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

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revision 1375 by gross, Wed Jan 9 00:15:05 2008 UTC revision 1859 by gross, Wed Oct 8 03:03:37 2008 UTC
# Line 1  Line 1 
1    
 /* $Id$ */  
   
2  /*******************************************************  /*******************************************************
3   *  *
4   *           Copyright 2003-2007 by ACceSS MNRF  * Copyright (c) 2003-2008 by University of Queensland
5   *       Copyright 2007 by University of Queensland  * Earth Systems Science Computational Center (ESSCC)
6   *  * http://www.uq.edu.au/esscc
7   *                http://esscc.uq.edu.au  *
8   *        Primary Business: Queensland, Australia  * Primary Business: Queensland, Australia
9   *  Licensed under the Open Software License version 3.0  * Licensed under the Open Software License version 3.0
10   *     http://www.opensource.org/licenses/osl-3.0.php  * http://www.opensource.org/licenses/osl-3.0.php
11   *  *
12   *******************************************************/  *******************************************************/
13    
14    
15  #include "MeshAdapter.h"  #include "MeshAdapter.h"
16  #include "escript/Data.h"  #include "escript/Data.h"
# Line 19  Line 18 
18  #ifdef USE_NETCDF  #ifdef USE_NETCDF
19  #include <netcdfcpp.h>  #include <netcdfcpp.h>
20  #endif  #endif
21    #ifdef PASO_MPI
22    #include <mpi.h>
23    #include "paso/Paso_MPI.h"
24    #endif
25  extern "C" {  extern "C" {
26  #include "escript/blocktimer.h"  #include "escript/blocktimer.h"
27  }  }
28  #include <vector>  #include <vector>
29    
30    #define IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH  256
31    
32  using namespace std;  using namespace std;
33  using namespace escript;  using namespace escript;
34    
# Line 48  const int MeshAdapter::ReducedContactEle Line 53  const int MeshAdapter::ReducedContactEle
53    
54  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
55  {  {
56    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
57    //     //
58    // need to use a null_deleter as Finley_Mesh_free deletes the pointer     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
59    // for us.     // for us.
60    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
61  }  }
62    
63  //  //
# Line 60  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 65  MeshAdapter::MeshAdapter(Finley_Mesh* fi
65  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
66  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
67  {  {
68    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
69  }  }
70    
71  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
72  {  {
73    //     //
74    // I hope the case for the pointer being zero has been taken care of.     // I hope the case for the pointer being zero has been taken care of.
75    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
76    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
77      Finley_Mesh_free(m_finleyMesh.get());        Finley_Mesh_free(m_finleyMesh.get());
78    }     }
79  }  }
80    
81  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
# Line 89  Finley_Mesh* MeshAdapter::getFinley_Mesh Line 94  Finley_Mesh* MeshAdapter::getFinley_Mesh
94    
95  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const std::string& fileName) const
96  {  {
97    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;
98    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
99    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
100    checkFinleyError();     checkFinleyError();
101    TMPMEMFREE(fName);     TMPMEMFREE(fName);
102  }  }
103    
104  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  void MeshAdapter::Print_Mesh_Info(const bool full=false) const
105  {  {
106    Finley_PrintMesh_Info(m_finleyMesh.get(), full);     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
107  }  }
108    
109  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const std::string& fileName) const
110  {  {
111  #ifdef USE_NETCDF  #ifdef USE_NETCDF
112     const NcDim* ncdims[12];     const NcDim* ncdims[12];
113     NcVar *ids, *data;     NcVar *ids;
114     int *int_ptr;     int *int_ptr;
115     Finley_Mesh *mesh = m_finleyMesh.get();     Finley_Mesh *mesh = m_finleyMesh.get();
116     Finley_TagMap* tag_map;     Finley_TagMap* tag_map;
# Line 121  void MeshAdapter::dump(const std::string Line 126  void MeshAdapter::dump(const std::string
126     int num_Elements_numNodes        = mesh->Elements->numNodes;     int num_Elements_numNodes        = mesh->Elements->numNodes;
127     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;     int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
128     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;     int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
129     char *newFileName = Paso_MPI_appendRankToFileName(strdup(fileName.c_str()), mpi_size, mpi_rank);  #ifdef PASO_MPI
130       MPI_Status status;
131    #endif
132    
133    /* Incoming token indicates it's my turn to write */
134    #ifdef PASO_MPI
135       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
136    #endif
137    
138       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
139                                                         mpi_size, mpi_rank);
140    
141     /* Figure out how much storage is required for tags */     /* Figure out how much storage is required for tags */
142     tag_map = mesh->TagMap;     tag_map = mesh->TagMap;
143       num_Tags = 0;
144     if (tag_map) {     if (tag_map) {
145       while (tag_map) {        while (tag_map) {
146      num_Tags++;           num_Tags++;
147          tag_map=tag_map->next;           tag_map=tag_map->next;
148       }        }
149     }     }
150    
151     // NetCDF error handler     // NetCDF error handler
# Line 138  void MeshAdapter::dump(const std::string Line 154  void MeshAdapter::dump(const std::string
154     NcFile dataFile(newFileName, NcFile::Replace);     NcFile dataFile(newFileName, NcFile::Replace);
155     // check if writing was successful     // check if writing was successful
156     if (!dataFile.is_valid())     if (!dataFile.is_valid())
157          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);
158    
159     // 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)
160     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )     if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
161          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);
162     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )     if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
163          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);
164     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)) )
165          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);
166     if (num_Elements>0)     if (num_Elements>0)
167        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )        if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
168          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);
169     if (num_FaceElements>0)     if (num_FaceElements>0)
170        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )        if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
171          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);
172     if (num_ContactElements>0)     if (num_ContactElements>0)
173        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )        if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
174          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);
175     if (num_Points>0)     if (num_Points>0)
176        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )        if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
177          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);
178     if (num_Elements>0)     if (num_Elements>0)
179        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )        if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
180          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);
181     if (num_FaceElements>0)     if (num_FaceElements>0)
182        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )        if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
183          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);
184     if (num_ContactElements>0)     if (num_ContactElements>0)
185        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )        if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
186          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);
187     if (num_Tags>0)     if (num_Tags>0)
188        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )        if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
189          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);
190    
191     // Attributes: MPI size, MPI rank, Name, order, reduced_order     // Attributes: MPI size, MPI rank, Name, order, reduced_order
192     if (!dataFile.add_att("mpi_size", mpi_size) )     if (!dataFile.add_att("mpi_size", mpi_size) )
193          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);
194     if (!dataFile.add_att("mpi_rank", mpi_rank) )     if (!dataFile.add_att("mpi_rank", mpi_rank) )
195          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);
196     if (!dataFile.add_att("Name",mesh->Name) )     if (!dataFile.add_att("Name",mesh->Name) )
197          throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending Name to NetCDF file failed: " + *newFileName);
198     if (!dataFile.add_att("numDim",numDim) )     if (!dataFile.add_att("numDim",numDim) )
199          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
200     if (!dataFile.add_att("order",mesh->order) )     if (!dataFile.add_att("order",mesh->order) )
201          throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending order to NetCDF file failed: " + *newFileName);
202     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )     if (!dataFile.add_att("reduced_order",mesh->reduced_order) )
203          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);
204     if (!dataFile.add_att("numNodes",numNodes) )     if (!dataFile.add_att("numNodes",numNodes) )
205          throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);        throw DataException("Error - MeshAdapter::dump: appending numNodes to NetCDF file failed: " + *newFileName);
206     if (!dataFile.add_att("num_Elements",num_Elements) )     if (!dataFile.add_att("num_Elements",num_Elements) )
207          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);
208     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )     if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
209          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);
210     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )     if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
211          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);
212     if (!dataFile.add_att("num_Points",num_Points) )     if (!dataFile.add_att("num_Points",num_Points) )
213          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);
214     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )     if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
215          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);
216     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )     if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
217          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);
218     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )     if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
219          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);
220     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )     if (!dataFile.add_att("Elements_TypeId", mesh->Elements->ReferenceElement->Type->TypeId) )
221        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);
222     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 233  void MeshAdapter::dump(const std::string
233     // 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)
234     if (numNodes>0) {     if (numNodes>0) {
235    
236     // Nodes Id        // Nodes Id
237     if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
238          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);
239     int_ptr = &mesh->Nodes->Id[0];        int_ptr = &mesh->Nodes->Id[0];
240     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
241          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);
242    
243     // Nodes Tag        // Nodes Tag
244     if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
245          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);
246     int_ptr = &mesh->Nodes->Tag[0];        int_ptr = &mesh->Nodes->Tag[0];
247     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
248          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);
249    
250     // Nodes gDOF        // Nodes gDOF
251     if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
252          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);
253     int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];        int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
254     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
255          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);
256    
257     // Nodes global node index        // Nodes global node index
258     if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
259          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);
260     int_ptr = &mesh->Nodes->globalNodesIndex[0];        int_ptr = &mesh->Nodes->globalNodesIndex[0];
261     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
262          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);
263    
264     // Nodes grDof        // Nodes grDof
265     if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
266          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);
267     int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];        int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
268     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
269          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);
270    
271     // Nodes grNI        // Nodes grNI
272     if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )        if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
273          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);
274     int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];        int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
275     if (! (ids->put(int_ptr, numNodes)) )        if (! (ids->put(int_ptr, numNodes)) )
