/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
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revision 1339 by ksteube, Wed Nov 7 01:53:12 2007 UTC revision 3911 by jfenwick, Thu Jun 14 01:01:03 2012 UTC
# Line 1  Line 1 
1    
 /* $Id$ */  
   
2  /*******************************************************  /*******************************************************
3   *  *
4   *           Copyright 2003-2007 by ACceSS MNRF  * Copyright (c) 2003-2012 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    #include <pasowrap/PasoException.h>
15    #include <pasowrap/TransportProblemAdapter.h>
16  #include "MeshAdapter.h"  #include "MeshAdapter.h"
17  #include "escript/Data.h"  #include "escript/Data.h"
18  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
19    #ifdef USE_NETCDF
20    #include <netcdfcpp.h>
21    #endif
22  extern "C" {  extern "C" {
23  #include "escript/blocktimer.h"  #include "esysUtils/blocktimer.h"
24  }  }
25  #include <vector>  
26    #include <boost/python/import.hpp>
27    
28  using namespace std;  using namespace std;
29  using namespace escript;  using namespace escript;
30    using namespace paso;
31    
32  namespace finley {  namespace finley {
33    
# Line 45  const int MeshAdapter::ReducedContactEle Line 50  const int MeshAdapter::ReducedContactEle
50    
51  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
52  {  {
53    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
54    //     //
55    // need to use a null_deleter as Finley_Mesh_free deletes the pointer     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
56    // for us.     // for us.
57    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
58  }  }
59    
60  //  //
# Line 57  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 62  MeshAdapter::MeshAdapter(Finley_Mesh* fi
62  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
63  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
64  {  {
65    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
66  }  }
67    
68  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
69  {  {
70    //     //
71    // I hope the case for the pointer being zero has been taken care of.     // I hope the case for the pointer being zero has been taken care of.
72    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
73    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
74      Finley_Mesh_free(m_finleyMesh.get());        Finley_Mesh_free(m_finleyMesh.get());
75    }     }
76  }  }
77    
78  int MeshAdapter::getMPISize() const  int MeshAdapter::getMPISize() const
# Line 78  int MeshAdapter::getMPIRank() const Line 83  int MeshAdapter::getMPIRank() const
83  {  {
84     return m_finleyMesh.get()->MPIInfo->rank;     return m_finleyMesh.get()->MPIInfo->rank;
85  }  }
86    void MeshAdapter::MPIBarrier() const
87    {
88    #ifdef ESYS_MPI
89       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
90    #endif
91       return;
92    }
93    bool MeshAdapter::onMasterProcessor() const
94    {
95       return m_finleyMesh.get()->MPIInfo->rank == 0;
96    }
97    
98    
99    #ifdef ESYS_MPI
100      MPI_Comm
101    #else
102      unsigned int
103    #endif
104    MeshAdapter::getMPIComm() const
105    {
106    #ifdef ESYS_MPI
107        return m_finleyMesh->MPIInfo->comm;
108    #else
109        return 0;
110    #endif
111    }
112    
113    
114  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
115     return m_finleyMesh.get();     return m_finleyMesh.get();
116  }  }
117    
118  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
119  {  {
120    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;
121    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
122    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
123    checkFinleyError();     checkFinleyError();
124    TMPMEMFREE(fName);     TMPMEMFREE(fName);
125  }  }
126    
127  void MeshAdapter::Print_Mesh_Info(const bool full=false) const  void MeshAdapter::Print_Mesh_Info(const bool full) const
128  {  {
129    Finley_PrintMesh_Info(m_finleyMesh.get(), full);     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
130  }  }
131    
132  void MeshAdapter::dump(const std::string& fileName) const  void MeshAdapter::dump(const string& fileName) const
133  {  {
134    char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;  #ifdef USE_NETCDF
135    strcpy(fName,fileName.c_str());     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
136    Finley_Mesh_dump(m_finleyMesh.get(),fName);     NcVar *ids;
137    checkFinleyError();     int *int_ptr;
138    TMPMEMFREE(fName);     Finley_Mesh *mesh = m_finleyMesh.get();
139       Finley_TagMap* tag_map;
140       int num_Tags = 0;
141       int mpi_size             = mesh->MPIInfo->size;
142       int mpi_rank             = mesh->MPIInfo->rank;
143       int numDim               = mesh->Nodes->numDim;
144       int numNodes             = mesh->Nodes->numNodes;
145       int num_Elements         = mesh->Elements->numElements;
146       int num_FaceElements         = mesh->FaceElements->numElements;
147       int num_ContactElements      = mesh->ContactElements->numElements;
148       int num_Points           = mesh->Points->numElements;
149       int num_Elements_numNodes        = mesh->Elements->numNodes;
150       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
151       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
152    #ifdef ESYS_MPI
153       MPI_Status status;
154    #endif
155    
156    /* Incoming token indicates it's my turn to write */
157    #ifdef ESYS_MPI
158       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
159    #endif
160    
161       char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
162                                                         mpi_size, mpi_rank);
163    
164       /* Figure out how much storage is required for tags */
165       tag_map = mesh->TagMap;
166       num_Tags = 0;
167       while (tag_map) {
168          num_Tags++;
169          tag_map=tag_map->next;
170       }
171    
172       // NetCDF error handler
173       NcError err(NcError::verbose_nonfatal);
174       // Create the file.
175       NcFile dataFile(newFileName, NcFile::Replace);
176       string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
177       // check if writing was successful
178       if (!dataFile.is_valid())
179          throw DataException(msgPrefix+"Open file for output");
180    
181       // Define dimensions (num_Elements and dim_Elements are identical,
182       // dim_Elements only appears if > 0)
183       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
184          throw DataException(msgPrefix+"add_dim(numNodes)");
185       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
186          throw DataException(msgPrefix+"add_dim(numDim)");
187       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
188          throw DataException(msgPrefix+"add_dim(mpi_size)");
189       if (num_Elements>0)
190          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
191             throw DataException(msgPrefix+"add_dim(dim_Elements)");
192       if (num_FaceElements>0)
193          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
194             throw DataException(msgPrefix+"add_dim(dim_FaceElements)");
195       if (num_ContactElements>0)
196          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
197             throw DataException(msgPrefix+"add_dim(dim_ContactElements)");
198       if (num_Points>0)
199          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
200             throw DataException(msgPrefix+"add_dim(dim_Points)");
201       if (num_Elements>0)
202          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
203             throw DataException(msgPrefix+"add_dim(dim_Elements_Nodes)");
204       if (num_FaceElements>0)
205          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
206             throw DataException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
207       if (num_ContactElements>0)
208          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
209             throw DataException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
210       if (num_Tags>0)
211          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
212             throw DataException(msgPrefix+"add_dim(dim_Tags)");
213    
214       // Attributes: MPI size, MPI rank, Name, order, reduced_order
215       if (!dataFile.add_att("mpi_size", mpi_size) )
216          throw DataException(msgPrefix+"add_att(mpi_size)");
217       if (!dataFile.add_att("mpi_rank", mpi_rank) )
218          throw DataException(msgPrefix+"add_att(mpi_rank)");
219       if (!dataFile.add_att("Name",mesh->Name) )
220          throw DataException(msgPrefix+"add_att(Name)");
221       if (!dataFile.add_att("numDim",numDim) )
222          throw DataException(msgPrefix+"add_att(order)");
223       if (!dataFile.add_att("order",mesh->integrationOrder) )
224          throw DataException(msgPrefix+"add_att(order)");
225       if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
226          throw DataException(msgPrefix+"add_att(reduced_order)");
227       if (!dataFile.add_att("numNodes",numNodes) )
228          throw DataException(msgPrefix+"add_att(numNodes)");
229       if (!dataFile.add_att("num_Elements",num_Elements) )
230          throw DataException(msgPrefix+"add_att(num_Elements)");
231       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
232          throw DataException(msgPrefix+"add_att(num_FaceElements)");
233       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
234          throw DataException(msgPrefix+"add_att(num_ContactElements)");
235       if (!dataFile.add_att("num_Points",num_Points) )
236          throw DataException(msgPrefix+"add_att(num_Points)");
237       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
238          throw DataException(msgPrefix+"add_att(num_Elements_numNodes)");
239       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
240          throw DataException(msgPrefix+"add_att(num_FaceElements_numNodes)");
241       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
242          throw DataException(msgPrefix+"add_att(num_ContactElements_numNodes)");
243       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
244          throw DataException(msgPrefix+"add_att(Elements_TypeId)");
245       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
246          throw DataException(msgPrefix+"add_att(FaceElements_TypeId)");
247       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
248          throw DataException(msgPrefix+"add_att(ContactElements_TypeId)");
249       if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
250          throw DataException(msgPrefix+"add_att(Points_TypeId)");
251       if (!dataFile.add_att("num_Tags", num_Tags) )
252          throw DataException(msgPrefix+"add_att(num_Tags)");
253    
254       // // // // // Nodes // // // // //
255    
256       // Nodes nodeDistribution
257       if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
258          throw DataException(msgPrefix+"add_var(Nodes_NodeDistribution)");
259       int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
260       if (! (ids->put(int_ptr, mpi_size+1)) )
261          throw DataException(msgPrefix+"put(Nodes_NodeDistribution)");
262    
263       // Nodes degreesOfFreedomDistribution
264       if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
265          throw DataException(msgPrefix+"add_var(Nodes_DofDistribution)");
266       int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
267       if (! (ids->put(int_ptr, mpi_size+1)) )
268          throw DataException(msgPrefix+"put(Nodes_DofDistribution)");
269    
270       // Only write nodes if non-empty because NetCDF doesn't like empty arrays
271       // (it treats them as NC_UNLIMITED)
272       if (numNodes>0) {
273    
274          // Nodes Id
275          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
276             throw DataException(msgPrefix+"add_var(Nodes_Id)");
277          int_ptr = &mesh->Nodes->Id[0];
278          if (! (ids->put(int_ptr, numNodes)) )
279             throw DataException(msgPrefix+"put(Nodes_Id)");
280    
281          // Nodes Tag
282          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
283             throw DataException(msgPrefix+"add_var(Nodes_Tag)");
284          int_ptr = &mesh->Nodes->Tag[0];
285          if (! (ids->put(int_ptr, numNodes)) )
286             throw DataException(msgPrefix+"put(Nodes_Tag)");
287    
288          // Nodes gDOF
289          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
290             throw DataException(msgPrefix+"add_var(Nodes_gDOF)");
291          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
292          if (! (ids->put(int_ptr, numNodes)) )
293             throw DataException(msgPrefix+"put(Nodes_gDOF)");
294    
295          // Nodes global node index
296          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
297             throw DataException(msgPrefix+"add_var(Nodes_gNI)");
298          int_ptr = &mesh->Nodes->globalNodesIndex[0];
299          if (! (ids->put(int_ptr, numNodes)) )
300             throw DataException(msgPrefix+"put(Nodes_gNI)");
301    
302          // Nodes grDof
303          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
304             throw DataException(msgPrefix+"add_var(Nodes_grDfI)");
305          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
306          if (! (ids->put(int_ptr, numNodes)) )
307             throw DataException(msgPrefix+"put(Nodes_grDfI)");
308    
309          // Nodes grNI
310          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
311             throw DataException(msgPrefix+"add_var(Nodes_grNI)");
312          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
313          if (! (ids->put(int_ptr, numNodes)) )
314             throw DataException(msgPrefix+"put(Nodes_grNI)");
315    
316          // Nodes Coordinates
317          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
318             throw DataException(msgPrefix+"add_var(Nodes_Coordinates)");
319          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
320             throw DataException(msgPrefix+"put(Nodes_Coordinates)");
321    
322       }
323    
324       // // // // // Elements // // // // //
325    
326       if (num_Elements>0) {
327    
328          // Elements_Id
329          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
330             throw DataException(msgPrefix+"add_var(Elements_Id)");
331          int_ptr = &mesh->Elements->Id[0];
332          if (! (ids->put(int_ptr, num_Elements)) )
333             throw DataException(msgPrefix+"put(Elements_Id)");
334    
335          // Elements_Tag
336          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
337             throw DataException(msgPrefix+"add_var(Elements_Tag)");
338          int_ptr = &mesh->Elements->Tag[0];
339          if (! (ids->put(int_ptr, num_Elements)) )
340             throw DataException(msgPrefix+"put(Elements_Tag)");
341    
342          // Elements_Owner
343          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
344             throw DataException(msgPrefix+"add_var(Elements_Owner)");
345          int_ptr = &mesh->Elements->Owner[0];
346          if (! (ids->put(int_ptr, num_Elements)) )
347             throw DataException(msgPrefix+"put(Elements_Owner)");
348    
349          // Elements_Color
350          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
351             throw DataException(msgPrefix+"add_var(Elements_Color)");
352          int_ptr = &mesh->Elements->Color[0];
353          if (! (ids->put(int_ptr, num_Elements)) )
354             throw DataException(msgPrefix+"put(Elements_Color)");
355    
356          // Elements_Nodes
