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

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revision 1388 by trankine, Fri Jan 11 07:45:58 2008 UTC revision 1632 by trankine, Sat Jul 12 07:17:50 2008 UTC
# Line 24  extern "C" { Line 24  extern "C" {
24  }  }
25  #include <vector>  #include <vector>
26    
27    #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH  256
28    
29  using namespace std;  using namespace std;
30  using namespace escript;  using namespace escript;
31    
# 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 89  Finley_Mesh* MeshAdapter::getFinley_Mesh Line 91  Finley_Mesh* MeshAdapter::getFinley_Mesh
91    
92  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
93  {  {
94    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;
95    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
96    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
97    checkFinleyError();     checkFinleyError();
98    TMPMEMFREE(fName);     TMPMEMFREE(fName);
99  }  }
100    
101  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  void MeshAdapter::Print_Mesh_Info(const bool full=false) const
102  {  {
103    Finley_PrintMesh_Info(m_finleyMesh.get(), full);     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
104  }  }
105    
106  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const std::string& fileName) const
107  {  {
108  #ifdef USE_NETCDF  #ifdef USE_NETCDF
109     const NcDim* ncdims[12];     const NcDim* ncdims[12];
110     NcVar *ids, *data;     NcVar *ids;
111     int *int_ptr;     int *int_ptr;
112     Finley_Mesh *mesh = m_finleyMesh.get();     Finley_Mesh *mesh = m_finleyMesh.get();
113     Finley_TagMap* tag_map;     Finley_TagMap* tag_map;
# Line 121  void MeshAdapter::dump(const std::string Line 123  void MeshAdapter::dump(const std::string
123     int num_Elements_numNodes        = mesh->Elements->numNodes;     int num_Elements_numNodes        = mesh->Elements->numNodes;
124     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
125     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
126     char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank);  
127       // I don't think the strdup is needed since Paso_MPI_appendRankToFileName
128       // does it's own allocation.
129       // char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank);
130    
131       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
132                                                         mpi_size, mpi_rank);
133    
134     /* Figure out how much storage is required for tags */     /* Figure out how much storage is required for tags */
135     tag_map = mesh->TagMap;     tag_map = mesh->TagMap;
136     if (tag_map) {     if (tag_map) {
137       while (tag_map) {        while (tag_map) {
138      num_Tags++;           num_Tags++;
139          tag_map=tag_map->next;           tag_map=tag_map->next;
140       }        }
141     }     }
142    
143     // NetCDF error handler     // NetCDF error handler
# Line 138  void MeshAdapter::dump(const std::string Line 146  void MeshAdapter::dump(const std::string
146     NcFile dataFile(newFileName, NcFile::Replace);     NcFile dataFile(newFileName, NcFile::Replace);
147     // check if writing was successful     // check if writing was successful
148     if (!dataFile.is_valid())     if (!dataFile.is_valid())
149          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);
150    
151     // 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)
152     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
153          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);
154     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
155          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);
156     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)) )
157          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);
158     if (num_Elements>0)     if (num_Elements>0)
159        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
160          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);
161     if (num_FaceElements>0)     if (num_FaceElements>0)
162        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
163          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);
164     if (num_ContactElements>0)     if (num_ContactElements>0)
165        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
166          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);
167     if (num_Points>0)     if (num_Points>0)
168        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
169          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);
170     if (num_Elements>0)     if (num_Elements>0)
171        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
172          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);
173     if (num_FaceElements>0)     if (num_FaceElements>0)
174        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
175          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);
176     if (num_ContactElements>0)     if (num_ContactElements>0)
177        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
178          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);
179     if (num_Tags>0)     if (num_Tags>0)
180        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
181          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);
182    
183     // Attributes: MPI size, MPI rank, Name, order, reduced_order     // Attributes: MPI size, MPI rank, Name, order, reduced_order
184     if (!dataFile.add_att("mpi_size", mpi_size) )     if (!dataFile.add_att("mpi_size", mpi_size) )
185          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);
186     if (!dataFile.add_att("mpi_rank", mpi_rank) )     if (!dataFile.add_att("mpi_rank", mpi_rank) )
187          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);
188     if (!dataFile.add_att("Name",mesh->Name) )     if (!dataFile.add_att("Name",mesh->Name) )
189          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
190     if (!dataFile.add_att("numDim",numDim) )     if (!dataFile.add_att("numDim",numDim) )
191          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
192     if (!dataFile.add_att("order",mesh->order) )     if (!dataFile.add_att("order",mesh->order) )
193          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
194     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
195          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);
196     if (!dataFile.add_att("numNodes",numNodes) )     if (!dataFile.add_att("numNodes",numNodes) )
197          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
198     if (!dataFile.add_att("num_Elements",num_Elements) )     if (!dataFile.add_att("num_Elements",num_Elements) )
199          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);
200     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
201          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);
202     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
203          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);
204     if (!dataFile.add_att("num_Points",num_Points) )     if (!dataFile.add_att("num_Points",num_Points) )
205          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);
206     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
207          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);
208     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
209          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);
210     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
211          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);
212     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
213        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);
214     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 225  void MeshAdapter::dump(const std::string
225     // 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)
226     if (numNodes>0) {     if (numNodes>0) {
227    
228     // Nodes Id        // Nodes Id
229     if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
230          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);
231     int_ptr = &mesh->Nodes->Id[0];        int_ptr = &mesh->Nodes->Id[0];
232     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
233          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);
234    
235     // Nodes Tag        // Nodes Tag
236     if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
237          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);
238     int_ptr = &mesh->Nodes->Tag[0];        int_ptr = &mesh->Nodes->Tag[0];
239     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
240          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);
241    
242     // Nodes gDOF        // Nodes gDOF
243     if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
244          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);
245     int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
246     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
247          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);
248    
249     // Nodes global node index        // Nodes global node index
250     if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
251          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);
252     int_ptr = &mesh->Nodes->globalNodesIndex[0];        int_ptr = &mesh->Nodes->globalNodesIndex[0];
253     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
254          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);
255    
256     // Nodes grDof        // Nodes grDof
257     if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
258          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);
259     int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
260     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
261          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);
262    
263     // Nodes grNI        // Nodes grNI
264     if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
265          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);
266     int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
267     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
268          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);
269    
270     // Nodes Coordinates        // Nodes Coordinates
271     if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
272          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);
273     if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
274          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);
275    
276     // Nodes degreesOfFreedomDistribution        // Nodes degreesOfFreedomDistribution
277     if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
278          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);
279     int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
280     if (! (ids->put(int_ptr, mpi_size+1)) )        if (! (ids->put(int_ptr, mpi_size+1)) )
281          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);
282    
283     }     }
284    
# Line 278  void MeshAdapter::dump(const std::string Line 286  void MeshAdapter::dump(const std::string
286    
287     if (num_Elements>0) {     if (num_Elements>0) {
288    
289       // Temp storage to gather node IDs        // Temp storage to gather node IDs
290       int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);        int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);
291    
292       // Elements_Id        // Elements_Id
293       if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
294          throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
295       int_ptr = &mesh->Elements->Id[0];        int_ptr = &mesh->Elements->Id[0];
296       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
297          throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
298    
299       // Elements_Tag        // Elements_Tag
300       if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
301          throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
302       int_ptr = &mesh->Elements->Tag[0];        int_ptr = &mesh->Elements->Tag[0];
303       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
304          throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
305    
306       // Elements_Owner        // Elements_Owner
307       if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
308          throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
309       int_ptr = &mesh->Elements->Owner[0];        int_ptr = &mesh->Elements->Owner[0];
310       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
311          throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
312    
313       // Elements_Color        // Elements_Color
314       if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
315          throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
316       int_ptr = &mesh->Elements->Color[0];        int_ptr = &mesh->Elements->Color[0];
317       if (! (ids->put(int_ptr, num_Elements)) )        if (! (ids->put(int_ptr, num_Elements)) )
318          throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
319    
320       // Elements_Nodes        // Elements_Nodes
321       for (int i=0; i<num_Elements; i++)        for (int i=0; i<num_Elements; i++)