276          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);
277    
278     // Nodes Coordinates        // Nodes Coordinates
279     if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )        if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
280          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);
281     if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )        if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
282          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);
283    
284     // Nodes degreesOfFreedomDistribution        // Nodes degreesOfFreedomDistribution
285     if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )        if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
286          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);
287     int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];        int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
288     if (! (ids->put(int_ptr, mpi_size+1)) )        if (! (ids->put(int_ptr, mpi_size+1)) )
289          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);
290    
291          // Nodes nodeDistribution
292          if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
293             throw DataException("Error - MeshAdapter::dump: appending Nodes_NodeDistribution to netCDF file failed: " + *newFileName);
294          int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
295          if (! (ids->put(int_ptr, mpi_size+1)) )
296             throw DataException("Error - MeshAdapter::dump: copy Nodes_NodeDistribution to netCDF buffer failed: " + *newFileName);
297    
298     }     }
299    
# Line 278  void MeshAdapter::dump(const std::string Line 301  void MeshAdapter::dump(const std::string
301    
302     if (num_Elements>0) {     if (num_Elements>0) {
303    
304       // Temp storage to gather node IDs        // Elements_Id
305       int *Elements_Nodes = TMPMEMALLOC(num_Elements*num_Elements_numNodes,int);        if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
306             throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);
307       // Elements_Id        int_ptr = &mesh->Elements->Id[0];
308       if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
309          throw DataException("Error - MeshAdapter::dump: appending Elements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);
310       int_ptr = &mesh->Elements->Id[0];  
311       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Tag
312          throw DataException("Error - MeshAdapter::dump: copy Elements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
313             throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);
314       // Elements_Tag        int_ptr = &mesh->Elements->Tag[0];
315       if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
316          throw DataException("Error - MeshAdapter::dump: appending Elements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);
317       int_ptr = &mesh->Elements->Tag[0];  
318       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Owner
319          throw DataException("Error - MeshAdapter::dump: copy Elements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
320             throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);
321       // Elements_Owner        int_ptr = &mesh->Elements->Owner[0];
322       if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
323          throw DataException("Error - MeshAdapter::dump: appending Elements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);
324       int_ptr = &mesh->Elements->Owner[0];  
325       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Color
326          throw DataException("Error - MeshAdapter::dump: copy Elements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
327             throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);
328       // Elements_Color        int_ptr = &mesh->Elements->Color[0];
329       if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )        if (! (ids->put(int_ptr, num_Elements)) )
330          throw DataException("Error - MeshAdapter::dump: appending Elements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);
331       int_ptr = &mesh->Elements->Color[0];  
332       if (! (ids->put(int_ptr, num_Elements)) )        // Elements_Nodes
333          throw DataException("Error - MeshAdapter::dump: copy Elements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
334             throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);
335       // Elements_Nodes        if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
336       for (int i=0; i<num_Elements; i++)           throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);
        for (int j=0; j<num_Elements_numNodes; j++)  
          Elements_Nodes[INDEX2(j,i,num_Elements_numNodes)] = mesh->Nodes->Id[mesh->Elements->Nodes[INDEX2(j,i,num_Elements_numNodes)]];  
      if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending Elements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(Elements_Nodes[0]), num_Elements, num_Elements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy Elements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(Elements_Nodes);  
337    
338     }     }
339    
# Line 326  void MeshAdapter::dump(const std::string Line 341  void MeshAdapter::dump(const std::string
341    
342     if (num_FaceElements>0) {     if (num_FaceElements>0) {
343    
344       // Temp storage to gather node IDs        // FaceElements_Id
345       int *FaceElements_Nodes = TMPMEMALLOC(num_FaceElements*num_FaceElements_numNodes,int);        if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
346             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);
347       // FaceElements_Id        int_ptr = &mesh->FaceElements->Id[0];
348       if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
349          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);
350       int_ptr = &mesh->FaceElements->Id[0];  
351       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Tag
352          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
353             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);
354       // FaceElements_Tag        int_ptr = &mesh->FaceElements->Tag[0];
355       if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
356          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);
357       int_ptr = &mesh->FaceElements->Tag[0];  
358       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Owner
359          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
360             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);
361       // FaceElements_Owner        int_ptr = &mesh->FaceElements->Owner[0];
362       if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
363          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);
364       int_ptr = &mesh->FaceElements->Owner[0];  
365       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Color
366          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
367             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);
368       // FaceElements_Color        int_ptr = &mesh->FaceElements->Color[0];
369       if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )        if (! (ids->put(int_ptr, num_FaceElements)) )
370          throw DataException("Error - MeshAdapter::dump: appending FaceElements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);
371       int_ptr = &mesh->FaceElements->Color[0];  
372       if (! (ids->put(int_ptr, num_FaceElements)) )        // FaceElements_Nodes
373          throw DataException("Error - MeshAdapter::dump: copy FaceElements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
374             throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);
375       // FaceElements_Nodes        if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
376       for (int i=0; i<num_FaceElements; i++)           throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);
        for (int j=0; j<num_FaceElements_numNodes; j++)  
          FaceElements_Nodes[INDEX2(j,i,num_FaceElements_numNodes)] = mesh->Nodes->Id[mesh->FaceElements->Nodes[INDEX2(j,i,num_FaceElements_numNodes)]];  
      if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending FaceElements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(FaceElements_Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy FaceElements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(FaceElements_Nodes);  
377    
378     }     }
379    
# Line 374  void MeshAdapter::dump(const std::string Line 381  void MeshAdapter::dump(const std::string
381    
382     if (num_ContactElements>0) {     if (num_ContactElements>0) {
383    
384       // Temp storage to gather node IDs        // ContactElements_Id
385       int *ContactElements_Nodes = TMPMEMALLOC(num_ContactElements*num_ContactElements_numNodes,int);        if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
386             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);
387       // ContactElements_Id        int_ptr = &mesh->ContactElements->Id[0];
388       if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
389          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Id to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);
390       int_ptr = &mesh->ContactElements->Id[0];  
391       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Tag
392          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Id to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
393             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);
394       // ContactElements_Tag        int_ptr = &mesh->ContactElements->Tag[0];
395       if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
396          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Tag to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);
397       int_ptr = &mesh->ContactElements->Tag[0];  
398       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Owner
399          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Tag to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
400             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);
401       // ContactElements_Owner        int_ptr = &mesh->ContactElements->Owner[0];
402       if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
403          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Owner to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);
404       int_ptr = &mesh->ContactElements->Owner[0];  
405       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Color
406          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Owner to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
407             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);
408       // ContactElements_Color        int_ptr = &mesh->ContactElements->Color[0];
409       if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )        if (! (ids->put(int_ptr, num_ContactElements)) )
410          throw DataException("Error - MeshAdapter::dump: appending ContactElements_Color to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);
411       int_ptr = &mesh->ContactElements->Color[0];  
412       if (! (ids->put(int_ptr, num_ContactElements)) )        // ContactElements_Nodes
413          throw DataException("Error - MeshAdapter::dump: copy ContactElements_Color to netCDF buffer failed: " + *newFileName);        if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
414             throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);
415       // ContactElements_Nodes        if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
416       for (int i=0; i<num_ContactElements; i++)           throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);
        for (int j=0; j<num_ContactElements_numNodes; j++)  
          ContactElements_Nodes[INDEX2(j,i,num_ContactElements_numNodes)] = mesh->Nodes->Id[mesh->ContactElements->Nodes[INDEX2(j,i,num_ContactElements_numNodes)]];  
      if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )  
         throw DataException("Error - MeshAdapter::dump: appending ContactElements_Nodes to netCDF file failed: " + *newFileName);  
      if (! (ids->put(&(ContactElements_Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )  
         throw DataException("Error - MeshAdapter::dump: copy ContactElements_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(ContactElements_Nodes);  
417    
418     }     }
419    
# Line 422  void MeshAdapter::dump(const std::string Line 421  void MeshAdapter::dump(const std::string
421    
422     if (num_Points>0) {     if (num_Points>0) {
423    
424       fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");        fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
   
      // Temp storage to gather node IDs  
      int *Points_Nodes = TMPMEMALLOC(num_Points,int);  
425    
426       // Points_Id        // Points_Id
427       if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
428          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);
429       int_ptr = &mesh->Points->Id[0];        int_ptr = &mesh->Points->Id[0];
430       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
431          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);
432    
433       // Points_Tag        // Points_Tag
434       if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
435          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);
436       int_ptr = &mesh->Points->Tag[0];        int_ptr = &mesh->Points->Tag[0];
437       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
438          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);
439    
440       // Points_Owner        // Points_Owner
441       if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
442          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);
443       int_ptr = &mesh->Points->Owner[0];        int_ptr = &mesh->Points->Owner[0];
444       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
445          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);
446    
447       // Points_Color        // Points_Color
448       if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )        if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
449          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);
450       int_ptr = &mesh->Points->Color[0];        int_ptr = &mesh->Points->Color[0];
451       if (! (ids->put(int_ptr, num_Points)) )        if (! (ids->put(int_ptr, num_Points)) )
452          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);
453    
454       // Points_Nodes        // Points_Nodes
455       // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]        // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
