case(ReducedFaceElements):     case(ReducedFaceElements):
1363            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1364            break;     break;
1365         case(Points):     case(Points):
1366            throw FinleyAdapterException("Error - Gradient at points is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1367            break;     break;
1368         case(ContactElementsZero):     case(ContactElementsZero):
1369            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1370            break;     break;
1371         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1372            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1373            break;     break;
1374         case(ContactElementsOne):     case(ContactElementsOne):
1375            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1376            break;     break;
1377         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1378            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1379            break;     break;
1380         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1381            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1382            break;     break;
1383         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1384            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1385            break;     break;
1386         default:     default:
1387            stringstream temp;        stringstream temp;
1388            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();        temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1389            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1390            break;        break;
1391    }     }
1392    checkFinleyError();     checkFinleyError();
1393  }  }
1394    
1395  //  //
# Line 1293  void MeshAdapter::setToGradient(escript: Line 1397  void MeshAdapter::setToGradient(escript:
1397  //  //
1398  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1399  {  {
1400    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1401    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1402    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1403         case(Nodes):     case(Nodes):
1404            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1405            break;     break;
1406         case(ReducedNodes):     case(ReducedNodes):
1407            throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1408            break;     break;
1409         case(Elements):     case(Elements):
1410            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1411            break;     break;
1412         case(ReducedElements):     case(ReducedElements):
1413            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1414            break;     break;
1415         case(FaceElements):     case(FaceElements):
1416            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1417            break;     break;
1418         case(ReducedFaceElements):     case(ReducedFaceElements):
1419            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1420            break;     break;
1421         case(Points):     case(Points):
1422            throw FinleyAdapterException("Error - Size of point elements is not supported.");     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1423            break;     break;
1424         case(ContactElementsZero):     case(ContactElementsZero):
1425         case(ContactElementsOne):     case(ContactElementsOne):
1426            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1427            break;     break;
1428         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1429         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1430            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1431            break;     break;
1432         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1433            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1434            break;     break;
1435         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1436            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1437            break;     break;
1438         default:     default:
1439            stringstream temp;        stringstream temp;
1440            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();        temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1441            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1442            break;        break;
1443    }     }
1444    checkFinleyError();     checkFinleyError();
1445  }  }
1446    
1447  // sets the location of nodes:  // sets the location of nodes:
1448  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1449  {  {
1450    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1451    escriptDataC tmp;     escriptDataC tmp;
1452    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1453    if (newDomain!=*this)     if (newDomain!=*this)
1454       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1455    tmp = new_x.getDataC();     tmp = new_x.getDataC();
1456    Finley_Mesh_setCoordinates(mesh,&tmp);     Finley_Mesh_setCoordinates(mesh,&tmp);
1457    checkFinleyError();     checkFinleyError();
1458  }  }
1459    
1460  // saves a data array in openDX format:  // saves a data array in openDX format:
1461  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const
1462  {  {
1463      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1464      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1465    /* win32 refactor */     /* win32 refactor */
1466    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1467    for(int i=0;i<num_data;i++)     for(int i=0;i<num_data;i++)
1468    {     {
1469      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1470    }     }
1471    
1472    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1473    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
   escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
   boost::python::list keys=arg.keys();  
   for (int i=0;i<num_data;++i) {  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
     checkFinleyError();  
       
       /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1474    
1475      return;     boost::python::list keys=arg.keys();
1476       for (int i=0;i<num_data;++i) {
1477          std::string n=boost::python::extract<std::string>(keys[i]);
1478          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1479          if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1480             throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1481          data[i]=d.getDataC();
1482          ptr_data[i]= &(data[i]);
1483          if (n.length()>MAX_namelength-1) {
1484             strncpy(names[i],n.c_str(),MAX_namelength-1);