322         for (int j=0; j<num_Elements_numNodes; j++)           for (int j=0; j<num_Elements_numNodes; j++)
323           Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]];              Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]];
324       if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
325          throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
326       if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) )        if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) )
327          throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
328    
329       TMPMEMFREE(Elements_Nodes);        TMPMEMFREE(Elements_Nodes);
330    
331     }     }
332    
# Line 326  void MeshAdapter::dump(const std::string Line 334  void MeshAdapter::dump(const std::string
334    
335     if (num_FaceElements>0) {     if (num_FaceElements>0) {
336    
337       // Temp storage to gather node IDs        // Temp storage to gather node IDs
338       int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);        int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);
339    
340       // FaceElements_Id        // FaceElements_Id
341       if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
342          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
343       int_ptr = &mesh->FaceElements->Id[0];        int_ptr = &mesh->FaceElements->Id[0];
344       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
345          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
346    
347       // FaceElements_Tag        // FaceElements_Tag
348       if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
349          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
350       int_ptr = &mesh->FaceElements->Tag[0];        int_ptr = &mesh->FaceElements->Tag[0];
351       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
352          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
353    
354       // FaceElements_Owner        // FaceElements_Owner
355       if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
356          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
357       int_ptr = &mesh->FaceElements->Owner[0];        int_ptr = &mesh->FaceElements->Owner[0];
358       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
359          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
360    
361       // FaceElements_Color        // FaceElements_Color
362       if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
363          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
364       int_ptr = &mesh->FaceElements->Color[0];        int_ptr = &mesh->FaceElements->Color[0];
365       if (! (ids->put(int_ptr, num_FaceElements)) )        if (! (ids->put(int_ptr, num_FaceElements)) )
366          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
367    
368       // FaceElements_Nodes        // FaceElements_Nodes
369       for (int i=0; i<num_FaceElements; i++)        for (int i=0; i<num_FaceElements; i++)
370         for (int j=0; j<num_FaceElements_numNodes; j++)           for (int j=0; j<num_FaceElements_numNodes; j++)
371           FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]];              FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]];
372       if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
373          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
374       if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )        if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
375          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
376    
377       TMPMEMFREE(FaceElements_Nodes);        TMPMEMFREE(FaceElements_Nodes);
378    
379     }     }
380    
# Line 374  void MeshAdapter::dump(const std::string Line 382  void MeshAdapter::dump(const std::string
382    
383     if (num_ContactElements>0) {     if (num_ContactElements>0) {
384    
385       // Temp storage to gather node IDs        // Temp storage to gather node IDs
386       int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);        int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);
387    
388       // ContactElements_Id        // ContactElements_Id
389       if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
390          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
391       int_ptr = &mesh->ContactElements->Id[0];        int_ptr = &mesh->ContactElements->Id[0];
392       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
393          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
394    
395       // ContactElements_Tag        // ContactElements_Tag
396       if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
397          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
398       int_ptr = &mesh->ContactElements->Tag[0];        int_ptr = &mesh->ContactElements->Tag[0];
399       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
400          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
401    
402       // ContactElements_Owner        // ContactElements_Owner
403       if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
404          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
405       int_ptr = &mesh->ContactElements->Owner[0];        int_ptr = &mesh->ContactElements->Owner[0];
406       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
407          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
408    
409       // ContactElements_Color        // ContactElements_Color
410       if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
411          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
412       int_ptr = &mesh->ContactElements->Color[0];        int_ptr = &mesh->ContactElements->Color[0];
413       if (! (ids->put(int_ptr, num_ContactElements)) )        if (! (ids->put(int_ptr, num_ContactElements)) )
414          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
415    
416       // ContactElements_Nodes        // ContactElements_Nodes
417       for (int i=0; i<num_ContactElements; i++)        for (int i=0; i<num_ContactElements; i++)
418         for (int j=0; j<num_ContactElements_numNodes; j++)           for (int j=0; j<num_ContactElements_numNodes; j++)
419           ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]];              ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]];
420       if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
421          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
422       if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )        if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
423          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
424    
425       TMPMEMFREE(ContactElements_Nodes);        TMPMEMFREE(ContactElements_Nodes);
426    
427     }     }
428    
# Line 422  void MeshAdapter::dump(const std::string Line 430  void MeshAdapter::dump(const std::string
430    
431     if (num_Points>0) {     if (num_Points>0) {
432    
433       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");
434    
435       // Temp storage to gather node IDs        // Temp storage to gather node IDs
436       int *Points_Nodes = TMPMEMALLOC(num_Points,int);        int *Points_Nodes = TMPMEMALLOC(num_Points,int);
437    
438       // Points_Id        // Points_Id
439       if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
440          throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Id to netCDF file failed: " + *newFileName);
441       int_ptr = &mesh->Points->Id[0];        int_ptr = &mesh->Points->Id[0];
442       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
443          throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Id to netCDF buffer failed: " + *newFileName);
444    
445       // Points_Tag        // Points_Tag
446       if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
447          throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Tag to netCDF file failed: " + *newFileName);
448       int_ptr = &mesh->Points->Tag[0];        int_ptr = &mesh->Points->Tag[0];
449       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
450          throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Tag to netCDF buffer failed: " + *newFileName);
451    
452       // Points_Owner        // Points_Owner
453       if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
454          throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Owner to netCDF file failed: " + *newFileName);
455       int_ptr = &mesh->Points->Owner[0];        int_ptr = &mesh->Points->Owner[0];
456       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
457          throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Owner to netCDF buffer failed: " + *newFileName);
458    
459       // Points_Color        // Points_Color
460       if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
461          throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Color to netCDF file failed: " + *newFileName);
462       int_ptr = &mesh->Points->Color[0];        int_ptr = &mesh->Points->Color[0];
463       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
464          throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Color to netCDF buffer failed: " + *newFileName);
465    
466       // Points_Nodes        // Points_Nodes
467       // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
468       for (int i=0; i<num_Points; i++)        for (int i=0; i<num_Points; i++)
469         Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];           Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];
470       if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
471          throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
472       if (! (ids->put(&(Points_Nodes[0]), num_Points)) )        if (! (ids->put(&(Points_Nodes[0]), num_Points)) )
473          throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
474    
475       TMPMEMFREE(Points_Nodes);        TMPMEMFREE(Points_Nodes);
476    
477     }     }
478    
# Line 472  void MeshAdapter::dump(const std::string Line 480  void MeshAdapter::dump(const std::string
480    
481     if (num_Tags>0) {     if (num_Tags>0) {
482    
483       // Temp storage to gather node IDs        // Temp storage to gather node IDs
484       int *Tags_keys = TMPMEMALLOC(num_Tags, int);        int *Tags_keys = TMPMEMALLOC(num_Tags, int);
485       char name_temp[4096];        char name_temp[4096];
486    
487       /* Copy tag data into temp arrays */        /* Copy tag data into temp arrays */
488       tag_map = mesh->TagMap;        tag_map = mesh->TagMap;
489       if (tag_map) {        if (tag_map) {
490         int i = 0;           int i = 0;
491         while (tag_map) {           while (tag_map) {
492      Tags_keys[i++] = tag_map->tag_key;              Tags_keys[i++] = tag_map->tag_key;
493          tag_map=tag_map->next;              tag_map=tag_map->next;
494         }           }
495       }        }
496    
497       // Tags_keys        // Tags_keys
498       if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )        if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
499          throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: appending Tags_keys to netCDF file failed: " + *newFileName);
500       int_ptr = &Tags_keys[0];        int_ptr = &Tags_keys[0];
501       if (! (ids->put(int_ptr, num_Tags)) )        if (! (ids->put(int_ptr, num_Tags)) )
502          throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Tags_keys to netCDF buffer failed: " + *newFileName);
503    
504       // Tags_names_*        // Tags_names_*
505       // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string        // This is an array of strings, it should be stored as an array but instead I have hacked in one attribute per string
506       // because the NetCDF manual doesn't tell how to do an array of strings        // because the NetCDF manual doesn't tell how to do an array of strings
507       tag_map = mesh->TagMap;        tag_map = mesh->TagMap;
508       if (tag_map) {        if (tag_map) {
509         int i = 0;           int i = 0;
510         while (tag_map) {           while (tag_map) {
511           sprintf(name_temp, "Tags_name_%d", i);              sprintf(name_temp, "Tags_name_%d", i);
512           if (!dataFile.add_att(name_temp, tag_map->name) )              if (!dataFile.add_att(name_temp, tag_map->name) )
513             throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);                 throw DataException("Error - MeshAdapter::dump: appending Tags_names_ to NetCDF file failed: " + *newFileName);
514           tag_map=tag_map->next;              tag_map=tag_map->next;
515       i++;              i++;
516         }           }
517       }        }
518    
519       TMPMEMFREE(Tags_keys);        TMPMEMFREE(Tags_keys);
520    
521     }     }
522    
# Line 522  void MeshAdapter::dump(const std::string Line 530  void MeshAdapter::dump(const std::string
530    
531  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
532  {  {
533    return "FinleyMesh";     return "FinleyMesh";
534  }  }
535    
536  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
537  {  {
538    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
539    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
540    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
541      return "Invalid function space type code.";        return "Invalid function space type code.";
