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

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revision 1116 by gross, Mon Apr 23 03:36:34 2007 UTC revision 3675 by jfenwick, Thu Nov 17 00:53:38 2011 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  
  *                                                                            *  
  * This software is the property of ACcESS. No part of this code              *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that person has a software    *  
  * license agreement with ACcESS.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
1    
2  #ifdef PASO_MPI  /*******************************************************
3  #include <mpi.h>  *
4  #endif  * Copyright (c) 2003-2010 by University of Queensland
5  #include "MeshAdapter.h"  * Earth Systems Science Computational Center (ESSCC)
6    * http://www.uq.edu.au/esscc
7    *
8    * Primary Business: Queensland, Australia
9    * Licensed under the Open Software License version 3.0
10    * 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"
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" {
23    #include "esysUtils/blocktimer.h"
24    }
25    
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_dealloc 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      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
75      Finley_Mesh_dealloc(m_finleyMesh.get());     }
     //   cout << "Finished dealloc." << endl;  
   }  
76  }  }
77    
78    int MeshAdapter::getMPISize() const
79    {
80       return m_finleyMesh.get()->MPIInfo->size;
81    }
82    int MeshAdapter::getMPIRank() const
83    {
84       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;
121       strcpy(fName,fileName.c_str());
122       Finley_Mesh_write(m_finleyMesh.get(),fName);
123       checkFinleyError();
124       TMPMEMFREE(fName);
125    }
126    
127    void MeshAdapter::Print_Mesh_Info(const bool full) const
128  {  {
129    char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
130    strcpy(fName,fileName.c_str());  }
131    Finley_Mesh_write(m_finleyMesh.get(),fName);  
132    checkFinleyError();  void MeshAdapter::dump(const string& fileName) const
133    TMPMEMFREE(fName);  {
134    #ifdef USE_NETCDF
135       const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
136       NcVar *ids;
137       int *int_ptr;
138       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 203  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 218  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             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
689             break;     break;
690        case(ReducedNodes):     case(ReducedNodes):
691             /* TODO: add ReducedNodes */     numDataPointsPerSample=1;
692             numDataPointsPerSample=1;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
693             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     break;
694             throw FinleyAdapterException("Error - ReducedNodes is not supported yet.");     case(Elements):
695             break;     if (mesh->Elements!=NULL) {
696        case(Elements):        numSamples=mesh->Elements->numElements;
697             if (mesh->Elements!=NULL) {        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
698               numSamples=mesh->Elements->numElements;     }
699               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
700             }     case(ReducedElements):
701             break;     if (mesh->Elements!=NULL) {
702        case(ReducedElements):        numSamples=mesh->Elements->numElements;
703             if (mesh->Elements!=NULL) {        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
704               numSamples=mesh->Elements->numElements;     }
705               numDataPointsPerSample=mesh->Elements->ReferenceElementReducedOrder->numQuadNodes;     break;
706             }     case(FaceElements):
707             break;     if (mesh->FaceElements!=NULL) {
708        case(FaceElements):        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
709             if (mesh->FaceElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
710                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
711                  numSamples=mesh->FaceElements->numElements;     break;
712             }     case(ReducedFaceElements):
713             break;     if (mesh->FaceElements!=NULL) {
714        case(ReducedFaceElements):        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
715             if (mesh->FaceElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
716                  numDataPointsPerSample=mesh->FaceElements->ReferenceElementReducedOrder->numQuadNodes;     }
717                  numSamples=mesh->FaceElements->numElements;     break;
718             }     case(Points):
719             break;     if (mesh->Points!=NULL) {
720        case(Points):        numDataPointsPerSample=1;
721             if (mesh->Points!=NULL) {        numSamples=mesh->Points->numElements;
722               numDataPointsPerSample=1;     }
723               numSamples=mesh->Points->numElements;     break;
724             }     case(ContactElementsZero):
725             break;     if (mesh->ContactElements!=NULL) {
726        case(ContactElementsZero):        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
727             if (mesh->ContactElements!=NULL) {        numSamples=mesh->ContactElements->numElements;
728               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
729               numSamples=mesh->ContactElements->numElements;     break;
730             }     case(ReducedContactElementsZero):
731             break;     if (mesh->ContactElements!=NULL) {
732        case(ReducedContactElementsZero):        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
733             if (mesh->ContactElements!=NULL) {        numSamples=mesh->ContactElements->numElements;
734               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;     }
735               numSamples=mesh->ContactElements->numElements;     break;
736             }     case(ContactElementsOne):
737             break;     if (mesh->ContactElements!=NULL) {
738        case(ContactElementsOne):        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
739             if (mesh->ContactElements!=NULL) {        numSamples=mesh->ContactElements->numElements;
740               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
741               numSamples=mesh->ContactElements->numElements;     break;
742             }     case(ReducedContactElementsOne):
743             break;     if (mesh->ContactElements!=NULL) {
744        case(ReducedContactElementsOne):        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
745             if (mesh->ContactElements!=NULL) {        numSamples=mesh->ContactElements->numElements;
746               numDataPointsPerSample=mesh->ContactElements->ReferenceElementReducedOrder->numQuadNodes;     }
747               numSamples=mesh->ContactElements->numElements;     break;
748             }     case(DegreesOfFreedom):
749             break;     if (mesh->Nodes!=NULL) {
750        case(DegreesOfFreedom):        numDataPointsPerSample=1;
751             if (mesh->Nodes!=NULL) {        numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
752               numDataPointsPerSample=1;     }
753  #ifndef PASO_MPI     break;
754               numSamples=mesh->Nodes->numDegreesOfFreedom;     case(ReducedDegreesOfFreedom):
755  #else     if (mesh->Nodes!=NULL) {
756               numSamples=mesh->Nodes->degreeOfFreedomDistribution->numLocal;        numDataPointsPerSample=1;
757  #endif        numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
758             }     }
759             break;     break;
760        case(ReducedDegreesOfFreedom):     default:
761             if (mesh->Nodes!=NULL) {        stringstream temp;
762               numDataPointsPerSample=1;        temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
763  #ifndef PASO_MPI        throw FinleyAdapterException(temp.str());
764               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;        break;
765  #else     }
766               numSamples=mesh->Nodes->reducedDegreeOfFreedomDistribution->numLocal;     return pair<int,int>(numDataPointsPerSample,numSamples);
 #endif  
            }  
            break;  
       default:  
         stringstream temp;  
         temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();  
         throw FinleyAdapterException(temp.str());  
         break;  
       }  
       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 its own 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 331  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();     checkFinleyError();
802    
803     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );     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->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );     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->Points, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
810       checkFinleyError();
811    }
812    
813    void  MeshAdapter::addPDEToLumpedSystem(
814                                            escript::Data& mat,
815                                            const escript::Data& D,
816                                            const escript::Data& d,
817                                            const escript::Data& d_dirac,
818                                            const bool useHRZ) const
819    {
820       escriptDataC _mat=mat.getDataC();
821       escriptDataC _D=D.getDataC();