1485             names[i][MAX_namelength-1]='\0';
1486          } else {
1487             strcpy(names[i],n.c_str());
1488          }
1489       }
1490       Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1491       checkFinleyError();
1492    
1493       /* win32 refactor */
1494       TMPMEMFREE(data);
1495       TMPMEMFREE(ptr_data);
1496       for(int i=0;i<num_data;i++)
1497       {
1498          TMPMEMFREE(names[i]);
1499       }
1500       TMPMEMFREE(names);
1501    
1502       return;
1503  }  }
1504    
1505  // saves a data array in openVTK format:  // saves a data array in openVTK format:
1506  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const
1507  {  {
1508      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1509      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1510    /* win32 refactor */     /* win32 refactor */
1511    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1512    for(int i=0;i<num_data;i++)     for(int i=0;i<num_data;i++)
1513    {     {
1514      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1515    }     }
1516    
1517    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1518    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
   escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
     boost::python::list keys=arg.keys();  
     for (int i=0;i<num_data;++i) {  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
1519    
1520    checkFinleyError();     boost::python::list keys=arg.keys();
1521    /* win32 refactor */     for (int i=0;i<num_data;++i) {
1522    TMPMEMFREE(c_names);        std::string n=boost::python::extract<std::string>(keys[i]);
1523    TMPMEMFREE(data);        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1524    TMPMEMFREE(ptr_data);        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1525    for(int i=0;i<num_data;i++)           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1526    {        data[i]=d.getDataC();
1527      TMPMEMFREE(names[i]);        ptr_data[i]=&(data[i]);
1528    }        if (n.length()>MAX_namelength-1) {
1529    TMPMEMFREE(names);           strncpy(names[i],n.c_str(),MAX_namelength-1);
1530             names[i][MAX_namelength-1]='\0';
1531          } else {
1532             strcpy(names[i],n.c_str());
1533          }
1534       }
1535       Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1536    
1537       checkFinleyError();
1538       /* win32 refactor */
1539       TMPMEMFREE(data);
1540       TMPMEMFREE(ptr_data);
1541       for(int i=0;i<num_data;i++)
1542       {
1543          TMPMEMFREE(names[i]);
1544       }
1545       TMPMEMFREE(names);
1546    
1547      return;     return;
1548  }  }
1549                                                                                                                                                                                                                                                                                                                                                
1550                                                                                                                                                                                                                                                                                                                                                
1551  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1552  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1553                        const int row_blocksize,                                                   const int row_blocksize,
1554                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1555                        const int column_blocksize,                                                   const int column_blocksize,
1556                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1557                        const int type) const                                                   const int type) const
1558  {  {
1559      int reduceRowOrder=0;     int reduceRowOrder=0;
1560      int reduceColOrder=0;     int reduceColOrder=0;
1561      // is the domain right?     // is the domain right?
1562      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1563      if (row_domain!=*this)     if (row_domain!=*this)
1564            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");        throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1565      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1566      if (col_domain!=*this)     if (col_domain!=*this)
1567            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1568      // is the function space type right     // is the function space type right
1569      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1570          reduceRowOrder=0;        reduceRowOrder=0;
1571      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1572          reduceRowOrder=1;        reduceRowOrder=1;
1573      } else {     } else {
1574          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1575      }     }
1576      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1577          reduceColOrder=0;        reduceColOrder=0;
1578      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1579          reduceColOrder=1;        reduceColOrder=1;
1580      } else {     } else {
1581          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1582      }     }
1583      // generate matrix:     // generate matrix:
1584        
1585      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1586      checkFinleyError();     checkFinleyError();
1587      Paso_SystemMatrix* fsystemMatrix;     Paso_SystemMatrix* fsystemMatrix;
1588      int trilinos = 0;     int trilinos = 0;
1589      if (trilinos) {     if (trilinos) {
1590  #ifdef TRILINOS  #ifdef TRILINOS
1591        /* Allocation Epetra_VrbMatrix here */        /* Allocation Epetra_VrbMatrix here */
1592  #endif  #endif
1593      }     }
1594      else {     else {
1595        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1596      }     }
1597      checkPasoError();     checkPasoError();
1598      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1599      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1600    }
1601    // creates a TransportProblemAdapter
1602    TransportProblemAdapter MeshAdapter::newTransportProblem(
1603                                                             const double theta,
1604                                                             const int blocksize,
1605                                                             const escript::FunctionSpace& functionspace,
1606                                                             const int type) const
1607    {
1608       int reduceOrder=0;
1609       // is the domain right?
