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

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revision 532 by gross, Wed Feb 15 09:45:53 2006 UTC revision 3981 by jfenwick, Fri Sep 21 02:47:54 2012 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    /*****************************************************************************
3    *
4    * Copyright (c) 2003-2012 by University of Queensland
5    * http://www.uq.edu.au
6    *
7    * Primary Business: Queensland, Australia
8    * Licensed under the Open Software License version 3.0
9    * http://www.opensource.org/licenses/osl-3.0.php
10    *
11    * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12    * Development since 2012 by School of Earth Sciences
13    *
14    *****************************************************************************/
15    
16    #include <pasowrap/PasoException.h>
17    #include <pasowrap/TransportProblemAdapter.h>
18  #include "MeshAdapter.h"  #include "MeshAdapter.h"
19    #include "escript/Data.h"
20    #include "escript/DataFactory.h"
21    #ifdef USE_NETCDF
22    #include <netcdfcpp.h>
23    #endif
24    extern "C" {
25    #include "esysUtils/blocktimer.h"
26    }
27    
28  #include "Data.h"  #include <boost/python/import.hpp>
 #include "DataFactory.h"  
29    
30  using namespace std;  using namespace std;
31  using namespace escript;  using namespace escript;
32    using namespace paso;
33    
34  namespace finley {  namespace finley {
35    
# Line 29  MeshAdapter::FunctionSpaceNamesMapType M Line 39  MeshAdapter::FunctionSpaceNamesMapType M
39  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
40  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
41  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
42    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
43  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
44    const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
45  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
46    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
47  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
48  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
49    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
50  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
51    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
52    
53  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
54  {  {
55    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
56    //     //
57    // 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
58    // for us.     // for us.
59    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
60  }  }
61    
62  //  //
# Line 49  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 64  MeshAdapter::MeshAdapter(Finley_Mesh* fi
64  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
65  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
66  {  {
67    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
68  }  }
69    
70  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
71  {  {
72    //     //
73    // 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.
74    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
75    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
76      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
77      Finley_Mesh_dealloc(m_finleyMesh.get());     }
78      //   cout << "Finished dealloc." << endl;  }
79    }  
80    int MeshAdapter::getMPISize() const
81    {
82       return m_finleyMesh.get()->MPIInfo->size;
83    }
84    int MeshAdapter::getMPIRank() const
85    {
86       return m_finleyMesh.get()->MPIInfo->rank;
87    }
88    void MeshAdapter::MPIBarrier() const
89    {
90    #ifdef ESYS_MPI
91       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
92    #endif
93       return;
94    }
95    bool MeshAdapter::onMasterProcessor() const
96    {
97       return m_finleyMesh.get()->MPIInfo->rank == 0;
98  }  }
99    
100    
101    #ifdef ESYS_MPI
102      MPI_Comm
103    #else
104      unsigned int
105    #endif
106    MeshAdapter::getMPIComm() const
107    {
108    #ifdef ESYS_MPI
109        return m_finleyMesh->MPIInfo->comm;
110    #else
111        return 0;
112    #endif
113    }
114    
115    
116  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
117     return m_finleyMesh.get();     return m_finleyMesh.get();
118  }  }
119    
120  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
121  {  {
122    char fName[fileName.size()+1];     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
123    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
124    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
125    checkFinleyError();     checkFinleyError();
126       TMPMEMFREE(fName);
127  }  }
128    
129  // void MeshAdapter::getTagList(int functionSpaceType,  void MeshAdapter::Print_Mesh_Info(const bool full) const
130  //                  int* numTags) const  {
131  // {     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
132  //   Finley_Mesh_tagList(m_finleyMesh.get(),functionSpaceType,tagList,numTags);  }
133  //   return;  
134  // }  void MeshAdapter::dump(const string& fileName) const
135    {
136    #ifdef USE_NETCDF
137       const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
138       NcVar *ids;
139       int *int_ptr;
140       Finley_Mesh *mesh = m_finleyMesh.get();
141       Finley_TagMap* tag_map;
142       int num_Tags = 0;
143       int mpi_size             = mesh->MPIInfo->size;
144       int mpi_rank             = mesh->MPIInfo->rank;
145       int numDim               = mesh->Nodes->numDim;
146       int numNodes             = mesh->Nodes->numNodes;
147       int num_Elements         = mesh->Elements->numElements;
148       int num_FaceElements         = mesh->FaceElements->numElements;
149       int num_ContactElements      = mesh->ContactElements->numElements;
150       int num_Points           = mesh->Points->numElements;
151       int num_Elements_numNodes        = mesh->Elements->numNodes;
152       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
153       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
154    #ifdef ESYS_MPI
155       MPI_Status status;
156    #endif
157    
158    /* Incoming token indicates it's my turn to write */
159    #ifdef ESYS_MPI
160       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
161    #endif
162    
163       char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
164                                                         mpi_size, mpi_rank);
165    
166       /* Figure out how much storage is required for tags */
167       tag_map = mesh->TagMap;
168       num_Tags = 0;
169       while (tag_map) {
170          num_Tags++;
171          tag_map=tag_map->next;
172       }
173    
174       // NetCDF error handler
175       NcError err(NcError::verbose_nonfatal);
176       // Create the file.
