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

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revision 1375 by gross, Wed Jan 9 00:15:05 2008 UTC revision 2519 by jfenwick, Mon Jul 6 00:43:08 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) 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[12];     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;     Finley_TagMap* tag_map;
# Line 121  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 */     /* Figure out how much storage is required for tags */
150     tag_map = mesh->TagMap;     tag_map = mesh->TagMap;
151       num_Tags = 0;
152     if (tag_map) {     if (tag_map) {
153       while (tag_map) {        while (tag_map) {
154      num_Tags++;           num_Tags++;
155          tag_map=tag_map->next;           tag_map=tag_map->next;
156       }        }
157     }     }
158    
159     // NetCDF error handler     // NetCDF error handler
# Line 138  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)     if (num_Tags>0)
196        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )        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);           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) )     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);        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) )     if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->ReferenceElement->Type->TypeId) )
# Line 217  void MeshAdapter::dump(const std::string Line 241  void MeshAdapter::dump(const std::string
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 278  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_Id        int_ptr = &mesh->Elements->Id[0];
316       if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
317          throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
318       int_ptr = &mesh->Elements->Id[0];  
319       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Tag
320          throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
321             throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
322       // Elements_Tag        int_ptr = &mesh->Elements->Tag[0];
323       if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
324          throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
325       int_ptr = &mesh->Elements->Tag[0];  
326       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Owner
327          throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
328             throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
329       // Elements_Owner        int_ptr = &mesh->Elements->Owner[0];
330       if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
331          throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
332       int_ptr = &mesh->Elements->Owner[0];  
333       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Color
334          throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
335             throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
336       // Elements_Color        int_ptr = &mesh->Elements->Color[0];
337       if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
338          throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
339       int_ptr = &mesh->Elements->Color[0];  
340       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Nodes
341          throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
342             throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
343       // Elements_Nodes        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
344       for (int i=0; i<num_Elements; i++)           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
        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 326  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_Id        int_ptr = &mesh->FaceElements->Id[0];
356       if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
357          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
358       int_ptr = &mesh->FaceElements->Id[0];  
359       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Tag
360          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
361             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
362       // FaceElements_Tag        int_ptr = &mesh->FaceElements->Tag[0];
363       if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
364          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
365       int_ptr = &mesh->FaceElements->Tag[0];  
366       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Owner
367          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
368             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
369       // FaceElements_Owner        int_ptr = &mesh->FaceElements->Owner[0];
370       if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
371          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
372       int_ptr = &mesh->FaceElements->Owner[0];  
373       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Color
374          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
375             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
376       // FaceElements_Color        int_ptr = &mesh->FaceElements->Color[0];
377       if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
378          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
379       int_ptr = &mesh->FaceElements->Color[0];  
380       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Nodes
381          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
382             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
383       // FaceElements_Nodes        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
384       for (int i=0; i<num_FaceElements; i++)           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
        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 374  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_Id        int_ptr = &mesh->ContactElements->Id[0];
396       if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
397          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
398       int_ptr = &mesh->ContactElements->Id[0];  
399       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Tag
400          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
401             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
402       // ContactElements_Tag        int_ptr = &mesh->ContactElements->Tag[0];
403       if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
404          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
405       int_ptr = &mesh->ContactElements->Tag[0];  
406       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Owner
407          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
408             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
409       // ContactElements_Owner        int_ptr = &mesh->ContactElements->Owner[0];
410       if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
411          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
412       int_ptr = &mesh->ContactElements->Owner[0];  
413       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Color
414          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
415             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
416       // ContactElements_Color        int_ptr = &mesh->ContactElements->Color[0];
417       if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
418          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
419       int_ptr = &mesh->ContactElements->Color[0];  
420       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Nodes
421          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
422             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
423       // ContactElements_Nodes        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
424       for (int i=0; i<num_ContactElements; i++)           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
        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 422  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_Id        int_ptr = &mesh->Points->Id[0];
438       if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )        if (! (ids->put(int_ptr, num_Points)) )
439          throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
440       int_ptr = &mesh->Points->Id[0];  
441       if (! (ids->put(int_ptr, num_Points)) )        // Points_Tag