357          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
358             throw DataException(msgPrefix+"add_var(Elements_Nodes)");
359          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
360             throw DataException(msgPrefix+"put(Elements_Nodes)");
361    
362       }
363    
364       // // // // // Face_Elements // // // // //
365    
366       if (num_FaceElements>0) {
367    
368          // FaceElements_Id
369          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
370             throw DataException(msgPrefix+"add_var(FaceElements_Id)");
371          int_ptr = &mesh->FaceElements->Id[0];
372          if (! (ids->put(int_ptr, num_FaceElements)) )
373             throw DataException(msgPrefix+"put(FaceElements_Id)");
374    
375          // FaceElements_Tag
376          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
377             throw DataException(msgPrefix+"add_var(FaceElements_Tag)");
378          int_ptr = &mesh->FaceElements->Tag[0];
379          if (! (ids->put(int_ptr, num_FaceElements)) )
380             throw DataException(msgPrefix+"put(FaceElements_Tag)");
381    
382          // FaceElements_Owner
383          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
384             throw DataException(msgPrefix+"add_var(FaceElements_Owner)");
385          int_ptr = &mesh->FaceElements->Owner[0];
386          if (! (ids->put(int_ptr, num_FaceElements)) )
387             throw DataException(msgPrefix+"put(FaceElements_Owner)");
388    
389          // FaceElements_Color
390          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
391             throw DataException(msgPrefix+"add_var(FaceElements_Color)");
392          int_ptr = &mesh->FaceElements->Color[0];
393          if (! (ids->put(int_ptr, num_FaceElements)) )
394             throw DataException(msgPrefix+"put(FaceElements_Color)");
395    
396          // FaceElements_Nodes
397          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
398             throw DataException(msgPrefix+"add_var(FaceElements_Nodes)");
399          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
400             throw DataException(msgPrefix+"put(FaceElements_Nodes)");
401    
402       }
403    
404       // // // // // Contact_Elements // // // // //
405    
406       if (num_ContactElements>0) {
407    
408          // ContactElements_Id
409          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
410             throw DataException(msgPrefix+"add_var(ContactElements_Id)");
411          int_ptr = &mesh->ContactElements->Id[0];
412          if (! (ids->put(int_ptr, num_ContactElements)) )
413             throw DataException(msgPrefix+"put(ContactElements_Id)");
414    
415          // ContactElements_Tag
416          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
417             throw DataException(msgPrefix+"add_var(ContactElements_Tag)");
418          int_ptr = &mesh->ContactElements->Tag[0];
419          if (! (ids->put(int_ptr, num_ContactElements)) )
420             throw DataException(msgPrefix+"put(ContactElements_Tag)");
421    
422          // ContactElements_Owner
423          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
424             throw DataException(msgPrefix+"add_var(ContactElements_Owner)");
425          int_ptr = &mesh->ContactElements->Owner[0];
426          if (! (ids->put(int_ptr, num_ContactElements)) )
427             throw DataException(msgPrefix+"put(ContactElements_Owner)");
428    
429          // ContactElements_Color
430          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
431             throw DataException(msgPrefix+"add_var(ContactElements_Color)");
432          int_ptr = &mesh->ContactElements->Color[0];
433          if (! (ids->put(int_ptr, num_ContactElements)) )
434             throw DataException(msgPrefix+"put(ContactElements_Color)");
435    
436          // ContactElements_Nodes
437          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
438             throw DataException(msgPrefix+"add_var(ContactElements_Nodes)");
439          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
440             throw DataException(msgPrefix+"put(ContactElements_Nodes)");
441    
442       }
443    
444       // // // // // Points // // // // //
445    
446       if (num_Points>0) {
447    
448          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
449    
450          // Points_Id
451          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
452             throw DataException(msgPrefix+"add_var(Points_Id)");
453          int_ptr = &mesh->Points->Id[0];
454          if (! (ids->put(int_ptr, num_Points)) )
455             throw DataException(msgPrefix+"put(Points_Id)");
456    
457          // Points_Tag
458          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
459             throw DataException(msgPrefix+"add_var(Points_Tag)");
460          int_ptr = &mesh->Points->Tag[0];
461          if (! (ids->put(int_ptr, num_Points)) )
462             throw DataException(msgPrefix+"put(Points_Tag)");
463    
464          // Points_Owner
465          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
466             throw DataException(msgPrefix+"add_var(Points_Owner)");
467          int_ptr = &mesh->Points->Owner[0];
468          if (! (ids->put(int_ptr, num_Points)) )
469             throw DataException(msgPrefix+"put(Points_Owner)");
470    
471          // Points_Color
472          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
473             throw DataException(msgPrefix+"add_var(Points_Color)");
474          int_ptr = &mesh->Points->Color[0];
475          if (! (ids->put(int_ptr, num_Points)) )
476             throw DataException(msgPrefix+"put(Points_Color)");
477    
478          // Points_Nodes
479          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
480          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
481             throw DataException(msgPrefix+"add_var(Points_Nodes)");
482          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
483             throw DataException(msgPrefix+"put(Points_Nodes)");
484    
485       }
486    
487       // // // // // TagMap // // // // //
488    
489       if (num_Tags>0) {
490    
491          // Temp storage to gather node IDs
492          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
493          char name_temp[4096];
494    
495          /* Copy tag data into temp arrays */
496          tag_map = mesh->TagMap;
497          if (tag_map) {
498             int i = 0;
499             while (tag_map) {
500                Tags_keys[i++] = tag_map->tag_key;
501                tag_map=tag_map->next;
502             }
503          }
504    
505          // Tags_keys
506          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
507             throw DataException(msgPrefix+"add_var(Tags_keys)");
508          int_ptr = &Tags_keys[0];
509          if (! (ids->put(int_ptr, num_Tags)) )
510             throw DataException(msgPrefix+"put(Tags_keys)");
511    
512          // Tags_names_*
513          // This is an array of strings, it should be stored as an array but
514          // instead I have hacked in one attribute per string because the NetCDF
515          // manual doesn't tell how to do an array of strings
516          tag_map = mesh->TagMap;
517          if (tag_map) {
518             int i = 0;
519             while (tag_map) {
520                sprintf(name_temp, "Tags_name_%d", i);
521                if (!dataFile.add_att(name_temp, tag_map->name) )
522                   throw DataException(msgPrefix+"add_att(Tags_names_XX)");
523                tag_map=tag_map->next;
524                i++;
525             }
526          }
527    
528          TMPMEMFREE(Tags_keys);
529       }
530    
531    /* Send token to next MPI process so he can take his turn */
532    #ifdef ESYS_MPI
533       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
534    #endif
535    
536       // NetCDF file is closed by destructor of NcFile object
537    
538    #else
539       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
540    #endif  /* USE_NETCDF */
541       checkFinleyError();
542  }  }
543    
544  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
545  {  {
546    return "FinleyMesh";     return "FinleyMesh";
547  }  }
548    
549  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
550  {  {
551    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
552    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
553    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
554      return "Invalid function space type code.";        return "Invalid function space type code.";
555    } else {     } else {
556      return loc->second;        return loc->second;
557    }     }
558  }  }
559    
560  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
561  {  {
562    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
563    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
564    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
565  }  }
566    
567  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
568  {  {
569    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
570      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
571    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
572      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
573    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
574      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
575    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
576      (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
577    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
578      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
579    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
580      (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
581    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
582      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
583    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
584      (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
585    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
586      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
587    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
588      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
589    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
590      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
591    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
592      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
593    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
594      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
595  }  }
596    
597  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
598  {  {
599    return Nodes;     return Nodes;
600  }  }
601  int MeshAdapter::getReducedContinuousFunctionCode() const  int MeshAdapter::getReducedContinuousFunctionCode() const
602  {  {
603    return ReducedNodes;     return ReducedNodes;
604  }  }
605    
606  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
607  {  {
608    return Elements;     return Elements;
609  }  }
610  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
611  {  {
612    return ReducedElements;     return ReducedElements;
613  }  }
614    
615  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
616  {  {
617    return FaceElements;     return FaceElements;
618  }  }
619  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
620  {  {
621    return ReducedFaceElements;     return ReducedFaceElements;
622  }  }
623    
624  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
625  {  {
626    return ContactElementsZero;     return ContactElementsZero;
627  }  }
628  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
629  {  {
630    return ReducedContactElementsZero;     return ReducedContactElementsZero;
631  }  }
632    
633  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
634  {  {
635    return ContactElementsOne;     return ContactElementsOne;
636  }  }
637  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
638  {  {
639    return ReducedContactElementsOne;     return ReducedContactElementsOne;
640  }  }
641    
642  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
643  {  {
644    return DegreesOfFreedom;     return DegreesOfFreedom;
645  }  }
646    
647  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
648  {  {
649    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
650  }  }
651    
652  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionsCode() const
653  {  {
654    return Points;     return Points;
655  }  }
656    
657  //  //
# Line 225  int MeshAdapter::getDiracDeltaFunctionCo Line 659  int MeshAdapter::getDiracDeltaFunctionCo
659  //  //
660  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
661  {  {
662    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     Finley_Mesh* mesh=m_finleyMesh.get();
663    checkFinleyError();     int numDim=Finley_Mesh_getDim(mesh);
664    return numDim;     checkFinleyError();
665       return numDim;
666    }
667    
668    //
669    // Return the number of data points summed across all MPI processes
670    //
671    int MeshAdapter::getNumDataPointsGlobal() const
672    {
673       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
674  }  }
675    
676  //  //
# Line 240  pair<int,int> MeshAdapter::getDataShape( Line 683  pair<int,int> MeshAdapter::getDataShape(
683     int numSamples=0;     int numSamples=0;
684     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
685     switch (functionSpaceCode) {     switch (functionSpaceCode) {
686        case(Nodes):     case(Nodes):
687             numDataPointsPerSample=1;     numDataPointsPerSample=1;
688             numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
689             break;     break;
690        case(ReducedNodes):     case(ReducedNodes):
691             numDataPointsPerSample=1;     numDataPointsPerSample=1;
692             numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
693             break;     break;
694        case(Elements):     case(Elements):
695             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
696               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
697               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
698             }     }
699             break;     break;
700        case(ReducedElements):     case(ReducedElements):
701             if (mesh->Elements!=NULL) {     if (mesh->Elements!=NULL) {
702               numSamples=mesh->Elements->numElements;        numSamples=mesh->Elements->numElements;
703               numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
704             }     }
705             break;     break;
706        case(FaceElements):     case(FaceElements):
707             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
708                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
709                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
710             }     }
711             break;     break;
712        case(ReducedFaceElements):     case(ReducedFaceElements):
713             if (mesh->FaceElements!=NULL) {     if (mesh->FaceElements!=NULL) {
714                  numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
715                  numSamples=mesh->FaceElements->numElements;        numSamples=mesh->FaceElements->numElements;
716             }     }
717             break;     break;
718        case(Points):     case(Points):
719             if (mesh->Points!=NULL) {     if (mesh->Points!=NULL) {
720               numDataPointsPerSample=1;        numDataPointsPerSample=1;
721               numSamples=mesh->Points->numElements;        numSamples=mesh->Points->numElements;