822       escriptDataC _d=d.getDataC();
823       escriptDataC _d_dirac=d_dirac.getDataC();
824    
825       Finley_Mesh* mesh=m_finleyMesh.get();
826    
827       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D, useHRZ);
828       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();
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 356  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 365  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       paso::TransportProblemAdapter* tpa=dynamic_cast<paso::TransportProblemAdapter*>(&tp);
878       if (tpa==0)
879       {
880        throw FinleyAdapterException("finley only supports its own 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 372  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             case(Nodes):    
1070             case(ReducedNodes):        case(Nodes):
1071                Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        case(ReducedNodes):
1072                break;        if (getMPISize()>1) {
1073  #ifndef PASO_MPI           escript::Data temp=escript::Data(in);
1074             case(Elements):           temp.expand();
1075             case(ReducedElements):           escriptDataC _in2 = temp.getDataC();
1076                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1077                break;        } else {
1078             case(FaceElements):           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1079             case(ReducedFaceElements):        }
1080                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        break;
1081                break;        case(Elements):
1082             case(Points):        case(ReducedElements):
1083                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        if (getMPISize()>1) {
1084                break;           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1085             case(ContactElementsZero):           escriptDataC _in2 = temp.getDataC();
1086             case(ContactElementsOne):           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1087             case(ReducedContactElementsZero):        } else {
1088             case(ReducedContactElementsOne):           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1089                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        }
1090               break;        break;
1091  #else        case(FaceElements):
1092             /* need to copy Degrees of freedom data to nodal data so that the external values are available */        case(ReducedFaceElements):
1093             case(Elements):        if (getMPISize()>1) {
1094             case(ReducedElements):           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1095                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );           escriptDataC _in2 = temp.getDataC();
1096                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(nodeTemp.getDataC()),&_target);           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1097                break;    
1098             case(FaceElements):        } else {
1099             case(ReducedFaceElements):           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1100                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );        }
1101                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(nodeTemp.getDataC()),&_target);        break;
1102                break;        case(Points):
1103             case(Points):        if (getMPISize()>1) {
1104                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );           //escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1105                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(nodeTemp.getDataC()),&_target);           //escriptDataC _in2 = temp.getDataC();
1106                break;        } else {
1107             case(ContactElementsZero):           Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1108             case(ContactElementsOne):        }
1109             case(ReducedContactElementsZero):        break;
1110             case(ReducedContactElementsOne):        case(ContactElementsZero):
1111                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );        case(ContactElementsOne):
1112                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(nodeTemp.getDataC()),&_target);        case(ReducedContactElementsZero):
1113               break;        case(ReducedContactElementsOne):
1114  #endif        if (getMPISize()>1) {
1115             default:           escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1116               stringstream temp;           escriptDataC _in2 = temp.getDataC();
1117               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1118               throw FinleyAdapterException(temp.str());        } else {
1119               break;           Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1120          }        }
1121          break;        break;
1122       case(ReducedDegreesOfFreedom):        default:
1123         switch(target.getFunctionSpace().getTypeCode()) {           stringstream temp;
1124            case(Nodes):           temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1125               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");           throw FinleyAdapterException(temp.str());
1126               break;           break;
1127            case(ReducedNodes):        }
1128               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        break;
1129               break;     case(ReducedDegreesOfFreedom):
1130            case(DegreesOfFreedom):        switch(target.getFunctionSpace().getTypeCode()) {
1131               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");        case(Nodes):
1132               break;        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1133            case(ReducedDegreesOfFreedom):        break;
1134               Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);        case(ReducedNodes):
1135               break;        if (getMPISize()>1) {
1136            case(Elements):           escript::Data temp=escript::Data(in);
1137            case(ReducedElements):           temp.expand();
1138               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);           escriptDataC _in2 = temp.getDataC();
1139               break;           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1140            case(FaceElements):        } else {
1141            case(ReducedFaceElements):           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1142               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);        }
1143               break;        break;
1144            case(Points):        case(DegreesOfFreedom):
1145               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);        throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1146               break;        break;
1147            case(ContactElementsZero):        case(ReducedDegreesOfFreedom):
1148            case(ContactElementsOne):        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1149            case(ReducedContactElementsZero):        break;
1150            case(ReducedContactElementsOne):        case(Elements):
1151               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);        case(ReducedElements):
1152               break;        if (getMPISize()>1) {
1153            default:           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1154               stringstream temp;           escriptDataC _in2 = temp.getDataC();
1155               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1156               throw FinleyAdapterException(temp.str());        } else {
1157               break;           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1158         }        }
1159         break;        break;
1160       default:        case(FaceElements):
1161          stringstream temp;        case(ReducedFaceElements):
1162          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();        if (getMPISize()>1) {
1163          throw FinleyAdapterException(temp.str());           escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1164          break;           escriptDataC _in2 = temp.getDataC();
1165    }           Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1166    checkFinleyError();        } else {
1167             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1168          }
1169          break;
1170          case(Points):
1171          if (getMPISize()>1) {
1172             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1173             escriptDataC _in2 = temp.getDataC();
1174             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1175          } else {
1176             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1177          }
1178          break;
1179          case(ContactElementsZero):
1180          case(ContactElementsOne):
1181          case(ReducedContactElementsZero):
1182          case(ReducedContactElementsOne):
1183          if (getMPISize()>1) {
1184             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1185             escriptDataC _in2 = temp.getDataC();
1186             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1187          } else {
1188             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1189          }
1190          break;
1191          default:
1192             stringstream temp;
1193             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1194             throw FinleyAdapterException(temp.str());