1610       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1611       if (domain!=*this)
1612          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1613       // is the function space type right
1614       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1615          reduceOrder=0;
1616       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1617          reduceOrder=1;
1618       } else {
1619          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1620       }
1621       // generate matrix:
1622    
1623       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1624       checkFinleyError();
1625       Paso_FCTransportProblem* transportProblem;
1626       transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1627       checkPasoError();
1628       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1629       return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1630  }  }
1631    
1632  //  //
# Line 1510  SystemMatrixAdapter MeshAdapter::newSyst Line 1638  SystemMatrixAdapter MeshAdapter::newSyst
1638  // returns true if data at the atom_type is considered as being cell centered:  // returns true if data at the atom_type is considered as being cell centered:
1639  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1640  {  {
1641    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1642         case(Nodes):     case(Nodes):
1643         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1644         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1645            return false;     return false;
1646            break;     break;
1647         case(Elements):     case(Elements):
1648         case(FaceElements):     case(FaceElements):
1649         case(Points):     case(Points):
1650         case(ContactElementsZero):     case(ContactElementsZero):
1651         case(ContactElementsOne):     case(ContactElementsOne):
1652         case(ReducedElements):     case(ReducedElements):
1653         case(ReducedFaceElements):     case(ReducedFaceElements):
1654         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1655         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1656            return true;     return true;
1657            break;     break;
1658         default:     default:
1659            stringstream temp;        stringstream temp;
1660            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1661            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1662            break;        break;
1663    }     }
1664    checkFinleyError();     checkFinleyError();
1665    return false;     return false;
1666  }  }
1667    
1668  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1669  {  {
1670    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1671       case(Nodes):     case(Nodes):
1672          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1673             case(Nodes):     case(Nodes):
1674             case(ReducedNodes):     case(ReducedNodes):
1675             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1676             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1677             case(Elements):     case(Elements):
1678             case(ReducedElements):     case(ReducedElements):
1679             case(FaceElements):     case(FaceElements):
1680             case(ReducedFaceElements):     case(ReducedFaceElements):
1681             case(Points):     case(Points):
1682             case(ContactElementsZero):     case(ContactElementsZero):
1683             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1684             case(ContactElementsOne):     case(ContactElementsOne):
1685             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1686                 return true;     return true;
1687             default:     default:
1688                 stringstream temp;        stringstream temp;
1689                 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;
1690                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1691          }     }
1692          break;     break;
1693       case(ReducedNodes):     case(ReducedNodes):
1694          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1695             case(ReducedNodes):     case(ReducedNodes):
1696             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1697             case(Elements):     case(Elements):
1698             case(ReducedElements):     case(ReducedElements):
1699             case(FaceElements):     case(FaceElements):
1700             case(ReducedFaceElements):     case(ReducedFaceElements):
1701             case(Points):     case(Points):
1702             case(ContactElementsZero):     case(ContactElementsZero):
1703             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1704             case(ContactElementsOne):     case(ContactElementsOne):
1705             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1706                 return true;     return true;
1707            case(Nodes):     case(Nodes):
1708            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1709               return false;     return false;
1710             default:     default:
1711                 stringstream temp;        stringstream temp;
1712                 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;
1713                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1714          }     }
1715          break;     break;
1716       case(Elements):     case(Elements):
1717          if (functionSpaceType_target==Elements) {     if (functionSpaceType_target==Elements) {
1718             return true;        return true;
1719          } else if (functionSpaceType_target==ReducedElements) {     } else if (functionSpaceType_target==ReducedElements) {
1720             return true;        return true;
1721          } else {     } else {
1722             return false;        return false;
1723          }     }
1724       case(ReducedElements):     case(ReducedElements):
1725          if (functionSpaceType_target==ReducedElements) {     if (functionSpaceType_target==ReducedElements) {
1726             return true;        return true;
1727          } else {     } else {
1728             return false;        return false;
1729          }     }
1730       case(FaceElements):     case(FaceElements):
1731          if (functionSpaceType_target==FaceElements) {     if (functionSpaceType_target==FaceElements) {
1732             return true;        return true;
1733          } else if (functionSpaceType_target==ReducedFaceElements) {     } else if (functionSpaceType_target==ReducedFaceElements) {
1734             return true;        return true;
1735          } else {     } else {
1736             return false;        return false;
1737          }     }
1738       case(ReducedFaceElements):     case(ReducedFaceElements):