722             }     }
723             break;     break;
724        case(ContactElementsZero):     case(ContactElementsZero):
725             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
726               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
727               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
728             }     }
729             break;     break;
730        case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
731             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
732               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
733               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
734             }     }
735             break;     break;
736        case(ContactElementsOne):     case(ContactElementsOne):
737             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
738               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
739               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
740             }     }
741             break;     break;
742        case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
743             if (mesh->ContactElements!=NULL) {     if (mesh->ContactElements!=NULL) {
744               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
745               numSamples=mesh->ContactElements->numElements;        numSamples=mesh->ContactElements->numElements;
746             }     }
747             break;     break;
748        case(DegreesOfFreedom):     case(DegreesOfFreedom):
749             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
750               numDataPointsPerSample=1;        numDataPointsPerSample=1;
751               numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
752             }     }
753             break;     break;
754        case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
755             if (mesh->Nodes!=NULL) {     if (mesh->Nodes!=NULL) {
756               numDataPointsPerSample=1;        numDataPointsPerSample=1;
757               numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
758             }     }
759             break;     break;
760        default:     default:
761          stringstream temp;        stringstream temp;
762          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
763          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
764          break;        break;
765        }     }
766        return pair<int,int>(numDataPointsPerSample,numSamples);     return pair<int,int>(numDataPointsPerSample,numSamples);
767  }  }
768    
769  //  //
770  // 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:
771  //  //
772  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
773                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   AbstractSystemMatrix& mat, escript::Data& rhs,
774                       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,
775                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
776                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact,
777  {                                   const escript::Data& d_dirac,const escript::Data& y_dirac) const
778    {
779       SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
780       if (smat==0)
781       {
782        throw FinleyAdapterException("finley only supports Paso system matrices.");
783       }
784     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
785     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
786     escriptDataC _B=B.getDataC();     escriptDataC _B=B.getDataC();
# Line 343  void MeshAdapter::addPDEToSystem( Line 792  void MeshAdapter::addPDEToSystem(
792     escriptDataC _y=y.getDataC();     escriptDataC _y=y.getDataC();
793     escriptDataC _d_contact=d_contact.getDataC();     escriptDataC _d_contact=d_contact.getDataC();
794     escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
795       escriptDataC _d_dirac=d_dirac.getDataC();
796       escriptDataC _y_dirac=y_dirac.getDataC();
797    
798     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
799    
800     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,smat->getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
801       checkFinleyError();
802    
803       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, smat->getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
804     checkFinleyError();     checkFinleyError();
805    
806     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
807     checkFinleyError();     checkFinleyError();
808    
809     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );      Finley_Assemble_PDE(mesh->Nodes,mesh->Points, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
810     checkFinleyError();     checkFinleyError();
811  }  }
812    
813  void  MeshAdapter::addPDEToLumpedSystem(  void  MeshAdapter::addPDEToLumpedSystem(
814                       escript::Data& mat,                                          escript::Data& mat,
815                       const escript::Data& D,                                          const escript::Data& D,
816                       const escript::Data& d) const                                          const escript::Data& d,
817                                            const escript::Data& d_dirac,
818                                            const bool useHRZ) const
819  {  {
820     escriptDataC _mat=mat.getDataC();     escriptDataC _mat=mat.getDataC();
821     escriptDataC _D=D.getDataC();     escriptDataC _D=D.getDataC();
822     escriptDataC _d=d.getDataC();     escriptDataC _d=d.getDataC();
823       escriptDataC _d_dirac=d_dirac.getDataC();
824    
825     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
826    
827     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D, useHRZ);
828     Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);     checkFinleyError();
829      
830       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d, useHRZ);
831       checkFinleyError();
832    
833       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Points,&_mat, &_d_dirac, useHRZ);
834     checkFinleyError();     checkFinleyError();
835    
836  }  }
837    
838    
839  //  //
840  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
841  //  //
842  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact,  const escript::Data& y_dirac) const
843  {  {
844     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
845    
# Line 386  void MeshAdapter::addPDEToRHS( escript:: Line 848  void MeshAdapter::addPDEToRHS( escript::
848     escriptDataC _Y=Y.getDataC();     escriptDataC _Y=Y.getDataC();
849     escriptDataC _y=y.getDataC();     escriptDataC _y=y.getDataC();
850     escriptDataC _y_contact=y_contact.getDataC();     escriptDataC _y_contact=y_contact.getDataC();
851       escriptDataC _y_dirac=y_dirac.getDataC();
852    
853     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
854     checkFinleyError();     checkFinleyError();
# Line 395  void MeshAdapter::addPDEToRHS( escript:: Line 858  void MeshAdapter::addPDEToRHS( escript::
858    
859     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
860     checkFinleyError();     checkFinleyError();
861    
862       Finley_Assemble_PDE(mesh->Nodes,mesh->Points, 0, &_rhs , 0, 0, 0, 0, 0, &_y_dirac );
863       checkFinleyError();
864    
865    }
866    //
867    // adds PDE of second order into a transport problem
868    //
869    void MeshAdapter::addPDEToTransportProblem(
870                                               AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,
871                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
872                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
873                                               const escript::Data& d, const escript::Data& y,
874                                               const escript::Data& d_contact,const escript::Data& y_contact,
875                                               const escript::Data& d_dirac, const escript::Data& y_dirac) const
876    {
877       TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
878       if (tpa==0)
879       {
880        throw FinleyAdapterException("finley only supports Paso transport problems.");
881       }
882    
883    
884       DataTypes::ShapeType shape;
885       source.expand();
886       escriptDataC _source=source.getDataC();
887       escriptDataC _M=M.getDataC();
888       escriptDataC _A=A.getDataC();
889       escriptDataC _B=B.getDataC();
890       escriptDataC _C=C.getDataC();
891       escriptDataC _D=D.getDataC();
892       escriptDataC _X=X.getDataC();
893       escriptDataC _Y=Y.getDataC();
894       escriptDataC _d=d.getDataC();
895       escriptDataC _y=y.getDataC();
896       escriptDataC _d_contact=d_contact.getDataC();
897       escriptDataC _y_contact=y_contact.getDataC();
898       escriptDataC _d_dirac=d_dirac.getDataC();
899       escriptDataC _y_dirac=y_dirac.getDataC();
900    
901    
902       Finley_Mesh* mesh=m_finleyMesh.get();
903       Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
904    
905       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
906       checkFinleyError();
907    
908       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
909       checkFinleyError();
910    
911       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
912       checkFinleyError();
913    
914       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
915       checkFinleyError();
916    
917       Finley_Assemble_PDE(mesh->Nodes,mesh->Points, _tp->transport_matrix, &_source , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
918       checkFinleyError();
919    
920  }  }
921    
922  //  //
# Line 402  void MeshAdapter::addPDEToRHS( escript:: Line 924  void MeshAdapter::addPDEToRHS( escript::
924  //  //
925  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
926  {  {
927    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
928    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
929    if (inDomain!=*this)       if (inDomain!=*this)  
930      throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
931    if (targetDomain!=*this)     if (targetDomain!=*this)
932      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
933    
934    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
935    escriptDataC _target=target.getDataC();     escriptDataC _target=target.getDataC();
936    escriptDataC _in=in.getDataC();     escriptDataC _in=in.getDataC();
937    switch(in.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
938       case(Nodes):     case(Nodes):
939          switch(target.getFunctionSpace().getTypeCode()) {        switch(target.getFunctionSpace().getTypeCode()) {
940             case(Nodes):        case(Nodes):
941             case(ReducedNodes):        case(ReducedNodes):
942             case(DegreesOfFreedom):        case(DegreesOfFreedom):
943             case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
944                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
945                 break;        break;
946             case(Elements):        case(Elements):
947             case(ReducedElements):        case(ReducedElements):
948                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
949                 break;        break;
950             case(FaceElements):        case(FaceElements):
951             case(ReducedFaceElements):        case(ReducedFaceElements):
952                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
953                 break;        break;
954             case(Points):        case(Points):
955                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
956                 break;        break;
957             case(ContactElementsZero):        case(ContactElementsZero):
958             case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
959                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
960                 break;        break;
961             case(ContactElementsOne):        case(ContactElementsOne):
962             case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
963                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
964                 break;        break;
965             default:        default:
966                 stringstream temp;           stringstream temp;
967                 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();
968                 throw FinleyAdapterException(temp.str());           throw FinleyAdapterException(temp.str());
969                 break;           break;
970          }        }
971          break;        break;
972       case(ReducedNodes):     case(ReducedNodes):
973          switch(target.getFunctionSpace().getTypeCode()) {        switch(target.getFunctionSpace().getTypeCode()) {
974             case(Nodes):        case(Nodes):
975             case(ReducedNodes):        case(ReducedNodes):
976             case(DegreesOfFreedom):        case(DegreesOfFreedom):
977             case(ReducedDegreesOfFreedom):        case(ReducedDegreesOfFreedom):
978                 Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
979                 break;        break;
980             case(Elements):        case(Elements):
981             case(ReducedElements):        case(ReducedElements):
982                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
983                 break;        break;
984             case(FaceElements):        case(FaceElements):
985             case(ReducedFaceElements):        case(ReducedFaceElements):
986                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
987                 break;        break;
988             case(Points):        case(Points):
989                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
990                 break;        break;
991             case(ContactElementsZero):        case(ContactElementsZero):
992             case(ReducedContactElementsZero):        case(ReducedContactElementsZero):
993                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
994                 break;        break;
995             case(ContactElementsOne):        case(ContactElementsOne):
996             case(ReducedContactElementsOne):        case(ReducedContactElementsOne):
997                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
998                 break;        break;
999             default:        default:
1000                 stringstream temp;           stringstream temp;
1001                 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();
1002                 throw FinleyAdapterException(temp.str());           throw FinleyAdapterException(temp.str());
1003                 break;           break;
1004          }        }
1005          break;        break;
1006       case(Elements):     case(Elements):
1007          if (target.getFunctionSpace().getTypeCode()==Elements) {        if (target.getFunctionSpace().getTypeCode()==Elements) {
1008             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
1009          } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
1010             Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
1011          } else {        } else {
1012             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
1013          }        }
1014          break;        break;
1015       case(ReducedElements):     case(ReducedElements):
1016          if (target.getFunctionSpace().getTypeCode()==ReducedElements) {        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
1017             Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
1018          } else {        } else {
1019             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.");
1020          }        }