1195             break;
1196          }
1197          break;
1198       default:
1199          stringstream temp;
1200          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1201          throw FinleyAdapterException(temp.str());
1202          break;
1203       }
1204       checkFinleyError();
1205  }  }
1206    
1207  //  //
# Line 619  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 642  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 697  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    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1309    escriptDataC _arg=arg.getDataC();     Finley_Mesh* mesh=m_finleyMesh.get();
1310    switch(arg.getFunctionSpace().getTypeCode()) {     escriptDataC _temp;
1311       case(Nodes):     escript::Data temp;
1312          /* TODO */     escriptDataC _arg=arg.getDataC();
1313          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");     switch(arg.getFunctionSpace().getTypeCode()) {
1314          break;     case(Nodes):
1315       case(ReducedNodes):     temp=escript::Data( arg, escript::function(*this) );
1316          /* TODO */     _temp=temp.getDataC();
1317          throw FinleyAdapterException("Error - Integral of data on reduced nodes is not supported.");     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1318          break;     break;
1319       case(Elements):     case(ReducedNodes):
1320          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     temp=escript::Data( arg, escript::function(*this) );
1321          break;     _temp=temp.getDataC();
1322       case(ReducedElements):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1323          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);     break;
1324          break;     case(Elements):
1325       case(FaceElements):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1326          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     break;
1327          break;     case(ReducedElements):
1328       case(ReducedFaceElements):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1329          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);     break;
1330          break;     case(FaceElements):
1331       case(Points):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1332          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     break;
1333          break;     case(ReducedFaceElements):
1334       case(ContactElementsZero):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1335          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     break;
1336          break;     case(Points):
1337       case(ReducedContactElementsZero):     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1338          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     break;
1339          break;     case(ContactElementsZero):
1340       case(ContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1341          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     break;
1342          break;     case(ReducedContactElementsZero):
1343       case(ReducedContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1344          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);     break;
1345          break;     case(ContactElementsOne):
1346       case(DegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1347          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");     break;
1348          break;     case(ReducedContactElementsOne):
1349       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1350          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");     break;
1351          break;     case(DegreesOfFreedom):
1352       default:     temp=escript::Data( arg, escript::function(*this) );
1353          stringstream temp;     _temp=temp.getDataC();
1354          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1355          throw FinleyAdapterException(temp.str());     break;
1356          break;     case(ReducedDegreesOfFreedom):
1357    }     temp=escript::Data( arg, escript::function(*this) );
1358    checkFinleyError();     _temp=temp.getDataC();
1359       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1360       break;
1361       default:
1362          stringstream temp;
1363          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1364          throw FinleyAdapterException(temp.str());
1365          break;
1366       }
1367       checkFinleyError();
1368       blocktimer_increment("integrate()", blocktimer_start);
1369  }  }
1370    
1371  //  //
# Line 771  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  #ifdef PASO_MPI     escript::Data temp;
1387    escript::Data nodeTemp( arg, continuousFunction(asAbstractContinuousDomain()) );     if (getMPISize()>1) {
1388    if( arg.getFunctionSpace().getTypeCode() != Nodes )        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1389    {           temp=escript::Data( arg,  continuousFunction(*this) );
1390      Finley_Assemble_CopyNodalData(mesh->Nodes,&(nodeTemp.getDataC()),&(arg.getDataC()));           nodeDataC = temp.getDataC();
1391      nodeDataC = nodeTemp.getDataC();        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1392    }           temp=escript::Data( arg,  reducedContinuousFunction(*this) );
1393    else           nodeDataC = temp.getDataC();
1394      nodeDataC = arg.getDataC();        } else {
1395  #else           nodeDataC = arg.getDataC();
1396    nodeDataC = arg.getDataC();        }
1397  #endif     } else {
1398    switch(grad.getFunctionSpace().getTypeCode()) {        nodeDataC = arg.getDataC();
1399         case(Nodes):     }
1400            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     switch(grad.getFunctionSpace().getTypeCode()) {
1401            break;     case(Nodes):
1402         case(ReducedNodes):     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1403            throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");     break;
1404            break;     case(ReducedNodes):
1405         case(Elements):     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1406            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     break;
1407            break;     case(Elements):
1408         case(ReducedElements):     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1409            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);     break;
1410            break;     case(ReducedElements):
1411         case(FaceElements):     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1412            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     break;
1413            break;     case(FaceElements):
1414         case(ReducedFaceElements):     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1415            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);     break;
1416            break;     case(ReducedFaceElements):
1417         case(Points):     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1418            throw FinleyAdapterException("Error - Gradient at points is not supported.");     break;
1419            break;     case(Points):
1420         case(ContactElementsZero):     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1421            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     break;
1422            break;     case(ContactElementsZero):
1423         case(ReducedContactElementsZero):     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1424            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     break;
1425            break;     case(ReducedContactElementsZero):
1426         case(ContactElementsOne):     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1427            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     break;
1428            break;     case(ContactElementsOne):
1429         case(ReducedContactElementsOne):     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1430            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);     break;
1431            break;     case(ReducedContactElementsOne):
1432         case(DegreesOfFreedom):     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1433            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     break;
1434            break;     case(DegreesOfFreedom):
1435         case(ReducedDegreesOfFreedom):     throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1436            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     break;
1437            break;     case(ReducedDegreesOfFreedom):
1438         default:     throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1439            stringstream temp;     break;
1440            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     default:
1441            throw FinleyAdapterException(temp.str());        stringstream temp;
1442            break;        temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1443    }        throw FinleyAdapterException(temp.str());
1444    checkFinleyError();        break;
1445       }
1446       checkFinleyError();
1447  }  }
1448    
1449  //  //
# Line 847  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();
1520      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;  
   }  
1521    
1522    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  //
1523    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  // Helper for the save* methods. Extracts optional data variable names and the
1524    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  // corresponding pointers from python dictionary. Caller must free arrays.