1739          if (functionSpaceType_target==ReducedFaceElements) {     if (functionSpaceType_target==ReducedFaceElements) {
1740             return true;        return true;
1741          } else {     } else {
1742             return false;        return false;
1743          }     }
1744       case(Points):     case(Points):
1745          if (functionSpaceType_target==Points) {     if (functionSpaceType_target==Points) {
1746             return true;        return true;
1747          } else {     } else {
1748             return false;        return false;
1749          }     }
1750       case(ContactElementsZero):     case(ContactElementsZero):
1751       case(ContactElementsOne):     case(ContactElementsOne):
1752          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1753             return true;        return true;
1754          } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1755             return true;        return true;
1756          } else {     } else {
1757             return false;        return false;
1758          }     }
1759       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1760       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1761          if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1762             return true;        return true;
1763          } else {     } else {
1764             return false;        return false;
1765          }     }
1766       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1767          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1768             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1769             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1770             case(Nodes):     case(Nodes):
1771             case(ReducedNodes):     case(ReducedNodes):
1772             case(Elements):     case(Elements):
1773             case(ReducedElements):     case(ReducedElements):
1774             case(Points):     case(Points):
1775             case(FaceElements):     case(FaceElements):
1776             case(ReducedFaceElements):     case(ReducedFaceElements):
1777             case(ContactElementsZero):     case(ContactElementsZero):
1778             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1779             case(ContactElementsOne):     case(ContactElementsOne):
1780             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1781                return true;     return true;
1782             default:     default:
1783               stringstream temp;        stringstream temp;
1784               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;
1785               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1786          }     }
1787          break;     break;
1788       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1789         switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1790            case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1791            case(ReducedNodes):     case(ReducedNodes):
1792            case(Elements):     case(Elements):
1793            case(ReducedElements):     case(ReducedElements):
1794            case(FaceElements):     case(FaceElements):
1795            case(ReducedFaceElements):     case(ReducedFaceElements):
1796            case(Points):     case(Points):
1797            case(ContactElementsZero):     case(ContactElementsZero):
1798            case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1799            case(ContactElementsOne):     case(ContactElementsOne):
1800            case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1801                return true;     return true;
1802            case(Nodes):     case(Nodes):
1803            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1804               return false;     return false;
1805            default:     default:
1806               stringstream temp;        stringstream temp;
1807               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;
1808               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1809         }     }
1810         break;     break;
1811       default:     default:
1812          stringstream temp;        stringstream temp;
1813          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;
1814          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1815          break;        break;
1816    }     }
1817    checkFinleyError();     checkFinleyError();
1818    return false;     return false;
1819  }  }
1820    
1821  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const
1822  {  {
1823      return false;     return false;
1824  }  }
1825    
1826  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1827  {  {
1828    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1829    if (temp!=0) {     if (temp!=0) {
1830      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1831    } else {     } else {
1832      return false;        return false;
1833    }     }
1834  }  }
1835    
1836  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1837  {  {
1838    return !(operator==(other));     return !(operator==(other));
1839  }  }
1840    
1841  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1842  {  {
1843     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1844       checkPasoError();
1845       return out;
1846    }
1847    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1848    {
1849       int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1850     checkPasoError();     checkPasoError();
1851     return out;     return out;
1852  }  }
1853    
1854  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1855  {  {
1856    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1857  }  }
1858    
1859  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1860  {  {
1861    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1862  }  }
1863    
1864  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1865  {  {
1866    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
1867  }  }
1868    
1869  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1870  {  {
1871    int *out=0,i;     int *out = NULL;
1872    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1873    switch (functionSpaceType) {     switch (functionSpaceType) {
1874      case(Nodes):     case(Nodes):
1875        out=mesh->Nodes->Id;     out=mesh->Nodes->Id;
1876        break;     break;
1877      case(ReducedNodes):     case(ReducedNodes):
1878        out=mesh->Nodes->reducedNodesId;     out=mesh->Nodes->reducedNodesId;
1879        break;     break;
1880      case(Elements):     case(Elements):
1881        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1882        break;     break;
1883      case(ReducedElements):     case(ReducedElements):