1021          break;        break;
1022       case(FaceElements):     case(FaceElements):
1023          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
1024             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1025          } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1026             Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
1027          } else {        } else {
1028             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
1029         }        }
1030         break;        break;
1031       case(ReducedFaceElements):     case(ReducedFaceElements):
1032          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1033             Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1034          } else {        } else {
1035             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.");
1036         }        }
1037         break;        break;
1038       case(Points):     case(Points):
1039          if (target.getFunctionSpace().getTypeCode()==Points) {        if (target.getFunctionSpace().getTypeCode()==Points) {
1040             Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1041          } else {        } else {
1042             throw FinleyAdapterException("Error - No interpolation with data on points possible.");           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1043          }        }
1044          break;        break;
1045       case(ContactElementsZero):     case(ContactElementsZero):
1046       case(ContactElementsOne):     case(ContactElementsOne):
1047          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1048             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1049          } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1050             Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
1051          } else {        } else {
1052             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1053             break;        }
1054          }        break;
1055          break;     case(ReducedContactElementsZero):
1056       case(ReducedContactElementsZero):     case(ReducedContactElementsOne):
1057       case(ReducedContactElementsOne):        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1058          if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1059             Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);        } else {
1060          } else {           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1061             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");        }
1062             break;        break;
1063          }     case(DegreesOfFreedom):      
1064          break;        switch(target.getFunctionSpace().getTypeCode()) {
1065       case(DegreesOfFreedom):              case(ReducedDegreesOfFreedom):
1066          switch(target.getFunctionSpace().getTypeCode()) {        case(DegreesOfFreedom):
1067             case(ReducedDegreesOfFreedom):        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1068             case(DegreesOfFreedom):        break;
1069                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);    
1070                break;        case(Nodes):
1071          case(ReducedNodes):
1072             case(Nodes):        if (getMPISize()>1) {
1073             case(ReducedNodes):           escript::Data temp=escript::Data(in);
1074                if (getMPISize()>1) {           temp.expand();
1075                    escript::Data temp=escript::Data(in);           escriptDataC _in2 = temp.getDataC();
1076                    temp.expand();           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1077                    escriptDataC _in2 = temp.getDataC();        } else {
1078                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1079                } else {        }
1080                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        break;
1081                }        case(Elements):
1082                break;        case(ReducedElements):
1083             case(Elements):        if (getMPISize()>1) {
1084             case(ReducedElements):           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1085                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1086                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1087                   escriptDataC _in2 = temp.getDataC();        } else {
1088                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1089                } else {        }
1090                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        break;
1091                }        case(FaceElements):
1092                break;        case(ReducedFaceElements):
1093             case(FaceElements):        if (getMPISize()>1) {
1094             case(ReducedFaceElements):           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1095                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1096                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1097                   escriptDataC _in2 = temp.getDataC();    
1098                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);        } else {
1099             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1100                } else {        }
1101                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        break;
1102                }        case(Points):
1103                break;        if (getMPISize()>1) {
1104             case(Points):           //escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1105                if (getMPISize()>1) {           //escriptDataC _in2 = temp.getDataC();
1106                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );        } else {
1107                   escriptDataC _in2 = temp.getDataC();           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1108                } else {        }
1109                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        break;
1110                }        case(ContactElementsZero):
1111                break;        case(ContactElementsOne):
1112             case(ContactElementsZero):        case(ReducedContactElementsZero):
1113             case(ContactElementsOne):        case(ReducedContactElementsOne):
1114             case(ReducedContactElementsZero):        if (getMPISize()>1) {
1115             case(ReducedContactElementsOne):           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1116                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1117                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1118                   escriptDataC _in2 = temp.getDataC();        } else {
1119                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1120                } else {        }
1121                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        break;
1122                }        default:
1123               break;           stringstream temp;
1124             default:           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1125               stringstream temp;           throw FinleyAdapterException(temp.str());
1126               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           break;
1127               throw FinleyAdapterException(temp.str());        }
1128               break;        break;
1129          }     case(ReducedDegreesOfFreedom):
1130          break;        switch(target.getFunctionSpace().getTypeCode()) {
1131       case(ReducedDegreesOfFreedom):        case(Nodes):
1132         switch(target.getFunctionSpace().getTypeCode()) {        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1133            case(Nodes):        break;
1134               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");        case(ReducedNodes):
1135               break;        if (getMPISize()>1) {
1136            case(ReducedNodes):           escript::Data temp=escript::Data(in);
1137                if (getMPISize()>1) {           temp.expand();
1138                    escript::Data temp=escript::Data(in);           escriptDataC _in2 = temp.getDataC();
1139                    temp.expand();           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1140                    escriptDataC _in2 = temp.getDataC();        } else {
1141                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1142                } else {        }
1143                    Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        break;
1144                }        case(DegreesOfFreedom):
1145                break;        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1146            case(DegreesOfFreedom):        break;
1147               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");        case(ReducedDegreesOfFreedom):
1148               break;        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1149            case(ReducedDegreesOfFreedom):        break;
1150               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        case(Elements):
1151               break;        case(ReducedElements):
1152            case(Elements):        if (getMPISize()>1) {
1153            case(ReducedElements):           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1154                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1155                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1156                   escriptDataC _in2 = temp.getDataC();        } else {
1157                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1158                } else {        }
1159                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);        break;
1160               }        case(FaceElements):
1161               break;        case(ReducedFaceElements):
1162            case(FaceElements):        if (getMPISize()>1) {
1163            case(ReducedFaceElements):           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1164                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1165                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1166                   escriptDataC _in2 = temp.getDataC();        } else {
1167                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1168                } else {        }
1169                   Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        break;
1170                }        case(Points):
1171               break;        if (getMPISize()>1) {
1172            case(Points):           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1173                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1174                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1175                   escriptDataC _in2 = temp.getDataC();        } else {
1176                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1177                } else {        }
1178                   Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        break;
1179               }        case(ContactElementsZero):
1180               break;        case(ContactElementsOne):
1181            case(ContactElementsZero):        case(ReducedContactElementsZero):
1182            case(ContactElementsOne):        case(ReducedContactElementsOne):
1183            case(ReducedContactElementsZero):        if (getMPISize()>1) {
1184            case(ReducedContactElementsOne):           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1185                if (getMPISize()>1) {           escriptDataC _in2 = temp.getDataC();
1186                   escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1187                   escriptDataC _in2 = temp.getDataC();        } else {
1188                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1189                } else {        }
1190                   Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        break;
1191               }        default:
1192               break;           stringstream temp;
1193            default:           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1194               stringstream temp;           throw FinleyAdapterException(temp.str());
1195               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           break;
1196               throw FinleyAdapterException(temp.str());        }
1197               break;        break;
1198         }     default:
1199         break;        stringstream temp;
1200       default:        temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1201          stringstream temp;        throw FinleyAdapterException(temp.str());
1202          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        break;
1203          throw FinleyAdapterException(temp.str());     }
1204          break;     checkFinleyError();
   }  
   checkFinleyError();  
1205  }  }
1206    
1207  //  //
# Line 689  void MeshAdapter::interpolateOnDomain(es Line 1209  void MeshAdapter::interpolateOnDomain(es
1209  //  //
1210  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1211  {  {
1212    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1213    if (argDomain!=*this)     if (argDomain!=*this)
1214       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1215    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1216    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1217    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1218       escriptDataC _arg=arg.getDataC();        escriptDataC _arg=arg.getDataC();
1219       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1220    } else {     } else {
1221       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);        escript::Data tmp_data=Vector(0.0,continuousFunction(*this),true);
1222       escriptDataC _tmp_data=tmp_data.getDataC();        escriptDataC _tmp_data=tmp_data.getDataC();
1223       Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1224       // this is then interpolated onto arg:        // this is then interpolated onto arg:
1225       interpolateOnDomain(arg,tmp_data);        interpolateOnDomain(arg,tmp_data);
1226    }     }
1227    checkFinleyError();     checkFinleyError();
1228  }  }
1229    
1230  //  //
# Line 712  void MeshAdapter::setToX(escript::Data& Line 1232  void MeshAdapter::setToX(escript::Data&
1232  //  //
1233  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1234  {  {
1235    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1236    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1237       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1238    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1239    escriptDataC _normal=normal.getDataC();     Finley_Mesh* mesh=m_finleyMesh.get();
1240    switch(normal.getFunctionSpace().getTypeCode()) {     escriptDataC _normal=normal.getDataC();
1241      case(Nodes):     switch(normal.getFunctionSpace().getTypeCode()) {
1242        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     case(Nodes):
1243        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1244      case(ReducedNodes):     break;
1245        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");     case(ReducedNodes):
1246        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1247      case(Elements):     break;
1248        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     case(Elements):
1249        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1250      case(ReducedElements):     break;
1251        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");     case(ReducedElements):
1252        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1253      case (FaceElements):     break;
1254        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     case (FaceElements):
1255        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1256      case (ReducedFaceElements):     break;