542    } else {     } else {
543      return loc->second;        return loc->second;
544    }     }
545  }  }
546    
547  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
548  {  {
549    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
550    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
551    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
552  }  }
553    
554  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
555  {  {
556    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
557      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
558    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
559      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
560    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
561      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
562    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
563      (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
564    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
565      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
566    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
567      (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
568    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
569      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
570    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
571      (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
572    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
573      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
574    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
575      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
576    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
577      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
578    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
579      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
580    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
581      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
582  }  }
583    
584  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
585  {  {
586    return Nodes;     return Nodes;
587  }  }
588  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
589  {  {
590    return ReducedNodes;     return ReducedNodes;
591  }  }
592    
593  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
594  {  {
595    return Elements;     return Elements;
596  }  }
597  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
598  {  {
599    return ReducedElements;     return ReducedElements;
600  }  }
601    
602  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
603  {  {
604    return FaceElements;     return FaceElements;
605  }  }
606  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
607  {  {
608    return ReducedFaceElements;     return ReducedFaceElements;
609  }  }
610    
611  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
612  {  {
613    return ContactElementsZero;     return ContactElementsZero;
614  }  }
615  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
616  {  {
617    return ReducedContactElementsZero;     return ReducedContactElementsZero;
618  }  }
619    
620  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
621  {  {
622    return ContactElementsOne;     return ContactElementsOne;
623  }  }
624  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
625  {  {
626    return ReducedContactElementsOne;     return ReducedContactElementsOne;
627  }  }
628    
629  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
630  {  {
631    return DegreesOfFreedom;     return DegreesOfFreedom;
632  }  }
633    
634  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
635  {  {
636    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
637  }  }
638    
639  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
640  {  {
641    return Points;     return Points;
642  }  }
643    
644  //  //
# Line 638  int MeshAdapter::getDiracDeltaFunctionCo Line 646  int MeshAdapter::getDiracDeltaFunctionCo
646  //  //
647  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
648  {  {
649    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());
650    checkFinleyError();     checkFinleyError();
651    return numDim;     return numDim;
652  }  }
653    
654  //  //
# Line 653  pair<int,int> MeshAdapter::getDataShape( Line 661  pair<int,int> MeshAdapter::getDataShape(
661     int numSamples=0;     int numSamples=0;
662     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
663     switch (functionSpaceCode) {     switch (functionSpaceCode) {
664        case(Nodes):     case(Nodes):
665             numDataPointsPerSample=1;     numDataPointsPerSample=1;
666             numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
667             break;     break;
668        case(ReducedNodes):     case(ReducedNodes):
669             numDataPointsPerSample=1;     numDataPointsPerSample=1;
670             numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
671             break;     break;
672        case(Elements):     case(Elements):
673             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
674               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
675               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
676             }     }
677             break;     break;
678        case(ReducedElements):     case(ReducedElements):
679             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
680               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
681               numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
682             }     }
683             break;     break;
684        case(FaceElements):     case(FaceElements):
685             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
686                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
687                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
688             }     }
689             break;     break;
690        case(ReducedFaceElements):     case(ReducedFaceElements):
691             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
692                  numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
693                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
694             }     }
695             break;     break;
696        case(Points):     case(Points):
697             if (mesh->Points!=NULL) {     if (mesh->Points!=NULL) {
698               numDataPointsPerSample=1;        numDataPointsPerSample=1;
699               numSamples=mesh->Points->numElements;        numSamples=mesh->Points->numElements;
700             }     }
701             break;     break;
702        case(ContactElementsZero):     case(ContactElementsZero):
703             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
704               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
705               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
706             }     }
707             break;     break;
708        case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
709             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
710               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
711               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
712             }     }
713             break;     break;
714        case(ContactElementsOne):     case(ContactElementsOne):
715             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
716               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
717               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
718             }     }
719             break;     break;
720        case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
721             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
722               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
723               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
724             }     }
725             break;     break;
726        case(DegreesOfFreedom):     case(DegreesOfFreedom):
727             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
728               numDataPointsPerSample=1;        numDataPointsPerSample=1;
729               numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
730             }     }
731             break;     break;
732        case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
733             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
734               numDataPointsPerSample=1;        numDataPointsPerSample=1;
735               numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
736             }     }
737             break;     break;
738        default:     default:
739          stringstream temp;        stringstream temp;
740          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
741          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
742          break;        break;
743        }     }
744        return pair<int,int>(numDataPointsPerSample,numSamples);     return pair<int,int>(numDataPointsPerSample,numSamples);
745  }  }
746    
747  //  //
748  // 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:
749  //  //
750  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
751                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
752                       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,
753                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
754                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
755  {  {
756     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
757     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
# Line 770  void MeshAdapter::addPDEToSystem( Line 778  void MeshAdapter::addPDEToSystem(
778  }  }
779    
780  void  MeshAdapter::addPDEToLumpedSystem(  void  MeshAdapter::addPDEToLumpedSystem(
781                       escript::Data& mat,                                          escript::Data& mat,
782                       const escript::Data& D,                                          const escript::Data& D,
783                       const escript::Data& d) const                                          const escript::Data& d) const
784  {  {
785     escriptDataC _mat=mat.getDataC();     escriptDataC _mat=mat.getDataC();
786     escriptDataC _D=D.getDataC();     escriptDataC _D=D.getDataC();
# Line 813  void MeshAdapter::addPDEToRHS( escript:: Line 821  void MeshAdapter::addPDEToRHS( escript::
821  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
822  //  //
823  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
824                       TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
825                       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,
826                       const escript::Data& d, const escript::Data& y,                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
827                       const escript::Data& d_contact,const escript::Data& y_contact) const                                             const escript::Data& d, const escript::Data& y,
828                                               const escript::Data& d_contact,const escript::Data& y_contact) const
829  {  {
830     DataArrayView::ShapeType shape;     DataArrayView::ShapeType shape;
831     source.expand();     source.expand();
    escript:: Data tmp(0.0,M.getDataPointShape(),tp.getFunctionSpace(),true);  
832     escriptDataC _source=source.getDataC();     escriptDataC _source=source.getDataC();
    escriptDataC _tmp=tmp.getDataC();  
833     escriptDataC _M=M.getDataC();     escriptDataC _M=M.getDataC();
834     escriptDataC _A=A.getDataC();     escriptDataC _A=A.getDataC();
835     escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
# Line 837  void MeshAdapter::addPDEToTransportProbl Line 844  void MeshAdapter::addPDEToTransportProbl
844    
845     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
846     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];  
847    
848     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 );
849     checkFinleyError();     checkFinleyError();
850    
851     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 );
852     checkFinleyError();     checkFinleyError();
853    
854     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 863  void MeshAdapter::addPDEToTransportProbl
863  //  //
864  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
865  {  {
866    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());
867    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
868    if (inDomain!=*this)       if (inDomain!=*this)  
869      throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
870    if (targetDomain!=*this)     if (targetDomain!=*this)
871      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
872    
873    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
874    escriptDataC _target=target.getDataC();     escriptDataC _target=target.getDataC();
875    escriptDataC _in=in.getDataC();     escriptDataC _in=in.getDataC();
876    switch(in.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
877       case(Nodes):     case(Nodes):
878          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
879             case(Nodes):     case(Nodes):
880             case(ReducedNodes):     case(ReducedNodes):