1884        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1885        break;     break;
1886      case(FaceElements):     case(FaceElements):
1887        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1888        break;     break;
1889      case(ReducedFaceElements):     case(ReducedFaceElements):
1890        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1891        break;     break;
1892      case(Points):     case(Points):
1893        out=mesh->Points->Id;     out=mesh->Points->Id;
1894        break;     break;
1895      case(ContactElementsZero):     case(ContactElementsZero):
1896        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1897        break;     break;
1898      case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1899        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1900        break;     break;
1901      case(ContactElementsOne):     case(ContactElementsOne):
1902        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1903        break;     break;
1904      case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1905        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1906        break;     break;
1907      case(DegreesOfFreedom):     case(DegreesOfFreedom):
1908        out=mesh->Nodes->degreesOfFreedomId;     out=mesh->Nodes->degreesOfFreedomId;
1909        break;     break;
1910      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1911        out=mesh->Nodes->reducedDegreesOfFreedomId;     out=mesh->Nodes->reducedDegreesOfFreedomId;
1912        break;     break;
1913      default:     default:
1914        stringstream temp;        stringstream temp;
1915        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1916        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1917        break;        break;
1918    }     }
1919    return out;     return out;
1920  }  }
1921  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1922  {  {
1923    int out=0;     int out=0;
1924    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1925    switch (functionSpaceType) {     switch (functionSpaceType) {
1926    case(Nodes):     case(Nodes):
1927      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
1928      break;     break;
1929    case(ReducedNodes):     case(ReducedNodes):
1930      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1931      break;     break;
1932    case(Elements):     case(Elements):
1933      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1934      break;     break;
1935    case(ReducedElements):     case(ReducedElements):
1936      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1937      break;     break;
1938    case(FaceElements):     case(FaceElements):
1939      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1940      break;     break;
1941    case(ReducedFaceElements):     case(ReducedFaceElements):
1942      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1943      break;     break;
1944    case(Points):     case(Points):
1945      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
1946      break;     break;
1947    case(ContactElementsZero):     case(ContactElementsZero):
1948      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1949      break;     break;
1950    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1951      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1952      break;     break;
1953    case(ContactElementsOne):     case(ContactElementsOne):
1954      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1955      break;     break;
1956    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1957      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1958      break;     break;
1959    case(DegreesOfFreedom):     case(DegreesOfFreedom):
1960      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1961      break;     break;
1962    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1963      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1964      break;     break;
1965    default:     default:
1966      stringstream temp;        stringstream temp;
1967      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1968      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1969      break;        break;
1970    }     }
1971    return out;     return out;
1972  }  }
1973    
1974    
1975  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
1976  {  {
1977       Finley_Mesh* mesh=m_finleyMesh.get();
1978       escriptDataC tmp=mask.getDataC();
1979       switch(functionSpaceType) {
1980       case(Nodes):
1981       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1982       break;
1983       case(ReducedNodes):
1984       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1985       break;
1986       case(DegreesOfFreedom):
1987       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1988       break;
1989       case(ReducedDegreesOfFreedom):
1990       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1991       break;
1992       case(Elements):
1993       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1994       break;
1995       case(ReducedElements):
1996       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1997       break;
1998       case(FaceElements):
1999       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2000       break;
2001       case(ReducedFaceElements):
2002       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2003       break;
2004       case(Points):
2005       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2006       break;
2007       case(ContactElementsZero):
2008       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2009       break;
2010       case(ReducedContactElementsZero):
2011       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2012       break;
2013       case(ContactElementsOne):
2014       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2015       break;
2016       case(ReducedContactElementsOne):
2017       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2018       break;
2019       default:
2020          stringstream temp;
2021          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2022          throw FinleyAdapterException(temp.str());
2023       }
2024       checkFinleyError();
2025       return;
2026    }
2027    
2028    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2029    {
2030       Finley_Mesh* mesh=m_finleyMesh.get();
2031       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2032       checkPasoError();
2033       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2034    }
2035    
2036    int MeshAdapter::getTag(const std::string& name) const
2037    {
2038       Finley_Mesh* mesh=m_finleyMesh.get();
2039       int tag=0;
2040       tag=Finley_Mesh_getTag(mesh, name.c_str());
2041       checkPasoError();
