/[escript]/trunk/finley/src/CPPAdapter/MeshAdapter.cpp
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Diff of /trunk/finley/src/CPPAdapter/MeshAdapter.cpp

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revision 1346 by ksteube, Wed Nov 14 22:48:12 2007 UTC revision 2315 by gross, Wed Mar 18 00:38:48 2009 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 "esysUtils/blocktimer.h"
27  }  }
 #include <vector>  
28    
29  using namespace std;  using namespace std;
30  using namespace escript;  using namespace escript;
# Line 48  const int MeshAdapter::ReducedContactEle Line 50  const int MeshAdapter::ReducedContactEle
50    
51  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
52  {  {
53    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
54    //     //
55    // 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
56    // for us.     // for us.
57    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
58  }  }
59    
60  //  //
# Line 60  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 62  MeshAdapter::MeshAdapter(Finley_Mesh* fi
62  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
63  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
64  {  {
65    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
66  }  }
67    
68  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
69  {  {
70    //     //
71    // 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.
72    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
73    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
74      Finley_Mesh_free(m_finleyMesh.get());        Finley_Mesh_free(m_finleyMesh.get());
75    }     }
76  }  }
77    
78  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
# Line 81  int MeshAdapter::getMPIRank() const Line 83  int MeshAdapter::getMPIRank() const
83  {  {
84     return m_finleyMesh.get()->MPIInfo->rank;     return m_finleyMesh.get()->MPIInfo->rank;
85  }  }
86    void MeshAdapter::MPIBarrier() const
87    {
88    #ifdef PASO_MPI
89       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
90    #endif
91       return;
92    }
93    bool MeshAdapter::onMasterProcessor() const
94    {
95       return m_finleyMesh.get()->MPIInfo->rank == 0;
96    }
97    
98    
99  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
# Line 89  Finley_Mesh* MeshAdapter::getFinley_Mesh Line 102  Finley_Mesh* MeshAdapter::getFinley_Mesh
102    
103  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
104  {  {
105    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;
106    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
107    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
108    checkFinleyError();     checkFinleyError();
109    TMPMEMFREE(fName);     TMPMEMFREE(fName);
110  }  }
111    
112  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  void MeshAdapter::Print_Mesh_Info(const bool full=false) const
113  {  {
114    Finley_PrintMesh_Info(m_finleyMesh.get(), full);     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
115  }  }
116    
117  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const std::string& fileName) const
118  {  {
119  #ifdef USE_NETCDF  #ifdef USE_NETCDF
120     const NcDim* ncdims[25]; /* ksteube how big should ncdims be? */     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
121     NcVar *ids, *data;     NcVar *ids;
122     int *int_ptr;     int *int_ptr;
123     Finley_Mesh *mesh = m_finleyMesh.get();     Finley_Mesh *mesh = m_finleyMesh.get();
124       Finley_TagMap* tag_map;
125       int num_Tags = 0;
126     int mpi_size             = mesh->MPIInfo->size;     int mpi_size             = mesh->MPIInfo->size;
127     int mpi_rank             = mesh->MPIInfo->rank;     int mpi_rank             = mesh->MPIInfo->rank;
128     int numDim               = mesh->Nodes->numDim;     int numDim               = mesh->Nodes->numDim;
# Line 119  void MeshAdapter::dump(const std::string Line 134  void MeshAdapter::dump(const std::string
134     int num_Elements_numNodes        = mesh->Elements->numNodes;     int num_Elements_numNodes        = mesh->Elements->numNodes;
135     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
136     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
137     char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank);  #ifdef PASO_MPI
138       MPI_Status status;
139    #endif
140    
141    /* Incoming token indicates it's my turn to write */
142    #ifdef PASO_MPI
143       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
144    #endif
145    
146       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
147                                                         mpi_size, mpi_rank);
148    
149       /* Figure out how much storage is required for tags */
150       tag_map = mesh->TagMap;
151       num_Tags = 0;
152       if (tag_map) {
153          while (tag_map) {
154             num_Tags++;
155             tag_map=tag_map->next;
156          }
157       }
158    
159     // NetCDF error handler     // NetCDF error handler
160     NcError err(NcError::verbose_nonfatal);     NcError err(NcError::verbose_nonfatal);
# Line 127  void MeshAdapter::dump(const std::string Line 162  void MeshAdapter::dump(const std::string
162     NcFile dataFile(newFileName, NcFile::Replace);     NcFile dataFile(newFileName, NcFile::Replace);
163     // check if writing was successful     // check if writing was successful
164     if (!dataFile.is_valid())     if (!dataFile.is_valid())
165          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);
166    
167     // 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)
168     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
169          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);
170     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
171          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);
172     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)) )
173          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);
174     if (num_Elements>0)     if (num_Elements>0)
175        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
176          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);
177     if (num_FaceElements>0)     if (num_FaceElements>0)
178        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
179          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);
180     if (num_ContactElements>0)     if (num_ContactElements>0)
181        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
182          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);
183     if (num_Points>0)     if (num_Points>0)
184        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
185          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);
186     if (num_Elements>0)     if (num_Elements>0)
187        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
188          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);
189     if (num_FaceElements>0)     if (num_FaceElements>0)
190        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
191          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);
192     if (num_ContactElements>0)     if (num_ContactElements>0)
193        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
194          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);
195       if (num_Tags>0)
196          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
197             throw DataException("Error - MeshAdapter::dump: appending dimension dim_Tags to netCDF file failed: " + *newFileName);
198    
199     // Attributes: MPI size, MPI rank, Name, order, reduced_order     // Attributes: MPI size, MPI rank, Name, order, reduced_order
200     if (!dataFile.add_att("mpi_size", mpi_size) )     if (!dataFile.add_att("mpi_size", mpi_size) )
201          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);
202     if (!dataFile.add_att("mpi_rank", mpi_rank) )     if (!dataFile.add_att("mpi_rank", mpi_rank) )
203          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);
204     if (!dataFile.add_att("Name",mesh->Name) )     if (!dataFile.add_att("Name",mesh->Name) )
205          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
206     if (!dataFile.add_att("numDim",numDim) )     if (!dataFile.add_att("numDim",numDim) )
207          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
208     if (!dataFile.add_att("order",mesh->order) )     if (!dataFile.add_att("order",mesh->order) )
209          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
210     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
211          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);
212     if (!dataFile.add_att("numNodes",numNodes) )     if (!dataFile.add_att("numNodes",numNodes) )
213          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
214     if (!dataFile.add_att("num_Elements",num_Elements) )     if (!dataFile.add_att("num_Elements",num_Elements) )
215          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);
216     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
217          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);
218     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
219          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);
220     if (!dataFile.add_att("num_Points",num_Points) )     if (!dataFile.add_att("num_Points",num_Points) )
221          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);
222     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
223          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);
224     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
225          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);
226     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
227          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);
228       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
229          throw DataException("Error - MeshAdapter::dump: appending Elements_TypeId to NetCDF file failed: " + *newFileName);
230       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
231          throw DataException("Error - MeshAdapter::dump: appending FaceElements_TypeId to NetCDF file failed: " + *newFileName);
232       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )
233          throw DataException("Error - MeshAdapter::dump: appending ContactElements_TypeId to NetCDF file failed: " + *newFileName);
234       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )
235          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);
236       if (!dataFile.add_att("num_Tags", num_Tags) )
237          throw DataException("Error - MeshAdapter::dump: appending num_Tags to NetCDF file failed: " + *newFileName);
238    
239     // // // // // Nodes // // // // //     // // // // // Nodes // // // // //
240    
241     // 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)
242     if (numNodes>0) {     if (numNodes>0) {
243    
244     // Nodes Id        // Nodes Id
245     if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
246          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);
247     int_ptr = &mesh->Nodes->Id[0];        int_ptr = &mesh->Nodes->Id[0];
248     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
249          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);
250    
251     // Nodes Tag        // Nodes Tag
252     if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
253          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);
254     int_ptr = &mesh->Nodes->Tag[0];        int_ptr = &mesh->Nodes->Tag[0];
255     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
256          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);
257    
258     // Nodes gDOF        // Nodes gDOF
259     if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
260          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);
261     int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
262     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
263          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);
264    
265     // Nodes global node index        // Nodes global node index
266     if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
267          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);
268     int_ptr = &mesh->Nodes->globalNodesIndex[0];        int_ptr = &mesh->Nodes->globalNodesIndex[0];
269     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
270          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);
271    
272     // Nodes grDof        // Nodes grDof
273     if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
274          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);
275     int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
276     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
277          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);
278    
279     // Nodes grNI        // Nodes grNI
280     if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
281          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);
282     int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
283     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
284          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);
285    
286     // Nodes Coordinates        // Nodes Coordinates
287     if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
288          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);
289     if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
290          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);
291    
292     // Nodes degreesOfFreedomDistribution        // Nodes degreesOfFreedomDistribution
293     if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
294          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);
295     int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
296     if (! (ids->put(int_ptr, mpi_size+1)) )        if (! (ids->put(int_ptr, mpi_size+1)) )
297          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);
298    
299          // Nodes nodeDistribution
300          if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
301             throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
302          int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
303          if (! (ids->put(int_ptr, mpi_size+1)) )
304             throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
305    
306     }     }
307    
# Line 254  void MeshAdapter::dump(const std::string Line 309  void MeshAdapter::dump(const std::string
309    
310     if (num_Elements>0) {     if (num_Elements>0) {
311    
312       // Temp storage to gather node IDs        // Elements_Id
313       int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
314             throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
315       // Elements ReferenceElement->ElementTypeId        int_ptr = &mesh->Elements->Id[0];