1525    //
1526      boost::python::list keys=arg.keys();  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1527      for (int i=0;i<num_data;++i) {  {
1528           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     numData = boost::python::extract<int>(arg.attr("__len__")());
1529           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     /* win32 refactor */
1530               throw FinleyAdapterException("Error  in saveDX: Data must be defined on same Domain");     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1531           data[i]=d.getDataC();     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1532           ptr_data[i]=&(data[i]);     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1533           std::string n=boost::python::extract<std::string>(keys[i]);  
1534           c_names[i]=&(names[i][0]);     boost::python::list keys=arg.keys();
1535           if (n.length()>MAX_namelength-1) {     for (int i=0; i<numData; ++i) {
1536              strncpy(c_names[i],n.c_str(),MAX_namelength-1);        string n=boost::python::extract<string>(keys[i]);
1537              c_names[i][MAX_namelength-1]='\0';        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1538           } else {        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1539              strcpy(c_names[i],n.c_str());           throw FinleyAdapterException("Error: Data must be defined on same Domain");
1540           }        data[i] = d.getDataC();
1541      }        dataPtr[i] = &(data[i]);
1542      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);        names[i] = TMPMEMALLOC(n.length()+1, char);
1543      checkFinleyError();        strcpy(names[i], n.c_str());
1544           }
1545        /* win32 refactor */  }
1546    TMPMEMFREE(c_names);  
1547    TMPMEMFREE(data);  //
1548    TMPMEMFREE(ptr_data);  // saves mesh and optionally data arrays in openDX format
1549    for(int i=0;i<num_data;i++)  //
1550    {  void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1551      TMPMEMFREE(names[i]);  {
1552    }     int num_data;
1553    TMPMEMFREE(names);     char **names;
1554       escriptDataC *data;
1555       escriptDataC **ptr_data;
1556    
1557       extractArgsFromDict(arg, num_data, names, data, ptr_data);
1558       Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1559       checkFinleyError();
1560    
1561       /* win32 refactor */
1562       TMPMEMFREE(data);
1563       TMPMEMFREE(ptr_data);
1564       for(int i=0; i<num_data; i++)
1565       {
1566          TMPMEMFREE(names[i]);
1567       }
1568       TMPMEMFREE(names);
1569    
1570      return;     return;
1571  }  }
1572    
1573  // saves a data array in openVTK format:  //
1574  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  // saves mesh and optionally data arrays in VTK format
1575    //
1576    void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1577  {  {
1578      int MAX_namelength=256;      boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("_saveVTK");
1579      const int num_data=boost::python::extract<int>(arg.attr("__len__")());      pySaveVTK(filename, const_cast<MeshAdapter*>(this)->getPtr(),
1580    /* win32 refactor */                metadata, metadata_schema, arg);
1581    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;  
   }  
1582    
1583    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1584    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  {
1585    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  #ifdef ESYS_MPI
1586        index_t myFirstNode=0, myLastNode=0, k=0;
1587      boost::python::list keys=arg.keys();      index_t* globalNodeIndex=0;
1588      for (int i=0;i<num_data;++i) {      Finley_Mesh* mesh_p=m_finleyMesh.get();
1589           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);      if (fs_code == FINLEY_REDUCED_NODES)
1590           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)      {
1591               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");      myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1592           data[i]=d.getDataC();      myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1593           ptr_data[i]=&(data[i]);      globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
          std::string n=boost::python::extract<std::string>(keys[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());  
          }  
1594      }      }
1595  #ifndef PASO_MPI          else
1596      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);      {
1597  #else      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1598      Finley_Mesh_saveVTK_MPIO(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1599        globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
1600        }
1601        k=globalNodeIndex[id];
1602        return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1603  #endif  #endif
1604        return true;
1605    }
1606    
 checkFinleyError();  
   /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1607    
1608      return;  
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
1651          /* Allocation Epetra_VrbMatrix here */
1652    #endif
1653       }
1654       else {
1655          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1656       }
1657       checkPasoError();
1658       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1659       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 SystemMatrixAdapter stiffness matrix an initializes it with zeros:  // creates a TransportProblemAdapter
1666  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  //
1667                        const int row_blocksize,  ATP_ptr MeshAdapter::newTransportProblem(
1668                        const escript::FunctionSpace& row_functionspace,                                                           const bool useBackwardEuler,
1669                        const int column_blocksize,                                                           const int blocksize,
1670                        const escript::FunctionSpace& column_functionspace,                                                           const escript::FunctionSpace& functionspace,
1671                        const int type) const                                                           const int type) const
1672  {  {
1673      int reduceRowOrder=0;     int reduceOrder=0;
1674      int reduceColOrder=0;     // is the domain right?
1675      // is the domain right?     const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1676      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     if (domain!=*this)
1677      if (row_domain!=*this)        throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1678            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");     // is the function space type right
1679      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     if (functionspace.getTypeCode()==DegreesOfFreedom) {
1680      if (col_domain!=*this)        reduceOrder=0;
1681            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");     } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1682      // is the function space type right        reduceOrder=1;
1683      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     } else {
1684          reduceRowOrder=0;        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1685      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     }
1686          reduceRowOrder=1;     // generate matrix:
1687      } else {  
1688          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1689      }     checkFinleyError();
1690      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     Paso_TransportProblem* transportProblem;
1691          reduceColOrder=0;     transportProblem=Paso_TransportProblem_alloc(useBackwardEuler,fsystemMatrixPattern,blocksize);
1692      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     checkPasoError();
1693          reduceColOrder=1;     Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1694      } else {     TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1695          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");     return ATP_ptr(tpa);
1696      }  //   return TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
     // generate matrix:  
       
     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);  
     checkFinleyError();  
     Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);  
     checkPasoError();  
     Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);  
     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  
1697  }  }
1698    
1699  //  //
# Line 1059  SystemMatrixAdapter MeshAdapter::newSyst Line 1705  SystemMatrixAdapter MeshAdapter::newSyst
1705  // 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:
1706  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1707  {  {
1708    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1709         case(Nodes):     case(Nodes):
1710         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1711         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1712            return false;     return false;
1713            break;     break;
1714         case(Elements):     case(Elements):
1715         case(FaceElements):     case(FaceElements):
1716         case(Points):     case(Points):
1717         case(ContactElementsZero):     case(ContactElementsZero):
1718         case(ContactElementsOne):     case(ContactElementsOne):
1719         case(ReducedElements):     case(ReducedElements):
1720         case(ReducedFaceElements):     case(ReducedFaceElements):
1721         case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
1722         case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
1723            return true;     return true;
1724            break;     break;
1725         default:     default:
1726            stringstream temp;        stringstream temp;
1727            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;
1728            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1729            break;        break;
1730    }     }
1731    checkFinleyError();     checkFinleyError();
1732    return false;     return false;
1733    }
1734    
1735    bool
1736    MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1737    {
1738       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1739        class 1: DOF <-> Nodes
1740        class 2: ReducedDOF <-> ReducedNodes
1741        class 3: Points
1742        class 4: Elements
1743        class 5: ReducedElements
1744        class 6: FaceElements
1745        class 7: ReducedFaceElements
1746        class 8: ContactElementZero <-> ContactElementOne
1747        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1748    
1749       There is also a set of lines. Interpolation is possible down a line but not between lines.
1750       class 1 and 2 belong to all lines so aren't considered.
1751        line 0: class 3
1752        line 1: class 4,5
1753        line 2: class 6,7
1754        line 3: class 8,9
1755    
1756       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1757       eg hasnodes is true if we have at least one instance of Nodes.