881             case(DegreesOfFreedom):     case(DegreesOfFreedom):
882             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
883                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
884                 break;     break;
885             case(Elements):     case(Elements):
886             case(ReducedElements):     case(ReducedElements):
887                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
888                 break;     break;
889             case(FaceElements):     case(FaceElements):
890             case(ReducedFaceElements):     case(ReducedFaceElements):
891                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
892                 break;     break;
893             case(Points):     case(Points):
894                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
895                 break;     break;
896             case(ContactElementsZero):     case(ContactElementsZero):
897             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
898                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
899                 break;     break;
900             case(ContactElementsOne):     case(ContactElementsOne):
901             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
902                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
903                 break;     break;
904             default:     default:
905                 stringstream temp;        stringstream temp;
906                 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();
907                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
908                 break;        break;
909          }     }
910          break;     break;
911       case(ReducedNodes):     case(ReducedNodes):
912          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
913             case(Nodes):     case(Nodes):
914             case(ReducedNodes):     case(ReducedNodes):
915             case(DegreesOfFreedom):     case(DegreesOfFreedom):
916             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
917                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
918                 break;     break;
919             case(Elements):     case(Elements):
920             case(ReducedElements):     case(ReducedElements):
921                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
922                 break;     break;
923             case(FaceElements):     case(FaceElements):
924             case(ReducedFaceElements):     case(ReducedFaceElements):
925                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
926                 break;     break;
927             case(Points):     case(Points):
928                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
929                 break;     break;
930             case(ContactElementsZero):     case(ContactElementsZero):
931             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
932                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
933                 break;     break;
934             case(ContactElementsOne):     case(ContactElementsOne):
935             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
936                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
937                 break;     break;
938             default:     default:
939                 stringstream temp;        stringstream temp;
940                 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();
941                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
942                 break;        break;
943          }     }
944          break;     break;
945       case(Elements):     case(Elements):
946          if (target.getFunctionSpace().getTypeCode()==Elements) {     if (target.getFunctionSpace().getTypeCode()==Elements) {
947             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
948          } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
949             Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
950          } else {     } else {
951             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
952          }     }
953          break;     break;
954       case(ReducedElements):     case(ReducedElements):
955          if (target.getFunctionSpace().getTypeCode()==ReducedElements) {     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
956             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
957          } else {     } else {
958             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.");
959          }     }
960          break;     break;
961       case(FaceElements):     case(FaceElements):
962          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
963             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
964          } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
965             Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
966          } else {     } else {
967             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
968          }     }
969          break;     break;
970       case(ReducedFaceElements):     case(ReducedFaceElements):
971          if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
972             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
973          } else {     } else {
974             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.");
975         }     }
976         break;     break;
977       case(Points):     case(Points):
978          if (target.getFunctionSpace().getTypeCode()==Points) {     if (target.getFunctionSpace().getTypeCode()==Points) {
979             Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
980          } else {     } else {
981             throw FinleyAdapterException("Error - No interpolation with data on points possible.");        throw FinleyAdapterException("Error - No interpolation with data on points possible.");
982          }     }
983          break;     break;
984       case(ContactElementsZero):     case(ContactElementsZero):
985       case(ContactElementsOne):     case(ContactElementsOne):
986          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
987             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
988          } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
989             Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
990          } else {     } else {
991             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
992          }     }
993          break;     break;
994       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
995       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
996          if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
997             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
998          } else {     } else {
999             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.");
1000          }     }
1001          break;     break;
1002       case(DegreesOfFreedom):           case(DegreesOfFreedom):      
1003          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
1004             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1005             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1006                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1007                break;     break;
1008    
1009             case(Nodes):     case(Nodes):
1010             case(ReducedNodes):     case(ReducedNodes):
1011                if (getMPISize()>1) {     if (getMPISize()>1) {
1012                    escript::Data temp=escript::Data(in);        escript::Data temp=escript::Data(in);
1013                    temp.expand();        temp.expand();
1014                    escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1015                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1016                } else {     } else {
1017                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1018                }     }
1019                break;     break;
1020             case(Elements):     case(Elements):
1021             case(ReducedElements):     case(ReducedElements):
1022                if (getMPISize()>1) {     if (getMPISize()>1) {
1023                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1024                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1025                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1026                } else {     } else {
1027                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1028                }     }
1029                break;     break;
1030             case(FaceElements):     case(FaceElements):
1031             case(ReducedFaceElements):     case(ReducedFaceElements):
1032                if (getMPISize()>1) {     if (getMPISize()>1) {
1033                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1034                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1035                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1036    
1037                } else {     } else {
1038                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1039                }     }
1040                break;     break;
1041             case(Points):     case(Points):
1042                if (getMPISize()>1) {     if (getMPISize()>1) {
1043                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1044                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1045                } else {     } else {
1046                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1047                }     }
1048                break;     break;
1049             case(ContactElementsZero):     case(ContactElementsZero):
1050             case(ContactElementsOne):     case(ContactElementsOne):
1051             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1052             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1053                if (getMPISize()>1) {     if (getMPISize()>1) {
1054                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1055                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1056                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1057                } else {     } else {
1058                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1059                }     }
1060               break;     break;
1061             default:     default:
1062               stringstream temp;        stringstream temp;
1063               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();
1064               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1065               break;        break;
1066          }     }
1067          break;     break;
1068       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1069         switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
1070            case(Nodes):     case(Nodes):
1071               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.");
1072               break;     break;
1073            case(ReducedNodes):     case(ReducedNodes):
1074                if (getMPISize()>1) {     if (getMPISize()>1) {
1075                    escript::Data temp=escript::Data(in);        escript::Data temp=escript::Data(in);
1076                    temp.expand();        temp.expand();
1077                    escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1078                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1079                } else {     } else {
1080                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1081                }     }
1082                break;     break;
1083            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1084               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");
1085               break;     break;
1086            case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1087               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1088               break;     break;
1089            case(Elements):     case(Elements):
1090            case(ReducedElements):     case(ReducedElements):
1091                if (getMPISize()>1) {     if (getMPISize()>1) {
1092                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1093                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1094                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1095                } else {     } else {
1096                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1097               }     }
1098               break;     break;
1099            case(FaceElements):     case(FaceElements):
1100            case(ReducedFaceElements):     case(ReducedFaceElements):
1101                if (getMPISize()>1) {     if (getMPISize()>1) {
1102                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1103                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1104                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1105                } else {     } else {
1106                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1107                }     }
1108               break;     break;
1109            case(Points):     case(Points):
1110                if (getMPISize()>1) {     if (getMPISize()>1) {