316       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )        if (! (ids->put(int_ptr, num_Elements)) )
317          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);
318    
319       // Elements_Id        // Elements_Tag
320       if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
321          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);
322       int_ptr = &mesh->Elements->Id[0];        int_ptr = &mesh->Elements->Tag[0];
323       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
324          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);
325    
326       // Elements_Tag        // Elements_Owner
327       if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
328          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);
329       int_ptr = &mesh->Elements->Tag[0];        int_ptr = &mesh->Elements->Owner[0];
330       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
331          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);
332    
333       // Elements_Owner        // Elements_Color
334       if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
335          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);
336       int_ptr = &mesh->Elements->Owner[0];        int_ptr = &mesh->Elements->Color[0];
337       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
338          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);
339    
340       // Elements_Color        // Elements_Nodes
341       if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
342          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);
343       int_ptr = &mesh->Elements->Color[0];        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
344       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);  
345    
346     }     }
347    
# Line 306  void MeshAdapter::dump(const std::string Line 349  void MeshAdapter::dump(const std::string
349    
350     if (num_FaceElements>0) {     if (num_FaceElements>0) {
351    
352       // Temp storage to gather node IDs        // FaceElements_Id
353       int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
354             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
355       // FaceElements ReferenceElement->ElementTypeId        int_ptr = &mesh->FaceElements->Id[0];
356       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )        if (! (ids->put(int_ptr, num_FaceElements)) )
357          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);
358    
359       // FaceElements_Id        // FaceElements_Tag
360       if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
361          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);
362       int_ptr = &mesh->FaceElements->Id[0];        int_ptr = &mesh->FaceElements->Tag[0];
363       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
364          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);
365    
366       // FaceElements_Tag        // FaceElements_Owner
367       if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
368          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);
369       int_ptr = &mesh->FaceElements->Tag[0];        int_ptr = &mesh->FaceElements->Owner[0];
370       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
371          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);
372    
373       // FaceElements_Owner        // FaceElements_Color
374       if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
375          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);
376       int_ptr = &mesh->FaceElements->Owner[0];        int_ptr = &mesh->FaceElements->Color[0];
377       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
378          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);
379    
380       // FaceElements_Color        // FaceElements_Nodes
381       if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
382          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);
383       int_ptr = &mesh->FaceElements->Color[0];        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
384       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);  
385    
386     }     }
387    
# Line 358  void MeshAdapter::dump(const std::string Line 389  void MeshAdapter::dump(const std::string
389    
390     if (num_ContactElements>0) {     if (num_ContactElements>0) {
391    
392       // Temp storage to gather node IDs        // ContactElements_Id
393       int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
394             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
395       // ContactElements ReferenceElement->ElementTypeId        int_ptr = &mesh->ContactElements->Id[0];
396       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->ReferenceElement->Type->TypeId) )        if (! (ids->put(int_ptr, num_ContactElements)) )
397          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);
398    
399       // ContactElements_Id        // ContactElements_Tag
400       if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
401          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);
402       int_ptr = &mesh->ContactElements->Id[0];        int_ptr = &mesh->ContactElements->Tag[0];
403       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
404          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);
405    
406       // ContactElements_Tag        // ContactElements_Owner
407       if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
408          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);
409       int_ptr = &mesh->ContactElements->Tag[0];        int_ptr = &mesh->ContactElements->Owner[0];
410       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
411          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);
412    
413       // ContactElements_Owner        // ContactElements_Color
414       if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
415          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);
416       int_ptr = &mesh->ContactElements->Owner[0];        int_ptr = &mesh->ContactElements->Color[0];
417       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
418          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);
419    
420       // ContactElements_Color        // ContactElements_Nodes
421       if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
422          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);
423       int_ptr = &mesh->ContactElements->Color[0];        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
424       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);  
425    
426     }     }
427    
# Line 410  void MeshAdapter::dump(const std::string Line 429  void MeshAdapter::dump(const std::string
429    
430     if (num_Points>0) {     if (num_Points>0) {
431    
432       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");
433    
434       // Temp storage to gather node IDs        // Points_Id
435       int *Points_Nodes = TMPMEMALLOC(num_Points,int);        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
436             throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
437       // Points ReferenceElement->ElementTypeId        int_ptr = &mesh->Points->Id[0];
438       if (!dataFile.add_att("Points_TypeId", mesh->Points->ReferenceElement->Type->TypeId) )        if (! (ids->put(int_ptr, num_Points)) )
439          throw DataException("Error - MeshAdapter::dump: appending Points_TypeId to NetCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
440    
441       // Points_Id        // Points_Tag
442       if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
443          throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
444       int_ptr = &mesh->Points->Id[0];        int_ptr = &mesh->Points->Tag[0];
445       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
446          throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
447    
448       // Points_Tag        // Points_Owner
449       if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
450          throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
451       int_ptr = &mesh->Points->Tag[0];        int_ptr = &mesh->Points->Owner[0];
452       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
453          throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
454    
455       // Points_Owner        // Points_Color
456       if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
457          throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
458       int_ptr = &mesh->Points->Owner[0];        int_ptr = &mesh->Points->Color[0];
459       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
460          throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
461    
462       // Points_Color        // Points_Nodes
463       if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
464          throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
465       int_ptr = &mesh->Points->Color[0];           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
466       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
467          throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
   
      // Points_Nodes  
      // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]  
      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);  
468    
469     }     }
470    
471     // // // // // TagMap // // // // //     // // // // // TagMap // // // // //
472    
473       fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump does not save the TagMap yet\n\n\n");     if (num_Tags>0) {
474    
475          // Temp storage to gather node IDs
476          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
477          char name_temp[4096];
478    
479          /* Copy tag data into temp arrays */
480          tag_map = mesh->TagMap;
481          if (tag_map) {
482             int i = 0;
483             while (tag_map) {
484                Tags_keys[i++] = tag_map->tag_key;
485                tag_map=tag_map->next;
486             }
487          }
488    
489          // Tags_keys
490          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
491             throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
492          int_ptr = &Tags_keys[0];
493          if (! (ids->put(int_ptr, num_Tags)) )
494             throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
495    
496          // Tags_names_*
497          // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
498          // because the NetCDF manual doesn't tell how to do an array of strings
499          tag_map = mesh->TagMap;
500          if (tag_map) {
501             int i = 0;
502             while (tag_map) {
503                sprintf(name_temp, "Tags_name_%d", i);
504                if (!dataFile.add_att(name_temp, tag_map->name) )
505                   throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
506                tag_map=tag_map->next;
507                i++;
508             }
509          }
510    
511          TMPMEMFREE(Tags_keys);
512    
513       }
514    
515    /* Send token to next MPI process so he can take his turn */
516    #ifdef PASO_MPI
517       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
518    #endif
519    
520     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
521    
522  #else  #else
523     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.");
524  #endif  /* USE_NETCDF */  #endif  /* USE_NETCDF */
# Line 473  void MeshAdapter::dump(const std::string Line 527  void MeshAdapter::dump(const std::string
527    
528  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
529  {  {
530    return "FinleyMesh";     return "FinleyMesh";
531  }  }
532    
533  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
534  {  {
535    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
536    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
537    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
538      return "Invalid function space type code.";        return "Invalid function space type code.";
539    } else {     } else {
540      return loc->second;        return loc->second;
541    }     }
542  }  }
543    
544  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
545  {  {
546    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
547    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
548    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
549  }  }
550    
551  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
552  {  {
553    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
554      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
555    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
556      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
557    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
558      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
559    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
560      (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
561    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
562      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
563    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
564      (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
565    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
566      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
567    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
568      (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
569    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
570      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
571    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
572      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
573    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
574      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
575    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
576      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
577    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
578      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
579  }  }
580    
581  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
582  {  {
583    return Nodes;     return Nodes;
584  }  }
585  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
586  {  {
587    return ReducedNodes;     return ReducedNodes;
588  }  }
589    
590  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
591  {  {
592    return Elements;     return Elements;
593  }  }
594  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
595  {  {
596    return ReducedElements;     return ReducedElements;
597  }  }
598    
599  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
600  {  {
601    return FaceElements;     return FaceElements;
602  }  }
603  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
604  {  {