1758       */
1759        if (fs.empty())
1760        {
1761            return false;
1762        }
1763        vector<int> hasclass(10);
1764        vector<int> hasline(4);
1765        bool hasnodes=false;
1766        bool hasrednodes=false;
1767        bool hascez=false;
1768        bool hasrcez=false;
1769        for (int i=0;i<fs.size();++i)
1770        {
1771        switch(fs[i])
1772        {
1773        case(Nodes):   hasnodes=true;   // no break is deliberate
1774        case(DegreesOfFreedom):
1775            hasclass[1]=1;
1776            break;
1777        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1778        case(ReducedDegreesOfFreedom):
1779            hasclass[2]=1;
1780            break;
1781        case(Points):
1782            hasline[0]=1;
1783            hasclass[3]=1;
1784            break;
1785        case(Elements):
1786            hasclass[4]=1;
1787            hasline[1]=1;
1788            break;
1789        case(ReducedElements):
1790            hasclass[5]=1;
1791            hasline[1]=1;
1792            break;
1793        case(FaceElements):
1794            hasclass[6]=1;
1795            hasline[2]=1;
1796            break;
1797        case(ReducedFaceElements):
1798            hasclass[7]=1;
1799            hasline[2]=1;
1800            break;
1801        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1802        case(ContactElementsOne):
1803            hasclass[8]=1;
1804            hasline[3]=1;
1805            break;
1806        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1807        case(ReducedContactElementsOne):
1808            hasclass[9]=1;
1809            hasline[3]=1;
1810            break;
1811        default:
1812            return false;
1813        }
1814        }
1815        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1816        // fail if we have more than one leaf group
1817    
1818        if (totlines>1)
1819        {
1820        return false;   // there are at least two branches we can't interpolate between
1821        }
1822        else if (totlines==1)
1823        {
1824        if (hasline[0]==1)      // we have points
1825        {
1826            resultcode=Points;
1827        }
1828        else if (hasline[1]==1)
1829        {
1830            if (hasclass[5]==1)
1831            {
1832            resultcode=ReducedElements;
1833            }
1834            else
1835            {
1836            resultcode=Elements;
1837            }
1838        }
1839        else if (hasline[2]==1)
1840        {
1841            if (hasclass[7]==1)
1842            {
1843            resultcode=ReducedFaceElements;
1844            }
1845            else
1846            {
1847            resultcode=FaceElements;
1848            }
1849        }
1850        else    // so we must be in line3
1851        {
1852            if (hasclass[9]==1)
1853            {
1854            // need something from class 9
1855            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1856            }
1857            else
1858            {
1859            // something from class 8
1860            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1861            }
1862        }
1863        }
1864        else    // totlines==0
1865        {
1866        if (hasclass[2]==1)
1867        {
1868            // something from class 2
1869            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1870        }
1871        else
1872        {   // something from class 1
1873            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1874        }
1875        }
1876        return true;
1877  }  }
1878    
1879  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1880  {  {
1881    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1882       case(Nodes):     case(Nodes):
1883          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1884             case(Nodes):      case(Nodes):
1885             case(ReducedNodes):      case(ReducedNodes):
1886             case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1887             case(DegreesOfFreedom):      case(DegreesOfFreedom):
1888             case(Elements):      case(Elements):
1889             case(ReducedElements):      case(ReducedElements):
1890             case(FaceElements):      case(FaceElements):
1891             case(ReducedFaceElements):      case(ReducedFaceElements):
1892             case(Points):      case(Points):
1893             case(ContactElementsZero):      case(ContactElementsZero):
1894             case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1895             case(ContactElementsOne):      case(ContactElementsOne):
1896             case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1897                 return true;      return true;
1898             default:      default:
1899                 stringstream temp;            stringstream temp;
1900                 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;
1901                 throw FinleyAdapterException(temp.str());            throw FinleyAdapterException(temp.str());
1902          }     }
1903          break;     break;
1904       case(ReducedNodes):     case(ReducedNodes):
1905          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1906             case(ReducedNodes):      case(ReducedNodes):
1907             case(ReducedDegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1908             case(Elements):      case(Elements):
1909             case(ReducedElements):      case(ReducedElements):
1910             case(FaceElements):      case(FaceElements):
1911             case(ReducedFaceElements):      case(ReducedFaceElements):
1912             case(Points):      case(Points):
1913             case(ContactElementsZero):      case(ContactElementsZero):
1914             case(ReducedContactElementsZero):      case(ReducedContactElementsZero):
1915             case(ContactElementsOne):      case(ContactElementsOne):
1916             case(ReducedContactElementsOne):      case(ReducedContactElementsOne):
1917                 return true;      return true;
1918            case(Nodes):      case(Nodes):
1919            case(DegreesOfFreedom):      case(DegreesOfFreedom):
1920               return false;      return false;
1921             default:      default:
1922                 stringstream temp;          stringstream temp;
1923                 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;
1924                 throw FinleyAdapterException(temp.str());          throw FinleyAdapterException(temp.str());
1925          }     }
1926          break;     break;
1927       case(Elements):     case(Elements):
1928          if (functionSpaceType_target==Elements) {      if (functionSpaceType_target==Elements) {
1929             return true;        return true;
1930          } else if (functionSpaceType_target==ReducedElements) {      } else if (functionSpaceType_target==ReducedElements) {
1931             return true;        return true;
1932          } else {          } else {
1933             return false;            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;  
         } else {  
            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());  
1934          }          }
1935          break;     case(ReducedElements):
1936       case(ReducedDegreesOfFreedom):      if (functionSpaceType_target==ReducedElements) {
1937         switch(functionSpaceType_target) {        return true;
1938            case(ReducedDegreesOfFreedom):      } else {
1939            case(ReducedNodes):            return false;
1940            case(Elements):      }
1941            case(ReducedElements):     case(FaceElements):
1942            case(FaceElements):      if (functionSpaceType_target==FaceElements) {
1943            case(ReducedFaceElements):              return true;
1944            case(Points):      } else if (functionSpaceType_target==ReducedFaceElements) {
1945            case(ContactElementsZero):              return true;
1946            case(ReducedContactElementsZero):      } else {
1947            case(ContactElementsOne):              return false;
1948            case(ReducedContactElementsOne):      }
1949                return true;     case(ReducedFaceElements):
1950            case(Nodes):      if (functionSpaceType_target==ReducedFaceElements) {
1951            case(DegreesOfFreedom):              return true;
1952               return false;      } else {
1953            default:          return false;
1954               stringstream temp;      }