456       for (int i=0; i<num_Points; i++)        if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
457         Points_Nodes[i] = mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]];           throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);
458       if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )        if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
459          throw DataException("Error - MeshAdapter::dump: appending Points_Nodes to netCDF file failed: " + *newFileName);           throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);
      if (! (ids->put(&(Points_Nodes[0]), num_Points)) )  
         throw DataException("Error - MeshAdapter::dump: copy Points_Nodes to netCDF buffer failed: " + *newFileName);  
   
      TMPMEMFREE(Points_Nodes);  
460    
461     }     }
462    
# Line 472  void MeshAdapter::dump(const std::string Line 464  void MeshAdapter::dump(const std::string
464    
465     if (num_Tags>0) {     if (num_Tags>0) {
466    
467       // Temp storage to gather node IDs        // Temp storage to gather node IDs
468       int *Tags_keys = TMPMEMALLOC(num_Tags, int);        int *Tags_keys = TMPMEMALLOC(num_Tags, int);
469       char name_temp[4096];        char name_temp[4096];
470    
471       /* Copy tag data into temp arrays */        /* Copy tag data into temp arrays */
472       tag_map = mesh->TagMap;        tag_map = mesh->TagMap;
473       if (tag_map) {        if (tag_map) {
474         int i = 0;           int i = 0;
475         while (tag_map) {           while (tag_map) {
476      Tags_keys[i++] = tag_map->tag_key;              Tags_keys[i++] = tag_map->tag_key;
477          tag_map=tag_map->next;              tag_map=tag_map->next;
478         }           }
479       }        }
480    
481       // Tags_keys        // Tags_keys
482       if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )        if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
483          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);
484       int_ptr = &Tags_keys[0];        int_ptr = &Tags_keys[0];
485       if (! (ids->put(int_ptr, num_Tags)) )        if (! (ids->put(int_ptr, num_Tags)) )
486          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);
487    
488       // Tags_names_*        // Tags_names_*
489       // 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
490       // 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
491       tag_map = mesh->TagMap;        tag_map = mesh->TagMap;
492       if (tag_map) {        if (tag_map) {
493         int i = 0;           int i = 0;
494         while (tag_map) {           while (tag_map) {
495           sprintf(name_temp, "Tags_name_%d", i);              sprintf(name_temp, "Tags_name_%d", i);
496           if (!dataFile.add_att(name_temp, tag_map->name) )              if (!dataFile.add_att(name_temp, tag_map->name) )
497             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);
498           tag_map=tag_map->next;              tag_map=tag_map->next;
499       i++;              i++;
500         }           }
501       }        }
502    
503       TMPMEMFREE(Tags_keys);        TMPMEMFREE(Tags_keys);
504    
505     }     }
506    
507    /* Send token to next MPI process so he can take his turn */
508    #ifdef PASO_MPI
509       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
510    #endif
511    
512     // NetCDF file is closed by destructor of NcFile object     // NetCDF file is closed by destructor of NcFile object
513    
514  #else  #else
515     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");     Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
516  #endif  /* USE_NETCDF */  #endif  /* USE_NETCDF */
# Line 522  void MeshAdapter::dump(const std::string Line 519  void MeshAdapter::dump(const std::string
519    
520  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
521  {  {
522    return "FinleyMesh";     return "FinleyMesh";
523  }  }
524    
525  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
526  {  {
527    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
528    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
529    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
530      return "Invalid function space type code.";        return "Invalid function space type code.";
531    } else {     } else {
532      return loc->second;        return loc->second;
533    }     }
534  }  }
535    
536  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
537  {  {
538    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
539    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
540    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
541  }  }
542    
543  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
544  {  {
545    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
546      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
547    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
548      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
549    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
550      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
551    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
552      (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
553    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
554      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
555    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
556      (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
557    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
558      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
559    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
560      (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
561    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
562      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
563    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
564      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
565    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
566      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
567    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
568      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
569    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
570      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
571  }  }
572    
573  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
574  {  {
575    return Nodes;     return Nodes;
576  }  }
577  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
578  {  {
579    return ReducedNodes;     return ReducedNodes;
580  }  }
581    
582  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
583  {  {
584    return Elements;     return Elements;
585  }  }
586  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
587  {  {
588    return ReducedElements;     return ReducedElements;
589  }  }
590    
591  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
592  {  {
593    return FaceElements;     return FaceElements;
594  }  }
595  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
596  {  {
597    return ReducedFaceElements;     return ReducedFaceElements;
598  }  }
599    
600  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
601  {  {
602    return ContactElementsZero;     return ContactElementsZero;
603  }  }
604  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
605  {  {
606    return ReducedContactElementsZero;     return ReducedContactElementsZero;
607  }  }
608    
609  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
610  {  {
611    return ContactElementsOne;     return ContactElementsOne;
612  }  }
613  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
614  {  {
615    return ReducedContactElementsOne;     return ReducedContactElementsOne;
616  }  }
617    
618  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
619  {  {
620    return DegreesOfFreedom;     return DegreesOfFreedom;
621  }  }
622    
623  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
624  {  {
625    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
626  }  }
627    
628  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
629  {  {
630    return Points;     return Points;
631  }  }
632    
633  //  //
# Line 638  int MeshAdapter::getDiracDeltaFunctionCo Line 635  int MeshAdapter::getDiracDeltaFunctionCo
635  //  //
636  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
637  {  {
638    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     int numDim=Finley_Mesh_getDim(m_finleyMesh.get());
639    checkFinleyError();     checkFinleyError();
640    return numDim;     return numDim;
641    }
642    
643    //
644    // Return the number of data points summed across all MPI processes
645    //
646    int MeshAdapter::getNumDataPointsGlobal() const
647    {
648       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
649  }  }
650    
651  //  //
# Line 653  pair<int,int> MeshAdapter::getDataShape( Line 658  pair<int,int> MeshAdapter::getDataShape(
658     int numSamples=0;     int numSamples=0;
659     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
660     switch (functionSpaceCode) {     switch (functionSpaceCode) {
661        case(Nodes):     case(Nodes):
662             numDataPointsPerSample=1;     numDataPointsPerSample=1;
663             numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
664             break;     break;
665        case(ReducedNodes):     case(ReducedNodes):
666             numDataPointsPerSample=1;     numDataPointsPerSample=1;
667             numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
668             break;     break;
669        case(Elements):     case(Elements):
670             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
671               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
672               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;
673             }     }
674             break;     break;
675        case(ReducedElements):     case(ReducedElements):
676             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
677               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
678               numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;
679             }     }
680             break;     break;
681        case(FaceElements):     case(FaceElements):
682             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
683                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;
684                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
685             }     }
686             break;     break;
687        case(ReducedFaceElements):     case(ReducedFaceElements):
688             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
689                  numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;
690                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
691             }     }
692             break;     break;
693        case(Points):     case(Points):
694             if (mesh->Points!=NULL) {     if (mesh->Points!=NULL) {
695               numDataPointsPerSample=1;        numDataPointsPerSample=1;
696               numSamples=mesh->Points->numElements;        numSamples=mesh->Points->numElements;
697             }     }
698             break;     break;
699        case(ContactElementsZero):     case(ContactElementsZero):
700             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
701               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
702               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
703             }     }
704             break;     break;
705        case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
706             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
707               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
708               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
709             }     }
710             break;     break;
711        case(ContactElementsOne):     case(ContactElementsOne):
712             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
713               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;
714               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
715             }     }
716             break;     break;
717        case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
718             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
719               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;
720               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
721             }     }
722             break;     break;
723        case(DegreesOfFreedom):     case(DegreesOfFreedom):
724             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
725               numDataPointsPerSample=1;        numDataPointsPerSample=1;
726               numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
727             }     }
728             break;     break;
729        case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
730             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
731               numDataPointsPerSample=1;        numDataPointsPerSample=1;
732               numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
733             }     }
734             break;     break;
735        default:     default:
736          stringstream temp;        stringstream temp;
737          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
738          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
739          break;        break;
740        }     }
741        return pair<int,int>(numDataPointsPerSample,numSamples);     return pair<int,int>(numDataPointsPerSample,numSamples);
742  }  }
743    
744  //  //
745  // 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:
746  //  //
747  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
748                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
749                       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,
750                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
751                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
752  {  {
753     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
754     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
# Line 770  void MeshAdapter::addPDEToSystem( Line 775  void MeshAdapter::addPDEToSystem(
775  }  }
776    
777  void  MeshAdapter::addPDEToLumpedSystem(  void  MeshAdapter::addPDEToLumpedSystem(
778                       escript::Data& mat,                                          escript::Data& mat,
779                       const escript::Data& D,                                          const escript::Data& D,