442          throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
443             throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
444       // Points_Tag        int_ptr = &mesh->Points->Tag[0];
445       if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )        if (! (ids->put(int_ptr, num_Points)) )
446          throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
447       int_ptr = &mesh->Points->Tag[0];  
448       if (! (ids->put(int_ptr, num_Points)) )        // Points_Owner
449          throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
450             throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
451       // Points_Owner        int_ptr = &mesh->Points->Owner[0];
452       if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )        if (! (ids->put(int_ptr, num_Points)) )
453          throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
454       int_ptr = &mesh->Points->Owner[0];  
455       if (! (ids->put(int_ptr, num_Points)) )        // Points_Color
456          throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
457             throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
458       // Points_Color        int_ptr = &mesh->Points->Color[0];
459       if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )        if (! (ids->put(int_ptr, num_Points)) )
460          throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
461       int_ptr = &mesh->Points->Color[0];  
462       if (! (ids->put(int_ptr, num_Points)) )        // Points_Nodes
463          throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
464          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
465       // Points_Nodes           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
466       // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
467       for (int i=0; i<num_Points; i++)           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
        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    
# Line 472  void MeshAdapter::dump(const std::string Line 472  void MeshAdapter::dump(const std::string
472    
473     if (num_Tags>0) {     if (num_Tags>0) {
474    
475       // Temp storage to gather node IDs        // Temp storage to gather node IDs
476       int *Tags_keys = TMPMEMALLOC(num_Tags, int);        int *Tags_keys = TMPMEMALLOC(num_Tags, int);
477       char name_temp[4096];        char name_temp[4096];
478    
479       /* Copy tag data into temp arrays */        /* Copy tag data into temp arrays */
480       tag_map = mesh->TagMap;        tag_map = mesh->TagMap;
481       if (tag_map) {        if (tag_map) {
482         int i = 0;           int i = 0;
483         while (tag_map) {           while (tag_map) {
484      Tags_keys[i++] = tag_map->tag_key;              Tags_keys[i++] = tag_map->tag_key;
485          tag_map=tag_map->next;              tag_map=tag_map->next;
486         }           }
487       }        }
   
      // Tags_keys  
      if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )  
         throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);  
      int_ptr = &Tags_keys[0];  
      if (! (ids->put(int_ptr, num_Tags)) )  
         throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);  
   
      // Tags_names_*  
      // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string  
      // because the NetCDF manual doesn't tell how to do an array of strings  
      tag_map = mesh->TagMap;  
      if (tag_map) {  
        int i = 0;  
        while (tag_map) {  
          sprintf(name_temp, "Tags_name_%d", i);  
          if (!dataFile.add_att(name_temp, tag_map->name) )  
            throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);  
          tag_map=tag_map->next;  
      i++;  
        }  
      }  
488    
489       TMPMEMFREE(Tags_keys);        // 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 522  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 638  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 653  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 770  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 813  void MeshAdapter::addPDEToRHS( escript:: Line 827  void MeshAdapter::addPDEToRHS( escript::
827  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
828  //  //
829  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
830                       TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
831                       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,
832                       const escript::Data& d, const escript::Data& y,                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
833                       const escript::Data& d_contact,const escript::Data& y_contact) const                                             const escript::Data& d, const escript::Data& y,
834                                               const escript::Data& d_contact,const escript::Data& y_contact) const
835  {  {
836     DataArrayView::ShapeType shape;     DataTypes::ShapeType shape;
837     source.expand();     source.expand();
    escript:: Data tmp(0.0,M.getDataPointShape(),tp.getFunctionSpace(),true);  
838     escriptDataC _source=source.getDataC();     escriptDataC _source=source.getDataC();
    escriptDataC _tmp=tmp.getDataC();  
839     escriptDataC _M=M.getDataC();     escriptDataC _M=M.getDataC();
840     escriptDataC _A=A.getDataC();     escriptDataC _A=A.getDataC();
841     escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
# Line 837  void MeshAdapter::addPDEToTransportProbl Line 850  void MeshAdapter::addPDEToTransportProbl
850    
851     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
852     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
     
   
    Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_tmp, &_M);  
    checkFinleyError();  
    /* add mass matix to lumped mass matrix of transport problem */  
    double* tmp_prt=getSampleData(&_tmp,0);  
    int i;  
    int n=Paso_FCTransportProblem_getTotalNumRows(_tp);  
    #pragma omp parallel for private(i) schedule(static)  
    for (i=0;i<n ;++i) _tp->lumped_mass_matrix[i]+=tmp_prt[i];  
853    
854     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, 0, 0, &_D, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
855     checkFinleyError();     checkFinleyError();
856    
857     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->flux_matrix, &_source, 0, &_B, &_C, 0, 0, 0 );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
858     checkFinleyError();     checkFinleyError();
859    
860     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
# Line 866  void MeshAdapter::addPDEToTransportProbl Line 869  void MeshAdapter::addPDEToTransportProbl
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()==ReducedFaceElements) {        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          }        }
999          break;        break;
1000       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1001       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1002          if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1003             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1004          } else {        } else {
1005             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1006          }        }
1007          break;        break;
1008       case(DegreesOfFreedom):           case(DegreesOfFreedom):      
1009          switch(target.getFunctionSpace().getTypeCode()) {        switch(target.getFunctionSpace().getTypeCode()) {
1010             case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
1011             case(DegreesOfFreedom):        case(DegreesOfFreedom):
1012                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1013                break;        break;
1014      
1015             case(Nodes):        case(Nodes):
1016             case(ReducedNodes):        case(ReducedNodes):
1017                if (getMPISize()>1) {        if (getMPISize()>1) {
1018                    escript::Data temp=escript::Data(in);           escript::Data temp=escript::Data(in);
1019                    temp.expand();           temp.expand();
1020                    escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1021                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1022                } else {        } else {
1023                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1024                }        }
1025                break;        break;