1955               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;     case(Points):
1956               throw FinleyAdapterException(temp.str());      if (functionSpaceType_target==Points) {
1957         }              return true;
1958         break;      } else {
1959       default:              return false;
1960          stringstream temp;      }
1961          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;     case(ContactElementsZero):
1962          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
1963          break;      if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1964    }              return true;
1965    checkFinleyError();      } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1966    return false;              return true;
1967        } else {
1968                return false;
1969        }
1970       case(ReducedContactElementsZero):
1971       case(ReducedContactElementsOne):
1972        if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1973                return true;
1974        } else {
1975                return false;
1976        }
1977       case(DegreesOfFreedom):
1978        switch(functionSpaceType_target) {
1979        case(ReducedDegreesOfFreedom):
1980        case(DegreesOfFreedom):
1981        case(Nodes):
1982        case(ReducedNodes):
1983        case(Elements):
1984        case(ReducedElements):
1985        case(Points):
1986        case(FaceElements):
1987        case(ReducedFaceElements):
1988        case(ContactElementsZero):
1989        case(ReducedContactElementsZero):
1990        case(ContactElementsOne):
1991        case(ReducedContactElementsOne):
1992        return true;
1993        default:
1994            stringstream temp;
1995            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1996            throw FinleyAdapterException(temp.str());
1997        }
1998        break;
1999       case(ReducedDegreesOfFreedom):
2000       switch(functionSpaceType_target) {
2001        case(ReducedDegreesOfFreedom):
2002        case(ReducedNodes):
2003        case(Elements):
2004        case(ReducedElements):
2005        case(FaceElements):
2006        case(ReducedFaceElements):
2007        case(Points):
2008        case(ContactElementsZero):
2009        case(ReducedContactElementsZero):
2010        case(ContactElementsOne):
2011        case(ReducedContactElementsOne):
2012        return true;
2013        case(Nodes):
2014        case(DegreesOfFreedom):
2015        return false;
2016        default:
2017            stringstream temp;
2018            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
2019            throw FinleyAdapterException(temp.str());
2020        }
2021        break;
2022       default:
2023          stringstream temp;
2024          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
2025          throw FinleyAdapterException(temp.str());
2026          break;
2027       }
2028       checkFinleyError();
2029       return false;
2030  }  }
2031    
2032  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
2033  {  {
2034      return false;     return false;
2035  }  }
2036    
2037  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
2038  {  {
2039    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
2040    if (temp!=0) {     if (temp!=0) {
2041      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
2042    } else {     } else {
2043      return false;        return false;
2044    }     }
2045  }  }
2046    
2047  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
2048  {  {
2049    return !(operator==(other));     return !(operator==(other));
2050  }  }
2051    
2052  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
2053  {  {
2054     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
2055       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2056       checkPasoError();
2057       return out;
2058    }
2059    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2060    {
2061       Finley_Mesh* mesh=m_finleyMesh.get();
2062       int out=Paso_TransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2063     checkPasoError();     checkPasoError();
2064     return out;     return out;
2065  }  }
2066    
2067  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2068  {  {
2069    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(*this).getX();
2070  }  }
2071    
2072  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2073  {  {
2074    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(*this).getNormal();
2075  }  }
2076    
2077  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2078  {  {
2079    return function(asAbstractContinuousDomain()).getSize();     return escript::function(*this).getSize();
2080  }  }
2081    
2082  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2083  {  {
2084    int *out=0,i;     int *out = NULL;
2085    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2086    switch (functionSpaceType) {     switch (functionSpaceType) {
2087      case(Nodes):     case(Nodes):
2088        if (mesh->Nodes!=NULL) {     out=mesh->Nodes->Id;
2089          out=mesh->Nodes->Id;     break;
2090          break;     case(ReducedNodes):
2091        }     out=mesh->Nodes->reducedNodesId;
2092      case(ReducedNodes):     break;
2093        throw FinleyAdapterException("Error -  ReducedNodes not supported yet.");     case(Elements):
2094        break;     out=mesh->Elements->Id;
2095      case(Elements):     break;
2096        out=mesh->Elements->Id;     case(ReducedElements):
2097        break;     out=mesh->Elements->Id;
2098      case(ReducedElements):     break;
2099        out=mesh->Elements->Id;     case(FaceElements):
2100        break;     out=mesh->FaceElements->Id;
2101      case(FaceElements):     break;
2102        out=mesh->FaceElements->Id;     case(ReducedFaceElements):
2103        break;     out=mesh->FaceElements->Id;
2104      case(ReducedFaceElements):     break;
2105        out=mesh->FaceElements->Id;     case(Points):
2106        break;     out=mesh->Points->Id;
2107      case(Points):     break;
2108        out=mesh->Points->Id;     case(ContactElementsZero):
2109        break;     out=mesh->ContactElements->Id;
2110      case(ContactElementsZero):     break;
2111        out=mesh->ContactElements->Id;     case(ReducedContactElementsZero):
2112        break;     out=mesh->ContactElements->Id;
2113      case(ReducedContactElementsZero):     break;
2114        out=mesh->ContactElements->Id;     case(ContactElementsOne):
2115        break;     out=mesh->ContactElements->Id;
2116      case(ContactElementsOne):     break;
2117        out=mesh->ContactElements->Id;     case(ReducedContactElementsOne):
2118        break;     out=mesh->ContactElements->Id;
2119      case(ReducedContactElementsOne):     break;
2120        out=mesh->ContactElements->Id;     case(DegreesOfFreedom):
2121        break;     out=mesh->Nodes->degreesOfFreedomId;
2122      case(DegreesOfFreedom):     break;
2123        out=mesh->Nodes->degreeOfFreedomId;     case(ReducedDegreesOfFreedom):
2124        break;     out=mesh->Nodes->reducedDegreesOfFreedomId;
2125      case(ReducedDegreesOfFreedom):     break;
2126        out=mesh->Nodes->reducedDegreeOfFreedomId;     default:
       break;  
     default:  
2127        stringstream temp;        stringstream temp;
2128        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2129        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2130        break;        break;
2131    }     }
2132    return out;     return out;
2133  }  }
2134  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2135  {  {
2136    int out=0;     int out=0;
2137    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2138    switch (functionSpaceType) {     switch (functionSpaceType) {
2139    case(Nodes):     case(Nodes):
2140      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Tag[sampleNo];
2141      break;     break;
2142    case(ReducedNodes):     case(ReducedNodes):
2143      throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");     throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
2144      break;     break;
2145    case(Elements):     case(Elements):
2146      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
2147      break;     break;
2148    case(ReducedElements):     case(ReducedElements):
2149      out=mesh->Elements->Tag[sampleNo];     out=mesh->Elements->Tag[sampleNo];
2150      break;     break;
2151    case(FaceElements):     case(FaceElements):