177       NcFile dataFile(newFileName, NcFile::Replace);
178       string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
179       // check if writing was successful
180       if (!dataFile.is_valid())
181          throw DataException(msgPrefix+"Open file for output");
182    
183       // Define dimensions (num_Elements and dim_Elements are identical,
184       // dim_Elements only appears if > 0)
185       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
186          throw DataException(msgPrefix+"add_dim(numNodes)");
187       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
188          throw DataException(msgPrefix+"add_dim(numDim)");
189       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
190          throw DataException(msgPrefix+"add_dim(mpi_size)");
191       if (num_Elements>0)
192          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
193             throw DataException(msgPrefix+"add_dim(dim_Elements)");
194       if (num_FaceElements>0)
195          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
196             throw DataException(msgPrefix+"add_dim(dim_FaceElements)");
197       if (num_ContactElements>0)
198          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
199             throw DataException(msgPrefix+"add_dim(dim_ContactElements)");
200       if (num_Points>0)
201          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
202             throw DataException(msgPrefix+"add_dim(dim_Points)");
203       if (num_Elements>0)
204          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
205             throw DataException(msgPrefix+"add_dim(dim_Elements_Nodes)");
206       if (num_FaceElements>0)
207          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
208             throw DataException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
209       if (num_ContactElements>0)
210          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
211             throw DataException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
212       if (num_Tags>0)
213          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
214             throw DataException(msgPrefix+"add_dim(dim_Tags)");
215    
216       // Attributes: MPI size, MPI rank, Name, order, reduced_order
217       if (!dataFile.add_att("mpi_size", mpi_size) )
218          throw DataException(msgPrefix+"add_att(mpi_size)");
219       if (!dataFile.add_att("mpi_rank", mpi_rank) )
220          throw DataException(msgPrefix+"add_att(mpi_rank)");
221       if (!dataFile.add_att("Name",mesh->Name) )
222          throw DataException(msgPrefix+"add_att(Name)");
223       if (!dataFile.add_att("numDim",numDim) )
224          throw DataException(msgPrefix+"add_att(order)");
225       if (!dataFile.add_att("order",mesh->integrationOrder) )
226          throw DataException(msgPrefix+"add_att(order)");
227       if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
228          throw DataException(msgPrefix+"add_att(reduced_order)");
229       if (!dataFile.add_att("numNodes",numNodes) )
230          throw DataException(msgPrefix+"add_att(numNodes)");
231       if (!dataFile.add_att("num_Elements",num_Elements) )
232          throw DataException(msgPrefix+"add_att(num_Elements)");
233       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
234          throw DataException(msgPrefix+"add_att(num_FaceElements)");
235       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
236          throw DataException(msgPrefix+"add_att(num_ContactElements)");
237       if (!dataFile.add_att("num_Points",num_Points) )
238          throw DataException(msgPrefix+"add_att(num_Points)");
239       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
240          throw DataException(msgPrefix+"add_att(num_Elements_numNodes)");
241       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
242          throw DataException(msgPrefix+"add_att(num_FaceElements_numNodes)");
243       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
244          throw DataException(msgPrefix+"add_att(num_ContactElements_numNodes)");
245       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
246          throw DataException(msgPrefix+"add_att(Elements_TypeId)");
247       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
248          throw DataException(msgPrefix+"add_att(FaceElements_TypeId)");
249       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
250          throw DataException(msgPrefix+"add_att(ContactElements_TypeId)");
251       if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
252          throw DataException(msgPrefix+"add_att(Points_TypeId)");
253       if (!dataFile.add_att("num_Tags", num_Tags) )
254          throw DataException(msgPrefix+"add_att(num_Tags)");
255    
256       // // // // // Nodes // // // // //
257    
258       // Nodes nodeDistribution
259       if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
260          throw DataException(msgPrefix+"add_var(Nodes_NodeDistribution)");
261       int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
262       if (! (ids->put(int_ptr, mpi_size+1)) )
263          throw DataException(msgPrefix+"put(Nodes_NodeDistribution)");
264    
265       // Nodes degreesOfFreedomDistribution
266       if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
267          throw DataException(msgPrefix+"add_var(Nodes_DofDistribution)");
268       int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
269       if (! (ids->put(int_ptr, mpi_size+1)) )
270          throw DataException(msgPrefix+"put(Nodes_DofDistribution)");
271    
272       // Only write nodes if non-empty because NetCDF doesn't like empty arrays
273       // (it treats them as NC_UNLIMITED)
274       if (numNodes>0) {
275    
276          // Nodes Id
277          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
278             throw DataException(msgPrefix+"add_var(Nodes_Id)");
279          int_ptr = &mesh->Nodes->Id[0];
280          if (! (ids->put(int_ptr, numNodes)) )
281             throw DataException(msgPrefix+"put(Nodes_Id)");
282    
283          // Nodes Tag
284          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
285             throw DataException(msgPrefix+"add_var(Nodes_Tag)");
286          int_ptr = &mesh->Nodes->Tag[0];
287          if (! (ids->put(int_ptr, numNodes)) )
288             throw DataException(msgPrefix+"put(Nodes_Tag)");
289    
290          // Nodes gDOF
291          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
292             throw DataException(msgPrefix+"add_var(Nodes_gDOF)");
293          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
294          if (! (ids->put(int_ptr, numNodes)) )
295             throw DataException(msgPrefix+"put(Nodes_gDOF)");
296    
297          // Nodes global node index
298          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
299             throw DataException(msgPrefix+"add_var(Nodes_gNI)");
300          int_ptr = &mesh->Nodes->globalNodesIndex[0];
301          if (! (ids->put(int_ptr, numNodes)) )
302             throw DataException(msgPrefix+"put(Nodes_gNI)");
303    
304          // Nodes grDof
305          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
306             throw DataException(msgPrefix+"add_var(Nodes_grDfI)");
307          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
308          if (! (ids->put(int_ptr, numNodes)) )
309             throw DataException(msgPrefix+"put(Nodes_grDfI)");
310    
311          // Nodes grNI
312          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
313             throw DataException(msgPrefix+"add_var(Nodes_grNI)");
314          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
315          if (! (ids->put(int_ptr, numNodes)) )
316             throw DataException(msgPrefix+"put(Nodes_grNI)");
317    
318          // Nodes Coordinates
319          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
320             throw DataException(msgPrefix+"add_var(Nodes_Coordinates)");
321          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
322             throw DataException(msgPrefix+"put(Nodes_Coordinates)");
323    
324       }
325    
326       // // // // // Elements // // // // //
327    
328       if (num_Elements>0) {
329    
330          // Elements_Id
331          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
332             throw DataException(msgPrefix+"add_var(Elements_Id)");
333          int_ptr = &mesh->Elements->Id[0];
334          if (! (ids->put(int_ptr, num_Elements)) )
335             throw DataException(msgPrefix+"put(Elements_Id)");
336    
337          // Elements_Tag
338          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
339             throw DataException(msgPrefix+"add_var(Elements_Tag)");
340          int_ptr = &mesh->Elements->Tag[0];
341          if (! (ids->put(int_ptr, num_Elements)) )
342             throw DataException(msgPrefix+"put(Elements_Tag)");
343    
344          // Elements_Owner
345          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
346             throw DataException(msgPrefix+"add_var(Elements_Owner)");
347          int_ptr = &mesh->Elements->Owner[0];
348          if (! (ids->put(int_ptr, num_Elements)) )
349             throw DataException(msgPrefix+"put(Elements_Owner)");
350    
351          // Elements_Color
352          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
353             throw DataException(msgPrefix+"add_var(Elements_Color)");
354          int_ptr = &mesh->Elements->Color[0];
355          if (! (ids->put(int_ptr, num_Elements)) )
356             throw DataException(msgPrefix+"put(Elements_Color)");
357    
358          // Elements_Nodes
359          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
360             throw DataException(msgPrefix+"add_var(Elements_Nodes)");
361          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
362             throw DataException(msgPrefix+"put(Elements_Nodes)");
363    
364       }
365    
366       // // // // // Face_Elements // // // // //
367    
368       if (num_FaceElements>0) {
369    
370          // FaceElements_Id
371          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
372             throw DataException(msgPrefix+"add_var(FaceElements_Id)");
373          int_ptr = &mesh->FaceElements->Id[0];
374          if (! (ids->put(int_ptr, num_FaceElements)) )
375             throw DataException(msgPrefix+"put(FaceElements_Id)");
376    
377          // FaceElements_Tag
378          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
379             throw DataException(msgPrefix+"add_var(FaceElements_Tag)");
380          int_ptr = &mesh->FaceElements->Tag[0];