1026             case(Elements):        case(Elements):
1027             case(ReducedElements):        case(ReducedElements):
1028                if (getMPISize()>1) {        if (getMPISize()>1) {
1029                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1030                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1031                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1032                } else {        } else {
1033                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1034                }        }
1035                break;        break;
1036             case(FaceElements):        case(FaceElements):
1037             case(ReducedFaceElements):        case(ReducedFaceElements):
1038                if (getMPISize()>1) {        if (getMPISize()>1) {
1039                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1040                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1041                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1042      
1043                } else {        } else {
1044                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1045                }        }
1046                break;        break;
1047             case(Points):        case(Points):
1048                if (getMPISize()>1) {        if (getMPISize()>1) {
1049                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1050                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1051                } else {        } else {
1052                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1053                }        }
1054                break;        break;
1055             case(ContactElementsZero):        case(ContactElementsZero):
1056             case(ContactElementsOne):        case(ContactElementsOne):
1057             case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
1058             case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
1059                if (getMPISize()>1) {        if (getMPISize()>1) {
1060                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1061                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1062                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1063                } else {        } else {
1064                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1065                }        }
1066               break;        break;
1067             default:        default:
1068               stringstream temp;           stringstream temp;
1069               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();
1070               throw FinleyAdapterException(temp.str());           throw FinleyAdapterException(temp.str());
1071               break;           break;
1072          }        }
1073          break;        break;
1074       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1075         switch(target.getFunctionSpace().getTypeCode()) {        switch(target.getFunctionSpace().getTypeCode()) {
1076            case(Nodes):        case(Nodes):
1077               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1078               break;        break;
1079            case(ReducedNodes):        case(ReducedNodes):
1080                if (getMPISize()>1) {        if (getMPISize()>1) {
1081                    escript::Data temp=escript::Data(in);           escript::Data temp=escript::Data(in);
1082                    temp.expand();           temp.expand();
1083                    escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1084                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1085                } else {        } else {
1086                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1087                }        }
1088                break;        break;
1089            case(DegreesOfFreedom):        case(DegreesOfFreedom):
1090               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1091               break;        break;
1092            case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
1093               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1094               break;        break;
1095            case(Elements):        case(Elements):
1096            case(ReducedElements):        case(ReducedElements):
1097                if (getMPISize()>1) {        if (getMPISize()>1) {
1098                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1099                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1100                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1101                } else {        } else {
1102                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1103               }        }
1104               break;        break;
1105            case(FaceElements):        case(FaceElements):
1106            case(ReducedFaceElements):        case(ReducedFaceElements):
1107                if (getMPISize()>1) {        if (getMPISize()>1) {
1108                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1109                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1110                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1111                } else {        } else {
1112                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1113                }        }
1114               break;        break;
1115            case(Points):        case(Points):
1116                if (getMPISize()>1) {        if (getMPISize()>1) {
1117                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1118                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1119                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1120                } else {        } else {
1121                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1122               }        }
1123               break;        break;
1124            case(ContactElementsZero):        case(ContactElementsZero):
1125            case(ContactElementsOne):        case(ContactElementsOne):
1126            case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
1127            case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
1128                if (getMPISize()>1) {        if (getMPISize()>1) {
1129                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1130                   escriptDataC _in2 = temp.getDataC();           escriptDataC _in2 = temp.getDataC();
1131                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1132                } else {        } else {
1133                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1134               }        }
1135               break;        break;
1136            default:        default:
1137               stringstream temp;           stringstream temp;
1138               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();
1139               throw FinleyAdapterException(temp.str());           throw FinleyAdapterException(temp.str());
1140               break;           break;
1141         }        }
1142         break;        break;
1143       default:     default:
1144          stringstream temp;        stringstream temp;
1145          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1146          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1147          break;        break;
1148    }     }
1149    checkFinleyError();     checkFinleyError();
1150  }  }
1151    
1152  //  //
# Line 1151  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 1174  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 1229  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 1241  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 1313  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 1391  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();     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {
1457    Finley_Mesh_setCoordinates(mesh,&tmp);         tmp = new_x.getDataC();
1458    checkFinleyError();         Finley_Mesh_setCoordinates(mesh,&tmp);
1459       } else {
1460           escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );
1461           tmp = new_x_inter.getDataC();
1462           Finley_Mesh_setCoordinates(mesh,&tmp);
1463       }
1464       checkFinleyError();
1465    }
1466    
1467    //
1468    // Helper for the save* methods. Extracts optional data variable names and the
1469    // corresponding pointers from python dictionary. Caller must free arrays.