1111                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1112                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1113                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1114                } else {     } else {
1115                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1116               }     }
1117               break;     break;
1118            case(ContactElementsZero):     case(ContactElementsZero):
1119            case(ContactElementsOne):     case(ContactElementsOne):
1120            case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1121            case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1122                if (getMPISize()>1) {     if (getMPISize()>1) {
1123                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1124                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1125                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1126                } else {     } else {
1127                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1128               }     }
1129               break;     break;
1130            default:     default:
1131               stringstream temp;        stringstream temp;
1132               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();
1133               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1134               break;        break;
1135         }     }
1136         break;     break;
1137       default:     default:
1138          stringstream temp;        stringstream temp;
1139          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();
1140          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1141          break;        break;
1142    }     }
1143    checkFinleyError();     checkFinleyError();
1144  }  }
1145    
1146  //  //
# Line 1151  void MeshAdapter::interpolateOnDomain(es Line 1148  void MeshAdapter::interpolateOnDomain(es
1148  //  //
1149  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1150  {  {
1151    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1152    if (argDomain!=*this)     if (argDomain!=*this)
1153       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1154    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1155    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1156    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1157       escriptDataC _arg=arg.getDataC();        escriptDataC _arg=arg.getDataC();
1158       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1159    } else {     } else {
1160       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1161       escriptDataC _tmp_data=tmp_data.getDataC();        escriptDataC _tmp_data=tmp_data.getDataC();
1162       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1163       // this is then interpolated onto arg:        // this is then interpolated onto arg:
1164       interpolateOnDomain(arg,tmp_data);        interpolateOnDomain(arg,tmp_data);
1165    }     }
1166    checkFinleyError();     checkFinleyError();
1167  }  }
1168    
1169  //  //
# Line 1174  void MeshAdapter::setToX(escript::Data& Line 1171  void MeshAdapter::setToX(escript::Data&
1171  //  //
1172  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1173  {  {
1174    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());
1175    if (normalDomain!=*this)     if (normalDomain!=*this)
1176       throw FinleyAdapterException("Error - Illegal domain of normal locations");        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1177    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1178    escriptDataC _normal=normal.getDataC();     escriptDataC _normal=normal.getDataC();
1179    switch(normal.getFunctionSpace().getTypeCode()) {     switch(normal.getFunctionSpace().getTypeCode()) {
1180      case(Nodes):     case(Nodes):
1181        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1182        break;     break;
1183      case(ReducedNodes):     case(ReducedNodes):
1184        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1185        break;     break;
1186      case(Elements):     case(Elements):
1187        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1188        break;     break;
1189      case(ReducedElements):     case(ReducedElements):
1190        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1191        break;     break;
1192      case (FaceElements):     case (FaceElements):
1193        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1194        break;     break;
1195      case (ReducedFaceElements):     case (ReducedFaceElements):
1196        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1197        break;     break;
1198      case(Points):     case(Points):
1199        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1200        break;     break;
1201      case (ContactElementsOne):     case (ContactElementsOne):
1202      case (ContactElementsZero):     case (ContactElementsZero):
1203        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1204        break;     break;
1205      case (ReducedContactElementsOne):     case (ReducedContactElementsOne):
1206      case (ReducedContactElementsZero):     case (ReducedContactElementsZero):
1207        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1208        break;     break;
1209      case(DegreesOfFreedom):     case(DegreesOfFreedom):
1210        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1211        break;     break;
1212      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1213        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1214        break;     break;
1215      default:     default:
1216        stringstream temp;        stringstream temp;
1217        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();
1218        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1219        break;        break;
1220    }     }
1221    checkFinleyError();     checkFinleyError();
1222  }  }
1223    
1224  //  //
# Line 1229  void MeshAdapter::setToNormal(escript::D Line 1226  void MeshAdapter::setToNormal(escript::D
1226  //  //
1227  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1228  {  {
1229    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
1230    if (targetDomain!=*this)     if (targetDomain!=*this)
1231       throw FinleyAdapterException("Error - Illegal domain of interpolation target");        throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1232    
1233    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1234  }  }
1235    
1236  //  //
# Line 1241  void MeshAdapter::interpolateACross(escr Line 1238  void MeshAdapter::interpolateACross(escr
1238  //  //
1239  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1240  {  {
1241    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1242    if (argDomain!=*this)     if (argDomain!=*this)
1243       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1244    
1245    double blocktimer_start = blocktimer_time();     double blocktimer_start = blocktimer_time();
1246    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1247    escriptDataC _temp;     escriptDataC _temp;
1248    escript::Data temp;     escript::Data temp;
1249    escriptDataC _arg=arg.getDataC();     escriptDataC _arg=arg.getDataC();
1250    switch(arg.getFunctionSpace().getTypeCode()) {     switch(arg.getFunctionSpace().getTypeCode()) {
1251       case(Nodes):     case(Nodes):
1252          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1253          _temp=temp.getDataC();     _temp=temp.getDataC();
1254          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1255          break;     break;
1256       case(ReducedNodes):     case(ReducedNodes):
1257          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1258          _temp=temp.getDataC();     _temp=temp.getDataC();
1259          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1260          break;     break;
1261       case(Elements):     case(Elements):
1262          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1263          break;     break;
1264       case(ReducedElements):     case(ReducedElements):
1265          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1266          break;     break;
1267       case(FaceElements):     case(FaceElements):
1268          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1269          break;     break;
1270       case(ReducedFaceElements):     case(ReducedFaceElements):
1271          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1272          break;     break;
1273       case(Points):     case(Points):
1274          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1275          break;     break;
1276       case(ContactElementsZero):     case(ContactElementsZero):
1277          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1278          break;     break;
1279       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1280          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1281          break;     break;
1282       case(ContactElementsOne):     case(ContactElementsOne):
1283          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1284          break;     break;
1285       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1286          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1287          break;     break;
1288       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1289          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1290          _temp=temp.getDataC();     _temp=temp.getDataC();
1291          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1292          break;     break;
1293       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1294          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1295          _temp=temp.getDataC();     _temp=temp.getDataC();
1296          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1297          break;     break;
1298       default:     default:
1299          stringstream temp;        stringstream temp;
1300          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();
1301          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1302          break;        break;
1303    }     }
1304    checkFinleyError();     checkFinleyError();
1305    blocktimer_increment("integrate()", blocktimer_start);     blocktimer_increment("integrate()", blocktimer_start);
1306  }  }
1307    
1308  //  //
# Line 1313  void MeshAdapter::setToIntegrals(std::ve Line 1310  void MeshAdapter::setToIntegrals(std::ve
1310  //  //
1311  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1312  {  {
1313    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1314    if (argDomain!=*this)     if (argDomain!=*this)
1315      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1316    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());
1317    if (gradDomain!=*this)     if (gradDomain!=*this)
1318       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1319    
1320    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1321    escriptDataC _grad=grad.getDataC();     escriptDataC _grad=grad.getDataC();
1322    escriptDataC nodeDataC;     escriptDataC nodeDataC;
1323    escript::Data temp;     escript::Data temp;
1324    if (getMPISize()>1) {     if (getMPISize()>1) {
1325        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1326          temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1327          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1328        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1329          temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1330          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1331        } else {        } else {
1332          nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1333        }        }
1334    } else {     } else {
1335       nodeDataC = arg.getDataC();        nodeDataC = arg.getDataC();
1336    }     }
1337    switch(grad.getFunctionSpace().getTypeCode()) {     switch(grad.getFunctionSpace().getTypeCode()) {
1338         case(Nodes):     case(Nodes):
1339            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1340            break;     break;
1341         case(ReducedNodes):     case(ReducedNodes):
1342            throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1343            break;     break;
1344         case(Elements):     case(Elements):
1345            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1346            break;     break;
1347         case(ReducedElements):     case(ReducedElements):
1348            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1349            break;     break;
1350         case(FaceElements):     case(FaceElements):
1351            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1352            break;     break;
1353         case(ReducedFaceElements):     case(ReducedFaceElements):
1354            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1355            break;     break;
1356         case(Points):     case(Points):
1357            throw FinleyAdapterException("Error - Gradient at points is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1358            break;     break;
1359         case(ContactElementsZero):     case(ContactElementsZero):
1360            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1361            break;     break;
1362         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1363            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1364            break;     break;