2152      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
2153      break;     break;
2154    case(ReducedFaceElements):     case(ReducedFaceElements):
2155      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->FaceElements->Tag[sampleNo];
2156      break;     break;
2157    case(Points):     case(Points):
2158      out=mesh->Points->Tag[sampleNo];     out=mesh->Points->Tag[sampleNo];
2159      break;     break;
2160    case(ContactElementsZero):     case(ContactElementsZero):
2161      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2162      break;     break;
2163    case(ReducedContactElementsZero):     case(ReducedContactElementsZero):
2164      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2165      break;     break;
2166    case(ContactElementsOne):     case(ContactElementsOne):
2167      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2168      break;     break;
2169    case(ReducedContactElementsOne):     case(ReducedContactElementsOne):
2170      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->ContactElements->Tag[sampleNo];
2171      break;     break;
2172    case(DegreesOfFreedom):     case(DegreesOfFreedom):
2173      throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2174      break;     break;
2175    case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2176      throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");     throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2177      break;     break;
2178    default:     default:
2179      stringstream temp;        stringstream temp;
2180      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();        temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2181      throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2182      break;        break;
2183    }     }
2184    return out;     return out;
2185  }  }
2186    
2187    
2188  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
2189  {  {
2190       Finley_Mesh* mesh=m_finleyMesh.get();
2191       escriptDataC tmp=mask.getDataC();
2192       switch(functionSpaceType) {
2193       case(Nodes):
2194       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
2195       break;
2196       case(ReducedNodes):
2197       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2198       break;
2199       case(DegreesOfFreedom):
2200       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2201       break;
2202       case(ReducedDegreesOfFreedom):
2203       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2204       break;
2205       case(Elements):
2206       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2207       break;
2208       case(ReducedElements):
2209       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2210       break;
2211       case(FaceElements):
2212       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2213       break;
2214       case(ReducedFaceElements):
2215       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2216       break;
2217       case(Points):
2218       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2219       break;
2220       case(ContactElementsZero):
2221       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2222       break;
2223       case(ReducedContactElementsZero):
2224       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2225       break;
2226       case(ContactElementsOne):
2227       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2228       break;
2229       case(ReducedContactElementsOne):
2230       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2231       break;
2232       default:
2233          stringstream temp;
2234          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2235          throw FinleyAdapterException(temp.str());
2236       }
2237       checkFinleyError();
2238       return;
2239    }
2240    
2241    void MeshAdapter::setTagMap(const string& name,  int tag)
2242    {
2243       Finley_Mesh* mesh=m_finleyMesh.get();
2244       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2245       checkPasoError();
2246       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2247    }
2248    
2249    int MeshAdapter::getTag(const string& name) const
2250    {
2251       Finley_Mesh* mesh=m_finleyMesh.get();
2252       int tag=0;
2253       tag=Finley_Mesh_getTag(mesh, name.c_str());
2254       checkPasoError();
2255       // throwStandardException("MeshAdapter::getTag is not implemented.");
2256       return tag;
2257    }
2258    
2259    bool MeshAdapter::isValidTagName(const string& name) const
2260    {
2261       Finley_Mesh* mesh=m_finleyMesh.get();
2262       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2263    }
2264    
2265    string MeshAdapter::showTagNames() const
2266    {
2267       stringstream temp;
2268       Finley_Mesh* mesh=m_finleyMesh.get();
2269       Finley_TagMap* tag_map=mesh->TagMap;
2270       while (tag_map) {
2271          temp << tag_map->name;
2272          tag_map=tag_map->next;
2273          if (tag_map) temp << ", ";
2274       }
2275       return temp.str();
2276    }
2277    
2278    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2279    {
2280    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2281    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2282    switch(functionSpaceType) {    switch(functionSpaceCode) {
2283         case(Nodes):     case(Nodes):
2284            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2285            break;            break;
2286         case(ReducedNodes):     case(ReducedNodes):
2287            throw FinleyAdapterException("Error - ReducedNodes does not support tags");            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2288            break;            break;
2289         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2290            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2291            break;            break;
2292         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2293            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2294            break;            break;
2295         case(Elements):     case(Elements):
2296            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2297              numTags=mesh->Elements->numTagsInUse;
2298              break;
2299       case(FaceElements):
2300       case(ReducedFaceElements):
2301              numTags=mesh->FaceElements->numTagsInUse;
2302              break;
2303       case(Points):
2304              numTags=mesh->Points->numTagsInUse;
2305              break;
2306       case(ContactElementsZero):
2307       case(ReducedContactElementsZero):
2308       case(ContactElementsOne):
2309       case(ReducedContactElementsOne):
2310              numTags=mesh->ContactElements->numTagsInUse;
2311            break;            break;
2312         case(ReducedElements):     default:
2313            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);        stringstream temp;
2314            break;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2315         case(FaceElements):        throw FinleyAdapterException(temp.str());
2316            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);    }
2317            break;    return numTags;
2318         case(ReducedFaceElements):  }
2319            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);  
2320            break;  const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2321         case(Points):  {
2322            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);    Finley_Mesh* mesh=m_finleyMesh.get();
2323      index_t* tags=NULL;
2324      switch(functionSpaceCode) {
2325       case(Nodes):
2326              tags=mesh->Nodes->tagsInUse;
2327            break;            break;
2328         case(ContactElementsZero):     case(ReducedNodes):
2329            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2330            break;            break;
2331         case(ReducedContactElementsZero):     case(DegreesOfFreedom):
2332            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2333            break;            break;
2334         case(ContactElementsOne):     case(ReducedDegreesOfFreedom):
2335            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2336            break;            break;
2337         case(ReducedContactElementsOne):     case(Elements):
2338            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2339              tags=mesh->Elements->tagsInUse;
2340              break;
2341       case(FaceElements):