1470    //
1471    void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1472    {
1473       numData = boost::python::extract<int>(arg.attr("__len__")());
1474       /* win32 refactor */
1475       names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1476       data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1477       dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1478    
1479       boost::python::list keys=arg.keys();
1480       for (int i=0; i<numData; ++i) {
1481          std::string n=boost::python::extract<std::string>(keys[i]);
1482          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1483          if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1484             throw FinleyAdapterException("Error: Data must be defined on same Domain");
1485          data[i] = d.getDataC();
1486          dataPtr[i] = &(data[i]);
1487          names[i] = TMPMEMALLOC(n.length()+1, char);
1488          strcpy(names[i], n.c_str());
1489       }
1490  }  }
1491    
1492  // saves a data array in openDX format:  //
1493    // saves mesh and optionally data arrays in openDX format
1494    //
1495  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
1496  {  {
1497      int MAX_namelength=256;     int num_data;
1498      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1499    /* win32 refactor */     escriptDataC *data;
1500    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;  
   }  
1501    
1502    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1503    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);
1504    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;     checkFinleyError();
1505    
1506    boost::python::list keys=arg.keys();     /* win32 refactor */
1507    for (int i=0;i<num_data;++i) {     TMPMEMFREE(data);
1508           std::string n=boost::python::extract<std::string>(keys[i]);     TMPMEMFREE(ptr_data);
1509           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     for(int i=0; i<num_data; i++)
1510           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     {
1511               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");        TMPMEMFREE(names[i]);
1512           data[i]=d.getDataC();     }
1513           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);  
1514    
1515      return;     return;
1516  }  }
1517    
1518  // saves a data array in openVTK format:  //
1519  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  // saves mesh and optionally data arrays in VTK format
1520    //
1521    void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg,  const std::string& metadata, const std::string& metadata_schema) const
1522  {  {
1523      int MAX_namelength=256;     int num_data;
1524      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1525    /* win32 refactor */     escriptDataC *data;
1526    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);  
1527    
1528    checkFinleyError();     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1529    /* win32 refactor */     Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data, metadata.c_str(), metadata_schema.c_str());
1530    TMPMEMFREE(c_names);     checkFinleyError();
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1531    
1532      return;     /* win32 refactor */
1533       TMPMEMFREE(data);
1534       TMPMEMFREE(ptr_data);
1535       for(int i=0; i<num_data; i++)
1536       {
1537          TMPMEMFREE(names[i]);
1538       }
1539       TMPMEMFREE(names);
1540  }  }
1541                                                                                                                                                                            
1542                                                                                                                                                                            //
1543  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1544    //
1545  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1546                        const int row_blocksize,                                                   const int row_blocksize,
1547                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1548                        const int column_blocksize,                                                   const int column_blocksize,
1549                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1550                        const int type) const                                                   const int type) const
1551  {  {
1552      int reduceRowOrder=0;     int reduceRowOrder=0;
1553      int reduceColOrder=0;     int reduceColOrder=0;
1554      // is the domain right?     // is the domain right?
1555      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1556      if (row_domain!=*this)     if (row_domain!=*this)
1557            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.");
1558      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1559      if (col_domain!=*this)     if (col_domain!=*this)
1560            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.");
1561      // is the function space type right     // is the function space type right
1562      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1563          reduceRowOrder=0;        reduceRowOrder=0;
1564      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1565          reduceRowOrder=1;        reduceRowOrder=1;
1566      } else {     } else {
1567          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1568      }     }
1569      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1570          reduceColOrder=0;        reduceColOrder=0;
1571      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1572          reduceColOrder=1;        reduceColOrder=1;
1573      } else {     } else {
1574          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1575      }     }
1576      // generate matrix:     // generate matrix:
1577        
1578      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1579      checkFinleyError();     checkFinleyError();
1580      Paso_SystemMatrix* fsystemMatrix;     Paso_SystemMatrix* fsystemMatrix;
1581      int trilinos = 0;     int trilinos = 0;
1582      if (trilinos) {     if (trilinos) {
1583  #ifdef TRILINOS  #ifdef TRILINOS
1584        /* Allocation Epetra_VrbMatrix here */        /* Allocation Epetra_VrbMatrix here */
1585  #endif  #endif
1586      }     }
1587      else {     else {
1588        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1589      }     }
1590      checkPasoError();     checkPasoError();
1591      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1592      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1593  }  }
1594    
1595    //
1596  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1597    //
1598  TransportProblemAdapter MeshAdapter::newTransportProblem(  TransportProblemAdapter MeshAdapter::newTransportProblem(
1599                        const double theta,                                                           const double theta,
1600                        const double dt_max,                                                           const int blocksize,
1601                        const int blocksize,                                                           const escript::FunctionSpace& functionspace,
1602                        const escript::FunctionSpace& functionspace,                                                           const int type) const
1603                        const int type) const  {
1604  {     int reduceOrder=0;
1605      int reduceOrder=0;     // is the domain right?