605    return ReducedFaceElements;     return ReducedFaceElements;
606  }  }
607    
608  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
609  {  {
610    return ContactElementsZero;     return ContactElementsZero;
611  }  }
612  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
613  {  {
614    return ReducedContactElementsZero;     return ReducedContactElementsZero;
615  }  }
616    
617  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
618  {  {
619    return ContactElementsOne;     return ContactElementsOne;
620  }  }
621  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
622  {  {
623    return ReducedContactElementsOne;     return ReducedContactElementsOne;
624  }  }
625    
626  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
627  {  {
628    return DegreesOfFreedom;     return DegreesOfFreedom;
629  }  }
630    
631  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
632  {  {
633    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
634  }  }
635    
636  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
637  {  {
638    return Points;     return Points;
639  }  }
640    
641  //  //
# Line 589  int MeshAdapter::getDiracDeltaFunctionCo Line 643  int MeshAdapter::getDiracDeltaFunctionCo
643  //  //
644  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
645  {  {
646    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     Finley_Mesh* mesh=m_finleyMesh.get();
647    checkFinleyError();     int numDim=Finley_Mesh_getDim(mesh);
648    return numDim;     checkFinleyError();
649       return numDim;
650    }
651    
652    //
653    // Return the number of data points summed across all MPI processes
654    //
655    int MeshAdapter::getNumDataPointsGlobal() const
656    {
657       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
658  }  }
659    
660  //  //
# Line 604  pair<int,int> MeshAdapter::getDataShape( Line 667  pair<int,int> MeshAdapter::getDataShape(
667     int numSamples=0;     int numSamples=0;
668     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
669     switch (functionSpaceCode) {     switch (functionSpaceCode) {
670        case(Nodes):     case(Nodes):
671             numDataPointsPerSample=1;     numDataPointsPerSample=1;
672             numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
673             break;     break;
674        case(ReducedNodes):     case(ReducedNodes):
675             numDataPointsPerSample=1;     numDataPointsPerSample=1;
676             numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
677             break;     break;
678        case(Elements):     case(Elements):
679             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
680               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
681               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
682             }     }
683             break;     break;
684        case(ReducedElements):     case(ReducedElements):
685             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
686               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
687               numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
688             }     }
689             break;     break;
690        case(FaceElements):     case(FaceElements):
691             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
692                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
693                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
694             }     }
695             break;     break;
696        case(ReducedFaceElements):     case(ReducedFaceElements):
697             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
698                  numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
699                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
700             }     }
701             break;     break;
702        case(Points):     case(Points):
703             if (mesh->Points!=NULL) {     if (mesh->Points!=NULL) {
704               numDataPointsPerSample=1;        numDataPointsPerSample=1;
705               numSamples=mesh->Points->numElements;        numSamples=mesh->Points->numElements;
706             }     }
707             break;     break;
708        case(ContactElementsZero):     case(ContactElementsZero):
709             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
710               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
711               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
712             }     }
713             break;     break;
714        case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
715             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
716               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
717               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
718             }     }
719             break;     break;
720        case(ContactElementsOne):     case(ContactElementsOne):
721             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
722               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
723               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
724             }     }
725             break;     break;
726        case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
727             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
728               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
729               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
730             }     }
731             break;     break;
732        case(DegreesOfFreedom):     case(DegreesOfFreedom):
733             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
734               numDataPointsPerSample=1;        numDataPointsPerSample=1;
735               numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
736             }     }
737             break;     break;
738        case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
739             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
740               numDataPointsPerSample=1;        numDataPointsPerSample=1;
741               numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
742             }     }
743             break;     break;
744        default:     default:
745          stringstream temp;        stringstream temp;
746          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
747          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
748          break;        break;
749        }     }
750        return pair<int,int>(numDataPointsPerSample,numSamples);     return pair<int,int>(numDataPointsPerSample,numSamples);
751  }  }
752    
753  //  //
754  // 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:
755  //  //
756  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
757                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
758                       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,
759                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
760                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
761  {  {
762     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
763     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
# Line 721  void MeshAdapter::addPDEToSystem( Line 784  void MeshAdapter::addPDEToSystem(
784  }  }
785    
786  void  MeshAdapter::addPDEToLumpedSystem(  void  MeshAdapter::addPDEToLumpedSystem(
787                       escript::Data& mat,                                          escript::Data& mat,
788                       const escript::Data& D,                                          const escript::Data& D,
789                       const escript::Data& d) const                                          const escript::Data& d) const
790  {  {
791     escriptDataC _mat=mat.getDataC();     escriptDataC _mat=mat.getDataC();
792     escriptDataC _D=D.getDataC();     escriptDataC _D=D.getDataC();
# Line 760  void MeshAdapter::addPDEToRHS( escript:: Line 823  void MeshAdapter::addPDEToRHS( escript::
823     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 );
824     checkFinleyError();     checkFinleyError();
825  }  }
826    //
827    // adds PDE of second order into a transport problem
828    //
829    void MeshAdapter::addPDEToTransportProblem(
830                                               TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
831                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
832                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
833                                               const escript::Data& d, const escript::Data& y,
834                                               const escript::Data& d_contact,const escript::Data& y_contact) const
835    {
836       DataTypes::ShapeType shape;
837       source.expand();
838       escriptDataC _source=source.getDataC();
839       escriptDataC _M=M.getDataC();
840       escriptDataC _A=A.getDataC();
841       escriptDataC _B=B.getDataC();
842       escriptDataC _C=C.getDataC();
843       escriptDataC _D=D.getDataC();
844       escriptDataC _X=X.getDataC();
845       escriptDataC _Y=Y.getDataC();
846       escriptDataC _d=d.getDataC();
847       escriptDataC _y=y.getDataC();
848       escriptDataC _d_contact=d_contact.getDataC();
849       escriptDataC _y_contact=y_contact.getDataC();
850    
851       Finley_Mesh* mesh=m_finleyMesh.get();
852       Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
853    
854       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
855       checkFinleyError();
856    
857       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
858       checkFinleyError();
859    
860       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
861       checkFinleyError();
862    
863       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
864       checkFinleyError();
865    }
866    
867  //  //
868  // interpolates data between different function spaces:  // interpolates data between different function spaces:
869  //  //
870  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
871  {  {
872    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
873    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
874    if (inDomain!=*this)       if (inDomain!=*this)  
875      throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
876    if (targetDomain!=*this)     if (targetDomain!=*this)
877      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
878    
879    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
880    escriptDataC _target=target.getDataC();     escriptDataC _target=target.getDataC();
881    escriptDataC _in=in.getDataC();     escriptDataC _in=in.getDataC();
882    switch(in.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
883       case(Nodes):     case(Nodes):
884          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
885             case(Nodes):     case(Nodes):
886             case(ReducedNodes):     case(ReducedNodes):
887             case(DegreesOfFreedom):     case(DegreesOfFreedom):
888             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
889                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
890                 break;     break;
891             case(Elements):     case(Elements):
892             case(ReducedElements):     case(ReducedElements):
893                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
894                 break;     break;
895             case(FaceElements):     case(FaceElements):
896             case(ReducedFaceElements):     case(ReducedFaceElements):
897                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
898                 break;     break;
899             case(Points):     case(Points):
900                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
901                 break;     break;
902             case(ContactElementsZero):     case(ContactElementsZero):
903             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
904                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
905                 break;     break;
906             case(ContactElementsOne):     case(ContactElementsOne):
907             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
908                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
909                 break;     break;
910             default:     default:
911                 stringstream temp;        stringstream temp;
912                 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();
913                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
914                 break;        break;
915          }     }
916          break;     break;
917       case(ReducedNodes):     case(ReducedNodes):
918          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
919             case(Nodes):     case(Nodes):
920             case(ReducedNodes):     case(ReducedNodes):
921             case(DegreesOfFreedom):     case(DegreesOfFreedom):
922             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
923                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
924                 break;     break;
925             case(Elements):     case(Elements):
926             case(ReducedElements):     case(ReducedElements):
927                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
928                 break;     break;
929             case(FaceElements):     case(FaceElements):
930             case(ReducedFaceElements):     case(ReducedFaceElements):
931                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
932                 break;     break;
933             case(Points):     case(Points):
934                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
935                 break;     break;
936             case(ContactElementsZero):     case(ContactElementsZero):
937             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
938                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
939                 break;     break;
940             case(ContactElementsOne):     case(ContactElementsOne):
941             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
942                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
943                 break;     break;
944             default:     default:
945                 stringstream temp;        stringstream temp;
946                 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();
947                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
948                 break;        break;
949          }     }
950          break;     break;
951       case(Elements):     case(Elements):
952          if (target.getFunctionSpace().getTypeCode()==Elements) {     if (target.getFunctionSpace().getTypeCode()==Elements) {
953             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