780                       const escript::Data& d) const                                          const escript::Data& d) const
781  {  {
782     escriptDataC _mat=mat.getDataC();     escriptDataC _mat=mat.getDataC();
783     escriptDataC _D=D.getDataC();     escriptDataC _D=D.getDataC();
# Line 813  void MeshAdapter::addPDEToRHS( escript:: Line 818  void MeshAdapter::addPDEToRHS( escript::
818  // adds PDE of second order into a transport problem  // adds PDE of second order into a transport problem
819  //  //
820  void MeshAdapter::addPDEToTransportProblem(  void MeshAdapter::addPDEToTransportProblem(
821                       TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,                                             TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
822                       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,
823                       const escript::Data& d, const escript::Data& y,                                             const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
824                       const escript::Data& d_contact,const escript::Data& y_contact) const                                             const escript::Data& d, const escript::Data& y,
825                                               const escript::Data& d_contact,const escript::Data& y_contact) const
826  {  {
827     DataArrayView::ShapeType shape;     DataTypes::ShapeType shape;
828     source.expand();     source.expand();
    escript:: Data tmp(0.0,M.getDataPointShape(),tp.getFunctionSpace(),true);  
829     escriptDataC _source=source.getDataC();     escriptDataC _source=source.getDataC();
    escriptDataC _tmp=tmp.getDataC();  
830     escriptDataC _M=M.getDataC();     escriptDataC _M=M.getDataC();
831     escriptDataC _A=A.getDataC();     escriptDataC _A=A.getDataC();
832     escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
# Line 837  void MeshAdapter::addPDEToTransportProbl Line 841  void MeshAdapter::addPDEToTransportProbl
841    
842     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
843     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();     Paso_FCTransportProblem* _tp = tp.getPaso_FCTransportProblem();
     
844    
845     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_tmp, &_M);     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
846     checkFinleyError();     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->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
    checkFinleyError();  
   
    Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->flux_matrix, &_source, 0, &_B, &_C, 0, 0, 0 );  
849     checkFinleyError();     checkFinleyError();
850    
851     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 860  void MeshAdapter::addPDEToTransportProbl
860  //  //
861  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
862  {  {
863    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());
864    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
865    if (inDomain!=*this)       if (inDomain!=*this)  
866      throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
867    if (targetDomain!=*this)     if (targetDomain!=*this)
868      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
869    
870    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
871    escriptDataC _target=target.getDataC();     escriptDataC _target=target.getDataC();
872    escriptDataC _in=in.getDataC();     escriptDataC _in=in.getDataC();
873    switch(in.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
874       case(Nodes):     case(Nodes):
875          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
876             case(Nodes):     case(Nodes):
877             case(ReducedNodes):     case(ReducedNodes):
878             case(DegreesOfFreedom):     case(DegreesOfFreedom):
879             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
880                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
881                 break;     break;
882             case(Elements):     case(Elements):
883             case(ReducedElements):     case(ReducedElements):
884                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
885                 break;     break;
886             case(FaceElements):     case(FaceElements):
887             case(ReducedFaceElements):     case(ReducedFaceElements):
888                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
889                 break;     break;
890             case(Points):     case(Points):
891                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
892                 break;     break;
893             case(ContactElementsZero):     case(ContactElementsZero):
894             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
895                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
896                 break;     break;
897             case(ContactElementsOne):     case(ContactElementsOne):
898             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
899                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
900                 break;     break;
901             default:     default:
902                 stringstream temp;        stringstream temp;
903                 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();
904                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
905                 break;        break;
906          }     }
907          break;     break;
908       case(ReducedNodes):     case(ReducedNodes):
909          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
910             case(Nodes):     case(Nodes):
911             case(ReducedNodes):     case(ReducedNodes):
912             case(DegreesOfFreedom):     case(DegreesOfFreedom):
913             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
914                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
915                 break;     break;
916             case(Elements):     case(Elements):
917             case(ReducedElements):     case(ReducedElements):
918                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
919                 break;     break;
920             case(FaceElements):     case(FaceElements):
921             case(ReducedFaceElements):     case(ReducedFaceElements):
922                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
923                 break;     break;
924             case(Points):     case(Points):
925                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
926                 break;     break;
927             case(ContactElementsZero):     case(ContactElementsZero):
928             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
929                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
930                 break;     break;
931             case(ContactElementsOne):     case(ContactElementsOne):
932             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
933                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);     Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
934                 break;     break;
935             default:     default:
936                 stringstream temp;        stringstream temp;
937                 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();
938                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
939                 break;        break;
940          }     }
941          break;     break;
942       case(Elements):     case(Elements):
943          if (target.getFunctionSpace().getTypeCode()==Elements) {     if (target.getFunctionSpace().getTypeCode()==Elements) {
944             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
945          } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
946             Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
947          } else {     } else {
948             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
949          }     }
950          break;     break;
951       case(ReducedElements):     case(ReducedElements):
952          if (target.getFunctionSpace().getTypeCode()==ReducedElements) {     if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
953             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
954          } else {     } else {
955             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.");
956          }     }
957          break;     break;
958       case(FaceElements):     case(FaceElements):
959          if (target.getFunctionSpace().getTypeCode()==FaceElements) {     if (target.getFunctionSpace().getTypeCode()==FaceElements) {
960             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
961          } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
962             Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
963          } else {     } else {
964             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
965          }     }
966          break;     break;
967       case(ReducedFaceElements):     case(ReducedFaceElements):
968          if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {     if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
969             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
970          } else {     } else {
971             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.");
972         }     }
973         break;     break;
974       case(Points):     case(Points):
975          if (target.getFunctionSpace().getTypeCode()==Points) {     if (target.getFunctionSpace().getTypeCode()==Points) {
976             Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
977          } else {     } else {
978             throw FinleyAdapterException("Error - No interpolation with data on points possible.");        throw FinleyAdapterException("Error - No interpolation with data on points possible.");
979          }     }
980          break;     break;
981       case(ContactElementsZero):     case(ContactElementsZero):
982       case(ContactElementsOne):     case(ContactElementsOne):
983          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {     if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
984             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
985          } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {     } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
986             Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
987          } else {     } else {
988             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");        throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
989          }     }
990          break;     break;
991       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
992       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
993          if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {     if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
994             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);        Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
995          } else {     } else {
996             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.");
997          }     }
998          break;     break;
999       case(DegreesOfFreedom):           case(DegreesOfFreedom):      
1000          switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
1001             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1002             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1003                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1004                break;     break;
1005    
1006             case(Nodes):     case(Nodes):
1007             case(ReducedNodes):     case(ReducedNodes):
1008                if (getMPISize()>1) {     if (getMPISize()>1) {
1009                    escript::Data temp=escript::Data(in);        escript::Data temp=escript::Data(in);
1010                    temp.expand();        temp.expand();
1011                    escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1012                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1013                } else {     } else {
1014                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1015                }     }
1016                break;     break;
1017             case(Elements):     case(Elements):
1018             case(ReducedElements):     case(ReducedElements):
1019                if (getMPISize()>1) {     if (getMPISize()>1) {
1020                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1021                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1022                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1023                } else {     } else {
1024                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1025                }     }
1026                break;     break;
1027             case(FaceElements):     case(FaceElements):
1028             case(ReducedFaceElements):     case(ReducedFaceElements):
1029                if (getMPISize()>1) {     if (getMPISize()>1) {
1030                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1031                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1032                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1033    
1034                } else {     } else {
1035                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1036                }     }
1037                break;     break;
1038             case(Points):     case(Points):
1039                if (getMPISize()>1) {     if (getMPISize()>1) {
1040                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1041                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1042                } else {     } else {
1043                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1044                }     }
1045                break;     break;
1046             case(ContactElementsZero):     case(ContactElementsZero):
1047             case(ContactElementsOne):     case(ContactElementsOne):
1048             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1049             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1050                if (getMPISize()>1) {     if (getMPISize()>1) {
1051                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1052                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1053                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1054                } else {     } else {
1055                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1056                }     }
1057               break;     break;
1058             default:     default:
1059               stringstream temp;        stringstream temp;