381          if (! (ids->put(int_ptr, num_FaceElements)) )
382             throw DataException(msgPrefix+"put(FaceElements_Tag)");
383    
384          // FaceElements_Owner
385          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
386             throw DataException(msgPrefix+"add_var(FaceElements_Owner)");
387          int_ptr = &mesh->FaceElements->Owner[0];
388          if (! (ids->put(int_ptr, num_FaceElements)) )
389             throw DataException(msgPrefix+"put(FaceElements_Owner)");
390    
391          // FaceElements_Color
392          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
393             throw DataException(msgPrefix+"add_var(FaceElements_Color)");
394          int_ptr = &mesh->FaceElements->Color[0];
395          if (! (ids->put(int_ptr, num_FaceElements)) )
396             throw DataException(msgPrefix+"put(FaceElements_Color)");
397    
398          // FaceElements_Nodes
399          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
400             throw DataException(msgPrefix+"add_var(FaceElements_Nodes)");
401          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
402             throw DataException(msgPrefix+"put(FaceElements_Nodes)");
403    
404       }
405    
406       // // // // // Contact_Elements // // // // //
407    
408       if (num_ContactElements>0) {
409    
410          // ContactElements_Id
411          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
412             throw DataException(msgPrefix+"add_var(ContactElements_Id)");
413          int_ptr = &mesh->ContactElements->Id[0];
414          if (! (ids->put(int_ptr, num_ContactElements)) )
415             throw DataException(msgPrefix+"put(ContactElements_Id)");
416    
417          // ContactElements_Tag
418          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
419             throw DataException(msgPrefix+"add_var(ContactElements_Tag)");
420          int_ptr = &mesh->ContactElements->Tag[0];
421          if (! (ids->put(int_ptr, num_ContactElements)) )
422             throw DataException(msgPrefix+"put(ContactElements_Tag)");
423    
424          // ContactElements_Owner
425          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
426             throw DataException(msgPrefix+"add_var(ContactElements_Owner)");
427          int_ptr = &mesh->ContactElements->Owner[0];
428          if (! (ids->put(int_ptr, num_ContactElements)) )
429             throw DataException(msgPrefix+"put(ContactElements_Owner)");
430    
431          // ContactElements_Color
432          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
433             throw DataException(msgPrefix+"add_var(ContactElements_Color)");
434          int_ptr = &mesh->ContactElements->Color[0];
435          if (! (ids->put(int_ptr, num_ContactElements)) )
436             throw DataException(msgPrefix+"put(ContactElements_Color)");
437    
438          // ContactElements_Nodes
439          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
440             throw DataException(msgPrefix+"add_var(ContactElements_Nodes)");
441          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
442             throw DataException(msgPrefix+"put(ContactElements_Nodes)");
443    
444       }
445    
446       // // // // // Points // // // // //
447    
448       if (num_Points>0) {
449    
450          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
451    
452          // Points_Id
453          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
454             throw DataException(msgPrefix+"add_var(Points_Id)");
455          int_ptr = &mesh->Points->Id[0];
456          if (! (ids->put(int_ptr, num_Points)) )
457             throw DataException(msgPrefix+"put(Points_Id)");
458    
459          // Points_Tag
460          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
461             throw DataException(msgPrefix+"add_var(Points_Tag)");
462          int_ptr = &mesh->Points->Tag[0];
463          if (! (ids->put(int_ptr, num_Points)) )
464             throw DataException(msgPrefix+"put(Points_Tag)");
465    
466          // Points_Owner
467          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
468             throw DataException(msgPrefix+"add_var(Points_Owner)");
469          int_ptr = &mesh->Points->Owner[0];
470          if (! (ids->put(int_ptr, num_Points)) )
471             throw DataException(msgPrefix+"put(Points_Owner)");
472    
473          // Points_Color
474          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
475             throw DataException(msgPrefix+"add_var(Points_Color)");
476          int_ptr = &mesh->Points->Color[0];
477          if (! (ids->put(int_ptr, num_Points)) )
478             throw DataException(msgPrefix+"put(Points_Color)");
479    
480          // Points_Nodes
481          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
482          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
483             throw DataException(msgPrefix+"add_var(Points_Nodes)");
484          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
485             throw DataException(msgPrefix+"put(Points_Nodes)");
486    
487       }
488    
489       // // // // // TagMap // // // // //
490    
491       if (num_Tags>0) {
492    
493          // Temp storage to gather node IDs
494          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
495          char name_temp[4096];
496    
497          /* Copy tag data into temp arrays */
498          tag_map = mesh->TagMap;
499          if (tag_map) {
500             int i = 0;
501             while (tag_map) {
502                Tags_keys[i++] = tag_map->tag_key;
503                tag_map=tag_map->next;
504             }
505          }
506    
507          // Tags_keys
508          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
509             throw DataException(msgPrefix+"add_var(Tags_keys)");
510          int_ptr = &Tags_keys[0];
511          if (! (ids->put(int_ptr, num_Tags)) )
512             throw DataException(msgPrefix+"put(Tags_keys)");
513    
514          // Tags_names_*
515          // This is an array of strings, it should be stored as an array but
516          // instead I have hacked in one attribute per string because the NetCDF
517          // manual doesn't tell how to do an array of strings
518          tag_map = mesh->TagMap;
519          if (tag_map) {
520             int i = 0;
521             while (tag_map) {
522                sprintf(name_temp, "Tags_name_%d", i);
523                if (!dataFile.add_att(name_temp, tag_map->name) )
524                   throw DataException(msgPrefix+"add_att(Tags_names_XX)");
525                tag_map=tag_map->next;
526                i++;
527             }
528          }
529    
530          TMPMEMFREE(Tags_keys);
531       }
532    
533    /* Send token to next MPI process so he can take his turn */
534    #ifdef ESYS_MPI
535       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
536    #endif
537    
538       // NetCDF file is closed by destructor of NcFile object
539    
540    #else
541       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
542    #endif  /* USE_NETCDF */
543       checkFinleyError();
544    }
545    
546  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
547  {  {
548    return "FinleyMesh";     return "FinleyMesh";
549  }  }
550    
551  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
552  {  {
553    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
554    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
555    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
556      return "Invalid function space type code.";        return "Invalid function space type code.";
557    } else {     } else {
558      return loc->second;        return loc->second;
559    }     }
560  }  }
561    
562  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
563  {  {
564    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
565    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
566    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
567  }  }
568    
569  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
570  {  {
571    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
572      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
573    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
574      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
575    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
576      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
577    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
578      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
579    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
580      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
581    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
582      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
583    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
584      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
585    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
586      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
587       m_functionSpaceTypeNames.insert
588       (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
589       m_functionSpaceTypeNames.insert
590       (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
591       m_functionSpaceTypeNames.insert
592       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
593       m_functionSpaceTypeNames.insert
594       (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
595       m_functionSpaceTypeNames.insert
596       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
597  }  }
598    
599  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
600  {  {
601    return Nodes;     return Nodes;
602    }
603    int MeshAdapter::getReducedContinuousFunctionCode() const
604    {
605       return ReducedNodes;
606  }  }
607    
608  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
609  {  {
610    return Elements;     return Elements;
611    }
612    int MeshAdapter::getReducedFunctionCode() const
613    {
614       return ReducedElements;
615  }  }
616    
617  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
618  {  {
619    return FaceElements;     return FaceElements;
620    }
621    int MeshAdapter::getReducedFunctionOnBoundaryCode() const
622    {
623       return ReducedFaceElements;
624  }  }
625    
626  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
627  {  {
628    return ContactElementsZero;     return ContactElementsZero;
629    }
630    int MeshAdapter::getReducedFunctionOnContactZeroCode() const
631    {
632       return ReducedContactElementsZero;
633  }  }
634    