1365         case(ContactElementsOne):     case(ContactElementsOne):
1366            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1367            break;     break;
1368         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1369            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1370            break;     break;
1371         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1372            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1373            break;     break;
1374         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1375            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1376            break;     break;
1377         default:     default:
1378            stringstream temp;        stringstream temp;
1379            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();
1380            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1381            break;        break;
1382    }     }
1383    checkFinleyError();     checkFinleyError();
1384  }  }
1385    
1386  //  //
# Line 1391  void MeshAdapter::setToGradient(escript: Line 1388  void MeshAdapter::setToGradient(escript:
1388  //  //
1389  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1390  {  {
1391    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1392    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1393    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1394         case(Nodes):     case(Nodes):
1395            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1396            break;     break;
1397         case(ReducedNodes):     case(ReducedNodes):
1398            throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1399            break;     break;
1400         case(Elements):     case(Elements):
1401            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1402            break;     break;
1403         case(ReducedElements):     case(ReducedElements):
1404            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1405            break;     break;
1406         case(FaceElements):     case(FaceElements):
1407            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1408            break;     break;
1409         case(ReducedFaceElements):     case(ReducedFaceElements):
1410            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1411            break;     break;
1412         case(Points):     case(Points):
1413            throw FinleyAdapterException("Error - Size of point elements is not supported.");     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1414            break;     break;
1415         case(ContactElementsZero):     case(ContactElementsZero):
1416         case(ContactElementsOne):     case(ContactElementsOne):
1417            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1418            break;     break;
1419         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1420         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1421            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1422            break;     break;
1423         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1424            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1425            break;     break;
1426         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1427            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1428            break;     break;
1429         default:     default:
1430            stringstream temp;        stringstream temp;
1431            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();
1432            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1433            break;        break;
1434    }     }
1435    checkFinleyError();     checkFinleyError();
1436  }  }
1437    
1438  // sets the location of nodes:  // sets the location of nodes:
1439  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1440  {  {
1441    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1442    escriptDataC tmp;     escriptDataC tmp;
1443    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());
1444    if (newDomain!=*this)     if (newDomain!=*this)
1445       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1446    tmp = new_x.getDataC();     tmp = new_x.getDataC();
1447    Finley_Mesh_setCoordinates(mesh,&tmp);     Finley_Mesh_setCoordinates(mesh,&tmp);
1448    checkFinleyError();     checkFinleyError();
1449  }  }
1450    
1451  // saves a data array in openDX format:  // saves a data array in openDX format:
1452  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
1453  {  {
1454      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1455      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1456    /* win32 refactor */     /* win32 refactor */
1457    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1458    for(int i=0;i<num_data;i++)     for(int i=0;i<num_data;i++)
1459    {     {
1460      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1461    }     }
   
   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_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);  
1462    
1463      return;     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1464       escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1465    
1466       boost::python::list keys=arg.keys();
1467       for (int i=0;i<num_data;++i) {
1468          std::string n=boost::python::extract<std::string>(keys[i]);
1469          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1470          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1471             throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1472          data[i]=d.getDataC();
1473          ptr_data[i]= &(data[i]);
1474          if (n.length()>MAX_namelength-1) {
1475             strncpy(names[i],n.c_str(),MAX_namelength-1);
1476             names[i][MAX_namelength-1]='\0';
1477          } else {
1478             strcpy(names[i],n.c_str());
1479          }
1480       }
1481       Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1482       checkFinleyError();
1483    
1484       /* win32 refactor */
1485       TMPMEMFREE(data);
1486       TMPMEMFREE(ptr_data);
1487       for(int i=0;i<num_data;i++)
1488       {
1489          TMPMEMFREE(names[i]);
1490       }
1491       TMPMEMFREE(names);
1492    
1493       return;
1494  }  }
1495    
1496  // saves a data array in openVTK format:  // saves a data array in openVTK format:
1497  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const
1498  {  {
1499      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1500      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1501    /* win32 refactor */     /* win32 refactor */
1502    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1503    for(int i=0;i<num_data;i++)     for(int i=0;i<num_data;i++)
1504    {     {
1505      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1506    }     }
1507    
1508    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1509    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
1510    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
1511       boost::python::list keys=arg.keys();
1512      boost::python::list keys=arg.keys();     for (int i=0;i<num_data;++i) {
1513      for (int i=0;i<num_data;++i) {        std::string n=boost::python::extract<std::string>(keys[i]);
1514           std::string n=boost::python::extract<std::string>(keys[i]);        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1515           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);        if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1516           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1517               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");        data[i]=d.getDataC();
1518           data[i]=d.getDataC();        ptr_data[i]=&(data[i]);
1519           ptr_data[i]=&(data[i]);        if (n.length()>MAX_namelength-1) {
1520           c_names[i]=&(names[i][0]);           strncpy(names[i],n.c_str(),MAX_namelength-1);
1521           if (n.length()>MAX_namelength-1) {           names[i][MAX_namelength-1]='\0';
1522              strncpy(c_names[i],n.c_str(),MAX_namelength-1);        } else {
1523              c_names[i][MAX_namelength-1]='\0';           strcpy(names[i],n.c_str());
1524           } else {        }
1525              strcpy(c_names[i],n.c_str());     }
1526           }     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
     }  
     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
1527    
1528    checkFinleyError();     checkFinleyError();
1529    /* win32 refactor */     /* win32 refactor */
1530    TMPMEMFREE(c_names);     TMPMEMFREE(data);
1531    TMPMEMFREE(data);     TMPMEMFREE(ptr_data);
1532    TMPMEMFREE(ptr_data);     for(int i=0;i<num_data;i++)
1533    for(int i=0;i<num_data;i++)     {
1534    {        TMPMEMFREE(names[i]);
1535      TMPMEMFREE(names[i]);     }
1536    }     TMPMEMFREE(names);
   TMPMEMFREE(names);  
1537    
1538      return;     return;
1539  }  }
1540                                                                                                                                                                                                                                                                                                                                                
1541                                                                                                                                                                                                                                                                                                                                                
1542  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1543  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1544                        const int row_blocksize,                                                   const int row_blocksize,
1545                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1546                        const int column_blocksize,                                                   const int column_blocksize,
1547                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1548                        const int type) const                                                   const int type) const
1549  {  {
1550      int reduceRowOrder=0;     int reduceRowOrder=0;
1551      int reduceColOrder=0;     int reduceColOrder=0;
1552      // is the domain right?     // is the domain right?
1553      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());
1554      if (row_domain!=*this)     if (row_domain!=*this)
1555            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.");
1556      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());
1557      if (col_domain!=*this)     if (col_domain!=*this)
1558            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.");
1559      // is the function space type right     // is the function space type right
1560      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1561          reduceRowOrder=0;        reduceRowOrder=0;
1562      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1563          reduceRowOrder=1;        reduceRowOrder=1;
1564      } else {     } else {
1565          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1566      }     }
1567      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1568          reduceColOrder=0;        reduceColOrder=0;
1569      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1570          reduceColOrder=1;        reduceColOrder=1;
1571      } else {     } else {
1572          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1573      }     }
1574      // generate matrix:     // generate matrix:
1575        
1576      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1577      checkFinleyError();     checkFinleyError();
1578      Paso_SystemMatrix* fsystemMatrix;     Paso_SystemMatrix* fsystemMatrix;
1579      int trilinos = 0;     int trilinos = 0;
1580      if (trilinos) {     if (trilinos) {
1581  #ifdef TRILINOS  #ifdef TRILINOS
1582        /* Allocation Epetra_VrbMatrix here */        /* Allocation Epetra_VrbMatrix here */
1583  #endif  #endif
1584      }     }
1585      else {     else {
1586        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1587      }     }
1588      checkPasoError();     checkPasoError();
1589      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1590      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1591  }  }
1592  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1593  TransportProblemAdapter MeshAdapter::newTransportProblem(  TransportProblemAdapter MeshAdapter::newTransportProblem(
1594                        const double theta,                                                           const double theta,
1595                        const double dt_max,                                                           const int blocksize,
1596                        const int blocksize,                                                           const escript::FunctionSpace& functionspace,
1597                        const escript::FunctionSpace& functionspace,                                                           const int type) const
1598                        const int type) const  {
1599  {     int reduceOrder=0;
1600      int reduceOrder=0;     // is the domain right?