954          } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
955             Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
956          } else {     } else {
957             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
958          }     }
959          break;     break;
960       case(ReducedElements):     case(ReducedElements):
961          if (target.getFunctionSpace().getTypeCode()==ReducedElements) {     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
962             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
963          } else {     } else {
964             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.");
965          }     }
966          break;     break;
967       case(FaceElements):     case(FaceElements):
968          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
969             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
970          } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
971             Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
972          } else {     } else {
973             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
974         }     }
975         break;     break;
976       case(ReducedFaceElements):     case(ReducedFaceElements):
977          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
978             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
979          } else {     } else {
980             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.");
981         }     }
982         break;     break;
983       case(Points):     case(Points):
984          if (target.getFunctionSpace().getTypeCode()==Points) {     if (target.getFunctionSpace().getTypeCode()==Points) {
985             Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
986          } else {     } else {
987             throw FinleyAdapterException("Error - No interpolation with data on points possible.");        throw FinleyAdapterException("Error - No interpolation with data on points possible.");
988          }     }
989          break;     break;
990       case(ContactElementsZero):     case(ContactElementsZero):
991       case(ContactElementsOne):     case(ContactElementsOne):
992          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
993             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
994          } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
995             Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
996          } else {     } else {
997             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
998             break;     }
999          }     break;
1000          break;     case(ReducedContactElementsZero):
1001       case(ReducedContactElementsZero):     case(ReducedContactElementsOne):
1002       case(ReducedContactElementsOne):     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1003          if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1004             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);     } else {
1005          } else {        throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1006             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");     }
1007             break;     break;
1008          }     case(DegreesOfFreedom):      
1009          break;     switch(target.getFunctionSpace().getTypeCode()) {
1010       case(DegreesOfFreedom):           case(ReducedDegreesOfFreedom):
1011          switch(target.getFunctionSpace().getTypeCode()) {     case(DegreesOfFreedom):
1012             case(ReducedDegreesOfFreedom):     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1013             case(DegreesOfFreedom):     break;
1014                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);  
1015                break;     case(Nodes):
1016       case(ReducedNodes):
1017             case(Nodes):     if (getMPISize()>1) {
1018             case(ReducedNodes):        escript::Data temp=escript::Data(in);
1019                if (getMPISize()>1) {        temp.expand();
1020                    escript::Data temp=escript::Data(in);        escriptDataC _in2 = temp.getDataC();
1021                    temp.expand();        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1022                    escriptDataC _in2 = temp.getDataC();     } else {
1023                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1024                } else {     }
1025                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     break;
1026                }     case(Elements):
1027                break;     case(ReducedElements):
1028             case(Elements):     if (getMPISize()>1) {
1029             case(ReducedElements):        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1030                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1031                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1032                   escriptDataC _in2 = temp.getDataC();     } else {
1033                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1034                } else {     }
1035                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     break;
1036                }     case(FaceElements):
1037                break;     case(ReducedFaceElements):
1038             case(FaceElements):     if (getMPISize()>1) {
1039             case(ReducedFaceElements):        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1040                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1041                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1042                   escriptDataC _in2 = temp.getDataC();  
1043                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);     } else {
1044          Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1045                } else {     }
1046                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     break;
1047                }     case(Points):
1048                break;     if (getMPISize()>1) {
1049             case(Points):        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1050                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1051                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );     } else {
1052                   escriptDataC _in2 = temp.getDataC();        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1053                } else {     }
1054                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     break;
1055                }     case(ContactElementsZero):
1056                break;     case(ContactElementsOne):
1057             case(ContactElementsZero):     case(ReducedContactElementsZero):
1058             case(ContactElementsOne):     case(ReducedContactElementsOne):
1059             case(ReducedContactElementsZero):     if (getMPISize()>1) {
1060             case(ReducedContactElementsOne):        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1061                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1062                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1063                   escriptDataC _in2 = temp.getDataC();     } else {
1064                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1065                } else {     }
1066                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     break;
1067                }     default:
1068               break;        stringstream temp;
1069             default:        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1070               stringstream temp;        throw FinleyAdapterException(temp.str());
1071               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        break;
1072               throw FinleyAdapterException(temp.str());     }
1073               break;     break;
1074          }     case(ReducedDegreesOfFreedom):
1075          break;     switch(target.getFunctionSpace().getTypeCode()) {
1076       case(ReducedDegreesOfFreedom):     case(Nodes):
1077         switch(target.getFunctionSpace().getTypeCode()) {     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1078            case(Nodes):     break;
1079               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");     case(ReducedNodes):
1080               break;     if (getMPISize()>1) {
1081            case(ReducedNodes):        escript::Data temp=escript::Data(in);
1082                if (getMPISize()>1) {        temp.expand();
1083                    escript::Data temp=escript::Data(in);        escriptDataC _in2 = temp.getDataC();
1084                    temp.expand();        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1085                    escriptDataC _in2 = temp.getDataC();     } else {
1086                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1087                } else {     }
1088                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     break;
1089                }     case(DegreesOfFreedom):
1090                break;     throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1091            case(DegreesOfFreedom):     break;
1092               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ReducedDegreesOfFreedom):
1093               break;     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1094            case(ReducedDegreesOfFreedom):     break;
1095               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     case(Elements):
1096               break;     case(ReducedElements):
1097            case(Elements):     if (getMPISize()>1) {
1098            case(ReducedElements):        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1099                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1100                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1101                   escriptDataC _in2 = temp.getDataC();     } else {
1102                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1103                } else {     }
1104                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     break;
1105               }     case(FaceElements):
1106               break;     case(ReducedFaceElements):
1107            case(FaceElements):     if (getMPISize()>1) {
1108            case(ReducedFaceElements):        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1109                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1110                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1111                   escriptDataC _in2 = temp.getDataC();     } else {
1112                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1113                } else {     }
1114                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     break;
1115                }     case(Points):
1116               break;     if (getMPISize()>1) {
1117            case(Points):        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1118                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1119                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1120                   escriptDataC _in2 = temp.getDataC();     } else {
1121                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1122                } else {     }
1123                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     break;
1124               }     case(ContactElementsZero):
1125               break;     case(ContactElementsOne):
1126            case(ContactElementsZero):     case(ReducedContactElementsZero):
1127            case(ContactElementsOne):     case(ReducedContactElementsOne):
1128            case(ReducedContactElementsZero):     if (getMPISize()>1) {
1129            case(ReducedContactElementsOne):        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1130                if (getMPISize()>1) {        escriptDataC _in2 = temp.getDataC();
1131                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1132                   escriptDataC _in2 = temp.getDataC();     } else {
1133                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1134                } else {     }
1135                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     break;
1136               }     default:
1137               break;        stringstream temp;
1138            default:        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1139               stringstream temp;        throw FinleyAdapterException(temp.str());
1140               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        break;
1141               throw FinleyAdapterException(temp.str());     }
1142               break;     break;
1143         }     default:
1144         break;        stringstream temp;
1145       default:        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1146          stringstream temp;        throw FinleyAdapterException(temp.str());
1147          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        break;
1148          throw FinleyAdapterException(temp.str());     }
1149          break;     checkFinleyError();
   }  
   checkFinleyError();  
1150  }  }
1151    
1152  //  //
# Line 1053  void MeshAdapter::interpolateOnDomain(es Line 1154  void MeshAdapter::interpolateOnDomain(es
1154  //  //
1155  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1156  {  {
1157    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1158    if (argDomain!=*this)     if (argDomain!=*this)
1159       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1160    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1161    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1162    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1163       escriptDataC _arg=arg.getDataC();        escriptDataC _arg=arg.getDataC();
1164       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1165    } else {     } else {
1166       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1167       escriptDataC _tmp_data=tmp_data.getDataC();        escriptDataC _tmp_data=tmp_data.getDataC();
1168       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1169       // this is then interpolated onto arg:        // this is then interpolated onto arg:
1170       interpolateOnDomain(arg,tmp_data);        interpolateOnDomain(arg,tmp_data);
1171    }     }
1172    checkFinleyError();     checkFinleyError();
1173  }  }
1174    
1175  //  //
# Line 1076  void MeshAdapter::setToX(escript::Data& Line 1177  void MeshAdapter::setToX(escript::Data&
1177  //  //
1178  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1179  {  {
1180    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1181    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1182       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1183    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1184    escriptDataC _normal=normal.getDataC();     Finley_Mesh* mesh=m_finleyMesh.get();
1185    switch(normal.getFunctionSpace().getTypeCode()) {     escriptDataC _normal=normal.getDataC();