1060               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();
1061               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1062               break;        break;
1063          }     }
1064          break;     break;
1065       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1066         switch(target.getFunctionSpace().getTypeCode()) {     switch(target.getFunctionSpace().getTypeCode()) {
1067            case(Nodes):     case(Nodes):
1068               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.");
1069               break;     break;
1070            case(ReducedNodes):     case(ReducedNodes):
1071                if (getMPISize()>1) {     if (getMPISize()>1) {
1072                    escript::Data temp=escript::Data(in);        escript::Data temp=escript::Data(in);
1073                    temp.expand();        temp.expand();
1074                    escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1075                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1076                } else {     } else {
1077                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1078                }     }
1079                break;     break;
1080            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1081               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");
1082               break;     break;
1083            case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1084               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);     Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1085               break;     break;
1086            case(Elements):     case(Elements):
1087            case(ReducedElements):     case(ReducedElements):
1088                if (getMPISize()>1) {     if (getMPISize()>1) {
1089                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1090                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1091                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1092                } else {     } else {
1093                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1094               }     }
1095               break;     break;
1096            case(FaceElements):     case(FaceElements):
1097            case(ReducedFaceElements):     case(ReducedFaceElements):
1098                if (getMPISize()>1) {     if (getMPISize()>1) {
1099                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1100                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1101                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1102                } else {     } else {
1103                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1104                }     }
1105               break;     break;
1106            case(Points):     case(Points):
1107                if (getMPISize()>1) {     if (getMPISize()>1) {
1108                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1109                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1110                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1111                } else {     } else {
1112                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1113               }     }
1114               break;     break;
1115            case(ContactElementsZero):     case(ContactElementsZero):
1116            case(ContactElementsOne):     case(ContactElementsOne):
1117            case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1118            case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1119                if (getMPISize()>1) {     if (getMPISize()>1) {
1120                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1121                   escriptDataC _in2 = temp.getDataC();        escriptDataC _in2 = temp.getDataC();
1122                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1123                } else {     } else {
1124                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1125               }     }
1126               break;     break;
1127            default:     default:
1128               stringstream temp;        stringstream temp;
1129               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();
1130               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1131               break;        break;
1132         }     }
1133         break;     break;
1134       default:     default:
1135          stringstream temp;        stringstream temp;
1136          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();
1137          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1138          break;        break;
1139    }     }
1140    checkFinleyError();     checkFinleyError();
1141  }  }
1142    
1143  //  //
# Line 1151  void MeshAdapter::interpolateOnDomain(es Line 1145  void MeshAdapter::interpolateOnDomain(es
1145  //  //
1146  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1147  {  {
1148    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1149    if (argDomain!=*this)     if (argDomain!=*this)
1150       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1151    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1152    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1153    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1154       escriptDataC _arg=arg.getDataC();        escriptDataC _arg=arg.getDataC();
1155       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1156    } else {     } else {
1157       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1158       escriptDataC _tmp_data=tmp_data.getDataC();        escriptDataC _tmp_data=tmp_data.getDataC();
1159       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1160       // this is then interpolated onto arg:        // this is then interpolated onto arg:
1161       interpolateOnDomain(arg,tmp_data);        interpolateOnDomain(arg,tmp_data);
1162    }     }
1163    checkFinleyError();     checkFinleyError();
1164  }  }
1165    
1166  //  //
# Line 1174  void MeshAdapter::setToX(escript::Data& Line 1168  void MeshAdapter::setToX(escript::Data&
1168  //  //
1169  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1170  {  {
1171    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());
1172    if (normalDomain!=*this)     if (normalDomain!=*this)
1173       throw FinleyAdapterException("Error - Illegal domain of normal locations");        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1174    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1175    escriptDataC _normal=normal.getDataC();     escriptDataC _normal=normal.getDataC();
1176    switch(normal.getFunctionSpace().getTypeCode()) {     switch(normal.getFunctionSpace().getTypeCode()) {
1177      case(Nodes):     case(Nodes):
1178        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1179        break;     break;
1180      case(ReducedNodes):     case(ReducedNodes):
1181        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");
1182        break;     break;
1183      case(Elements):     case(Elements):
1184        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1185        break;     break;
1186      case(ReducedElements):     case(ReducedElements):
1187        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");
1188        break;     break;
1189      case (FaceElements):     case (FaceElements):
1190        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1191        break;     break;
1192      case (ReducedFaceElements):     case (ReducedFaceElements):
1193        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1194        break;     break;
1195      case(Points):     case(Points):
1196        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");
1197        break;     break;
1198      case (ContactElementsOne):     case (ContactElementsOne):
1199      case (ContactElementsZero):     case (ContactElementsZero):
1200        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1201        break;     break;
1202      case (ReducedContactElementsOne):     case (ReducedContactElementsOne):
1203      case (ReducedContactElementsZero):     case (ReducedContactElementsZero):
1204        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1205        break;     break;
1206      case(DegreesOfFreedom):     case(DegreesOfFreedom):
1207        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.");
1208        break;     break;
1209      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1210        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.");
1211        break;     break;
1212      default:     default:
1213        stringstream temp;        stringstream temp;
1214        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();
1215        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1216        break;        break;
1217    }     }
1218    checkFinleyError();     checkFinleyError();
1219  }  }
1220    
1221  //  //
# Line 1229  void MeshAdapter::setToNormal(escript::D Line 1223  void MeshAdapter::setToNormal(escript::D
1223  //  //
1224  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1225  {  {
1226    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());
1227    if (targetDomain!=*this)     if (targetDomain!=*this)
1228       throw FinleyAdapterException("Error - Illegal domain of interpolation target");        throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1229    
1230    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1231  }  }
1232    
1233  //  //
# Line 1241  void MeshAdapter::interpolateACross(escr Line 1235  void MeshAdapter::interpolateACross(escr
1235  //  //
1236  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const
1237  {  {
1238    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1239    if (argDomain!=*this)     if (argDomain!=*this)
1240       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1241    
1242    double blocktimer_start = blocktimer_time();     double blocktimer_start = blocktimer_time();
1243    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1244    escriptDataC _temp;     escriptDataC _temp;
1245    escript::Data temp;     escript::Data temp;
1246    escriptDataC _arg=arg.getDataC();     escriptDataC _arg=arg.getDataC();
1247    switch(arg.getFunctionSpace().getTypeCode()) {     switch(arg.getFunctionSpace().getTypeCode()) {
1248       case(Nodes):     case(Nodes):
1249          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1250          _temp=temp.getDataC();     _temp=temp.getDataC();
1251          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1252          break;     break;
1253       case(ReducedNodes):     case(ReducedNodes):
1254          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1255          _temp=temp.getDataC();     _temp=temp.getDataC();
1256          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1257          break;     break;
1258       case(Elements):     case(Elements):
1259          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1260          break;     break;
1261       case(ReducedElements):     case(ReducedElements):
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(FaceElements):     case(FaceElements):
1265          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1266          break;     break;
1267       case(ReducedFaceElements):     case(ReducedFaceElements):
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(Points):     case(Points):
1271          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1272          break;     break;
1273       case(ContactElementsZero):     case(ContactElementsZero):
1274          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1275          break;     break;
1276       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
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(ContactElementsOne):     case(ContactElementsOne):
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(ReducedContactElementsOne):     case(ReducedContactElementsOne):
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(DegreesOfFreedom):     case(DegreesOfFreedom):
1286          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1287          _temp=temp.getDataC();     _temp=temp.getDataC();
1288          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1289          break;     break;
1290       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1291          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, function(asAbstractContinuousDomain()) );
1292          _temp=temp.getDataC();     _temp=temp.getDataC();
1293          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1294          break;     break;
1295       default:     default:
1296          stringstream temp;        stringstream temp;
1297          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();
1298          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1299          break;        break;
1300    }     }
1301    checkFinleyError();     checkFinleyError();
1302    blocktimer_increment("integrate()", blocktimer_start);     blocktimer_increment("integrate()", blocktimer_start);
1303  }  }
1304    
1305  //  //
# Line 1313  void MeshAdapter::setToIntegrals(std::ve Line 1307  void MeshAdapter::setToIntegrals(std::ve
1307  //  //
1308  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1309  {  {
1310    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());
1311    if (argDomain!=*this)     if (argDomain!=*this)
1312      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1313    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());
1314    if (gradDomain!=*this)     if (gradDomain!=*this)
1315       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1316    
1317    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1318    escriptDataC _grad=grad.getDataC();     escriptDataC _grad=grad.getDataC();
1319    escriptDataC nodeDataC;     escriptDataC nodeDataC;
1320    escript::Data temp;     escript::Data temp;
1321    if (getMPISize()>1) {     if (getMPISize()>1) {
1322        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1323          temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1324          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1325        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1326          temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1327          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1328        } else {        } else {
1329          nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1330        }        }
1331    } else {     } else {
1332       nodeDataC = arg.getDataC();        nodeDataC = arg.getDataC();
1333    }     }
1334    switch(grad.getFunctionSpace().getTypeCode()) {     switch(grad.getFunctionSpace().getTypeCode()) {