1257        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);     case (ReducedFaceElements):
1258        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1259      case(Points):     break;
1260        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     case(Points):
1261        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1262      case (ContactElementsOne):     break;
1263      case (ContactElementsZero):     case (ContactElementsOne):
1264        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     case (ContactElementsZero):
1265        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1266      case (ReducedContactElementsOne):     break;
1267      case (ReducedContactElementsZero):     case (ReducedContactElementsOne):
1268        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);     case (ReducedContactElementsZero):
1269        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1270      case(DegreesOfFreedom):     break;
1271        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case(DegreesOfFreedom):
1272        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1273      case(ReducedDegreesOfFreedom):     break;
1274        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(ReducedDegreesOfFreedom):
1275        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1276      default:     break;
1277       default:
1278        stringstream temp;        stringstream temp;
1279        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();
1280        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1281        break;        break;
1282    }     }
1283    checkFinleyError();     checkFinleyError();
1284  }  }
1285    
1286  //  //
# Line 767  void MeshAdapter::setToNormal(escript::D Line 1288  void MeshAdapter::setToNormal(escript::D
1288  //  //
1289  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1290  {  {
1291    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1292    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1293       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1294          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1295    
1296    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1297  }  }
1298    
1299  //  //
1300  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined of arg:
1301  //  //
1302  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(vector<double>& integrals,const escript::Data& arg) const
1303  {  {
1304    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1305    if (argDomain!=*this)     if (argDomain!=*this)
1306       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1307    
1308    double blocktimer_start = blocktimer_time();     double blocktimer_start = blocktimer_time();
1309    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1310    escriptDataC _temp;     escriptDataC _temp;
1311    escript::Data temp;     escript::Data temp;
1312    escriptDataC _arg=arg.getDataC();     escriptDataC _arg=arg.getDataC();
1313    switch(arg.getFunctionSpace().getTypeCode()) {     switch(arg.getFunctionSpace().getTypeCode()) {
1314       case(Nodes):     case(Nodes):
1315          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1316          _temp=temp.getDataC();     _temp=temp.getDataC();
1317          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1318          break;     break;
1319       case(ReducedNodes):     case(ReducedNodes):
1320          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1321          _temp=temp.getDataC();     _temp=temp.getDataC();
1322          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1323          break;     break;
1324       case(Elements):     case(Elements):
1325          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1326          break;     break;
1327       case(ReducedElements):     case(ReducedElements):
1328          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1329          break;     break;
1330       case(FaceElements):     case(FaceElements):
1331          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1332          break;     break;
1333       case(ReducedFaceElements):     case(ReducedFaceElements):
1334          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1335          break;     break;
1336       case(Points):     case(Points):
1337          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1338          break;     break;
1339       case(ContactElementsZero):     case(ContactElementsZero):
1340          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1341          break;     break;
1342       case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1343          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1344          break;     break;
1345       case(ContactElementsOne):     case(ContactElementsOne):
1346          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1347          break;     break;
1348       case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1349          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1350          break;     break;
1351       case(DegreesOfFreedom):     case(DegreesOfFreedom):
1352          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1353          _temp=temp.getDataC();     _temp=temp.getDataC();
1354          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1355          break;     break;
1356       case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1357          temp=escript::Data( arg, function(asAbstractContinuousDomain()) );     temp=escript::Data( arg, escript::function(*this) );
1358          _temp=temp.getDataC();     _temp=temp.getDataC();
1359          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1360          break;     break;
1361       default:     default:
1362          stringstream temp;        stringstream temp;
1363          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();
1364          throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1365          break;        break;
1366    }     }
1367    checkFinleyError();     checkFinleyError();
1368    blocktimer_increment("integrate()", blocktimer_start);     blocktimer_increment("integrate()", blocktimer_start);
1369  }  }
1370    
1371  //  //
# Line 851  void MeshAdapter::setToIntegrals(std::ve Line 1373  void MeshAdapter::setToIntegrals(std::ve
1373  //  //
1374  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1375  {  {
1376    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1377    if (argDomain!=*this)     if (argDomain!=*this)
1378      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1379    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1380    if (gradDomain!=*this)     if (gradDomain!=*this)
1381       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1382    
1383    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1384    escriptDataC _grad=grad.getDataC();     escriptDataC _grad=grad.getDataC();
1385    escriptDataC nodeDataC;     escriptDataC nodeDataC;
1386    escript::Data temp;     escript::Data temp;
1387    if (getMPISize()>1) {     if (getMPISize()>1) {
1388        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1389          temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  continuousFunction(*this) );
1390          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1391        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1392          temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );           temp=escript::Data( arg,  reducedContinuousFunction(*this) );
1393          nodeDataC = temp.getDataC();           nodeDataC = temp.getDataC();
1394        } else {        } else {
1395          nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1396        }        }
1397    } else {     } else {
1398       nodeDataC = arg.getDataC();        nodeDataC = arg.getDataC();
1399    }     }
1400    switch(grad.getFunctionSpace().getTypeCode()) {     switch(grad.getFunctionSpace().getTypeCode()) {
1401         case(Nodes):     case(Nodes):
1402            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1403            break;     break;
1404         case(ReducedNodes):     case(ReducedNodes):
1405            throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1406            break;     break;
1407         case(Elements):     case(Elements):
1408            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1409            break;     break;
1410         case(ReducedElements):     case(ReducedElements):
1411            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1412            break;     break;
1413         case(FaceElements):     case(FaceElements):
1414            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1415            break;     break;
1416         case(ReducedFaceElements):     case(ReducedFaceElements):
1417            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1418            break;     break;
1419         case(Points):     case(Points):
1420            throw FinleyAdapterException("Error - Gradient at points is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1421            break;     break;
1422         case(ContactElementsZero):     case(ContactElementsZero):
1423            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1424            break;     break;
1425         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1426            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1427            break;     break;
1428         case(ContactElementsOne):     case(ContactElementsOne):
1429            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1430            break;     break;
1431         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1432            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1433            break;     break;
1434         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1435            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1436            break;     break;
1437         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1438            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1439            break;     break;
1440         default:     default:
1441            stringstream temp;        stringstream temp;
1442            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();
1443            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1444            break;        break;
1445    }     }
1446    checkFinleyError();     checkFinleyError();
1447  }  }
1448    
1449  //  //
# Line 929  void MeshAdapter::setToGradient(escript: Line 1451  void MeshAdapter::setToGradient(escript:
1451  //  //
1452  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1453  {  {
1454    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1455    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1456    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1457         case(Nodes):     case(Nodes):
1458            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1459            break;     break;
1460         case(ReducedNodes):     case(ReducedNodes):
1461            throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1462            break;     break;
1463         case(Elements):     case(Elements):
1464            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1465            break;     break;
1466         case(ReducedElements):     case(ReducedElements):
1467            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1468            break;     break;
1469         case(FaceElements):     case(FaceElements):
1470            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1471            break;     break;
1472         case(ReducedFaceElements):     case(ReducedFaceElements):
1473            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1474            break;     break;
1475         case(Points):     case(Points):
1476            throw FinleyAdapterException("Error - Size of point elements is not supported.");     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1477            break;     break;
1478         case(ContactElementsZero):     case(ContactElementsZero):
1479         case(ContactElementsOne):     case(ContactElementsOne):
1480            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1481            break;     break;
1482         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1483         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1484            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1485            break;     break;
1486         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1487            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1488            break;     break;
1489         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1490            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1491            break;     break;
1492         default:     default:
1493            stringstream temp;        stringstream temp;
1494            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();
1495            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1496            break;        break;
1497    }     }
1498    checkFinleyError();     checkFinleyError();
1499  }  }
1500    
1501  // sets the location of nodes:  //
1502    // sets the location of nodes
1503    //
1504  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1505  {  {
1506    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1507    escriptDataC tmp;     escriptDataC tmp;
1508    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1509    if (newDomain!=*this)     if (newDomain!=*this)
1510       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1511    tmp = new_x.getDataC();     if ( new_x.getFunctionSpace() == continuousFunction(*this) ) {
1512    Finley_Mesh_setCoordinates(mesh,&tmp);         tmp = new_x.getDataC();
1513    checkFinleyError();         Finley_Mesh_setCoordinates(mesh,&tmp);
1514  }     } else {
1515           escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(*this) );
1516  // saves a data array in openDX format:         tmp = new_x_inter.getDataC();
1517  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const         Finley_Mesh_setCoordinates(mesh,&tmp);
1518  {     }
1519      int MAX_namelength=256;     checkFinleyError();
     const int num_data=boost::python::extract<int>(arg.attr("__len__")());  
   /* win32 refactor */  
   char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
   
   char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  
   escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  
   escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  
   
   boost::python::list keys=arg.keys();  
   for (int i=0;i<num_data;++i) {  
          std::string n=boost::python::extract<std::string>(keys[i]);  
          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
          if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  
              throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  
          data[i]=d.getDataC();  
          ptr_data[i]=&(data[i]);  
          c_names[i]=&(names[i][0]);  
          if (n.length()>MAX_namelength-1) {  
             strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
             c_names[i][MAX_namelength-1]='\0';  
          } else {  
             strcpy(c_names[i],n.c_str());  
          }  
     }  
     Finley_Mesh_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);  
   
     return;  
1520  }  }
1521    
1522  // saves a data array in openVTK format:  //
1523  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  // Helper for the save* methods. Extracts optional data variable names and the
1524    // corresponding pointers from python dictionary. Caller must free arrays.