1606      // is the domain right?     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1607      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());     if (domain!=*this)
1608      if (domain!=*this)        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1609            throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");     // is the function space type right
1610      // is the function space type right     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1611      if (functionspace.getTypeCode()==DegreesOfFreedom) {        reduceOrder=0;
1612          reduceOrder=0;     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1613      } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {        reduceOrder=1;
1614          reduceOrder=1;     } else {
1615      } else {        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1616          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");     }
1617      }     // generate matrix:
1618      // generate matrix:  
1619           Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1620      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);     checkFinleyError();
1621      checkFinleyError();     Paso_FCTransportProblem* transportProblem;
1622      Paso_FCTransportProblem* transportProblem;     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1623      transportProblem=Paso_FCTransportProblem_alloc(theta,dt_max,fsystemMatrixPattern,blocksize);     checkPasoError();
1624      checkPasoError();     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1625      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
     return TransportProblemAdapter(transportProblem,theta,dt_max,blocksize,functionspace);  
1626  }  }
1627    
1628  //  //
# Line 1639  TransportProblemAdapter MeshAdapter::new Line 1634  TransportProblemAdapter MeshAdapter::new
1634  // 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:
1635  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1636  {  {
1637    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1638         case(Nodes):     case(Nodes):
1639         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1640         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1641            return false;     return false;
1642            break;     break;
1643         case(Elements):     case(Elements):
1644         case(FaceElements):     case(FaceElements):
1645         case(Points):     case(Points):
1646         case(ContactElementsZero):     case(ContactElementsZero):
1647         case(ContactElementsOne):     case(ContactElementsOne):
1648         case(ReducedElements):     case(ReducedElements):
1649         case(ReducedFaceElements):     case(ReducedFaceElements):
1650         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1651         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1652            return true;     return true;
1653            break;     break;
1654         default:     default:
1655            stringstream temp;        stringstream temp;
1656            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;
1657            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1658            break;        break;
1659    }     }
1660    checkFinleyError();     checkFinleyError();
1661    return false;     return false;
1662  }  }
1663    
1664  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1665  {  {
1666    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1667       case(Nodes):     case(Nodes):
1668          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1669             case(Nodes):     case(Nodes):
1670             case(ReducedNodes):     case(ReducedNodes):
1671             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1672             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1673             case(Elements):     case(Elements):
1674             case(ReducedElements):     case(ReducedElements):
1675             case(FaceElements):     case(FaceElements):
1676             case(ReducedFaceElements):     case(ReducedFaceElements):
1677             case(Points):     case(Points):
1678             case(ContactElementsZero):     case(ContactElementsZero):
1679             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1680             case(ContactElementsOne):     case(ContactElementsOne):
1681             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1682                 return true;     return true;
1683             default:     default:
1684                 stringstream temp;        stringstream temp;
1685                 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;
1686                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1687          }     }
1688          break;     break;
1689       case(ReducedNodes):     case(ReducedNodes):
1690          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1691             case(ReducedNodes):     case(ReducedNodes):
1692             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1693             case(Elements):     case(Elements):
1694             case(ReducedElements):     case(ReducedElements):
1695             case(FaceElements):     case(FaceElements):
1696             case(ReducedFaceElements):     case(ReducedFaceElements):
1697             case(Points):     case(Points):
1698             case(ContactElementsZero):     case(ContactElementsZero):
1699             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1700             case(ContactElementsOne):     case(ContactElementsOne):
1701             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1702                 return true;     return true;
1703            case(Nodes):     case(Nodes):
1704            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1705               return false;     return false;
1706             default:     default:
1707                 stringstream temp;        stringstream temp;
1708                 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;
1709                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1710          }     }
1711          break;     break;
1712       case(Elements):     case(Elements):
1713          if (functionSpaceType_target==Elements) {     if (functionSpaceType_target==Elements) {
1714             return true;        return true;
1715          } else if (functionSpaceType_target==ReducedElements) {     } else if (functionSpaceType_target==ReducedElements) {
1716             return true;        return true;
1717          } else {     } else {
1718             return false;        return false;
1719          }     }
1720       case(ReducedElements):     case(ReducedElements):
1721          if (functionSpaceType_target==ReducedElements) {     if (functionSpaceType_target==ReducedElements) {
1722             return true;        return true;
1723          } else {     } else {