1335         case(Nodes):     case(Nodes):
1336            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1337            break;     break;
1338         case(ReducedNodes):     case(ReducedNodes):
1339            throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1340            break;     break;
1341         case(Elements):     case(Elements):
1342            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1343            break;     break;
1344         case(ReducedElements):     case(ReducedElements):
1345            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1346            break;     break;
1347         case(FaceElements):     case(FaceElements):
1348            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1349            break;     break;
1350         case(ReducedFaceElements):     case(ReducedFaceElements):
1351            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1352            break;     break;
1353         case(Points):     case(Points):
1354            throw FinleyAdapterException("Error - Gradient at points is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1355            break;     break;
1356         case(ContactElementsZero):     case(ContactElementsZero):
1357            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1358            break;     break;
1359         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1360            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1361            break;     break;
1362         case(ContactElementsOne):     case(ContactElementsOne):
1363            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1364            break;     break;
1365         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1366            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1367            break;     break;
1368         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1369            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1370            break;     break;
1371         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1372            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1373            break;     break;
1374         default:     default:
1375            stringstream temp;        stringstream temp;
1376            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();
1377            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1378            break;        break;
1379    }     }
1380    checkFinleyError();     checkFinleyError();
1381  }  }
1382    
1383  //  //
# Line 1391  void MeshAdapter::setToGradient(escript: Line 1385  void MeshAdapter::setToGradient(escript:
1385  //  //
1386  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1387  {  {
1388    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1389    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1390    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1391         case(Nodes):     case(Nodes):
1392            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1393            break;     break;
1394         case(ReducedNodes):     case(ReducedNodes):
1395            throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1396            break;     break;
1397         case(Elements):     case(Elements):
1398            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1399            break;     break;
1400         case(ReducedElements):     case(ReducedElements):
1401            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1402            break;     break;
1403         case(FaceElements):     case(FaceElements):
1404            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1405            break;     break;
1406         case(ReducedFaceElements):     case(ReducedFaceElements):
1407            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1408            break;     break;
1409         case(Points):     case(Points):
1410            throw FinleyAdapterException("Error - Size of point elements is not supported.");     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1411            break;     break;
1412         case(ContactElementsZero):     case(ContactElementsZero):
1413         case(ContactElementsOne):     case(ContactElementsOne):
1414            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1415            break;     break;
1416         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1417         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1418            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1419            break;     break;
1420         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1421            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1422            break;     break;
1423         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1424            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1425            break;     break;
1426         default:     default:
1427            stringstream temp;        stringstream temp;
1428            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();
1429            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1430            break;        break;
1431    }     }
1432    checkFinleyError();     checkFinleyError();
1433  }  }
1434    
1435  // sets the location of nodes:  // sets the location of nodes:
1436  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1437  {  {
1438    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1439    escriptDataC tmp;     escriptDataC tmp;
1440    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());
1441    if (newDomain!=*this)     if (newDomain!=*this)
1442       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1443    tmp = new_x.getDataC();     tmp = new_x.getDataC();
1444    Finley_Mesh_setCoordinates(mesh,&tmp);     Finley_Mesh_setCoordinates(mesh,&tmp);
1445    checkFinleyError();     checkFinleyError();
1446  }  }
1447    
1448  // saves a data array in openDX format:  // saves a data array in openDX format:
1449  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
1450  {  {
1451      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1452      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1453    /* win32 refactor */     /* win32 refactor */
1454    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1455    for(int i=0;i<num_data;i++)     for(int i=0;i<num_data;i++)
1456    {     {
1457      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1458    }     }
1459    
1460    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1461    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
   escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
   boost::python::list keys=arg.keys();  
   for (int i=0;i<num_data;++i) {  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
     checkFinleyError();  
       
       /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1462    
1463      return;     boost::python::list keys=arg.keys();
1464       for (int i=0;i<num_data;++i) {
1465          std::string n=boost::python::extract<std::string>(keys[i]);
1466          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1467          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1468             throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1469          data[i]=d.getDataC();
1470          ptr_data[i]= &(data[i]);
1471          if (n.length()>MAX_namelength-1) {
1472             strncpy(names[i],n.c_str(),MAX_namelength-1);
1473             names[i][MAX_namelength-1]='\0';
1474          } else {
1475             strcpy(names[i],n.c_str());
1476          }
1477       }
1478       Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1479       checkFinleyError();
1480    
1481       /* win32 refactor */
1482       TMPMEMFREE(data);
1483       TMPMEMFREE(ptr_data);
1484       for(int i=0;i<num_data;i++)
1485       {
1486          TMPMEMFREE(names[i]);
1487       }
1488       TMPMEMFREE(names);
1489    
1490       return;
1491  }  }
1492    
1493  // saves a data array in openVTK format:  // saves a data array in openVTK format:
1494  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
1495  {  {
1496      int MAX_namelength=256;     unsigned int MAX_namelength=IS_THERE_A_REASON_FOR_THIS_MAGIC_NAME_LENGTH;
1497      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     const int num_data=boost::python::extract<int>(arg.attr("__len__")());
1498    /* win32 refactor */     /* win32 refactor */
1499    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;
1500    for(int i=0;i<num_data;i++)     for(int i=0;i<num_data;i++)
1501    {     {
1502      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;        names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;
1503    }     }
1504    
1505    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;
1506    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;
   escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
     boost::python::list keys=arg.keys();  
     for (int i=0;i<num_data;++i) {  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);  
1507    
1508    checkFinleyError();     boost::python::list keys=arg.keys();
1509    /* win32 refactor */     for (int i=0;i<num_data;++i) {
1510    TMPMEMFREE(c_names);        std::string n=boost::python::extract<std::string>(keys[i]);
1511    TMPMEMFREE(data);        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1512    TMPMEMFREE(ptr_data);        if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)
1513    for(int i=0;i<num_data;i++)           throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");
1514    {        data[i]=d.getDataC();
1515      TMPMEMFREE(names[i]);        ptr_data[i]=&(data[i]);
1516    }        if (n.length()>MAX_namelength-1) {
1517    TMPMEMFREE(names);           strncpy(names[i],n.c_str(),MAX_namelength-1);
1518             names[i][MAX_namelength-1]='\0';
1519          } else {
1520             strcpy(names[i],n.c_str());
1521          }
1522       }
1523       Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,names,ptr_data);
1524    
1525      return;     checkFinleyError();
1526       /* win32 refactor */
1527       TMPMEMFREE(data);
1528       TMPMEMFREE(ptr_data);
1529       for(int i=0;i<num_data;i++)
1530       {
1531          TMPMEMFREE(names[i]);
1532       }
1533       TMPMEMFREE(names);
1534    
1535       return;
1536  }  }
1537                                                                                                                                                                                                                                                                                                                                                
1538                                                                                                                                                                                                                                                                                                                                                
1539  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:
1540  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1541                        const int row_blocksize,                                                   const int row_blocksize,
1542                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1543                        const int column_blocksize,                                                   const int column_blocksize,
1544                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1545                        const int type) const                                                   const int type) const
1546  {  {
1547      int reduceRowOrder=0;     int reduceRowOrder=0;
1548      int reduceColOrder=0;     int reduceColOrder=0;
1549      // is the domain right?     // is the domain right?
1550      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());
1551      if (row_domain!=*this)     if (row_domain!=*this)
1552            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.");
1553      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());
1554      if (col_domain!=*this)     if (col_domain!=*this)
1555            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.");
1556      // is the function space type right     // is the function space type right
1557      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1558          reduceRowOrder=0;        reduceRowOrder=0;
1559      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1560          reduceRowOrder=1;        reduceRowOrder=1;
1561      } else {     } else {
1562          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1563      }     }
1564      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1565          reduceColOrder=0;        reduceColOrder=0;
1566      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1567          reduceColOrder=1;        reduceColOrder=1;
1568      } else {     } else {
1569          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1570      }     }
1571      // generate matrix:     // generate matrix:
1572        
1573      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1574      checkFinleyError();     checkFinleyError();
1575      Paso_SystemMatrix* fsystemMatrix;     Paso_SystemMatrix* fsystemMatrix;
1576      int trilinos = 0;     int trilinos = 0;
1577      if (trilinos) {     if (trilinos) {
1578  #ifdef TRILINOS  #ifdef TRILINOS
1579        /* Allocation Epetra_VrbMatrix here */        /* Allocation Epetra_VrbMatrix here */
1580  #endif  #endif
1581      }     }
1582      else {     else {
1583        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);
1584      }     }
1585      checkPasoError();     checkPasoError();
1586      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1587      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1588  }  }
1589  // creates a TransportProblemAdapter  // creates a TransportProblemAdapter
1590  TransportProblemAdapter MeshAdapter::newTransportProblem(  TransportProblemAdapter MeshAdapter::newTransportProblem(
1591                        const double theta,                                                           const double theta,
1592                        const double dt_max,                                                           const int blocksize,
1593                        const int blocksize,                                                           const escript::FunctionSpace& functionspace,
1594                        const escript::FunctionSpace& functionspace,                                                           const int type) const
1595                        const int type) const  {
1596  {     int reduceOrder=0;
1597      int reduceOrder=0;     // is the domain right?