2342       case(ReducedFaceElements):
2343              tags=mesh->FaceElements->tagsInUse;
2344              break;
2345       case(Points):
2346              tags=mesh->Points->tagsInUse;
2347              break;
2348       case(ContactElementsZero):
2349       case(ReducedContactElementsZero):
2350       case(ContactElementsOne):
2351       case(ReducedContactElementsOne):
2352              tags=mesh->ContactElements->tagsInUse;
2353            break;            break;
2354         default:     default:
2355            stringstream temp;        stringstream temp;
2356            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2357            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2358    }    }
2359    checkFinleyError();    return tags;
   return;  
2360  }  }
2361    
2362  void MeshAdapter::setTagMap(const std::string& name,  int tag)  
2363    bool MeshAdapter::canTag(int functionSpaceCode) const
2364  {  {
2365    Finley_Mesh* mesh=m_finleyMesh.get();    switch(functionSpaceCode) {
2366    Finley_Mesh_addTagMap(mesh, name.c_str(),tag);     case(Nodes):
2367    checkPasoError();     case(Elements):
2368    // throwStandardException("MeshAdapter::set TagMap is not implemented.");     case(ReducedElements):
2369       case(FaceElements):
2370       case(ReducedFaceElements):
2371       case(Points):
2372       case(ContactElementsZero):
2373       case(ReducedContactElementsZero):
2374       case(ContactElementsOne):
2375       case(ReducedContactElementsOne):
2376              return true;
2377       case(ReducedNodes):
2378       case(DegreesOfFreedom):
2379       case(ReducedDegreesOfFreedom):
2380          return false;
2381       default:
2382        return false;
2383      }
2384  }  }
2385    
2386  int MeshAdapter::getTag(const std::string& name) const  AbstractDomain::StatusType MeshAdapter::getStatus() const
2387  {  {
2388    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2389    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;  
2390  }  }
2391    
2392  bool MeshAdapter::isValidTagName(const std::string& name) const  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2393  {  {
2394      
2395    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2396    return Finley_Mesh_isValidTagName(mesh,name.c_str());    int order =-1;
2397      switch(functionSpaceCode) {
2398       case(Nodes):
2399       case(DegreesOfFreedom):
2400              order=mesh->approximationOrder;
2401              break;
2402       case(ReducedNodes):
2403       case(ReducedDegreesOfFreedom):
2404              order=mesh->reducedApproximationOrder;
2405              break;
2406       case(Elements):
2407       case(FaceElements):
2408       case(Points):
2409       case(ContactElementsZero):
2410       case(ContactElementsOne):
2411              order=mesh->integrationOrder;
2412              break;
2413       case(ReducedElements):
2414       case(ReducedFaceElements):
2415       case(ReducedContactElementsZero):
2416       case(ReducedContactElementsOne):
2417              order=mesh->reducedIntegrationOrder;
2418              break;
2419       default:
2420          stringstream temp;
2421          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2422          throw FinleyAdapterException(temp.str());
2423      }
2424      return order;
2425  }  }
2426    
2427  std::string MeshAdapter::showTagNames() const  bool MeshAdapter::supportsContactElements() const
2428  {  {
2429    stringstream temp;    return true;
2430    Finley_Mesh* mesh=m_finleyMesh.get();  }
2431    Finley_TagMap* tag_map=mesh->TagMap;  
2432    while (tag_map) {  ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2433       temp << tag_map->name;  {
2434       tag_map=tag_map->next;    m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2435       if (tag_map) temp << ", ";  }
2436    }  
2437    return temp.str();  ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2438    {
2439      Finley_ReferenceElementSet_dealloc(m_refSet);
2440    }
2441    
2442    // points will be flattened
2443    void MeshAdapter:: addDiracPoints(const std::vector<double>& points, const std::vector<int>& tags) const
2444    {
2445          const int dim = getDim();
2446          int numPoints=points.size()/dim;
2447          int numTags=tags.size();
2448          Finley_Mesh* mesh=m_finleyMesh.get();
2449          
2450          if ( points.size() % dim != 0 )
2451          {
2452        throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2453          }
2454          
2455          if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2456         throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2457          
2458          double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2459          int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2460          
2461          for (int i=0;i<numPoints;++i) {
2462           points_ptr[ i * dim     ] = points[i * dim ];
2463           if ( dim > 1 ) points_ptr[ i * dim + 1 ] = points[i * dim + 1];
2464           if ( dim > 2 ) points_ptr[ i * dim + 2 ] = points[i * dim + 2];    
2465               tags_ptr[i]=tags[i];
2466          }
2467          
2468          Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2469          checkPasoError();
2470          
2471          TMPMEMFREE(points_ptr);
2472          TMPMEMFREE(tags_ptr);
2473    }
2474    
2475    
2476    // void MeshAdapter:: addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2477    // {
2478    //       const int dim = getDim();
2479    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2480    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2481    //       Finley_Mesh* mesh=m_finleyMesh.get();
2482    //      
2483    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2484    //   throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2485    //      
2486    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2487    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2488    //      
2489    //       for (int i=0;i<numPoints;++i) {
2490    //     int tag_id=-1;
2491    //     int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2492    //     if  ( numComps !=   dim ) {
2493    //                stringstream temp;            
2494    //                temp << "Error - illegal number of components " << numComps << " for point " << i;              
2495    //                throw FinleyAdapterException(temp.str());
2496    //     }
2497    //     points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2498    //     if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2499    //     if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2500    //    
2501    //     if ( numTags > 0) {
2502    //            boost::python::extract<string> ex_str(tags[i]);
2503    //        if  ( ex_str.check() ) {
2504    //            tag_id=getTag( ex_str());
2505    //        } else {
2506    //             boost::python::extract<int> ex_int(tags[i]);
2507    //             if ( ex_int.check() ) {
2508    //                 tag_id=ex_int();
2509    //             } else {
2510    //              stringstream temp;          
2511    //                  temp << "Error - unable to extract tag for point " << i;
2512    //              throw FinleyAdapterException(temp.str());
2513    //            }
2514    //        }
2515    //     }      
2516    //            tags_ptr[i]=tag_id;
2517    //       }
2518    //      
2519    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2520    //       checkPasoError();
2521    //      
2522    //       TMPMEMFREE(points_ptr);
2523    //       TMPMEMFREE(tags_ptr);
2524    // }
2525    
2526    /*
2527    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2528    {  
2529        boost::python::list points =  boost::python::list();
2530        boost::python::list tags =  boost::python::list();
2531        points.append(point);
2532        tags.append(tag);
2533        addDiracPoints(points, tags);
2534  }  }
2535    */
2536    
2537    /*
2538    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const std::string& tag) const
2539    {
2540            boost::python::list points =   boost::python::list();
2541            boost::python::list tags =   boost::python::list();
2542            points.append(point);
2543            tags.append(tag);
2544            addDiracPoints(points, tags);
2545    }
2546    */
2547  }  // end of namespace  }  // end of namespace

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