1186      case(Nodes):     switch(normal.getFunctionSpace().getTypeCode()) {
1187        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     case(Nodes):
1188        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1189      case(ReducedNodes):     break;
1190        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");     case(ReducedNodes):
1191        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1192      case(Elements):     break;
1193        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     case(Elements):
1194        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1195      case(ReducedElements):     break;
1196        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");     case(ReducedElements):
1197        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1198      case (FaceElements):     break;
1199        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     case (FaceElements):
1200        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1201      case (ReducedFaceElements):     break;
1202        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     case (ReducedFaceElements):
1203        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1204      case(Points):     break;
1205        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     case(Points):
1206        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1207      case (ContactElementsOne):     break;
1208      case (ContactElementsZero):     case (ContactElementsOne):
1209        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     case (ContactElementsZero):
1210        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1211      case (ReducedContactElementsOne):     break;
1212      case (ReducedContactElementsZero):     case (ReducedContactElementsOne):
1213        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     case (ReducedContactElementsZero):
1214        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1215      case(DegreesOfFreedom):     break;
1216        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case(DegreesOfFreedom):
1217        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1218      case(ReducedDegreesOfFreedom):     break;
1219        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(ReducedDegreesOfFreedom):
1220        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1221      default:     break;
1222       default:
1223        stringstream temp;        stringstream temp;
1224        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();
1225        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1226        break;        break;
1227    }     }
1228    checkFinleyError();     checkFinleyError();
1229  }  }
1230    
1231  //  //
# Line 1131  void MeshAdapter::setToNormal(escript::D Line 1233  void MeshAdapter::setToNormal(escript::D
1233  //  //
1234  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1235  {  {
1236    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1237    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1238       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1239          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1240    
1241    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1242  }  }
1243    
1244  //  //
# Line 1143  void MeshAdapter::interpolateACross(escr Line 1246  void MeshAdapter::interpolateACross(escr
1246  //  //
1247  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1248  {  {
1249    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1250    if (argDomain!=*this)     if (argDomain!=*this)
1251       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1252    
1253    double blocktimer_start = blocktimer_time();     double blocktimer_start = blocktimer_time();
1254    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1255    escriptDataC _temp;     escriptDataC _temp;
1256    escript::Data temp;     escript::Data temp;
1257    escriptDataC _arg=arg.getDataC();     escriptDataC _arg=arg.getDataC();
1258    switch(arg.getFunctionSpace().getTypeCode()) {     switch(arg.getFunctionSpace().getTypeCode()) {
1259       case(Nodes):     case(Nodes):
1260          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1261          _temp=temp.getDataC();     _temp=temp.getDataC();
1262          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1263          break;     break;
1264       case(ReducedNodes):     case(ReducedNodes):
1265          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1266          _temp=temp.getDataC();     _temp=temp.getDataC();
1267          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1268          break;     break;
1269       case(Elements):     case(Elements):
1270          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1271          break;     break;
1272       case(ReducedElements):     case(ReducedElements):
1273          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1274          break;     break;
1275       case(FaceElements):     case(FaceElements):
1276          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1277          break;     break;
1278       case(ReducedFaceElements):     case(ReducedFaceElements):
1279          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1280          break;     break;
1281       case(Points):     case(Points):
1282          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1283          break;     break;
1284       case(ContactElementsZero):     case(ContactElementsZero):
1285          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1286          break;     break;
1287       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1288          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1289          break;     break;
1290       case(ContactElementsOne):     case(ContactElementsOne):
1291          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1292          break;     break;
1293       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1294          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1295          break;     break;
1296       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1297          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1298          _temp=temp.getDataC();     _temp=temp.getDataC();
1299          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1300          break;     break;
1301       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1302          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1303          _temp=temp.getDataC();     _temp=temp.getDataC();
1304          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1305          break;     break;
1306       default:     default:
1307          stringstream temp;        stringstream temp;
1308          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();
1309          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1310          break;        break;
1311    }     }
1312    checkFinleyError();     checkFinleyError();
1313    blocktimer_increment("integrate()", blocktimer_start);     blocktimer_increment("integrate()", blocktimer_start);
1314  }  }
1315    
1316  //  //
# Line 1215  void MeshAdapter::setToIntegrals(std::ve Line 1318  void MeshAdapter::setToIntegrals(std::ve
1318  //  //
1319  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1320  {  {
1321    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1322    if (argDomain!=*this)     if (argDomain!=*this)
1323      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1324    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1325    if (gradDomain!=*this)     if (gradDomain!=*this)
1326       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1327    
1328    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1329    escriptDataC _grad=grad.getDataC();     escriptDataC _grad=grad.getDataC();
1330    escriptDataC nodeDataC;     escriptDataC nodeDataC;
1331    escript::Data temp;     escript::Data temp;
1332    if (getMPISize()>1) {     if (getMPISize()>1) {
1333        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1334          temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1335          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1336        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1337          temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1338          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1339        } else {        } else {
1340          nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1341        }        }
1342    } else {     } else {
1343       nodeDataC = arg.getDataC();        nodeDataC = arg.getDataC();
1344    }     }
1345    switch(grad.getFunctionSpace().getTypeCode()) {     switch(grad.getFunctionSpace().getTypeCode()) {
1346         case(Nodes):     case(Nodes):
1347            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1348            break;     break;
1349         case(ReducedNodes):     case(ReducedNodes):
1350            throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1351            break;     break;
1352         case(Elements):     case(Elements):
1353            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1354            break;     break;
1355         case(ReducedElements):     case(ReducedElements):
1356            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1357            break;     break;
1358         case(FaceElements):     case(FaceElements):
1359            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1360            break;     break;
1361         case(ReducedFaceElements):     case(ReducedFaceElements):
1362            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1363            break;     break;
1364         case(Points):     case(Points):
1365            throw FinleyAdapterException("Error - Gradient at points is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1366            break;     break;
1367         case(ContactElementsZero):     case(ContactElementsZero):
1368            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1369            break;     break;
1370         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1371            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1372            break;     break;
1373         case(ContactElementsOne):     case(ContactElementsOne):
1374            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1375            break;     break;
1376         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1377            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1378            break;     break;
1379         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1380            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1381            break;     break;
1382         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1383            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1384            break;     break;
1385         default:     default:
1386            stringstream temp;        stringstream temp;
1387            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();
1388            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1389            break;        break;
1390    }     }
1391    checkFinleyError();     checkFinleyError();
1392  }  }
1393    
1394  //  //
# Line 1293  void MeshAdapter::setToGradient(escript: Line 1396  void MeshAdapter::setToGradient(escript:
1396  //  //
1397  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1398  {  {
1399    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1400    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1401    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1402         case(Nodes):     case(Nodes):
1403            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1404            break;     break;
1405         case(ReducedNodes):     case(ReducedNodes):
1406            throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1407            break;     break;
1408         case(Elements):     case(Elements):
1409            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1410            break;     break;
1411         case(ReducedElements):     case(ReducedElements):
1412            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1413            break;     break;
1414         case(FaceElements):     case(FaceElements):
1415            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1416            break;     break;
1417         case(ReducedFaceElements):     case(ReducedFaceElements):
1418            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1419            break;     break;
1420         case(Points):     case(Points):
1421            throw FinleyAdapterException("Error - Size of point elements is not supported.");     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1422            break;     break;
1423         case(ContactElementsZero):     case(ContactElementsZero):
1424         case(ContactElementsOne):     case(ContactElementsOne):
1425            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1426            break;     break;
1427         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1428         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1429            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1430            break;     break;
1431         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1432            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1433            break;     break;
1434         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1435            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1436            break;     break;
1437         default:     default:
1438            stringstream temp;        stringstream temp;
1439            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();
1440            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1441            break;        break;
1442    }     }
1443    checkFinleyError();     checkFinleyError();
1444  }  }
1445    
1446  // sets the location of nodes:  //
1447    // sets the location of nodes
1448    //
1449  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1450  {  {
1451    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1452    escriptDataC tmp;     escriptDataC tmp;
1453    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1454    if (newDomain!=*this)     if (newDomain!=*this)
1455       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1456    tmp = new_x.getDataC();     tmp = new_x.getDataC();
1457    Finley_Mesh_setCoordinates(mesh,&tmp);     Finley_Mesh_setCoordinates(mesh,&tmp);
1458    checkFinleyError();     checkFinleyError();
1459    }
1460    
1461    //
1462    // Helper for the save* methods. Extracts optional data variable names and the
1463    // corresponding pointers from python dictionary. Caller must free arrays.