1598      // is the domain right?     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());
1599      const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(functionspace.getDomain());     if (domain!=*this)
1600      if (domain!=*this)        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1601            throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");     // is the function space type right
1602      // is the function space type right     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1603      if (functionspace.getTypeCode()==DegreesOfFreedom) {        reduceOrder=0;
1604          reduceOrder=0;     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1605      } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {        reduceOrder=1;
1606          reduceOrder=1;     } else {
1607      } else {        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1608          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");     }
1609      }     // generate matrix:
1610      // generate matrix:  
1611           Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1612      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);     checkFinleyError();
1613      checkFinleyError();     Paso_FCTransportProblem* transportProblem;
1614      Paso_FCTransportProblem* transportProblem;     transportProblem=Paso_FCTransportProblem_alloc(theta,fsystemMatrixPattern,blocksize);
1615      transportProblem=Paso_FCTransportProblem_alloc(theta,dt_max,fsystemMatrixPattern,blocksize);     checkPasoError();
1616      checkPasoError();     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1617      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     return TransportProblemAdapter(transportProblem,theta,blocksize,functionspace);
     return TransportProblemAdapter(transportProblem,theta,dt_max,blocksize,functionspace);  
1618  }  }
1619    
1620  //  //
# Line 1639  TransportProblemAdapter MeshAdapter::new Line 1626  TransportProblemAdapter MeshAdapter::new
1626  // 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:
1627  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1628  {  {
1629    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1630         case(Nodes):     case(Nodes):
1631         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1632         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1633            return false;     return false;
1634            break;     break;
1635         case(Elements):     case(Elements):
1636         case(FaceElements):     case(FaceElements):
1637         case(Points):     case(Points):
1638         case(ContactElementsZero):     case(ContactElementsZero):
1639         case(ContactElementsOne):     case(ContactElementsOne):
1640         case(ReducedElements):     case(ReducedElements):
1641         case(ReducedFaceElements):     case(ReducedFaceElements):
1642         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1643         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1644            return true;     return true;
1645            break;     break;
1646         default:     default:
1647            stringstream temp;        stringstream temp;
1648            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;
1649            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1650            break;        break;
1651    }     }
1652    checkFinleyError();     checkFinleyError();
1653    return false;     return false;
1654  }  }
1655    
1656  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1657  {  {
1658    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1659       case(Nodes):     case(Nodes):
1660          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1661             case(Nodes):     case(Nodes):
1662             case(ReducedNodes):     case(ReducedNodes):
1663             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1664             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1665             case(Elements):     case(Elements):
1666             case(ReducedElements):     case(ReducedElements):
1667             case(FaceElements):     case(FaceElements):
1668             case(ReducedFaceElements):     case(ReducedFaceElements):
1669             case(Points):     case(Points):
1670             case(ContactElementsZero):     case(ContactElementsZero):
1671             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1672             case(ContactElementsOne):     case(ContactElementsOne):
1673             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1674                 return true;     return true;
1675             default:     default:
1676                 stringstream temp;        stringstream temp;
1677                 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;
1678                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1679          }     }
1680          break;     break;
1681       case(ReducedNodes):     case(ReducedNodes):
1682          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1683             case(ReducedNodes):     case(ReducedNodes):
1684             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1685             case(Elements):     case(Elements):
1686             case(ReducedElements):     case(ReducedElements):
1687             case(FaceElements):     case(FaceElements):
1688             case(ReducedFaceElements):     case(ReducedFaceElements):
1689             case(Points):     case(Points):
1690             case(ContactElementsZero):     case(ContactElementsZero):
1691             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1692             case(ContactElementsOne):     case(ContactElementsOne):
1693             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1694                 return true;     return true;
1695            case(Nodes):     case(Nodes):
1696            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1697               return false;     return false;
1698             default:     default:
1699                 stringstream temp;        stringstream temp;
1700                 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;
1701                 throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1702          }     }
1703          break;     break;
1704       case(Elements):     case(Elements):
1705          if (functionSpaceType_target==Elements) {     if (functionSpaceType_target==Elements) {
1706             return true;        return true;
1707          } else if (functionSpaceType_target==ReducedElements) {     } else if (functionSpaceType_target==ReducedElements) {
1708             return true;        return true;
1709          } else {     } else {
1710             return false;        return false;
1711          }     }
1712       case(ReducedElements):     case(ReducedElements):
1713          if (functionSpaceType_target==ReducedElements) {     if (functionSpaceType_target==ReducedElements) {
1714             return true;        return true;
1715          } else {     } else {
1716             return false;        return false;
1717          }     }
1718       case(FaceElements):     case(FaceElements):
1719          if (functionSpaceType_target==FaceElements) {     if (functionSpaceType_target==FaceElements) {
1720             return true;        return true;
1721          } else if (functionSpaceType_target==ReducedFaceElements) {     } else if (functionSpaceType_target==ReducedFaceElements) {
1722             return true;        return true;
1723          } else {     } else {
1724             return false;        return false;
1725          }     }
1726       case(ReducedFaceElements):     case(ReducedFaceElements):
1727          if (functionSpaceType_target==ReducedFaceElements) {     if (functionSpaceType_target==ReducedFaceElements) {
1728             return true;        return true;
1729          } else {     } else {
1730             return false;        return false;
1731          }     }
1732       case(Points):     case(Points):
1733          if (functionSpaceType_target==Points) {     if (functionSpaceType_target==Points) {
1734             return true;        return true;
1735          } else {     } else {
1736             return false;        return false;
1737          }     }
1738       case(ContactElementsZero):     case(ContactElementsZero):
1739       case(ContactElementsOne):     case(ContactElementsOne):
1740          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {     if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1741             return true;        return true;
1742          } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1743             return true;        return true;
1744          } else {     } else {
1745             return false;        return false;
1746          }     }
1747       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1748       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1749          if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {     if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1750             return true;        return true;
1751          } else {     } else {
1752             return false;        return false;
1753          }     }
1754       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1755          switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1756             case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1757             case(DegreesOfFreedom):     case(DegreesOfFreedom):
1758             case(Nodes):     case(Nodes):
1759             case(ReducedNodes):     case(ReducedNodes):
1760             case(Elements):     case(Elements):
1761             case(ReducedElements):     case(ReducedElements):
1762             case(Points):     case(Points):
1763             case(FaceElements):     case(FaceElements):
1764             case(ReducedFaceElements):     case(ReducedFaceElements):
1765             case(ContactElementsZero):     case(ContactElementsZero):
1766             case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1767             case(ContactElementsOne):     case(ContactElementsOne):
1768             case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1769                return true;     return true;
1770             default:     default:
1771               stringstream temp;        stringstream temp;
1772               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;
1773               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1774          }     }
1775          break;     break;
1776       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1777         switch(functionSpaceType_target) {     switch(functionSpaceType_target) {
1778            case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1779            case(ReducedNodes):     case(ReducedNodes):
1780            case(Elements):     case(Elements):
1781            case(ReducedElements):     case(ReducedElements):
1782            case(FaceElements):     case(FaceElements):
1783            case(ReducedFaceElements):     case(ReducedFaceElements):
1784            case(Points):     case(Points):
1785            case(ContactElementsZero):     case(ContactElementsZero):
1786            case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1787            case(ContactElementsOne):     case(ContactElementsOne):
1788            case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1789                return true;     return true;
1790            case(Nodes):     case(Nodes):
1791            case(DegreesOfFreedom):     case(DegreesOfFreedom):
1792               return false;     return false;
1793            default:     default:
1794               stringstream temp;        stringstream temp;
1795               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;
1796               throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1797         }     }
1798         break;     break;
1799       default:     default:
1800          stringstream temp;        stringstream temp;
1801          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;
1802          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1803          break;        break;
1804    }     }
1805    checkFinleyError();     checkFinleyError();
1806    return false;     return false;
1807  }  }
1808    
1809  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
1810  {  {
1811      return false;     return false;
1812  }  }
1813    
1814  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
1815  {  {
1816    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
1817    if (temp!=0) {     if (temp!=0) {
1818      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
1819    } else {     } else {
1820      return false;        return false;
1821    }     }
1822  }  }
1823    
1824  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
1825  {  {
1826    return !(operator==(other));     return !(operator==(other));
1827  }  }
1828    
1829  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const  int MeshAdapter::getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1830  {  {
1831     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1832       checkPasoError();
1833       return out;
1834    }
1835    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
1836    {
1837       int out=Paso_FCTransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);
1838     checkPasoError();     checkPasoError();
1839     return out;     return out;
1840  }  }
1841    
1842  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
1843  {  {
1844    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
1845  }  }
1846    
1847  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
1848  {  {
1849    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
1850  }  }
1851    
1852  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
1853  {  {
1854    return function(asAbstractContinuousDomain()).getSize();     return function(asAbstractContinuousDomain()).getSize();
1855  }  }
1856    
1857  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
1858  {  {
1859    int *out=0,i;     int *out = NULL;