635  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
636  {  {
637    return ContactElementsOne;     return ContactElementsOne;
638  }  }
639    int MeshAdapter::getReducedFunctionOnContactOneCode() const
 int MeshAdapter::getSolutionCode() const  
640  {  {
641    return DegreesOfFreedom;     return ReducedContactElementsOne;
642  }  }
643    
644  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getSolutionCode() const
645  {  {
646    return ReducedDegreesOfFreedom;     return DegreesOfFreedom;
647  }  }
648    
649  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getReducedSolutionCode() const
650  {  {
651    return Points;     return ReducedDegreesOfFreedom;
652  }  }
653    
654  //  int MeshAdapter::getDiracDeltaFunctionsCode() const
 // returns a pointer to the tag list of samples of functionSpaceType  
 //  
 void MeshAdapter::getTagList(int functionSpaceType, int** tagList,  
                  int* numTags) const  
655  {  {
656    *tagList=NULL;     return Points;
   *numTags=0;  
   Finley_Mesh* mesh=m_finleyMesh.get();  
   switch (functionSpaceType) {  
   case(Nodes):  
     if (mesh->Nodes!=NULL) {  
       *tagList=mesh->Nodes->Tag;  
       *numTags=mesh->Nodes->numNodes;  
     }  
     break;  
   case(Elements):  
     if (mesh->Elements!=NULL) {  
       *tagList=mesh->Elements->Tag;  
       *numTags=mesh->Elements->numElements;  
     }  
     break;  
   case(FaceElements):  
     if (mesh->FaceElements!=NULL) {  
       *tagList=mesh->FaceElements->Tag;  
       *numTags=mesh->FaceElements->numElements;  
     }  
     break;  
   case(Points):  
     if (mesh->Points!=NULL) {  
       *tagList=mesh->Points->Tag;  
       *numTags=mesh->Points->numElements;  
     }  
     break;  
   case(ContactElementsZero):  
     if (mesh->ContactElements!=NULL) {  
       *tagList=mesh->ContactElements->Tag;  
       *numTags=mesh->ContactElements->numElements;  
     }  
     break;  
   case(ContactElementsOne):  
     if (mesh->ContactElements!=NULL) {  
       *tagList=mesh->ContactElements->Tag;  
       *numTags=mesh->ContactElements->numElements;  
     }  
     break;  
   case(DegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *tagList=NULL;  
       *numTags=0;  
     }  
     break;  
   case(ReducedDegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *tagList=NULL;  
       *numTags=0;  
     }  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
   }  
   if (*tagList==NULL) {  
     stringstream temp;  
     temp << "Error - no tags available for " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
   }  
   return;  
657  }  }
658    
659  //  //
660  // returns a pointer to the reference no list of samples of functionSpaceType  // return the spatial dimension of the Mesh:
661  //  //
662  void MeshAdapter::getReferenceNoList(int functionSpaceType, int** referenceNoList,  int MeshAdapter::getDim() const
                  int* numReferenceNo) const  
663  {  {
664    *referenceNoList=NULL;     Finley_Mesh* mesh=m_finleyMesh.get();
665    *numReferenceNo=0;     int numDim=Finley_Mesh_getDim(mesh);
666    Finley_Mesh* mesh=m_finleyMesh.get();     checkFinleyError();
667    switch (functionSpaceType) {     return numDim;
   case(Nodes):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=mesh->Nodes->Id;  
       *numReferenceNo=mesh->Nodes->numNodes;  
     }  
     break;  
   case(Elements):  
     if (mesh->Elements!=NULL) {  
       *referenceNoList=mesh->Elements->Id;  
       *numReferenceNo=mesh->Elements->numElements;  
     }  
     break;  
   case(FaceElements):  
     if (mesh->FaceElements!=NULL) {  
       *referenceNoList=mesh->FaceElements->Id;  
       *numReferenceNo=mesh->FaceElements->numElements;  
     }  
     break;  
   case(Points):  
     if (mesh->Points!=NULL) {  
       *referenceNoList=mesh->Points->Id;  
       *numReferenceNo=mesh->Points->numElements;  
     }  
     break;  
   case(ContactElementsZero):  
     if (mesh->ContactElements!=NULL) {  
       *referenceNoList=mesh->ContactElements->Id;  
       *numReferenceNo=mesh->ContactElements->numElements;  
     }  
     break;  
   case(ContactElementsOne):  
     if (mesh->ContactElements!=NULL) {  
       *referenceNoList=mesh->ContactElements->Id;  
       *numReferenceNo=mesh->ContactElements->numElements;  
     }  
     break;  
   case(DegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=NULL;  
       *numReferenceNo=0;  
     }  
     break;  
   case(ReducedDegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *referenceNoList=NULL;  
       *numReferenceNo=0;  
     }  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
   }  
   if (*referenceNoList==NULL) {  
     stringstream temp;  
     temp << "Error - reference number list available for " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
   }  
   return;  
668  }  }
669    
670  //  //
671  // return the spatial dimension of the Mesh:  // Return the number of data points summed across all MPI processes
672  //  //
673  int MeshAdapter::getDim() const  int MeshAdapter::getNumDataPointsGlobal() const
674  {  {
675    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
   checkFinleyError();  
   return numDim;  
676  }  }
677    
678  //  //
# Line 330  pair<int,int> MeshAdapter::getDataShape( Line 685  pair<int,int> MeshAdapter::getDataShape(
685     int numSamples=0;     int numSamples=0;
686     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
687     switch (functionSpaceCode) {     switch (functionSpaceCode) {
688        case(Nodes):     case(Nodes):
689             numDataPointsPerSample=1;     numDataPointsPerSample=1;
690             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
691             break;     break;
692        case(Elements):     case(ReducedNodes):
693             if (mesh->Elements!=NULL) {     numDataPointsPerSample=1;
694               numSamples=mesh->Elements->numElements;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
695               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
696             }     case(Elements):
697             break;     if (mesh->Elements!=NULL) {
698        case(FaceElements):        numSamples=mesh->Elements->numElements;
699             if (mesh->FaceElements!=NULL) {        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
700                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
701                  numSamples=mesh->FaceElements->numElements;     break;
702             }     case(ReducedElements):
703             break;     if (mesh->Elements!=NULL) {
704        case(Points):        numSamples=mesh->Elements->numElements;
705             if (mesh->Points!=NULL) {        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
706               numDataPointsPerSample=1;     }
707               numSamples=mesh->Points->numElements;     break;
708             }     case(FaceElements):
709             break;     if (mesh->FaceElements!=NULL) {
710        case(ContactElementsZero):        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
711             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
712               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
713               numSamples=mesh->ContactElements->numElements;     break;
714             }     case(ReducedFaceElements):
715             break;     if (mesh->FaceElements!=NULL) {
716        case(ContactElementsOne):        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
717             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
718               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
719               numSamples=mesh->ContactElements->numElements;     break;
720             }     case(Points):
721             break;     if (mesh->Points!=NULL) {
722        case(DegreesOfFreedom):        numDataPointsPerSample=1;
723             if (mesh->Nodes!=NULL) {        numSamples=mesh->Points->numElements;
724               numDataPointsPerSample=1;     }
725               numSamples=mesh->Nodes->numDegreesOfFreedom;     break;
726             }     case(ContactElementsZero):
727             break;     if (mesh->ContactElements!=NULL) {
728        case(ReducedDegreesOfFreedom):        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
729             if (mesh->Nodes!=NULL) {        numSamples=mesh->ContactElements->numElements;
730               numDataPointsPerSample=1;     }
731               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     break;
732             }     case(ReducedContactElementsZero):
733             break;     if (mesh->ContactElements!=NULL) {
734        default:        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
735          stringstream temp;        numSamples=mesh->ContactElements->numElements;
736          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();     }
737          throw FinleyAdapterException(temp.str());     break;
738          break;     case(ContactElementsOne):
739        }     if (mesh->ContactElements!=NULL) {
740        return pair<int,int>(numDataPointsPerSample,numSamples);        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
741          numSamples=mesh->ContactElements->numElements;
742       }
743       break;
744       case(ReducedContactElementsOne):
745       if (mesh->ContactElements!=NULL) {
746          numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
747          numSamples=mesh->ContactElements->numElements;
748       }
749       break;
750       case(DegreesOfFreedom):
751       if (mesh->Nodes!=NULL) {
752          numDataPointsPerSample=1;
753          numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
754       }
755       break;
756       case(ReducedDegreesOfFreedom):
757       if (mesh->Nodes!=NULL) {
758          numDataPointsPerSample=1;
759          numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
760       }
761       break;
762       default:
763          stringstream temp;
764          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
765          throw FinleyAdapterException(temp.str());
766          break;
767       }
768       return pair<int,int>(numDataPointsPerSample,numSamples);
769  }  }
770    
771  //  //
772  // 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:
773  //  //
774  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
775                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   AbstractSystemMatrix& mat, escript::Data& rhs,
776                       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,
777                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
778                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact,