1464    //
1465    void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1466    {
1467       numData = boost::python::extract<int>(arg.attr("__len__")());
1468       /* win32 refactor */
1469       names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1470       data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1471       dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1472    
1473       boost::python::list keys=arg.keys();
1474       for (int i=0; i<numData; ++i) {
1475          std::string n=boost::python::extract<std::string>(keys[i]);
1476          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1477          if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1478             throw FinleyAdapterException("Error: Data must be defined on same Domain");
1479          data[i] = d.getDataC();
1480          dataPtr[i] = &(data[i]);
1481          names[i] = TMPMEMALLOC(n.length()+1, char);
1482          strcpy(names[i], n.c_str());
1483       }
1484  }  }
1485    
1486  // saves a data array in openDX format:  //
1487    // saves mesh and optionally data arrays in openDX format
1488    //
1489  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
1490  {  {
1491      int MAX_namelength=256;     int num_data;
1492      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1493    /* win32 refactor */     escriptDataC *data;
1494    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC **ptr_data;
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
1495    
1496    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1497    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1498    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;     checkFinleyError();
1499    
1500    boost::python::list keys=arg.keys();     /* win32 refactor */
1501    for (int i=0;i<num_data;++i) {     TMPMEMFREE(data);
1502           std::string n=boost::python::extract<std::string>(keys[i]);     TMPMEMFREE(ptr_data);
1503           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     for(int i=0; i<num_data; i++)
1504           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     {
1505               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");        TMPMEMFREE(names[i]);
1506           data[i]=d.getDataC();     }
1507           ptr_data[i]=&(data[i]);     TMPMEMFREE(names);
          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);  
1508    
1509      return;     return;
1510  }  }
1511    
1512  // saves a data array in openVTK format:  //
1513    // saves mesh and optionally data arrays in VTK format
1514    //
1515  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
1516  {  {
1517      int MAX_namelength=256;     int num_data;
1518      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1519    /* win32 refactor */     escriptDataC *data;
1520    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC **ptr_data;
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
   
   char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  
   escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  
   escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
     boost::python::list keys=arg.keys();  
     for (int i=0;i<num_data;++i) {  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          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);  
1521    
1522    checkFinleyError();     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1523    /* win32 refactor */     Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1524    TMPMEMFREE(c_names);     checkFinleyError();
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1525    
1526      return;     /* win32 refactor */
1527       TMPMEMFREE(data);
1528       TMPMEMFREE(ptr_data);
1529       for(int i=0; i<num_data; i++)
1530       {
1531          TMPMEMFREE(names[i]);
1532       }
1533       TMPMEMFREE(names);
1534  }  }
1535                                                                                                                                                                            
1536                                                                                                                                                                            //
1537  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1538    //
1539  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1540                        const int row_blocksize,                                                   const int row_blocksize,
1541                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1542                        const int column_blocksize,                                                   const int column_blocksize,
1543                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1544                        const int type) const                                                   const int type) const
1545  {  {
1546      int reduceRowOrder=0;     int reduceRowOrder=0;
1547      int reduceColOrder=0;     int reduceColOrder=0;
1548      // is the domain right?     // is the domain right?
1549      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1550      if (row_domain!=*this)     if (row_domain!=*this)
1551            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.");
1552      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1553      if (col_domain!=*this)     if (col_domain!=*this)
1554            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.");
1555      // is the function space type right     // is the function space type right
1556      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1557          reduceRowOrder=0;        reduceRowOrder=0;
1558      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1559          reduceRowOrder=1;        reduceRowOrder=1;
1560      } else {     } else {
1561          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1562      }     }
1563      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1564          reduceColOrder=0;        reduceColOrder=0;
1565      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1566          reduceColOrder=1;        reduceColOrder=1;
1567      } else {     } else {
1568          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1569      }     }
1570      // generate matrix:     // generate matrix:
1571        
1572      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1573      checkFinleyError();     checkFinleyError();
1574      Paso_SystemMatrix* fsystemMatrix;     Paso_SystemMatrix* fsystemMatrix;
1575      int trilinos = 0;     int trilinos = 0;
1576      if (trilinos) {     if (trilinos) {
1577  #ifdef TRILINOS  #ifdef TRILINOS
1578        /* Allocation Epetra_VrbMatrix here */        /* Allocation Epetra_VrbMatrix here */
1579  #endif  #endif
1580      }     }
1581      else {     else {
1582        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1583      }     }
1584      checkPasoError();     checkPasoError();
1585      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1586      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1587    }
1588    
1589    //
1590    // creates a TransportProblemAdapter
1591    //
1592    TransportProblemAdapter MeshAdapter::newTransportProblem(
1593                                                             const double theta,
1594                                                             const int blocksize,
1595                                                             const escript::FunctionSpace& functionspace,
1596                                                             const int type) const
1597    {
1598       int reduceOrder=0;
1599       // is the domain right?