1724             return false;        return false;
1725          }     }
1726       case(FaceElements):     case(FaceElements):
1727          if (functionSpaceType_target==FaceElements) {     if (functionSpaceType_target==FaceElements) {
1728             return true;        return true;
1729          } else if (functionSpaceType_target==ReducedFaceElements) {     } else if (functionSpaceType_target==ReducedFaceElements) {
1730             return true;        return true;
1731          } else {     } else {
1732             return false;        return false;
1733          }     }
1734       case(ReducedFaceElements):     case(ReducedFaceElements):
1735          if (functionSpaceType_target==ReducedFaceElements) {     if (functionSpaceType_target==ReducedFaceElements) {
1736             return true;        return true;
1737          } else {     } else {
1738             return false;        return false;
1739          }     }
1740       case(Points):     case(Points):
1741          if (functionSpaceType_target==Points) {     if (functionSpaceType_target==Points) {
1742             return true;        return true;
1743          } else {     } else {
1744             return false;        return false;
1745          }     }
1746       case(ContactElementsZero):     case(ContactElementsZero):
1747       case(ContactElementsOne):     case(ContactElementsOne):
1748          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1749             return true;        return true;
1750          } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1751             return true;        return true;
1752          } else {     } else {
1753             return false;        return false;
1754          }     }
1755       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1756       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1757          if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1758             return true;        return true;
1759          } else {     } else {
1760             return false;        return false;
1761          }     }
1762       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1763          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1764             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1765             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1766             case(Nodes):     case(Nodes):
1767             case(ReducedNodes):     case(ReducedNodes):
1768             case(Elements):     case(Elements):
1769             case(ReducedElements):     case(ReducedElements):
1770             case(Points):     case(Points):
1771             case(FaceElements):     case(FaceElements):
1772             case(ReducedFaceElements):     case(ReducedFaceElements):
1773             case(ContactElementsZero):     case(ContactElementsZero):
1774             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1775             case(ContactElementsOne):     case(ContactElementsOne):
1776             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1777                return true;     return true;
1778             default:     default:
1779               stringstream temp;        stringstream temp;
1780               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;
1781               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1782          }     }
1783          break;     break;
1784       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1785         switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1786            case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1787            case(ReducedNodes):     case(ReducedNodes):
1788            case(Elements):     case(Elements):
1789            case(ReducedElements):     case(ReducedElements):
1790            case(FaceElements):     case(FaceElements):
1791            case(ReducedFaceElements):     case(ReducedFaceElements):
1792            case(Points):     case(Points):
1793            case(ContactElementsZero):     case(ContactElementsZero):
1794            case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1795            case(ContactElementsOne):     case(ContactElementsOne):
1796            case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1797                return true;     return true;
1798            case(Nodes):     case(Nodes):
1799            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1800               return false;     return false;
1801            default:     default:
1802               stringstream temp;        stringstream temp;
1803               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;
1804               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1805         }     }
1806         break;     break;
1807       default:     default:
1808          stringstream temp;        stringstream temp;
1809          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;
1810          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1811          break;        break;
1812    }     }
1813    checkFinleyError();     checkFinleyError();
1814    return false;     return false;
1815  }  }
1816    
1817  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
1818  {  {
1819      return false;     return false;
1820  }  }
1821    
1822  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1823  {  {
1824    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1825    if (temp!=0) {     if (temp!=0) {
1826      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1827    } else {     } else {
1828      return false;        return false;
1829    }     }
1830  }  }
1831    
1832  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1833  {  {
1834    return !(operator==(other));     return !(operator==(other));
1835  }  }
1836    
1837  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
1838    {
1839       Finley_Mesh* mesh=m_finleyMesh.get();
1840       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
1841       checkPasoError();
1842       return out;
1843    }
1844    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1845  {  {
1846     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
1847       int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
1848     checkPasoError();     checkPasoError();
1849     return out;     return out;
1850  }  }
1851    
1852  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1853  {  {
1854    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1855  }  }
1856    
1857  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1858  {  {
1859    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1860  }  }
1861    
1862  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1863  {  {
1864    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
1865  }  }
1866    
1867  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1868  {  {
1869    int *out=0,i;     int *out = NULL;