779  {                                   const escript::Data& d_dirac,const escript::Data& y_dirac) const
780     Finley_Mesh* mesh=m_finleyMesh.get();  {
781     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(),&(rhs.getDataC()),     SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
782                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     if (smat==0)
783     checkFinleyError();     {
784     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,      throw FinleyAdapterException("finley only supports Paso system matrices.");
785                    mat.getPaso_SystemMatrix(),     }
786                    &(rhs.getDataC()),     escriptDataC _rhs=rhs.getDataC();
787                                    &(d.getDataC()),&(y.getDataC()),     escriptDataC _A  =A.getDataC();
788                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     escriptDataC _B=B.getDataC();
789     checkFinleyError();     escriptDataC _C=C.getDataC();
790     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,     escriptDataC _D=D.getDataC();
791                    mat.getPaso_SystemMatrix(),     escriptDataC _X=X.getDataC();
792                    &(rhs.getDataC()),     escriptDataC _Y=Y.getDataC();
793                                    &(d_contact.getDataC()),     escriptDataC _d=d.getDataC();
794                    &(y_contact.getDataC()),     escriptDataC _y=y.getDataC();
795                                    Finley_Assemble_handelShapeMissMatch_Step_out);     escriptDataC _d_contact=d_contact.getDataC();
796       escriptDataC _y_contact=y_contact.getDataC();
797       escriptDataC _d_dirac=d_dirac.getDataC();
798       escriptDataC _y_dirac=y_dirac.getDataC();
799    
800       Finley_Mesh* mesh=m_finleyMesh.get();
801    
802       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,smat->getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
803       checkFinleyError();
804    
805       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, smat->getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
806       checkFinleyError();
807    
808       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
809       checkFinleyError();
810    
811        Finley_Assemble_PDE(mesh->Nodes,mesh->Points, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
812     checkFinleyError();     checkFinleyError();
813  }  }
814    
815    void  MeshAdapter::addPDEToLumpedSystem(
816                                            escript::Data& mat,
817                                            const escript::Data& D,
818                                            const escript::Data& d,
819                                            const escript::Data& d_dirac,
820                                            const bool useHRZ) const
821    {
822       escriptDataC _mat=mat.getDataC();
823       escriptDataC _D=D.getDataC();
824       escriptDataC _d=d.getDataC();
825       escriptDataC _d_dirac=d_dirac.getDataC();
826    
827       Finley_Mesh* mesh=m_finleyMesh.get();
828    
829       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D, useHRZ);
830       checkFinleyError();
831      
832       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d, useHRZ);
833       checkFinleyError();
834    
835       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Points,&_mat, &_d_dirac, useHRZ);
836       checkFinleyError();
837    
838    }
839    
840    
841  //  //
842  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
843  //  //
844  void MeshAdapter::addPDEToRHS( escript::Data& rhs,  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
                      const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const  
845  {  {
846     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
847    
848     // Finley_Assemble_PDE_RHS(mesh->Nodes,mesh->Elements,&(rhs.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _rhs=rhs.getDataC();
849     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));     escriptDataC _X=X.getDataC();
850       escriptDataC _Y=Y.getDataC();
851       escriptDataC _y=y.getDataC();
852       escriptDataC _y_contact=y_contact.getDataC();
853       escriptDataC _y_dirac=y_dirac.getDataC();
854    
855       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
856     checkFinleyError();     checkFinleyError();
857    
858     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->FaceElements,&(rhs.getDataC()),&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
859     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),Finley_Assemble_handelShapeMissMatch_Mean_out);     checkFinleyError();
860    
861       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
862     checkFinleyError();     checkFinleyError();
863     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->ContactElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);  
864     // Finley_Assemble_RobinCondition_RHS(mesh->Nodes,mesh->ContactElements,&(rhs.getDataC()),&(y_contact.getDataC()),Finley_Assemble_handelShapeMissMatch_Step_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->Points, 0, &_rhs , 0, 0, 0, 0, 0, &_y_dirac );
865     checkFinleyError();     checkFinleyError();
866    
867    }
868    //
869    // adds PDE of second order into a transport problem
870    //
871    void MeshAdapter::addPDEToTransportProblem(
872                                               AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,
873                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
874                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
875                                               const escript::Data& d, const escript::Data& y,
876                                               const escript::Data& d_contact,const escript::Data& y_contact,
877                                               const escript::Data& d_dirac, const escript::Data& y_dirac) const
878    {
879       TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
880       if (tpa==0)
881       {
882        throw FinleyAdapterException("finley only supports Paso transport problems.");
883       }
884    
885    
886       DataTypes::ShapeType shape;
887       source.expand();
888       escriptDataC _source=source.getDataC();
889       escriptDataC _M=M.getDataC();
890       escriptDataC _A=A.getDataC();
891       escriptDataC _B=B.getDataC();
892       escriptDataC _C=C.getDataC();
893       escriptDataC _D=D.getDataC();
894       escriptDataC _X=X.getDataC();
895       escriptDataC _Y=Y.getDataC();
896       escriptDataC _d=d.getDataC();
897       escriptDataC _y=y.getDataC();
898       escriptDataC _d_contact=d_contact.getDataC();
899       escriptDataC _y_contact=y_contact.getDataC();
900       escriptDataC _d_dirac=d_dirac.getDataC();
901       escriptDataC _y_dirac=y_dirac.getDataC();
902    
903    
904       Finley_Mesh* mesh=m_finleyMesh.get();
905       Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
906    
907       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
908       checkFinleyError();
909    
910       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
911       checkFinleyError();
912    
913       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
914       checkFinleyError();
915    
916       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
917       checkFinleyError();
918    
919       Finley_Assemble_PDE(mesh->Nodes,mesh->Points, _tp->transport_matrix, &_source , 0, 0, 0, &_d_dirac, 0, &_y_dirac );
920       checkFinleyError();
921    
922  }  }
923    
924  //  //
# Line 439  void MeshAdapter::addPDEToRHS( escript:: Line 926  void MeshAdapter::addPDEToRHS( escript::
926  //  //
927  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
928  {  {
929    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
930    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
931    if (inDomain!=*this)     if (inDomain!=*this)  
932       throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
933    if (targetDomain!=*this)     if (targetDomain!=*this)
934       throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
935    
936    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
937    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
938       case(Nodes):     escriptDataC _in=in.getDataC();
939          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
940             case(Nodes):     case(Nodes):
941             case(ReducedDegreesOfFreedom):        switch(target.getFunctionSpace().getTypeCode()) {
942             case(DegreesOfFreedom):        case(Nodes):
943                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        case(ReducedNodes):
944                 break;        case(DegreesOfFreedom):
945             case(Elements):        case(ReducedDegreesOfFreedom):
946                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
947                 break;        break;
948             case(FaceElements):        case(Elements):
949                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        case(ReducedElements):
950                 break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
951             case(Points):        break;
952                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        case(FaceElements):
953                 break;        case(ReducedFaceElements):
954             case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
955                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
956                 break;        case(Points):
957             case(ContactElementsOne):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
958                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
959                 break;        case(ContactElementsZero):
960             default:        case(ReducedContactElementsZero):
961                 stringstream temp;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
962                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        break;
963                 throw FinleyAdapterException(temp.str());        case(ContactElementsOne):
964                 break;        case(ReducedContactElementsOne):
965          }        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
966          break;        break;
967       case(Elements):        default:
968          if (target.getFunctionSpace().getTypeCode()==Elements) {           stringstream temp;
969             Finley_Assemble_CopyElementData(mesh->Elements,&(target.getDataC()),&(in.getDataC()));           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
970          } else {           throw FinleyAdapterException(temp.str());
971             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");           break;