1600       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1601       if (domain!=*this)
1602          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1603       // is the function space type right
1604       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1605          reduceOrder=0;
1606       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1607          reduceOrder=1;
1608       } else {
1609          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1610       }
1611       // generate matrix:
1612    
1613       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1614       checkFinleyError();
1615       Paso_FCTransportProblem* transportProblem;
1616       transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1617       checkPasoError();
1618       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1619       return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
1620  }  }
1621    
1622  //  //
# Line 1510  SystemMatrixAdapter MeshAdapter::newSyst Line 1628  SystemMatrixAdapter MeshAdapter::newSyst
1628  // 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:
1629  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1630  {  {
1631    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1632         case(Nodes):     case(Nodes):
1633         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1634         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1635            return false;     return false;
1636            break;     break;
1637         case(Elements):     case(Elements):
1638         case(FaceElements):     case(FaceElements):
1639         case(Points):     case(Points):
1640         case(ContactElementsZero):     case(ContactElementsZero):
1641         case(ContactElementsOne):     case(ContactElementsOne):
1642         case(ReducedElements):     case(ReducedElements):
1643         case(ReducedFaceElements):     case(ReducedFaceElements):
1644         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1645         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1646            return true;     return true;
1647            break;     break;
1648         default:     default:
1649            stringstream temp;        stringstream temp;
1650            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;
1651            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1652            break;        break;
1653    }     }
1654    checkFinleyError();     checkFinleyError();
1655    return false;     return false;
1656  }  }
1657    
1658  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1659  {  {
1660    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1661       case(Nodes):     case(Nodes):
1662          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1663             case(Nodes):     case(Nodes):
1664             case(ReducedNodes):     case(ReducedNodes):
1665             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1666             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1667             case(Elements):     case(Elements):
1668             case(ReducedElements):     case(ReducedElements):
1669             case(FaceElements):     case(FaceElements):
1670             case(ReducedFaceElements):     case(ReducedFaceElements):
1671             case(Points):     case(Points):
1672             case(ContactElementsZero):     case(ContactElementsZero):
1673             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1674             case(ContactElementsOne):     case(ContactElementsOne):
1675             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1676                 return true;     return true;
1677             default:     default:
1678                 stringstream temp;        stringstream temp;
1679                 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;
1680                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1681          }     }
1682          break;     break;
1683       case(ReducedNodes):     case(ReducedNodes):
1684          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1685             case(ReducedNodes):     case(ReducedNodes):
1686             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1687             case(Elements):     case(Elements):
1688             case(ReducedElements):     case(ReducedElements):
1689             case(FaceElements):     case(FaceElements):
1690             case(ReducedFaceElements):     case(ReducedFaceElements):
1691             case(Points):     case(Points):
1692             case(ContactElementsZero):     case(ContactElementsZero):
1693             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1694             case(ContactElementsOne):     case(ContactElementsOne):
1695             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1696                 return true;     return true;
1697            case(Nodes):     case(Nodes):
1698            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1699               return false;     return false;
1700             default:     default:
1701                 stringstream temp;        stringstream temp;
1702                 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;
1703                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1704          }     }
1705          break;     break;
1706       case(Elements):     case(Elements):
1707          if (functionSpaceType_target==Elements) {     if (functionSpaceType_target==Elements) {
1708             return true;        return true;
1709          } else if (functionSpaceType_target==ReducedElements) {     } else if (functionSpaceType_target==ReducedElements) {
1710             return true;        return true;
1711          } else {     } else {
1712             return false;        return false;
1713          }     }
1714       case(ReducedElements):     case(ReducedElements):
1715          if (functionSpaceType_target==ReducedElements) {     if (functionSpaceType_target==ReducedElements) {
1716             return true;        return true;
1717          } else {     } else {
1718             return false;        return false;
1719          }     }
1720       case(FaceElements):     case(FaceElements):
1721          if (functionSpaceType_target==FaceElements) {     if (functionSpaceType_target==FaceElements) {
1722             return true;        return true;
1723          } else if (functionSpaceType_target==ReducedFaceElements) {     } else if (functionSpaceType_target==ReducedFaceElements) {
1724             return true;        return true;
1725          } else {     } else {
1726             return false;        return false;
1727          }     }
1728       case(ReducedFaceElements):     case(ReducedFaceElements):
1729          if (functionSpaceType_target==ReducedFaceElements) {     if (functionSpaceType_target==ReducedFaceElements) {
1730             return true;        return true;
1731          } else {     } else {
1732             return false;        return false;
1733          }     }
1734       case(Points):     case(Points):
1735          if (functionSpaceType_target==Points) {     if (functionSpaceType_target==Points) {
1736             return true;        return true;
1737          } else {     } else {
1738             return false;        return false;
1739          }     }
1740       case(ContactElementsZero):     case(ContactElementsZero):
1741       case(ContactElementsOne):     case(ContactElementsOne):
1742          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1743             return true;        return true;
1744          } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1745             return true;        return true;
1746          } else {     } else {
1747             return false;        return false;
1748          }     }
1749       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1750       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1751          if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1752             return true;        return true;
1753          } else {     } else {
1754             return false;        return false;
1755          }     }
1756       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1757          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1758             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1759             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1760             case(Nodes):     case(Nodes):
1761             case(ReducedNodes):     case(ReducedNodes):
1762             case(Elements):     case(Elements):
1763             case(ReducedElements):     case(ReducedElements):
1764             case(Points):     case(Points):
1765             case(FaceElements):     case(FaceElements):
1766             case(ReducedFaceElements):     case(ReducedFaceElements):
1767             case(ContactElementsZero):     case(ContactElementsZero):
1768             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1769             case(ContactElementsOne):     case(ContactElementsOne):
1770             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1771                return true;     return true;
1772             default:     default:
1773               stringstream temp;        stringstream temp;
1774               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;
1775               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1776          }     }
1777          break;     break;
1778       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1779         switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1780            case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1781            case(ReducedNodes):     case(ReducedNodes):
1782            case(Elements):     case(Elements):
1783            case(ReducedElements):     case(ReducedElements):
1784            case(FaceElements):     case(FaceElements):
1785            case(ReducedFaceElements):     case(ReducedFaceElements):
1786            case(Points):     case(Points):
1787            case(ContactElementsZero):     case(ContactElementsZero):
1788            case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1789            case(ContactElementsOne):     case(ContactElementsOne):
1790            case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1791                return true;     return true;
1792            case(Nodes):     case(Nodes):
1793            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1794               return false;     return false;
1795            default:     default:
1796               stringstream temp;        stringstream temp;
1797               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;
1798               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1799         }     }
1800         break;     break;
1801       default:     default:
1802          stringstream temp;        stringstream temp;
1803          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;
1804          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1805          break;        break;
1806    }     }
1807    checkFinleyError();     checkFinleyError();
1808    return false;     return false;
1809  }  }
1810    
1811  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
1812  {  {
1813      return false;     return false;
1814  }  }
1815    
1816  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1817  {  {
1818    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1819    if (temp!=0) {     if (temp!=0) {
1820      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1821    } else {     } else {
1822      return false;        return false;
1823    }     }
1824  }  }
1825    
1826  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1827  {  {
1828    return !(operator==(other));     return !(operator==(other));
1829  }  }
1830    
1831  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
1832  {  {
1833     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
1834       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
1835       checkPasoError();
1836       return out;
1837    }
1838    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1839    {
1840       Finley_Mesh* mesh=m_finleyMesh.get();
1841       int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
1842     checkPasoError();     checkPasoError();
1843     return out;     return out;
1844  }  }
1845    
1846  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1847  {  {
1848    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1849  }  }
1850    
1851  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1852  {  {
1853    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1854  }  }
1855    
1856  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1857  {  {
1858    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
1859  }  }
1860    
1861  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1862  {  {
1863    int *out=0,i;     int *out = NULL;
1864    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1865    switch (functionSpaceType) {     switch (functionSpaceType) {
1866      case(Nodes):     case(Nodes):
1867        out=mesh->Nodes->Id;     out=mesh->Nodes->Id;
1868        break;     break;
1869      case(ReducedNodes):     case(ReducedNodes):
1870        out=mesh->Nodes->reducedNodesId;     out=mesh->Nodes->reducedNodesId;
1871        break;     break;