1525    //
1526    void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1527  {  {
1528      int MAX_namelength=256;     numData = boost::python::extract<int>(arg.attr("__len__")());
1529      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     /* win32 refactor */
1530    /* win32 refactor */     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1531    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1532    for(int i=0;i<num_data;i++)     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1533    {  
1534      names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;     boost::python::list keys=arg.keys();
1535    }     for (int i=0; i<numData; ++i) {
1536          string n=boost::python::extract<string>(keys[i]);
1537          escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1538          if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1539             throw FinleyAdapterException("Error: Data must be defined on same Domain");
1540          data[i] = d.getDataC();
1541          dataPtr[i] = &(data[i]);
1542          names[i] = TMPMEMALLOC(n.length()+1, char);
1543          strcpy(names[i], n.c_str());
1544       }
1545    }
1546    
1547    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  //
1548    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  // saves mesh and optionally data arrays in openDX format
1549    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  //
1550    void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1551      boost::python::list keys=arg.keys();  {
1552      for (int i=0;i<num_data;++i) {     int num_data;
1553           std::string n=boost::python::extract<std::string>(keys[i]);     char **names;
1554           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     escriptDataC *data;
1555           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     escriptDataC **ptr_data;
              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);  
1556    
1557    checkFinleyError();     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1558    /* win32 refactor */     Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1559    TMPMEMFREE(c_names);     checkFinleyError();
1560    TMPMEMFREE(data);  
1561    TMPMEMFREE(ptr_data);     /* win32 refactor */
1562    for(int i=0;i<num_data;i++)     TMPMEMFREE(data);
1563    {     TMPMEMFREE(ptr_data);
1564      TMPMEMFREE(names[i]);     for(int i=0; i<num_data; i++)
1565    }     {
1566    TMPMEMFREE(names);        TMPMEMFREE(names[i]);
1567       }
1568       TMPMEMFREE(names);
1569    
1570      return;     return;
1571  }  }
1572                                                                                                                                                                            
1573                                                                                                                                                                            //
1574  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // saves mesh and optionally data arrays in VTK format
1575  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  //
1576                        const int row_blocksize,  void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1577                        const escript::FunctionSpace& row_functionspace,  {
1578                        const int column_blocksize,      boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("_saveVTK");
1579                        const escript::FunctionSpace& column_functionspace,      pySaveVTK(filename, const_cast<MeshAdapter*>(this)->getPtr(),
1580                        const int type) const                metadata, metadata_schema, arg);
1581  {  }
1582      int reduceRowOrder=0;  
1583      int reduceColOrder=0;  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1584      // is the domain right?  {
1585      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());  #ifdef ESYS_MPI
1586      if (row_domain!=*this)      index_t myFirstNode=0, myLastNode=0, k=0;
1587            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");      index_t* globalNodeIndex=0;
1588      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());      Finley_Mesh* mesh_p=m_finleyMesh.get();
1589      if (col_domain!=*this)      if (fs_code == FINLEY_REDUCED_NODES)
1590            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");      {
1591      // is the function space type right      myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1592      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {      myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1593          reduceRowOrder=0;      globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {  
         reduceRowOrder=1;  
     } else {  
         throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");  
1594      }      }
1595      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      else
1596          reduceColOrder=0;      {
1597      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1598          reduceColOrder=1;      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1599      } else {      globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
         throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");  
1600      }      }
1601      // generate matrix:      k=globalNodeIndex[id];
1602            return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1603      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);  #endif
1604      checkFinleyError();      return true;
1605      Paso_SystemMatrix* fsystemMatrix;  }
1606      int trilinos = 0;  
1607      if (trilinos) {  
1608    
1609    //
1610    // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1611    //
1612    ASM_ptr MeshAdapter::newSystemMatrix(
1613                                                     const int row_blocksize,
1614                                                     const escript::FunctionSpace& row_functionspace,
1615                                                     const int column_blocksize,
1616                                                     const escript::FunctionSpace& column_functionspace,
1617                                                     const int type) const
1618    {
1619       int reduceRowOrder=0;
1620       int reduceColOrder=0;
1621       // is the domain right?
1622       const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1623       if (row_domain!=*this)
1624          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1625       const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1626       if (col_domain!=*this)
1627          throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1628       // is the function space type right
1629       if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1630          reduceRowOrder=0;
1631       } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1632          reduceRowOrder=1;
1633       } else {
1634          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1635       }
1636       if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1637          reduceColOrder=0;
1638       } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1639          reduceColOrder=1;
1640       } else {
1641          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1642       }
1643       // generate matrix:
1644    
1645       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1646       checkFinleyError();
1647       Paso_SystemMatrix* fsystemMatrix;
1648       int trilinos = 0;
1649       if (trilinos) {
1650  #ifdef TRILINOS  #ifdef TRILINOS
1651        /* Allocation Epetra_VrbMatrix here */        /* Allocation Epetra_VrbMatrix here */
1652  #endif  #endif
1653      }     }
1654      else {     else {
1655        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);        fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1656      }     }
1657      checkPasoError();     checkPasoError();
1658      Paso_SystemMatrixPattern_free(fsystemMatrixPattern);     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1659      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);     SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1660       return ASM_ptr(sma);
1661    //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1662    }
1663    
1664    //
1665    // creates a TransportProblemAdapter
1666    //
1667    ATP_ptr MeshAdapter::newTransportProblem(
1668                                                             const int blocksize,
1669                                                             const escript::FunctionSpace& functionspace,
1670                                                             const int type) const
1671    {
1672       int reduceOrder=0;
1673       // is the domain right?
1674       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1675       if (domain!=*this)
1676          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1677       // is the function space type right
1678       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1679          reduceOrder=0;
1680       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1681          reduceOrder=1;
1682       } else {
1683          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1684       }
1685       // generate matrix:
1686    
1687       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1688       checkFinleyError();
1689       Paso_TransportProblem* transportProblem;
1690       transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern,blocksize);
1691       checkPasoError();
1692       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1693       TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,blocksize,functionspace);
1694       return ATP_ptr(tpa);
1695    //   return TransportProblemAdapter(transportProblem, blocksize,functionspace);
1696  }  }
1697    
1698  //  //
# Line 1146  SystemMatrixAdapter MeshAdapter::newSyst Line 1704  SystemMatrixAdapter MeshAdapter::newSyst
1704  // 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:
1705  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1706  {  {
1707    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1708         case(Nodes):     case(Nodes):
1709         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1710         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1711            return false;     return false;
1712            break;     break;
1713         case(Elements):     case(Elements):
1714         case(FaceElements):     case(FaceElements):
1715         case(Points):     case(Points):
1716         case(ContactElementsZero):     case(ContactElementsZero):
1717         case(ContactElementsOne):     case(ContactElementsOne):
1718         case(ReducedElements):     case(ReducedElements):
1719         case(ReducedFaceElements):     case(ReducedFaceElements):
1720         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1721         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1722            return true;     return true;
1723            break;     break;
1724         default:     default:
1725            stringstream temp;        stringstream temp;
1726            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;
1727            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1728            break;        break;
1729    }     }
1730    checkFinleyError();     checkFinleyError();
1731    return false;     return false;
1732    }
1733    
1734    bool
1735    MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1736    {
1737       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1738        class 1: DOF <-> Nodes
1739        class 2: ReducedDOF <-> ReducedNodes
1740        class 3: Points
1741        class 4: Elements
1742        class 5: ReducedElements
1743        class 6: FaceElements
1744        class 7: ReducedFaceElements
1745        class 8: ContactElementZero <-> ContactElementOne
1746        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1747    
1748       There is also a set of lines. Interpolation is possible down a line but not between lines.
1749       class 1 and 2 belong to all lines so aren't considered.
1750        line 0: class 3
1751        line 1: class 4,5
1752        line 2: class 6,7
1753        line 3: class 8,9
1754    
1755       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1756       eg hasnodes is true if we have at least one instance of Nodes.
1757       */
1758        if (fs.empty())
1759        {
1760            return false;
1761        }
1762        vector<int> hasclass(10);
1763        vector<int> hasline(4);
1764        bool hasnodes=false;
1765        bool hasrednodes=false;
1766        bool hascez=false;
1767        bool hasrcez=false;
1768        for (int i=0;i<fs.size();++i)
1769        {
1770        switch(fs[i])
1771        {
1772        case(Nodes):   hasnodes=true;   // no break is deliberate
1773        case(DegreesOfFreedom):
1774            hasclass[1]=1;
1775            break;
1776        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1777        case(ReducedDegreesOfFreedom):
1778            hasclass[2]=1;
1779            break;
1780        case(Points):
1781            hasline[0]=1;
1782            hasclass[3]=1;
1783            break;
1784        case(Elements):
1785            hasclass[4]=1;
1786            hasline[1]=1;
1787            break;
1788        case(ReducedElements):
1789            hasclass[5]=1;
1790            hasline[1]=1;
1791            break;
1792        case(FaceElements):
1793            hasclass[6]=1;
1794            hasline[2]=1;
1795            break;
1796        case(ReducedFaceElements):
1797            hasclass[7]=1;
1798            hasline[2]=1;
1799            break;
1800        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1801        case(ContactElementsOne):
1802            hasclass[8]=1;
1803            hasline[3]=1;
1804            break;
1805        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1806        case(ReducedContactElementsOne):
1807            hasclass[9]=1;
1808            hasline[3]=1;
1809            break;
1810        default:
1811            return false;
1812        }
1813        }
1814        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1815        // fail if we have more than one leaf group
1816    
1817        if (totlines>1)
1818        {
1819        return false;   // there are at least two branches we can't interpolate between
1820        }
1821        else if (totlines==1)
1822        {
1823        if (hasline[0]==1)      // we have points
1824        {
1825            resultcode=Points;
1826        }
1827        else if (hasline[1]==1)
1828        {
1829            if (hasclass[5]==1)
1830            {
1831            resultcode=ReducedElements;
1832            }
1833            else
1834            {
1835            resultcode=Elements;
1836            }
1837        }
1838        else if (hasline[2]==1)
1839        {
1840            if (hasclass[7]==1)
1841            {
1842            resultcode=ReducedFaceElements;
1843            }
1844            else
1845            {
1846            resultcode=FaceElements;
1847            }
1848        }
1849        else    // so we must be in line3
1850        {
1851            if (hasclass[9]==1)
1852            {
1853            // need something from class 9
1854            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1855            }
1856            else
1857            {
1858            // something from class 8
1859            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1860            }
1861        }
1862        }
1863        else    // totlines==0
1864        {
1865        if (hasclass[2]==1)
1866        {
1867            // something from class 2
1868            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1869        }
1870        else
1871        {   // something from class 1
1872            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1873        }
1874        }