972          }        }
973          break;        break;
974       case(FaceElements):     case(ReducedNodes):
975          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        switch(target.getFunctionSpace().getTypeCode()) {
976             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));        case(Nodes):
977          } else {        case(ReducedNodes):
978             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");        case(DegreesOfFreedom):
979             break;        case(ReducedDegreesOfFreedom):
980         }        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
981       case(Points):        break;
982          if (target.getFunctionSpace().getTypeCode()==Points) {        case(Elements):
983             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));        case(ReducedElements):
984          } else {        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
985             throw FinleyAdapterException("Error - No interpolation with data on points possible.");        break;
986             break;        case(FaceElements):
987          }        case(ReducedFaceElements):
988          break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
989       case(ContactElementsZero):        break;
990       case(ContactElementsOne):        case(Points):
991          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
992             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));        break;
993          } else {        case(ContactElementsZero):
994             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");        case(ReducedContactElementsZero):
995             break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
996          }        break;
997          break;        case(ContactElementsOne):
998       case(DegreesOfFreedom):        case(ReducedContactElementsOne):
999          switch(target.getFunctionSpace().getTypeCode()) {        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1000             case(ReducedDegreesOfFreedom):        break;
1001             case(DegreesOfFreedom):        default:
1002             case(Nodes):           stringstream temp;
1003                Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1004                break;           throw FinleyAdapterException(temp.str());
1005             case(Elements):           break;
1006                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        }
1007                break;        break;
1008             case(FaceElements):     case(Elements):
1009                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Elements) {
1010                break;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
1011             case(Points):        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
1012                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
1013                break;        } else {
1014             case(ContactElementsZero):           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
1015             case(ContactElementsOne):        }
1016                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
1017               break;     case(ReducedElements):
1018             default:        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
1019               stringstream temp;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
1020               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        } else {
1021               throw FinleyAdapterException(temp.str());           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
1022               break;        }
1023          }        break;
1024          break;     case(FaceElements):
1025       case(ReducedDegreesOfFreedom):        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
1026         switch(target.getFunctionSpace().getTypeCode()) {           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1027            case(ReducedDegreesOfFreedom):        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1028               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
1029               break;        } else {
1030            case(Elements):           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
1031               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        }
1032               break;        break;
1033            case(FaceElements):     case(ReducedFaceElements):
1034               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1035               break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1036            case(Points):        } else {
1037               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
1038               break;        }
1039            case(ContactElementsZero):        break;
1040            case(ContactElementsOne):     case(Points):
1041               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Points) {
1042               break;           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1043            case(Nodes):        } else {
1044               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1045               break;        }
1046            case(DegreesOfFreedom):        break;
1047               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ContactElementsZero):
1048               break;     case(ContactElementsOne):
1049            default:        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1050               stringstream temp;           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1051               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1052               throw FinleyAdapterException(temp.str());           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
1053               break;        } else {
1054         }           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1055         break;        }
1056       default:        break;
1057          stringstream temp;     case(ReducedContactElementsZero):
1058          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();     case(ReducedContactElementsOne):
1059          throw FinleyAdapterException(temp.str());        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1060          break;           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1061    }        } else {
1062    checkFinleyError();           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1063          }
1064          break;
1065       case(DegreesOfFreedom):      
1066          switch(target.getFunctionSpace().getTypeCode()) {
1067          case(ReducedDegreesOfFreedom):
1068          case(DegreesOfFreedom):
1069          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1070          break;
1071      
1072          case(Nodes):
1073          case(ReducedNodes):
1074          if (getMPISize()>1) {
1075             escript::Data temp=escript::Data(in);
1076             temp.expand();
1077             escriptDataC _in2 = temp.getDataC();
1078             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1079          } else {
1080             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1081          }
1082          break;
1083          case(Elements):
1084          case(ReducedElements):
1085          if (getMPISize()>1) {
1086             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1087             escriptDataC _in2 = temp.getDataC();
1088             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1089          } else {
1090             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1091          }
1092          break;
1093          case(FaceElements):
1094          case(ReducedFaceElements):
1095          if (getMPISize()>1) {
1096             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1097             escriptDataC _in2 = temp.getDataC();
1098             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1099      
1100          } else {
1101             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1102          }
1103          break;
1104          case(Points):
1105          if (getMPISize()>1) {
1106             //escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1107             //escriptDataC _in2 = temp.getDataC();
1108          } else {
1109             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1110          }
1111          break;
1112          case(ContactElementsZero):
1113          case(ContactElementsOne):
1114          case(ReducedContactElementsZero):
1115          case(ReducedContactElementsOne):
1116          if (getMPISize()>1) {
1117             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1118             escriptDataC _in2 = temp.getDataC();
1119             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1120          } else {
1121             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1122          }
1123          break;
1124          default:
1125             stringstream temp;
1126             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1127             throw FinleyAdapterException(temp.str());
1128             break;
1129          }
1130          break;
1131       case(ReducedDegreesOfFreedom):
1132          switch(target.getFunctionSpace().getTypeCode()) {
1133          case(Nodes):
1134          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1135          break;
1136          case(ReducedNodes):
1137          if (getMPISize()>1) {
1138             escript::Data temp=escript::Data(in);
1139             temp.expand();
1140             escriptDataC _in2 = temp.getDataC();
1141             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1142          } else {
1143             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1144          }
1145          break;
1146          case(DegreesOfFreedom):
1147          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1148          break;
1149          case(ReducedDegreesOfFreedom):
1150          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1151          break;
1152          case(Elements):
1153          case(ReducedElements):
1154          if (getMPISize()>1) {
1155             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1156             escriptDataC _in2 = temp.getDataC();
1157             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1158          } else {
1159             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1160          }
1161          break;
1162          case(FaceElements):
1163          case(ReducedFaceElements):
1164          if (getMPISize()>1) {
1165             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1166             escriptDataC _in2 = temp.getDataC();