1870    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1871    switch (functionSpaceType) {     switch (functionSpaceType) {
1872      case(Nodes):     case(Nodes):
1873        out=mesh->Nodes->Id;     out=mesh->Nodes->Id;
1874        break;     break;
1875      case(ReducedNodes):     case(ReducedNodes):
1876        out=mesh->Nodes->reducedNodesId;     out=mesh->Nodes->reducedNodesId;
1877        break;     break;
1878      case(Elements):     case(Elements):
1879        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1880        break;     break;
1881      case(ReducedElements):     case(ReducedElements):
1882        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1883        break;     break;
1884      case(FaceElements):     case(FaceElements):
1885        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1886        break;     break;
1887      case(ReducedFaceElements):     case(ReducedFaceElements):
1888        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1889        break;     break;
1890      case(Points):     case(Points):
1891        out=mesh->Points->Id;     out=mesh->Points->Id;
1892        break;     break;
1893      case(ContactElementsZero):     case(ContactElementsZero):
1894        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1895        break;     break;
1896      case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1897        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1898        break;     break;
1899      case(ContactElementsOne):     case(ContactElementsOne):
1900        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1901        break;     break;
1902      case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1903        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1904        break;     break;
1905      case(DegreesOfFreedom):     case(DegreesOfFreedom):
1906        out=mesh->Nodes->degreesOfFreedomId;     out=mesh->Nodes->degreesOfFreedomId;
1907        break;     break;
1908      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1909        out=mesh->Nodes->reducedDegreesOfFreedomId;     out=mesh->Nodes->reducedDegreesOfFreedomId;
1910        break;     break;
1911      default:     default:
1912        stringstream temp;        stringstream temp;
1913        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1914        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1915        break;        break;
1916    }     }
1917    return out;     return out;
1918  }  }
1919  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1920  {  {
1921    int out=0;     int out=0;
1922    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1923    switch (functionSpaceType) {     switch (functionSpaceType) {
1924    case(Nodes):     case(Nodes):
1925      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
1926      break;     break;
1927    case(ReducedNodes):     case(ReducedNodes):
1928      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1929      break;     break;
1930    case(Elements):     case(Elements):
1931      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1932      break;     break;
1933    case(ReducedElements):     case(ReducedElements):
1934      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1935      break;     break;
1936    case(FaceElements):     case(FaceElements):
1937      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1938      break;     break;
1939    case(ReducedFaceElements):     case(ReducedFaceElements):
1940      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1941      break;     break;
1942    case(Points):     case(Points):
1943      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
1944      break;     break;
1945    case(ContactElementsZero):     case(ContactElementsZero):
1946      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1947      break;     break;
1948    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1949      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1950      break;     break;
1951    case(ContactElementsOne):     case(ContactElementsOne):
1952      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1953      break;     break;
1954    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1955      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1956      break;     break;
1957    case(DegreesOfFreedom):     case(DegreesOfFreedom):
1958      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1959      break;     break;
1960    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1961      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1962      break;     break;
1963    default:     default:
1964      stringstream temp;        stringstream temp;
1965      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1966      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1967      break;        break;
1968    }     }
1969    return out;     return out;
1970  }  }
1971    
1972    
1973  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
1974  {  {
1975       Finley_Mesh* mesh=m_finleyMesh.get();
1976       escriptDataC tmp=mask.getDataC();
1977       switch(functionSpaceType) {
1978       case(Nodes):
1979       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1980       break;
1981       case(ReducedNodes):
1982       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1983       break;
1984       case(DegreesOfFreedom):
1985       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1986       break;
1987       case(ReducedDegreesOfFreedom):
1988       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1989       break;
1990       case(Elements):
1991       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1992       break;
1993       case(ReducedElements):
1994       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1995       break;
1996       case(FaceElements):
1997       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1998       break;
1999       case(ReducedFaceElements):
2000       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2001       break;
2002       case(Points):
2003       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2004       break;
2005       case(ContactElementsZero):
2006       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2007       break;
2008       case(ReducedContactElementsZero):
2009       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2010       break;
2011       case(ContactElementsOne):
2012       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2013       break;
2014       case(ReducedContactElementsOne):
2015       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2016       break;
2017       default:
2018          stringstream temp;
2019          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2020          throw FinleyAdapterException(temp.str());
2021       }
2022       checkFinleyError();
2023       return;
2024    }
2025    