1875        return true;
1876  }  }
1877    
1878  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1879  {  {
1880    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1881       case(Nodes):     case(Nodes):
1882          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1883             case(Nodes):      case(Nodes):
1884             case(ReducedNodes):      case(ReducedNodes):
1885             case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1886             case(DegreesOfFreedom):      case(DegreesOfFreedom):
1887             case(Elements):      case(Elements):
1888             case(ReducedElements):      case(ReducedElements):
1889             case(FaceElements):      case(FaceElements):
1890             case(ReducedFaceElements):      case(ReducedFaceElements):
1891             case(Points):      case(Points):
1892             case(ContactElementsZero):      case(ContactElementsZero):
1893             case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1894             case(ContactElementsOne):      case(ContactElementsOne):
1895             case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1896                 return true;      return true;
1897             default:      default:
1898                 stringstream temp;            stringstream temp;
1899                 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;
1900                 throw FinleyAdapterException(temp.str());            throw FinleyAdapterException(temp.str());
1901          }     }
1902          break;     break;
1903       case(ReducedNodes):     case(ReducedNodes):
1904          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1905             case(ReducedNodes):      case(ReducedNodes):
1906             case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1907             case(Elements):      case(Elements):
1908             case(ReducedElements):      case(ReducedElements):
1909             case(FaceElements):      case(FaceElements):
1910             case(ReducedFaceElements):      case(ReducedFaceElements):
1911             case(Points):      case(Points):
1912             case(ContactElementsZero):      case(ContactElementsZero):
1913             case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1914             case(ContactElementsOne):      case(ContactElementsOne):
1915             case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1916                 return true;      return true;
1917            case(Nodes):      case(Nodes):
1918            case(DegreesOfFreedom):      case(DegreesOfFreedom):
1919               return false;      return false;
1920             default:      default:
1921                 stringstream temp;          stringstream temp;
1922                 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;
1923                 throw FinleyAdapterException(temp.str());          throw FinleyAdapterException(temp.str());
1924          }     }
1925          break;     break;
1926       case(Elements):     case(Elements):
1927          if (functionSpaceType_target==Elements) {      if (functionSpaceType_target==Elements) {
1928             return true;        return true;
1929          } else if (functionSpaceType_target==ReducedElements) {      } else if (functionSpaceType_target==ReducedElements) {
1930             return true;        return true;
         } else {  
            return false;  
         }  
      case(ReducedElements):  
         if (functionSpaceType_target==ReducedElements) {  
            return true;  
         } else {  
            return false;  
         }  
      case(FaceElements):  
         if (functionSpaceType_target==FaceElements) {  
            return true;  
         } else if (functionSpaceType_target==ReducedFaceElements) {  
            return true;  
         } else {  
            return false;  
         }  
      case(ReducedFaceElements):  
         if (functionSpaceType_target==ReducedFaceElements) {  
            return true;  
         } else {  
            return false;  
         }  
      case(Points):  
         if (functionSpaceType_target==Points) {  
            return true;  
1931          } else {          } else {
1932             return false;            return false;
         }  
      case(ContactElementsZero):  
      case(ContactElementsOne):  
         if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {  
            return true;  
         } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {  
            return true;  
         } else {  
            return false;  
         }  
      case(ReducedContactElementsZero):  
      case(ReducedContactElementsOne):  
         if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {  
            return true;  
         } else {  
            return false;  
         }  
      case(DegreesOfFreedom):  
         switch(functionSpaceType_target) {  
            case(ReducedDegreesOfFreedom):  
            case(DegreesOfFreedom):  
            case(Nodes):  
            case(ReducedNodes):  
            case(Elements):  
            case(ReducedElements):  
            case(Points):  
            case(FaceElements):  
            case(ReducedFaceElements):  
            case(ContactElementsZero):  
            case(ReducedContactElementsZero):  
            case(ContactElementsOne):  
            case(ReducedContactElementsOne):  
               return true;  
            default:  
              stringstream temp;  
              temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;  
              throw FinleyAdapterException(temp.str());  
1933          }          }
1934          break;     case(ReducedElements):
1935       case(ReducedDegreesOfFreedom):      if (functionSpaceType_target==ReducedElements) {
1936         switch(functionSpaceType_target) {        return true;
1937            case(ReducedDegreesOfFreedom):      } else {
1938            case(ReducedNodes):            return false;
1939            case(Elements):      }
1940            case(ReducedElements):     case(FaceElements):
1941            case(FaceElements):      if (functionSpaceType_target==FaceElements) {
1942            case(ReducedFaceElements):              return true;
1943            case(Points):      } else if (functionSpaceType_target==ReducedFaceElements) {
1944            case(ContactElementsZero):              return true;
1945            case(ReducedContactElementsZero):      } else {
1946            case(ContactElementsOne):              return false;
1947            case(ReducedContactElementsOne):      }
1948                return true;     case(ReducedFaceElements):
1949            case(Nodes):      if (functionSpaceType_target==ReducedFaceElements) {
1950            case(DegreesOfFreedom):              return true;
1951               return false;      } else {
1952            default:          return false;
1953               stringstream temp;      }
1954               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1955               throw FinleyAdapterException(temp.str());      if (functionSpaceType_target==Points) {
1956         }              return true;
1957         break;      } else {
1958       default:              return false;
1959          stringstream temp;      }
1960          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1961          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1962          break;      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1963    }              return true;
1964    checkFinleyError();      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1965    return false;              return true;
1966        } else {
1967                return false;
1968        }
1969       case(ReducedContactElementsZero):
1970       case(ReducedContactElementsOne):
1971        if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1972                return true;
1973        } else {
1974                return false;
1975        }
1976       case(DegreesOfFreedom):
1977        switch(functionSpaceType_target) {
1978        case(ReducedDegreesOfFreedom):
1979        case(DegreesOfFreedom):
1980        case(Nodes):
1981        case(ReducedNodes):
1982        case(Elements):
1983        case(ReducedElements):
1984        case(Points):
1985        case(FaceElements):
1986        case(ReducedFaceElements):
1987        case(ContactElementsZero):
1988        case(ReducedContactElementsZero):
1989        case(ContactElementsOne):
1990        case(ReducedContactElementsOne):
1991        return true;
1992        default:
1993            stringstream temp;
1994            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1995            throw FinleyAdapterException(temp.str());
1996        }
1997        break;
1998       case(ReducedDegreesOfFreedom):
1999       switch(functionSpaceType_target) {
2000        case(ReducedDegreesOfFreedom):
2001        case(ReducedNodes):
2002        case(Elements):
2003        case(ReducedElements):
2004        case(FaceElements):
2005        case(ReducedFaceElements):
2006        case(Points):
2007        case(ContactElementsZero):
2008        case(ReducedContactElementsZero):
2009        case(ContactElementsOne):
2010        case(ReducedContactElementsOne):
2011        return true;
2012        case(Nodes):
2013        case(DegreesOfFreedom):
2014        return false;
2015        default:
2016            stringstream temp;
2017            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
2018            throw FinleyAdapterException(temp.str());
2019        }
2020        break;
2021       default:
2022          stringstream temp;
2023          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
2024          throw FinleyAdapterException(temp.str());
2025          break;
2026       }
2027       checkFinleyError();
2028       return false;
2029  }  }
2030    
2031  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
2032  {  {
2033      return false;     return false;
2034  }  }
2035    
2036  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
2037  {  {
2038    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
2039    if (temp!=0) {     if (temp!=0) {
2040      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
2041    } else {     } else {
2042      return false;        return false;
2043    }     }
2044  }  }
2045    
2046  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
2047  {  {
2048    return !(operator==(other));     return !(operator==(other));
2049  }  }
2050    
2051  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
2052  {  {
2053     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
2054     checkPasoError();     return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
2055     return out;             package, symmetry, mesh->MPIInfo);
2056    }
2057    
2058    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2059    {
2060       Finley_Mesh* mesh=m_finleyMesh.get();
2061       return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
2062               package, symmetry, mesh->MPIInfo);
2063  }  }
2064    
2065  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2066  {  {
2067    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(*this).getX();
2068  }  }
2069    
2070  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2071  {  {
2072    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(*this).getNormal();
2073  }  }
2074    
2075  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2076  {  {
2077    return function(asAbstractContinuousDomain()).getSize();     return escript::function(*this).getSize();
2078  }  }
2079    
2080  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2081  {  {
2082    int *out=0,i;     int *out = NULL;
2083    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2084    switch (functionSpaceType) {     switch (functionSpaceType) {
2085      case(Nodes):     case(Nodes):
2086        out=mesh->Nodes->Id;     out=mesh->Nodes->Id;
2087        break;     break;
2088      case(ReducedNodes):     case(ReducedNodes):
2089        out=mesh->Nodes->reducedNodesId;     out=mesh->Nodes->reducedNodesId;
2090        break;     break;
2091      case(Elements):     case(Elements):
2092        out=mesh->Elements->Id;     out=mesh->Elements->Id;
2093        break;     break;
2094      case(ReducedElements):     case(ReducedElements):
2095        out=mesh->Elements->Id;     out=mesh->Elements->Id;
2096        break;     break;
2097      case(FaceElements):     case(FaceElements):
2098        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
2099        break;     break;
2100      case(ReducedFaceElements):     case(ReducedFaceElements):
2101        out=mesh->FaceElements->Id;     out=mesh->FaceElements->Id;
2102        break;     break;
2103      case(Points):     case(Points):
2104        out=mesh->Points->Id;     out=mesh->Points->Id;
2105        break;     break;
2106      case(ContactElementsZero):     case(ContactElementsZero):
2107        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2108        break;     break;
2109      case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
2110        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2111        break;     break;
2112      case(ContactElementsOne):     case(ContactElementsOne):
2113        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2114        break;     break;
2115      case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
2116        out=mesh->ContactElements->Id;     out=mesh->ContactElements->Id;
2117        break;     break;
2118      case(DegreesOfFreedom):     case(DegreesOfFreedom):
2119        out=mesh->Nodes->degreesOfFreedomId;     out=mesh->Nodes->degreesOfFreedomId;
2120        break;     break;
2121      case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2122        out=mesh->Nodes->reducedDegreesOfFreedomId;     out=mesh->Nodes->reducedDegreesOfFreedomId;
2123        break;     break;
2124      default:     default:
2125        stringstream temp;        stringstream temp;
2126        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2127        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2128        break;        break;
2129    }     }
2130    return out;     return out;
2131  }  }
2132  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2133  {  {
2134    int out=0;     int out=0;
2135    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2136    switch (functionSpaceType) {     switch (functionSpaceType) {
2137    case(Nodes):     case(Nodes):
2138      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
2139      break;     break;
2140    case(ReducedNodes):     case(ReducedNodes):
2141      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
2142      break;     break;
2143    case(Elements):     case(Elements):
2144      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
2145      break;     break;
2146    case(ReducedElements):     case(ReducedElements):
2147      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
2148      break;     break;
2149    case(FaceElements):     case(FaceElements):
2150      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
2151      break;     break;
2152    case(ReducedFaceElements):     case(ReducedFaceElements):
2153      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
2154      break;     break;
2155    case(Points):     case(Points):
2156      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
2157      break;     break;
2158    case(ContactElementsZero):     case(ContactElementsZero):
2159      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2160      break;     break;
2161    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
2162      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2163      break;     break;
2164    case(ContactElementsOne):     case(ContactElementsOne):
2165      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2166      break;     break;
2167    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
2168      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2169      break;     break;