1167             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1168          } else {
1169             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1170          }
1171          break;
1172          case(Points):
1173          if (getMPISize()>1) {
1174             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1175             escriptDataC _in2 = temp.getDataC();
1176             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1177          } else {
1178             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1179          }
1180          break;
1181          case(ContactElementsZero):
1182          case(ContactElementsOne):
1183          case(ReducedContactElementsZero):
1184          case(ReducedContactElementsOne):
1185          if (getMPISize()>1) {
1186             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1187             escriptDataC _in2 = temp.getDataC();
1188             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1189          } else {
1190             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1191          }
1192          break;
1193          default:
1194             stringstream temp;
1195             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1196             throw FinleyAdapterException(temp.str());
1197             break;
1198          }
1199          break;
1200       default:
1201          stringstream temp;
1202          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1203          throw FinleyAdapterException(temp.str());
1204          break;
1205       }
1206       checkFinleyError();
1207  }  }
1208    
1209  //  //
# Line 580  void MeshAdapter::interpolateOnDomain(es Line 1211  void MeshAdapter::interpolateOnDomain(es
1211  //  //
1212  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1213  {  {
1214    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1215    if (argDomain!=*this)     if (argDomain!=*this)
1216       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1217    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1218    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1219    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1220       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1221    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1222       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1223       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(*this),true);
1224       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1225       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1226    }        // this is then interpolated onto arg:
1227    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1228       }
1229       checkFinleyError();
1230  }  }
1231    
1232  //  //
# Line 601  void MeshAdapter::setToX(escript::Data& Line 1234  void MeshAdapter::setToX(escript::Data&
1234  //  //
1235  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1236  {  {
1237    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1238    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1239       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1240    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1241    switch(normal.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1242      case(Nodes):     escriptDataC _normal=normal.getDataC();
1243        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     switch(normal.getFunctionSpace().getTypeCode()) {
1244        break;     case(Nodes):
1245      case(Elements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1246        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     break;
1247        break;     case(ReducedNodes):
1248      case (FaceElements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1249        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     break;
1250        break;     case(Elements):
1251      case(Points):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1252        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     break;
1253        break;     case(ReducedElements):
1254      case (ContactElementsOne):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1255      case (ContactElementsZero):     break;
1256        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (FaceElements):
1257        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1258      case(DegreesOfFreedom):     break;
1259        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case (ReducedFaceElements):
1260        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1261      case(ReducedDegreesOfFreedom):     break;
1262        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(Points):
1263        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1264      default:     break;
1265       case (ContactElementsOne):
1266       case (ContactElementsZero):
1267       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1268       break;
1269       case (ReducedContactElementsOne):
1270       case (ReducedContactElementsZero):
1271       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1272       break;
1273       case(DegreesOfFreedom):
1274       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1275       break;
1276       case(ReducedDegreesOfFreedom):
1277       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1278       break;
1279       default:
1280        stringstream temp;        stringstream temp;
1281        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();
1282        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1283        break;        break;
1284    }     }
1285    checkFinleyError();     checkFinleyError();
1286  }  }
1287    
1288  //  //
# Line 642  void MeshAdapter::setToNormal(escript::D Line 1290  void MeshAdapter::setToNormal(escript::D
1290  //  //
1291  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1292  {  {
1293    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1294    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1295       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1296          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1297    
1298    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1299  }  }
1300    
1301  //  //
1302  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined of arg:
1303  //  //
1304  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(vector<double>& integrals,const escript::Data& arg) const
1305  {  {
1306    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1307    if (argDomain!=*this)     if (argDomain!=*this)
1308       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1309    
1310    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1311    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1312       case(Nodes):     escriptDataC _temp;
1313          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");     escript::Data temp;
1314          break;     escriptDataC _arg=arg.getDataC();
1315       case(Elements):     switch(arg.getFunctionSpace().getTypeCode()) {
1316          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     case(Nodes):
1317          break;     temp=escript::Data( arg, escript::function(*this) );
1318       case(FaceElements):     _temp=temp.getDataC();
1319          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1320          break;     break;
1321       case(Points):     case(ReducedNodes):
1322          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     temp=escript::Data( arg, escript::function(*this) );
1323          break;     _temp=temp.getDataC();
1324       case(ContactElementsZero):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1325          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1326          break;     case(Elements):
1327       case(ContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1328          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1329          break;     case(ReducedElements):
1330       case(DegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1331          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");     break;
1332          break;     case(FaceElements):
1333       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1334          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");     break;
1335          break;     case(ReducedFaceElements):
1336       default:     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1337          stringstream temp;     break;
1338          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     case(Points):
1339          throw FinleyAdapterException(temp.str());     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1340          break;     break;
1341    }     case(ContactElementsZero):
1342    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1343       break;
1344       case(ReducedContactElementsZero):
1345       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1346       break;
1347       case(ContactElementsOne):
1348       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1349       break;
1350       case(ReducedContactElementsOne):
1351       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1352       break;
1353       case(DegreesOfFreedom):
1354       temp=escript::Data( arg, escript::function(*this) );
1355       _temp=temp.getDataC();
1356       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1357       break;
1358       case(ReducedDegreesOfFreedom):
1359       temp=escript::Data( arg, escript::function(*this) );
1360       _temp=temp.getDataC();
1361       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1362       break;
1363       default:
1364          stringstream temp;
1365          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1366          throw FinleyAdapterException(temp.str());
1367          break;
1368       }
1369       checkFinleyError();
1370       blocktimer_increment("integrate()", blocktimer_start);
1371  }  }
1372    
1373  //  //
# Line 698  void MeshAdapter::setToIntegrals(std::ve Line 1375  void MeshAdapter::setToIntegrals(std::ve
1375  //  //
1376  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1377  {  {
1378    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1379    if (argDomain!=*this)     if (argDomain!=*this)
1380      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1381    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1382    if (gradDomain!=*this)     if (gradDomain!=*this)
1383       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1384    
1385    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1386    switch(grad.getFunctionSpace().getTypeCode()) {     escriptDataC _grad=grad.getDataC();