2026    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2027    {
2028       Finley_Mesh* mesh=m_finleyMesh.get();
2029       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2030       checkPasoError();
2031       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2032    }
2033    
2034    int MeshAdapter::getTag(const std::string& name) const
2035    {
2036       Finley_Mesh* mesh=m_finleyMesh.get();
2037       int tag=0;
2038       tag=Finley_Mesh_getTag(mesh, name.c_str());
2039       checkPasoError();
2040       // throwStandardException("MeshAdapter::getTag is not implemented.");
2041       return tag;
2042    }
2043    
2044    bool MeshAdapter::isValidTagName(const std::string& name) const
2045    {
2046       Finley_Mesh* mesh=m_finleyMesh.get();
2047       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2048    }
2049    
2050    std::string MeshAdapter::showTagNames() const
2051    {
2052       stringstream temp;
2053       Finley_Mesh* mesh=m_finleyMesh.get();
2054       Finley_TagMap* tag_map=mesh->TagMap;
2055       while (tag_map) {
2056          temp << tag_map->name;
2057          tag_map=tag_map->next;
2058          if (tag_map) temp << ", ";
2059       }
2060       return temp.str();
2061    }
2062    
2063    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2064    {
2065    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2066    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2067    switch(functionSpaceType) {    switch(functionSpaceCode) {
2068         case(Nodes):     case(Nodes):
2069            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2070            break;            break;
2071         case(ReducedNodes):     case(ReducedNodes):
2072            throw FinleyAdapterException("Error - ReducedNodes does not support tags");            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2073            break;            break;
2074         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2075            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2076            break;            break;
2077         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2078            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2079            break;            break;
2080         case(Elements):     case(Elements):
2081            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2082            break;            numTags=mesh->Elements->numTagsInUse;
2083         case(ReducedElements):            break;
2084            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(FaceElements):
2085            break;     case(ReducedFaceElements):
2086         case(FaceElements):            numTags=mesh->FaceElements->numTagsInUse;
2087            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);            break;
2088            break;     case(Points):
2089         case(ReducedFaceElements):            numTags=mesh->Points->numTagsInUse;
2090            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);            break;
2091       case(ContactElementsZero):
2092       case(ReducedContactElementsZero):
2093       case(ContactElementsOne):
2094       case(ReducedContactElementsOne):
2095              numTags=mesh->ContactElements->numTagsInUse;
2096            break;            break;
2097         case(Points):     default:
2098            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);        stringstream temp;
2099          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2100          throw FinleyAdapterException(temp.str());
2101      }
2102      return numTags;
2103    }
2104    
2105    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2106    {
2107      Finley_Mesh* mesh=m_finleyMesh.get();
2108      index_t* tags=NULL;
2109      switch(functionSpaceCode) {
2110       case(Nodes):
2111              tags=mesh->Nodes->tagsInUse;
2112            break;            break;
2113         case(ContactElementsZero):     case(ReducedNodes):
2114            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2115            break;            break;
2116         case(ReducedContactElementsZero):     case(DegreesOfFreedom):
2117            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2118            break;            break;
2119         case(ContactElementsOne):     case(ReducedDegreesOfFreedom):
2120            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2121            break;            break;
2122         case(ReducedContactElementsOne):     case(Elements):
2123            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2124              tags=mesh->Elements->tagsInUse;
2125              break;
2126       case(FaceElements):
2127       case(ReducedFaceElements):
2128              tags=mesh->FaceElements->tagsInUse;
2129              break;
2130       case(Points):
2131              tags=mesh->Points->tagsInUse;
2132              break;
2133       case(ContactElementsZero):
2134       case(ReducedContactElementsZero):
2135       case(ContactElementsOne):
2136       case(ReducedContactElementsOne):
2137              tags=mesh->ContactElements->tagsInUse;
2138            break;            break;
2139         default:     default:
2140            stringstream temp;        stringstream temp;
2141            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2142            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2143    }    }
2144    checkFinleyError();    return tags;
   return;  
2145  }  }
2146    
 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.");  
 }  
2147    
2148  int MeshAdapter::getTag(const std::string& name) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2149  {  {
2150    Finley_Mesh* mesh=m_finleyMesh.get();    switch(functionSpaceCode) {
2151    int tag=0;     case(Nodes):
2152    tag=Finley_Mesh_getTag(mesh, name.c_str());     case(Elements):
2153    checkPasoError();     case(ReducedElements):
2154    // throwStandardException("MeshAdapter::getTag is not implemented.");     case(FaceElements):
2155    return tag;     case(ReducedFaceElements):
2156  }     case(Points):
2157       case(ContactElementsZero):
2158  bool MeshAdapter::isValidTagName(const std::string& name) const     case(ReducedContactElementsZero):
2159  {     case(ContactElementsOne):
2160    Finley_Mesh* mesh=m_finleyMesh.get();     case(ReducedContactElementsOne):
2161    return Finley_Mesh_isValidTagName(mesh,name.c_str());            return true;
2162  }     case(ReducedNodes):
2163       case(DegreesOfFreedom):
2164  std::string MeshAdapter::showTagNames() const     case(ReducedDegreesOfFreedom):
2165  {        return false;
2166    stringstream temp;     default:
2167    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 << ", ";  
2168    }    }
   return temp.str();  
2169  }  }
2170    
2171    
2172  }  // end of namespace  }  // end of namespace

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