2170    case(DegreesOfFreedom):     case(DegreesOfFreedom):
2171      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2172      break;     break;
2173    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2174      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2175      break;     break;
2176    default:     default:
2177      stringstream temp;        stringstream temp;
2178      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2179      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2180      break;        break;
2181    }     }
2182    return out;     return out;
2183  }  }
2184    
2185    
2186  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
2187  {  {
2188       Finley_Mesh* mesh=m_finleyMesh.get();
2189       escriptDataC tmp=mask.getDataC();
2190       switch(functionSpaceType) {
2191       case(Nodes):
2192       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
2193       break;
2194       case(ReducedNodes):
2195       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2196       break;
2197       case(DegreesOfFreedom):
2198       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2199       break;
2200       case(ReducedDegreesOfFreedom):
2201       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2202       break;
2203       case(Elements):
2204       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2205       break;
2206       case(ReducedElements):
2207       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2208       break;
2209       case(FaceElements):
2210       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2211       break;
2212       case(ReducedFaceElements):
2213       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2214       break;
2215       case(Points):
2216       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2217       break;
2218       case(ContactElementsZero):
2219       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2220       break;
2221       case(ReducedContactElementsZero):
2222       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2223       break;
2224       case(ContactElementsOne):
2225       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2226       break;
2227       case(ReducedContactElementsOne):
2228       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2229       break;
2230       default:
2231          stringstream temp;
2232          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2233          throw FinleyAdapterException(temp.str());
2234       }
2235       checkFinleyError();
2236       return;
2237    }
2238    
2239    void MeshAdapter::setTagMap(const string& name,  int tag)
2240    {
2241       Finley_Mesh* mesh=m_finleyMesh.get();
2242       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2243       checkFinleyError();
2244       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2245    }
2246    
2247    int MeshAdapter::getTag(const string& name) const
2248    {
2249       Finley_Mesh* mesh=m_finleyMesh.get();
2250       int tag=0;
2251       tag=Finley_Mesh_getTag(mesh, name.c_str());
2252       checkFinleyError();
2253       // throwStandardException("MeshAdapter::getTag is not implemented.");
2254       return tag;
2255    }
2256    
2257    bool MeshAdapter::isValidTagName(const string& name) const
2258    {
2259       Finley_Mesh* mesh=m_finleyMesh.get();
2260       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2261    }
2262    
2263    string MeshAdapter::showTagNames() const
2264    {
2265       stringstream temp;
2266       Finley_Mesh* mesh=m_finleyMesh.get();
2267       Finley_TagMap* tag_map=mesh->TagMap;
2268       while (tag_map) {
2269          temp << tag_map->name;
2270          tag_map=tag_map->next;
2271          if (tag_map) temp << ", ";
2272       }
2273       return temp.str();
2274    }
2275    
2276    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2277    {
2278    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2279    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2280    switch(functionSpaceType) {    switch(functionSpaceCode) {
2281         case(Nodes):     case(Nodes):
2282            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2283            break;            break;
2284         case(ReducedNodes):     case(ReducedNodes):
2285            throw FinleyAdapterException("Error - ReducedNodes does not support tags");            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2286            break;            break;
2287         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2288            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2289            break;            break;
2290         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2291            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2292            break;            break;
2293         case(Elements):     case(Elements):
2294            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2295              numTags=mesh->Elements->numTagsInUse;
2296              break;
2297       case(FaceElements):
2298       case(ReducedFaceElements):
2299              numTags=mesh->FaceElements->numTagsInUse;
2300              break;
2301       case(Points):
2302              numTags=mesh->Points->numTagsInUse;
2303              break;
2304       case(ContactElementsZero):
2305       case(ReducedContactElementsZero):
2306       case(ContactElementsOne):
2307       case(ReducedContactElementsOne):
2308              numTags=mesh->ContactElements->numTagsInUse;
2309            break;            break;
2310         case(ReducedElements):     default:
2311            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);        stringstream temp;
2312            break;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2313         case(FaceElements):        throw FinleyAdapterException(temp.str());
2314            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);    }
2315            break;    return numTags;
2316         case(ReducedFaceElements):  }
2317            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);  
2318            break;  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2319         case(Points):  {
2320            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);    Finley_Mesh* mesh=m_finleyMesh.get();
2321      index_t* tags=NULL;
2322      switch(functionSpaceCode) {
2323       case(Nodes):
2324              tags=mesh->Nodes->tagsInUse;
2325            break;            break;
2326         case(ContactElementsZero):     case(ReducedNodes):
2327            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2328            break;            break;
2329         case(ReducedContactElementsZero):     case(DegreesOfFreedom):
2330            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2331            break;            break;
2332         case(ContactElementsOne):     case(ReducedDegreesOfFreedom):
2333            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2334            break;            break;
2335         case(ReducedContactElementsOne):     case(Elements):
2336            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2337              tags=mesh->Elements->tagsInUse;
2338              break;
2339       case(FaceElements):
2340       case(ReducedFaceElements):
2341              tags=mesh->FaceElements->tagsInUse;
2342              break;
2343       case(Points):
2344              tags=mesh->Points->tagsInUse;
2345              break;
2346       case(ContactElementsZero):
2347       case(ReducedContactElementsZero):
2348       case(ContactElementsOne):
2349       case(ReducedContactElementsOne):
2350              tags=mesh->ContactElements->tagsInUse;
2351            break;            break;
2352         default:     default:
2353            stringstream temp;        stringstream temp;
2354            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2355            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2356    }    }
2357    checkFinleyError();    return tags;
   return;  
2358  }  }
2359    
2360  void MeshAdapter::setTagMap(const std::string& name,  int tag)  
2361    bool MeshAdapter::canTag(int functionSpaceCode) const
2362  {  {
2363    Finley_Mesh* mesh=m_finleyMesh.get();    switch(functionSpaceCode) {
2364    Finley_Mesh_addTagMap(mesh, name.c_str(),tag);     case(Nodes):
2365    checkPasoError();     case(Elements):
2366    // throwStandardException("MeshAdapter::set TagMap is not implemented.");     case(ReducedElements):
2367       case(FaceElements):
2368       case(ReducedFaceElements):
2369       case(Points):
2370       case(ContactElementsZero):
2371       case(ReducedContactElementsZero):
2372       case(ContactElementsOne):
2373       case(ReducedContactElementsOne):
2374              return true;
2375       case(ReducedNodes):
2376       case(DegreesOfFreedom):
2377       case(ReducedDegreesOfFreedom):
2378          return false;
2379       default:
2380        return false;
2381      }
2382  }  }
2383    
2384  int MeshAdapter::getTag(const std::string& name) const  AbstractDomain::StatusType MeshAdapter::getStatus() const
2385  {  {
2386    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2387    int tag=0;    return Finley_Mesh_getStatus(mesh);
   tag=Finley_Mesh_getTag(mesh, name.c_str());  
   checkPasoError();  
   // throwStandardException("MeshAdapter::getTag is not implemented.");  
   return tag;  
2388  }  }
2389    
2390  bool MeshAdapter::isValidTagName(const std::string& name) const  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2391  {  {
2392      
2393    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2394    return Finley_Mesh_isValidTagName(mesh,name.c_str());    int order =-1;
2395      switch(functionSpaceCode) {
2396       case(Nodes):
2397       case(DegreesOfFreedom):
2398              order=mesh->approximationOrder;
2399              break;
2400       case(ReducedNodes):
2401       case(ReducedDegreesOfFreedom):
2402              order=mesh->reducedApproximationOrder;
2403              break;
2404       case(Elements):
2405       case(FaceElements):
2406       case(Points):
2407       case(ContactElementsZero):
2408       case(ContactElementsOne):
2409              order=mesh->integrationOrder;
2410              break;
2411       case(ReducedElements):
2412       case(ReducedFaceElements):
2413       case(ReducedContactElementsZero):
2414       case(ReducedContactElementsOne):
2415              order=mesh->reducedIntegrationOrder;
2416              break;
2417       default:
2418          stringstream temp;
2419          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2420          throw FinleyAdapterException(temp.str());
2421      }
2422      return order;
2423  }  }
2424    
2425  std::string MeshAdapter::showTagNames() const  bool MeshAdapter::supportsContactElements() const
2426  {  {
2427    stringstream temp;    return true;
   Finley_Mesh* mesh=m_finleyMesh.get();  
   Finley_TagMap* tag_map=mesh->TagMap;  
   while (tag_map) {  
      temp << tag_map->name;  
      tag_map=tag_map->next;  
      if (tag_map) temp << ", ";  
   }  
   return temp.str();  
2428  }  }
2429    
2430    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2431    {
2432      m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2433    }
2434    
2435    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2436    {
2437      Finley_ReferenceElementSet_dealloc(m_refSet);
2438    }
2439    
2440    // points will be flattened
2441    void MeshAdapter:: addDiracPoints(const std::vector<double>& points, const std::vector<int>& tags) const
2442    {
2443          const int dim = getDim();
2444          int numPoints=points.size()/dim;
2445          int numTags=tags.size();
2446          Finley_Mesh* mesh=m_finleyMesh.get();
2447          
2448          if ( points.size() % dim != 0 )
2449          {
2450        throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2451          }
2452          
2453          if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2454         throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2455          
2456          double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2457          int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2458          
2459          for (int i=0;i<numPoints;++i) {
2460           points_ptr[ i * dim     ] = points[i * dim ];
2461           if ( dim > 1 ) points_ptr[ i * dim + 1 ] = points[i * dim + 1];
2462           if ( dim > 2 ) points_ptr[ i * dim + 2 ] = points[i * dim + 2];    
2463               tags_ptr[i]=tags[i];
2464          }
2465          
2466          Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2467          checkFinleyError();
2468          
2469          TMPMEMFREE(points_ptr);
2470          TMPMEMFREE(tags_ptr);
2471    }
2472    
2473    
2474    // void MeshAdapter:: addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2475    // {
2476    //       const int dim = getDim();
2477    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2478    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2479    //       Finley_Mesh* mesh=m_finleyMesh.get();
2480    //      
2481    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2482    //   throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2483    //      
2484    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2485    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2486    //      
2487    //       for (int i=0;i<numPoints;++i) {
2488    //     int tag_id=-1;
2489    //     int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2490    //     if  ( numComps !=   dim ) {
2491    //                stringstream temp;            
2492    //                temp << "Error - illegal number of components " << numComps << " for point " << i;              
2493    //                throw FinleyAdapterException(temp.str());
2494    //     }
2495    //     points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2496    //     if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2497    //     if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2498    //    
2499    //     if ( numTags > 0) {
2500    //            boost::python::extract<string> ex_str(tags[i]);
2501    //        if  ( ex_str.check() ) {
2502    //            tag_id=getTag( ex_str());
2503    //        } else {
2504    //             boost::python::extract<int> ex_int(tags[i]);
2505    //             if ( ex_int.check() ) {
2506    //                 tag_id=ex_int();
2507    //             } else {
2508    //              stringstream temp;          
2509    //                  temp << "Error - unable to extract tag for point " << i;
2510    //              throw FinleyAdapterException(temp.str());
2511    //            }
2512    //        }
2513    //     }      
2514    //            tags_ptr[i]=tag_id;
2515    //       }
2516    //      
2517    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2518    //       checkPasoError();
2519    //      
2520    //       TMPMEMFREE(points_ptr);
2521    //       TMPMEMFREE(tags_ptr);
2522    // }
2523    
2524    /*
2525    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2526    {  
2527        boost::python::list points =  boost::python::list();
2528        boost::python::list tags =  boost::python::list();
2529        points.append(point);
2530        tags.append(tag);
2531        addDiracPoints(points, tags);
2532    }
2533    */
2534    
2535    /*
2536    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const std::string& tag) const
2537    {
2538            boost::python::list points =   boost::python::list();
2539            boost::python::list tags =   boost::python::list();
2540            points.append(point);
2541            tags.append(tag);
2542            addDiracPoints(points, tags);
2543    }
2544    */
2545  }  // end of namespace  }  // end of namespace

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