1860    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1861    switch (functionSpaceType) {     switch (functionSpaceType) {
1862      case(Nodes):     case(Nodes):
1863        out=mesh->Nodes->Id;     out=mesh->Nodes->Id;
1864        break;     break;
1865      case(ReducedNodes):     case(ReducedNodes):
1866        out=mesh->Nodes->reducedNodesId;     out=mesh->Nodes->reducedNodesId;
1867        break;     break;
1868      case(Elements):     case(Elements):
1869        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1870        break;     break;
1871      case(ReducedElements):     case(ReducedElements):
1872        out=mesh->Elements->Id;     out=mesh->Elements->Id;
1873        break;     break;
1874      case(FaceElements):     case(FaceElements):
1875        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1876        break;     break;
1877      case(ReducedFaceElements):     case(ReducedFaceElements):
1878        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
1879        break;     break;
1880      case(Points):     case(Points):
1881        out=mesh->Points->Id;     out=mesh->Points->Id;
1882        break;     break;
1883      case(ContactElementsZero):     case(ContactElementsZero):
1884        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1885        break;     break;
1886      case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1887        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1888        break;     break;
1889      case(ContactElementsOne):     case(ContactElementsOne):
1890        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1891        break;     break;
1892      case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1893        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
1894        break;     break;
1895      case(DegreesOfFreedom):     case(DegreesOfFreedom):
1896        out=mesh->Nodes->degreesOfFreedomId;     out=mesh->Nodes->degreesOfFreedomId;
1897        break;     break;
1898      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1899        out=mesh->Nodes->reducedDegreesOfFreedomId;     out=mesh->Nodes->reducedDegreesOfFreedomId;
1900        break;     break;
1901      default:     default:
1902        stringstream temp;        stringstream temp;
1903        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1904        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1905        break;        break;
1906    }     }
1907    return out;     return out;
1908  }  }
1909  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
1910  {  {
1911    int out=0;     int out=0;
1912    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1913    switch (functionSpaceType) {     switch (functionSpaceType) {
1914    case(Nodes):     case(Nodes):
1915      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
1916      break;     break;
1917    case(ReducedNodes):     case(ReducedNodes):
1918      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
1919      break;     break;
1920    case(Elements):     case(Elements):
1921      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1922      break;     break;
1923    case(ReducedElements):     case(ReducedElements):
1924      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
1925      break;     break;
1926    case(FaceElements):     case(FaceElements):
1927      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1928      break;     break;
1929    case(ReducedFaceElements):     case(ReducedFaceElements):
1930      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
1931      break;     break;
1932    case(Points):     case(Points):
1933      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
1934      break;     break;
1935    case(ContactElementsZero):     case(ContactElementsZero):
1936      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1937      break;     break;
1938    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1939      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1940      break;     break;
1941    case(ContactElementsOne):     case(ContactElementsOne):
1942      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1943      break;     break;
1944    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1945      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
1946      break;     break;
1947    case(DegreesOfFreedom):     case(DegreesOfFreedom):
1948      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
1949      break;     break;
1950    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1951      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
1952      break;     break;
1953    default:     default:
1954      stringstream temp;        stringstream temp;
1955      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
1956      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1957      break;        break;
1958    }     }
1959    return out;     return out;
1960  }  }
1961    
1962    
1963  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
1964  {  {
1965       Finley_Mesh* mesh=m_finleyMesh.get();
1966       escriptDataC tmp=mask.getDataC();
1967       switch(functionSpaceType) {
1968       case(Nodes):
1969       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
1970       break;
1971       case(ReducedNodes):
1972       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
1973       break;
1974       case(DegreesOfFreedom):
1975       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
1976       break;
1977       case(ReducedDegreesOfFreedom):
1978       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
1979       break;
1980       case(Elements):
1981       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1982       break;
1983       case(ReducedElements):
1984       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
1985       break;
1986       case(FaceElements):
1987       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1988       break;
1989       case(ReducedFaceElements):
1990       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
1991       break;
1992       case(Points):
1993       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
1994       break;
1995       case(ContactElementsZero):
1996       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
1997       break;
1998       case(ReducedContactElementsZero):
1999       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2000       break;
2001       case(ContactElementsOne):
2002       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2003       break;
2004       case(ReducedContactElementsOne):
2005       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2006       break;
2007       default:
2008          stringstream temp;
2009          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2010          throw FinleyAdapterException(temp.str());
2011       }
2012       checkFinleyError();
2013       return;
2014    }
2015    
2016    void MeshAdapter::setTagMap(const std::string& name,  int tag)
2017    {
2018       Finley_Mesh* mesh=m_finleyMesh.get();
2019       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2020       checkPasoError();
2021       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2022    }
2023    
2024    int MeshAdapter::getTag(const std::string& name) const
2025    {
2026       Finley_Mesh* mesh=m_finleyMesh.get();
2027       int tag=0;
2028       tag=Finley_Mesh_getTag(mesh, name.c_str());
2029       checkPasoError();
2030       // throwStandardException("MeshAdapter::getTag is not implemented.");
2031       return tag;
2032    }
2033    
2034    bool MeshAdapter::isValidTagName(const std::string& name) const
2035    {
2036       Finley_Mesh* mesh=m_finleyMesh.get();
2037       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2038    }
2039    
2040    std::string MeshAdapter::showTagNames() const
2041    {
2042       stringstream temp;
2043       Finley_Mesh* mesh=m_finleyMesh.get();
2044       Finley_TagMap* tag_map=mesh->TagMap;
2045       while (tag_map) {
2046          temp << tag_map->name;
2047          tag_map=tag_map->next;
2048          if (tag_map) temp << ", ";
2049       }
2050       return temp.str();
2051    }
2052    
2053    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2054    {
2055    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2056    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2057    switch(functionSpaceType) {    switch(functionSpaceCode) {
2058         case(Nodes):     case(Nodes):
2059            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2060            break;            break;
2061         case(ReducedNodes):     case(ReducedNodes):
2062            throw FinleyAdapterException("Error - ReducedNodes does not support tags");            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2063            break;            break;
2064         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2065            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2066            break;            break;
2067         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2068            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2069            break;            break;
2070         case(Elements):     case(Elements):
2071            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2072            break;            numTags=mesh->Elements->numTagsInUse;
2073         case(ReducedElements):            break;
2074            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(FaceElements):
2075            break;     case(ReducedFaceElements):
2076         case(FaceElements):            numTags=mesh->FaceElements->numTagsInUse;
2077            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);            break;
2078            break;     case(Points):
2079         case(ReducedFaceElements):            numTags=mesh->Points->numTagsInUse;
2080            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);            break;
2081       case(ContactElementsZero):
2082       case(ReducedContactElementsZero):
2083       case(ContactElementsOne):
2084       case(ReducedContactElementsOne):
2085              numTags=mesh->ContactElements->numTagsInUse;
2086            break;            break;
2087         case(Points):     default:
2088            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);        stringstream temp;
2089          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2090          throw FinleyAdapterException(temp.str());
2091      }
2092      return numTags;
2093    }
2094    int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2095    {
2096      Finley_Mesh* mesh=m_finleyMesh.get();
2097      index_t* tags=NULL;
2098      switch(functionSpaceCode) {
2099       case(Nodes):
2100              tags=mesh->Nodes->tagsInUse;
2101            break;            break;
2102         case(ContactElementsZero):     case(ReducedNodes):
2103            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2104            break;            break;
2105         case(ReducedContactElementsZero):     case(DegreesOfFreedom):
2106            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2107            break;            break;
2108         case(ContactElementsOne):     case(ReducedDegreesOfFreedom):
2109            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2110            break;            break;
2111         case(ReducedContactElementsOne):     case(Elements):
2112            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2113              tags=mesh->Elements->tagsInUse;
2114              break;
2115       case(FaceElements):
2116       case(ReducedFaceElements):
2117              tags=mesh->FaceElements->tagsInUse;
2118              break;
2119       case(Points):
2120              tags=mesh->Points->tagsInUse;
2121              break;
2122       case(ContactElementsZero):
2123       case(ReducedContactElementsZero):
2124       case(ContactElementsOne):
2125       case(ReducedContactElementsOne):
2126              tags=mesh->ContactElements->tagsInUse;
2127            break;            break;
2128         default:     default:
2129            stringstream temp;        stringstream temp;
2130            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2131            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2132    }    }
2133    checkFinleyError();    return tags;
   return;  
2134  }  }
2135    
 void MeshAdapter::setTagMap(const std::string& name,  int tag)  
 {  
   Finley_Mesh* mesh=m_finleyMesh.get();  
   Finley_Mesh_addTagMap(mesh, name.c_str(),tag);  
   checkPasoError();  
   // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
 }  
2136    
2137  int MeshAdapter::getTag(const std::string& name) const  bool MeshAdapter::canTag(int functionSpaceCode) const
2138  {  {
2139    Finley_Mesh* mesh=m_finleyMesh.get();    switch(functionSpaceCode) {
2140    int tag=0;     case(Nodes):
2141    tag=Finley_Mesh_getTag(mesh, name.c_str());     case(Elements):
2142    checkPasoError();     case(ReducedElements):
2143    // throwStandardException("MeshAdapter::getTag is not implemented.");     case(FaceElements):
2144    return tag;     case(ReducedFaceElements):
2145  }     case(Points):
2146       case(ContactElementsZero):
2147  bool MeshAdapter::isValidTagName(const std::string& name) const     case(ReducedContactElementsZero):
2148  {     case(ContactElementsOne):
2149    Finley_Mesh* mesh=m_finleyMesh.get();     case(ReducedContactElementsOne):
2150    return Finley_Mesh_isValidTagName(mesh,name.c_str());            return true;
2151  }     case(ReducedNodes):
2152       case(DegreesOfFreedom):
2153  std::string MeshAdapter::showTagNames() const     case(ReducedDegreesOfFreedom):
2154  {        return false;
2155    stringstream temp;     default:
2156    Finley_Mesh* mesh=m_finleyMesh.get();      return false;
   Finley_TagMap* tag_map=mesh->TagMap;  
   while (tag_map) {  
      temp << tag_map->name;  
      tag_map=tag_map->next;  
      if (tag_map) temp << ", ";  
2157    }    }
   return temp.str();  
2158  }  }
2159    
2160    
2161  }  // end of namespace  }  // end of namespace

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