1601      // is the domain right?     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());
1602      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());     if (domain!=*this)
1603      if (domain!=*this)        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1604            throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");     // is the function space type right
1605      // is the function space type right     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1606      if (functionspace.getTypeCode()==DegreesOfFreedom) {        reduceOrder=0;
1607          reduceOrder=0;     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1608      } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {        reduceOrder=1;
1609          reduceOrder=1;     } else {
1610      } else {        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1611          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");     }
1612      }     // generate matrix:
1613      // generate matrix:  
1614           Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1615      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);     checkFinleyError();
1616      checkFinleyError();     Paso_FCTransportProblem* transportProblem;
1617      Paso_FCTransportProblem* transportProblem;     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1618      transportProblem=Paso_FCTransportProblem_alloc(theta,dt_max,fsystemMatrixPattern,blocksize);     checkPasoError();
1619      checkPasoError();     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1620      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
     return TransportProblemAdapter(transportProblem,theta,dt_max,blocksize,functionspace);  
1621  }  }
1622    
1623  //  //
# Line 1639  TransportProblemAdapter MeshAdapter::new Line 1629  TransportProblemAdapter MeshAdapter::new
1629  // 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:
1630  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1631  {  {
1632    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1633         case(Nodes):     case(Nodes):
1634         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1635         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1636            return false;     return false;
1637            break;     break;
1638         case(Elements):     case(Elements):
1639         case(FaceElements):     case(FaceElements):
1640         case(Points):     case(Points):
1641         case(ContactElementsZero):     case(ContactElementsZero):
1642         case(ContactElementsOne):     case(ContactElementsOne):
1643         case(ReducedElements):     case(ReducedElements):
1644         case(ReducedFaceElements):     case(ReducedFaceElements):
1645         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1646         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1647            return true;     return true;
1648            break;     break;
1649         default:     default:
1650            stringstream temp;        stringstream temp;
1651            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;
1652            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1653            break;        break;
1654    }     }
1655    checkFinleyError();     checkFinleyError();
1656    return false;     return false;
1657  }  }
1658    
1659  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1660  {  {
1661    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1662       case(Nodes):     case(Nodes):
1663          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1664             case(Nodes):     case(Nodes):
1665             case(ReducedNodes):     case(ReducedNodes):
1666             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1667             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1668             case(Elements):     case(Elements):
1669             case(ReducedElements):     case(ReducedElements):
1670             case(FaceElements):     case(FaceElements):
1671             case(ReducedFaceElements):     case(ReducedFaceElements):
1672             case(Points):     case(Points):
1673             case(ContactElementsZero):     case(ContactElementsZero):
1674             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1675             case(ContactElementsOne):     case(ContactElementsOne):
1676             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1677                 return true;     return true;
1678             default:     default:
1679                 stringstream temp;        stringstream temp;
1680                 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;
1681                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1682          }     }
1683          break;     break;
1684       case(ReducedNodes):     case(ReducedNodes):
1685          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1686             case(ReducedNodes):     case(ReducedNodes):
1687             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1688             case(Elements):     case(Elements):
1689             case(ReducedElements):     case(ReducedElements):
1690             case(FaceElements):     case(FaceElements):
1691             case(ReducedFaceElements):     case(ReducedFaceElements):
1692             case(Points):     case(Points):
1693             case(ContactElementsZero):     case(ContactElementsZero):
1694             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1695             case(ContactElementsOne):     case(ContactElementsOne):
1696             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1697                 return true;     return true;
1698            case(Nodes):     case(Nodes):
1699            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1700               return false;     return false;
1701             default:     default:
1702                 stringstream temp;        stringstream temp;
1703                 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;
1704                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1705          }     }
1706          break;     break;
1707       case(Elements):     case(Elements):
1708          if (functionSpaceType_target==Elements) {     if (functionSpaceType_target==Elements) {
1709             return true;        return true;
1710          } else if (functionSpaceType_target==ReducedElements) {     } else if (functionSpaceType_target==ReducedElements) {
1711             return true;        return true;
1712          } else {     } else {
1713             return false;        return false;
1714          }     }
1715       case(ReducedElements):     case(ReducedElements):
1716          if (functionSpaceType_target==ReducedElements) {     if (functionSpaceType_target==ReducedElements) {
1717             return true;        return true;
1718          } else {     } else {
1719             return false;        return false;
1720          }     }
1721       case(FaceElements):     case(FaceElements):
1722          if (functionSpaceType_target==FaceElements) {     if (functionSpaceType_target==FaceElements) {
1723             return true;        return true;
1724          } else if (functionSpaceType_target==ReducedFaceElements) {     } else if (functionSpaceType_target==ReducedFaceElements) {
1725             return true;        return true;
1726          } else {     } else {
1727             return false;        return false;
1728          }     }
1729       case(ReducedFaceElements):     case(ReducedFaceElements):
1730          if (functionSpaceType_target==ReducedFaceElements) {     if (functionSpaceType_target==ReducedFaceElements) {
1731             return true;        return true;
1732          } else {     } else {
1733             return false;        return false;
1734          }     }
1735       case(Points):     case(Points):
1736          if (functionSpaceType_target==Points) {     if (functionSpaceType_target==Points) {
1737             return true;        return true;
1738          } else {     } else {
1739             return false;        return false;
1740          }     }
1741       case(ContactElementsZero):     case(ContactElementsZero):
1742       case(ContactElementsOne):     case(ContactElementsOne):
1743          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1744             return true;        return true;
1745          } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1746             return true;        return true;
1747          } else {     } else {
1748             return false;        return false;
1749          }     }
1750       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1751       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1752          if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1753             return true;        return true;
1754          } else {     } else {
1755             return false;        return false;
1756          }     }
1757       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1758          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1759             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1760             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1761             case(Nodes):     case(Nodes):
1762             case(ReducedNodes):     case(ReducedNodes):
1763             case(Elements):     case(Elements):
1764             case(ReducedElements):     case(ReducedElements):
1765             case(Points):     case(Points):
1766             case(FaceElements):     case(FaceElements):
1767             case(ReducedFaceElements):     case(ReducedFaceElements):
1768             case(ContactElementsZero):     case(ContactElementsZero):
1769             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1770             case(ContactElementsOne):     case(ContactElementsOne):
1771             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1772                return true;     return true;
1773             default:     default:
1774               stringstream temp;        stringstream temp;
1775               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;
1776               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1777          }     }
1778          break;     break;
1779       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1780         switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1781            case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1782            case(ReducedNodes):     case(ReducedNodes):
1783            case(Elements):     case(Elements):
1784            case(ReducedElements):     case(ReducedElements):
1785            case(FaceElements):     case(FaceElements):
1786            case(ReducedFaceElements):     case(ReducedFaceElements):
1787            case(Points):     case(Points):
1788            case(ContactElementsZero):     case(ContactElementsZero):
1789            case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1790            case(ContactElementsOne):     case(ContactElementsOne):
1791            case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1792                return true;     return true;
1793            case(Nodes):     case(Nodes):
1794            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1795               return false;     return false;
1796            default:     default:
1797               stringstream temp;        stringstream temp;
1798               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;
1799               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1800         }     }
1801         break;     break;
1802       default:     default:
1803          stringstream temp;        stringstream temp;
1804          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;
1805          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1806          break;        break;