1872      case(Elements):     case(Elements):
1873        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1874        break;     break;
1875      case(ReducedElements):     case(ReducedElements):
1876        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1877        break;     break;
1878      case(FaceElements):     case(FaceElements):
1879        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1880        break;     break;
1881      case(ReducedFaceElements):     case(ReducedFaceElements):
1882        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1883        break;     break;
1884      case(Points):     case(Points):
1885        out=mesh->Points->Id;     out=mesh->Points->Id;
1886        break;     break;
1887      case(ContactElementsZero):     case(ContactElementsZero):
1888        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1889        break;     break;
1890      case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1891        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1892        break;     break;
1893      case(ContactElementsOne):     case(ContactElementsOne):
1894        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1895        break;     break;
1896      case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1897        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1898        break;     break;
1899      case(DegreesOfFreedom):     case(DegreesOfFreedom):
1900        out=mesh->Nodes->degreesOfFreedomId;     out=mesh->Nodes->degreesOfFreedomId;
1901        break;     break;
1902      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1903        out=mesh->Nodes->reducedDegreesOfFreedomId;     out=mesh->Nodes->reducedDegreesOfFreedomId;
1904        break;     break;
1905      default:     default:
1906        stringstream temp;        stringstream temp;
1907        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1908        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1909        break;        break;
1910    }     }
1911    return out;     return out;
1912  }  }
1913  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1914  {  {
1915    int out=0;     int out=0;
1916    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1917    switch (functionSpaceType) {     switch (functionSpaceType) {
1918    case(Nodes):     case(Nodes):
1919      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
1920      break;     break;
1921    case(ReducedNodes):     case(ReducedNodes):
1922      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1923      break;     break;
1924    case(Elements):     case(Elements):
1925      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1926      break;     break;
1927    case(ReducedElements):     case(ReducedElements):
1928      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1929      break;     break;
1930    case(FaceElements):     case(FaceElements):
1931      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1932      break;     break;
1933    case(ReducedFaceElements):     case(ReducedFaceElements):
1934      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1935      break;     break;
1936    case(Points):     case(Points):
1937      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
1938      break;     break;
1939    case(ContactElementsZero):     case(ContactElementsZero):
1940      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1941      break;     break;
1942    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1943      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1944      break;     break;
1945    case(ContactElementsOne):     case(ContactElementsOne):
1946      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1947      break;     break;
1948    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1949      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1950      break;     break;
1951    case(DegreesOfFreedom):     case(DegreesOfFreedom):
1952      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1953      break;     break;
1954    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1955      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1956      break;     break;
1957    default:     default:
1958      stringstream temp;        stringstream temp;
1959      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1960      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1961      break;        break;
1962    }     }
1963    return out;     return out;
1964  }  }
1965    
1966    
1967  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
1968  {  {
1969       Finley_Mesh* mesh=m_finleyMesh.get();
1970       escriptDataC tmp=mask.getDataC();
1971       switch(functionSpaceType) {
1972       case(Nodes):
1973       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1974       break;
1975       case(ReducedNodes):
1976       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1977       break;
1978       case(DegreesOfFreedom):
1979       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1980       break;
1981       case(ReducedDegreesOfFreedom):
1982       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1983       break;
1984       case(Elements):
1985       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1986       break;
1987       case(ReducedElements):
1988       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1989       break;
1990       case(FaceElements):
1991       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1992       break;
1993       case(ReducedFaceElements):
1994       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1995       break;
1996       case(Points):
1997       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1998       break;
1999       case(ContactElementsZero):
2000       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2001       break;
2002       case(ReducedContactElementsZero):
2003       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2004       break;
2005       case(ContactElementsOne):
2006       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2007       break;
2008       case(ReducedContactElementsOne):
2009       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2010       break;
2011       default:
2012          stringstream temp;
2013          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2014          throw FinleyAdapterException(temp.str());
2015       }
2016       checkFinleyError();
2017       return;
2018    }
2019    
2020    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2021    {
2022       Finley_Mesh* mesh=m_finleyMesh.get();
2023       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2024       checkPasoError();
2025       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2026    }
2027    
2028    int MeshAdapter::getTag(const std::string& name) const
2029    {
2030       Finley_Mesh* mesh=m_finleyMesh.get();
2031       int tag=0;
2032       tag=Finley_Mesh_getTag(mesh, name.c_str());
2033       checkPasoError();
2034       // throwStandardException("MeshAdapter::getTag is not implemented.");
2035       return tag;
2036    }
2037    
2038    bool MeshAdapter::isValidTagName(const std::string& name) const
2039    {
2040       Finley_Mesh* mesh=m_finleyMesh.get();
2041       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2042    }
2043    
2044    std::string MeshAdapter::showTagNames() const
2045    {
2046       stringstream temp;
2047       Finley_Mesh* mesh=m_finleyMesh.get();
2048       Finley_TagMap* tag_map=mesh->TagMap;
2049       while (tag_map) {
2050          temp << tag_map->name;
2051          tag_map=tag_map->next;
2052          if (tag_map) temp << ", ";
2053       }
2054       return temp.str();
2055    }
2056    
2057    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2058    {
2059    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2060    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2061    switch(functionSpaceType) {    switch(functionSpaceCode) {
2062         case(Nodes):     case(Nodes):
2063            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2064            break;            break;
2065         case(ReducedNodes):     case(ReducedNodes):
2066            throw FinleyAdapterException("Error - ReducedNodes does not support tags");            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2067            break;            break;
2068         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2069            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2070            break;            break;
2071         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2072            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2073            break;            break;
2074         case(Elements):     case(Elements):
2075            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2076            break;            numTags=mesh->Elements->numTagsInUse;
2077         case(ReducedElements):            break;
2078            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(FaceElements):
2079            break;     case(ReducedFaceElements):
2080         case(FaceElements):            numTags=mesh->FaceElements->numTagsInUse;
2081            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);            break;
2082       case(Points):
2083              numTags=mesh->Points->numTagsInUse;
2084              break;
2085       case(ContactElementsZero):
2086       case(ReducedContactElementsZero):
2087       case(ContactElementsOne):
2088       case(ReducedContactElementsOne):
2089              numTags=mesh->ContactElements->numTagsInUse;
2090            break;            break;
2091         case(ReducedFaceElements):     default:
2092            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);        stringstream temp;
2093            break;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2094         case(Points):        throw FinleyAdapterException(temp.str());
2095            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);    }
2096      return numTags;
2097    }
2098    int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2099    {
2100      Finley_Mesh* mesh=m_finleyMesh.get();
2101      index_t* tags=NULL;
2102      switch(functionSpaceCode) {
2103       case(Nodes):
2104              tags=mesh->Nodes->tagsInUse;
2105            break;            break;
2106         case(ContactElementsZero):     case(ReducedNodes):
2107            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2108            break;            break;
2109         case(ReducedContactElementsZero):     case(DegreesOfFreedom):
2110            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2111            break;            break;
2112         case(ContactElementsOne):     case(ReducedDegreesOfFreedom):
2113            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2114            break;            break;
2115         case(ReducedContactElementsOne):     case(Elements):
2116            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2117              tags=mesh->Elements->tagsInUse;
2118              break;
2119       case(FaceElements):
2120       case(ReducedFaceElements):
2121              tags=mesh->FaceElements->tagsInUse;
2122              break;
2123       case(Points):
2124              tags=mesh->Points->tagsInUse;
2125              break;
2126       case(ContactElementsZero):
2127       case(ReducedContactElementsZero):
2128       case(ContactElementsOne):
2129       case(ReducedContactElementsOne):
2130              tags=mesh->ContactElements->tagsInUse;
2131            break;            break;
2132         default:     default:
2133            stringstream temp;        stringstream temp;
2134            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2135            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2136    }    }
2137    checkFinleyError();    return tags;
   return;  
2138  }  }
2139    
 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.");  
 }  
2140    
2141  int MeshAdapter::getTag(const std::string& name) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2142  {  {
2143    Finley_Mesh* mesh=m_finleyMesh.get();    switch(functionSpaceCode) {
2144    int tag=0;     case(Nodes):
2145    tag=Finley_Mesh_getTag(mesh, name.c_str());     case(Elements):
2146    checkPasoError();     case(ReducedElements):
2147    // throwStandardException("MeshAdapter::getTag is not implemented.");     case(FaceElements):
2148    return tag;     case(ReducedFaceElements):
2149  }     case(Points):
2150       case(ContactElementsZero):
2151  bool MeshAdapter::isValidTagName(const std::string& name) const     case(ReducedContactElementsZero):
2152  {     case(ContactElementsOne):
2153    Finley_Mesh* mesh=m_finleyMesh.get();     case(ReducedContactElementsOne):
2154    return Finley_Mesh_isValidTagName(mesh,name.c_str());            return true;
2155  }     case(ReducedNodes):
2156       case(DegreesOfFreedom):
2157  std::string MeshAdapter::showTagNames() const     case(ReducedDegreesOfFreedom):
2158  {        return false;
2159    stringstream temp;     default:
2160    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 << ", ";  
2161    }    }
   return temp.str();  
2162  }  }
2163    
2164    
2165  }  // end of namespace  }  // end of namespace

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