2042       // throwStandardException("MeshAdapter::getTag is not implemented.");
2043       return tag;
2044    }
2045    
2046    bool MeshAdapter::isValidTagName(const std::string& name) const
2047    {
2048       Finley_Mesh* mesh=m_finleyMesh.get();
2049       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2050    }
2051    
2052    std::string MeshAdapter::showTagNames() const
2053    {
2054       stringstream temp;
2055       Finley_Mesh* mesh=m_finleyMesh.get();
2056       Finley_TagMap* tag_map=mesh->TagMap;
2057       while (tag_map) {
2058          temp << tag_map->name;
2059          tag_map=tag_map->next;
2060          if (tag_map) temp << ", ";
2061       }
2062       return temp.str();
2063    }
2064    
2065    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2066    {
2067    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2068    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2069    switch(functionSpaceType) {    switch(functionSpaceCode) {
2070         case(Nodes):     case(Nodes):
2071            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2072            break;            break;
2073         case(ReducedNodes):     case(ReducedNodes):
2074            throw FinleyAdapterException("Error - ReducedNodes does not support tags");            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2075            break;            break;
2076         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2077            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2078            break;            break;
2079         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2080            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2081            break;            break;
2082         case(Elements):     case(Elements):
2083            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2084              numTags=mesh->Elements->numTagsInUse;
2085              break;
2086       case(FaceElements):
2087       case(ReducedFaceElements):
2088              numTags=mesh->FaceElements->numTagsInUse;
2089              break;
2090       case(Points):
2091              numTags=mesh->Points->numTagsInUse;
2092              break;
2093       case(ContactElementsZero):
2094       case(ReducedContactElementsZero):
2095       case(ContactElementsOne):
2096       case(ReducedContactElementsOne):
2097              numTags=mesh->ContactElements->numTagsInUse;
2098            break;            break;
2099         case(ReducedElements):     default:
2100            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);        stringstream temp;
2101            break;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2102         case(FaceElements):        throw FinleyAdapterException(temp.str());
2103            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);    }
2104            break;    return numTags;
2105         case(ReducedFaceElements):  }
2106            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);  int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2107            break;  {
2108         case(Points):    Finley_Mesh* mesh=m_finleyMesh.get();
2109            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);    index_t* tags=NULL;
2110      switch(functionSpaceCode) {
2111       case(Nodes):
2112              tags=mesh->Nodes->tagsInUse;
2113            break;            break;
2114         case(ContactElementsZero):     case(ReducedNodes):
2115            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2116            break;            break;
2117         case(ReducedContactElementsZero):     case(DegreesOfFreedom):
2118            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2119            break;            break;
2120         case(ContactElementsOne):     case(ReducedDegreesOfFreedom):
2121            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2122            break;            break;
2123         case(ReducedContactElementsOne):     case(Elements):
2124            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2125              tags=mesh->Elements->tagsInUse;
2126              break;
2127       case(FaceElements):
2128       case(ReducedFaceElements):
2129              tags=mesh->FaceElements->tagsInUse;
2130              break;
2131       case(Points):
2132              tags=mesh->Points->tagsInUse;
2133              break;
2134       case(ContactElementsZero):
2135       case(ReducedContactElementsZero):
2136       case(ContactElementsOne):
2137       case(ReducedContactElementsOne):
2138              tags=mesh->ContactElements->tagsInUse;
2139            break;            break;
2140         default:     default:
2141            stringstream temp;        stringstream temp;
2142            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2143            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2144    }    }
2145    checkFinleyError();    return tags;
   return;  
2146  }  }
2147    
 void MeshAdapter::setTagMap(const std::string& name,  int tag)  
 {  
   Finley_Mesh* mesh=m_finleyMesh.get();  
   Finley_Mesh_addTagMap(mesh, name.c_str(),tag);  
   checkPasoError();  
   // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
 }  
2148    
2149  int MeshAdapter::getTag(const std::string& name) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2150  {  {
2151    Finley_Mesh* mesh=m_finleyMesh.get();    switch(functionSpaceCode) {
2152    int tag=0;     case(Nodes):
2153    tag=Finley_Mesh_getTag(mesh, name.c_str());     case(Elements):
2154    checkPasoError();     case(ReducedElements):
2155    // throwStandardException("MeshAdapter::getTag is not implemented.");     case(FaceElements):
2156    return tag;     case(ReducedFaceElements):
2157  }     case(Points):
2158       case(ContactElementsZero):
2159  bool MeshAdapter::isValidTagName(const std::string& name) const     case(ReducedContactElementsZero):
2160  {     case(ContactElementsOne):
2161    Finley_Mesh* mesh=m_finleyMesh.get();     case(ReducedContactElementsOne):
2162    return Finley_Mesh_isValidTagName(mesh,name.c_str());            return true;
2163  }     case(ReducedNodes):
2164       case(DegreesOfFreedom):
2165  std::string MeshAdapter::showTagNames() const     case(ReducedDegreesOfFreedom):
2166  {        return false;
2167    stringstream temp;     default:
2168    Finley_Mesh* mesh=m_finleyMesh.get();      return false;
   Finley_TagMap* tag_map=mesh->TagMap;  
   while (tag_map) {  
      temp << tag_map->name;  
      tag_map=tag_map->next;  
      if (tag_map) temp << ", ";  
2169    }    }
   return temp.str();  
2170  }  }
2171    
2172    
2173  }  // end of namespace  }  // end of namespace

Legend:
Removed from v.1346  
changed lines
  Added in v.1877

  ViewVC Help
Powered by ViewVC 1.1.26