1807    }     }
1808    checkFinleyError();     checkFinleyError();
1809    return false;     return false;
1810  }  }
1811    
1812  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
1813  {  {
1814      return false;     return false;
1815  }  }
1816    
1817  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1818  {  {
1819    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1820    if (temp!=0) {     if (temp!=0) {
1821      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1822    } else {     } else {
1823      return false;        return false;
1824    }     }
1825  }  }
1826    
1827  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1828  {  {
1829    return !(operator==(other));     return !(operator==(other));
1830  }  }
1831    
1832  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const
# Line 1848  int MeshAdapter::getSystemMatrixTypeId(c Line 1838  int MeshAdapter::getSystemMatrixTypeId(c
1838    
1839  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1840  {  {
1841    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1842  }  }
1843    
1844  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1845  {  {
1846    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1847  }  }
1848    
1849  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1850  {  {
1851    return function(asAbstractContinuousDomain()).getSize();     return function(asAbstractContinuousDomain()).getSize();
1852  }  }
1853    
1854  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1855  {  {
1856    int *out=0,i;     int *out = NULL;
1857    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1858    switch (functionSpaceType) {     switch (functionSpaceType) {
1859      case(Nodes):     case(Nodes):
1860        out=mesh->Nodes->Id;     out=mesh->Nodes->Id;
1861        break;     break;
1862      case(ReducedNodes):     case(ReducedNodes):
1863        out=mesh->Nodes->reducedNodesId;     out=mesh->Nodes->reducedNodesId;
1864        break;     break;
1865      case(Elements):     case(Elements):
1866        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1867        break;     break;
1868      case(ReducedElements):     case(ReducedElements):
1869        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1870        break;     break;
1871      case(FaceElements):     case(FaceElements):
1872        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1873        break;     break;
1874      case(ReducedFaceElements):     case(ReducedFaceElements):
1875        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1876        break;     break;
1877      case(Points):     case(Points):
1878        out=mesh->Points->Id;     out=mesh->Points->Id;
1879        break;     break;
1880      case(ContactElementsZero):     case(ContactElementsZero):
1881        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1882        break;     break;
1883      case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1884        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1885        break;     break;
1886      case(ContactElementsOne):     case(ContactElementsOne):
1887        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1888        break;     break;
1889      case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1890        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1891        break;     break;
1892      case(DegreesOfFreedom):     case(DegreesOfFreedom):
1893        out=mesh->Nodes->degreesOfFreedomId;     out=mesh->Nodes->degreesOfFreedomId;
1894        break;     break;
1895      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1896        out=mesh->Nodes->reducedDegreesOfFreedomId;     out=mesh->Nodes->reducedDegreesOfFreedomId;
1897        break;     break;
1898      default:     default:
1899        stringstream temp;        stringstream temp;
1900        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1901        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1902        break;        break;
1903    }     }
1904    return out;     return out;
1905  }  }
1906  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1907  {  {
1908    int out=0;     int out=0;
1909    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1910    switch (functionSpaceType) {     switch (functionSpaceType) {
1911    case(Nodes):     case(Nodes):
1912      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
1913      break;     break;
1914    case(ReducedNodes):     case(ReducedNodes):
1915      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1916      break;     break;
1917    case(Elements):     case(Elements):
1918      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1919      break;     break;
1920    case(ReducedElements):     case(ReducedElements):
1921      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1922      break;     break;
1923    case(FaceElements):     case(FaceElements):
1924      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1925      break;     break;
1926    case(ReducedFaceElements):     case(ReducedFaceElements):
1927      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1928      break;     break;
1929    case(Points):     case(Points):
1930      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
1931      break;     break;
1932    case(ContactElementsZero):     case(ContactElementsZero):
1933      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1934      break;     break;
1935    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1936      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1937      break;     break;
1938    case(ContactElementsOne):     case(ContactElementsOne):
1939      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1940      break;     break;
1941    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1942      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1943      break;     break;
1944    case(DegreesOfFreedom):     case(DegreesOfFreedom):
1945      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1946      break;     break;
1947    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1948      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1949      break;     break;
1950    default:     default:
1951      stringstream temp;        stringstream temp;
1952      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1953      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1954      break;        break;
1955    }     }
1956    return out;     return out;
1957  }  }
1958    
1959    
1960  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
1961  {  {
1962    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1963    escriptDataC tmp=mask.getDataC();     escriptDataC tmp=mask.getDataC();
1964    switch(functionSpaceType) {     switch(functionSpaceType) {
1965         case(Nodes):     case(Nodes):
1966            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);     Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1967            break;     break;
1968         case(ReducedNodes):     case(ReducedNodes):
1969            throw FinleyAdapterException("Error - ReducedNodes does not support tags");     throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1970            break;     break;
1971         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1972            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");     throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1973            break;     break;
1974         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1975            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");     throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1976            break;     break;
1977         case(Elements):     case(Elements):
1978            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1979            break;     break;
1980         case(ReducedElements):     case(ReducedElements):
1981            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1982            break;     break;
1983         case(FaceElements):     case(FaceElements):
1984            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1985            break;     break;
1986         case(ReducedFaceElements):     case(ReducedFaceElements):
1987            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);     Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1988            break;     break;
1989         case(Points):     case(Points):
1990            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);     Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1991            break;     break;
1992         case(ContactElementsZero):     case(ContactElementsZero):
1993            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1994            break;     break;
1995         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1996            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1997            break;     break;
1998         case(ContactElementsOne):     case(ContactElementsOne):
1999            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2000            break;     break;
2001         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
2002            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2003            break;     break;
2004         default:     default:
2005            stringstream temp;        stringstream temp;
2006            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2007            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2008    }     }
2009    checkFinleyError();     checkFinleyError();
2010    return;     return;
2011  }  }
2012    
2013  void MeshAdapter::setTagMap(const std::string& name,  int tag)  void MeshAdapter::setTagMap(const std::string& name,  int tag)
2014  {  {
2015    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2016    Finley_Mesh_addTagMap(mesh, name.c_str(),tag);     Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2017    checkPasoError();     checkPasoError();
2018    // throwStandardException("MeshAdapter::set TagMap is not implemented.");     // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2019  }  }
2020    
2021  int MeshAdapter::getTag(const std::string& name) const  int MeshAdapter::getTag(const std::string& name) const
2022  {  {
2023    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2024    int tag=0;     int tag=0;
2025    tag=Finley_Mesh_getTag(mesh, name.c_str());     tag=Finley_Mesh_getTag(mesh, name.c_str());
2026    checkPasoError();     checkPasoError();
2027    // throwStandardException("MeshAdapter::getTag is not implemented.");     // throwStandardException("MeshAdapter::getTag is not implemented.");
2028    return tag;     return tag;
2029  }  }
2030    
2031  bool MeshAdapter::isValidTagName(const std::string& name) const  bool MeshAdapter::isValidTagName(const std::string& name) const
2032  {  {
2033    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2034    return Finley_Mesh_isValidTagName(mesh,name.c_str());     return Finley_Mesh_isValidTagName(mesh,name.c_str());
2035  }  }
2036    
2037  std::string MeshAdapter::showTagNames() const  std::string MeshAdapter::showTagNames() const
2038  {  {
2039    stringstream temp;     stringstream temp;
2040    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2041    Finley_TagMap* tag_map=mesh->TagMap;     Finley_TagMap* tag_map=mesh->TagMap;
2042    while (tag_map) {     while (tag_map) {
2043       temp << tag_map->name;        temp << tag_map->name;
2044       tag_map=tag_map->next;        tag_map=tag_map->next;
2045       if (tag_map) temp << ", ";        if (tag_map) temp << ", ";
2046    }     }
2047    return temp.str();     return temp.str();
2048  }  }
2049    
2050  }  // end of namespace  }  // end of namespace

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