1387         case(Nodes):     escriptDataC nodeDataC;
1388            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     escript::Data temp;
1389            break;     if (getMPISize()>1) {
1390         case(Elements):        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1391            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  continuousFunction(*this) );
1392            break;           nodeDataC = temp.getDataC();
1393         case(FaceElements):        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1394            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  reducedContinuousFunction(*this) );
1395            break;           nodeDataC = temp.getDataC();
1396         case(Points):        } else {
1397            throw FinleyAdapterException("Error - Gradient at points is not supported.");           nodeDataC = arg.getDataC();
1398            break;        }
1399         case(ContactElementsZero):     } else {
1400            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));        nodeDataC = arg.getDataC();
1401            break;     }
1402         case(ContactElementsOne):     switch(grad.getFunctionSpace().getTypeCode()) {
1403            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     case(Nodes):
1404            break;     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1405         case(DegreesOfFreedom):     break;
1406            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     case(ReducedNodes):
1407            break;     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1408         case(ReducedDegreesOfFreedom):     break;
1409            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     case(Elements):
1410            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1411         default:     break;
1412            stringstream temp;     case(ReducedElements):
1413            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1414            throw FinleyAdapterException(temp.str());     break;
1415            break;     case(FaceElements):
1416    }     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1417    checkFinleyError();     break;
1418       case(ReducedFaceElements):
1419       Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1420       break;
1421       case(Points):
1422       throw FinleyAdapterException("Error - Gradient at points is not supported.");
1423       break;
1424       case(ContactElementsZero):
1425       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1426       break;
1427       case(ReducedContactElementsZero):
1428       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1429       break;
1430       case(ContactElementsOne):
1431       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1432       break;
1433       case(ReducedContactElementsOne):
1434       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1435       break;
1436       case(DegreesOfFreedom):
1437       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1438       break;
1439       case(ReducedDegreesOfFreedom):
1440       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1441       break;
1442       default:
1443          stringstream temp;
1444          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1445          throw FinleyAdapterException(temp.str());
1446          break;
1447       }
1448       checkFinleyError();
1449  }  }
1450    
1451  //  //
# Line 745  void MeshAdapter::setToGradient(escript: Line 1453  void MeshAdapter::setToGradient(escript:
1453  //  //
1454  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1455  {  {
1456    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1457    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1458    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1459         case(Nodes):     case(Nodes):
1460            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1461            break;     break;
1462         case(Elements):     case(ReducedNodes):
1463            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1464            break;     break;
1465         case(FaceElements):     case(Elements):
1466            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1467            break;     break;
1468         case(Points):     case(ReducedElements):
1469            throw FinleyAdapterException("Error - Size of point elements is not supported.");     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1470            break;     break;
1471         case(ContactElementsZero):     case(FaceElements):
1472         case(ContactElementsOne):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1473            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     break;
1474            break;     case(ReducedFaceElements):
1475         case(DegreesOfFreedom):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1476            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     break;
1477            break;     case(Points):
1478         case(ReducedDegreesOfFreedom):     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1479            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     break;
1480            break;     case(ContactElementsZero):
1481         default:     case(ContactElementsOne):
1482            stringstream temp;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1483            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();     break;
1484            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1485            break;     case(ReducedContactElementsOne):
1486    }     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1487    checkFinleyError();     break;
1488       case(DegreesOfFreedom):
1489       throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1490       break;
1491       case(ReducedDegreesOfFreedom):
1492       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1493       break;
1494       default:
1495          stringstream temp;
1496          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1497          throw FinleyAdapterException(temp.str());
1498          break;
1499       }
1500       checkFinleyError();
1501  }  }
1502    
1503  // sets the location of nodes:  //
1504    // sets the location of nodes
1505    //
1506  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1507  {  {
1508    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1509    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     escriptDataC tmp;
1510    if (newDomain!=*this)     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1511       throw FinleyAdapterException("Error - Illegal domain of new point locations");     if (newDomain!=*this)
1512    Finley_Mesh_setCoordinates(mesh,&(new_x.getDataC()));        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1513    checkFinleyError();     if ( new_x.getFunctionSpace() == continuousFunction(*this) ) {
1514  }         tmp = new_x.getDataC();
1515           Finley_Mesh_setCoordinates(mesh,&tmp);
1516  // saves a data array in openDX format:     } else {
1517  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const         throw FinleyAdapterException("As of version escript3.3 - SetNewX only accepts ContinuousFunction arguments please interpolate.");    
1518  {  /*       escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(*this) );
1519      int MAX_namelength=256;         tmp = new_x_inter.getDataC();
1520      const int num_data=boost::python::extract<int>(arg.attr("__len__")());         Finley_Mesh_setCoordinates(mesh,&tmp);*/
1521      char names[num_data][MAX_namelength];     }
1522      char* c_names[num_data];     checkFinleyError();
1523      escriptDataC data[num_data];  }
1524      escriptDataC* ptr_data[num_data];  
1525    //
1526      boost::python::list keys=arg.keys();  // Helper for the save* methods. Extracts optional data variable names and the
1527      for (int i=0;i<num_data;++i) {  // corresponding pointers from python dictionary. Caller must free arrays.
1528           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  //
1529           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1530               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");  {
1531           data[i]=d.getDataC();     numData = boost::python::extract<int>(arg.attr("__len__")());
1532           ptr_data[i]=&(data[i]);     /* win32 refactor */
1533           std::string n=boost::python::extract<std::string>(keys[i]);     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1534           c_names[i]=&(names[i][0]);     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1535           if (n.length()>MAX_namelength-1) {     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1536              strncpy(c_names[i],n.c_str(),MAX_namelength-1);  
1537              c_names[i][MAX_namelength-1]='\0';     boost::python::list keys=arg.keys();
1538           } else {     for (int i=0; i<numData; ++i) {
1539              strcpy(c_names[i],n.c_str());        string n=boost::python::extract<string>(keys[i]);
1540           }        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1541      }        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1542      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);           throw FinleyAdapterException("Error: Data must be defined on same Domain");
1543      checkFinleyError();        data[i] = d.getDataC();
1544      return;        dataPtr[i] = &(data[i]);
1545  }        names[i] = TMPMEMALLOC(n.length()+1, char);
1546          strcpy(names[i], n.c_str());
1547  // saves a data array in openVTK format:     }
1548  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  }
1549  {  
1550      int MAX_namelength=256;  //
1551      const int num_data=boost::python::extract<int>(arg.attr("__len__")());  // saves mesh and optionally data arrays in openDX format
1552      char names[num_data][MAX_namelength];  //
1553      char* c_names[num_data];  void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1554      escriptDataC data[num_data];  {
1555      escriptDataC* ptr_data[num_data];     int num_data;
1556       char **names;
1557      boost::python::list keys=arg.keys();     escriptDataC *data;
1558      for (int i=0;i<num_data;++i) {     escriptDataC **ptr_data;
1559           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);  
1560           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1561               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1562           data[i]=d.getDataC();     checkFinleyError();
1563           ptr_data[i]=&(data[i]);  
1564           std::string n=boost::python::extract<std::string>(keys[i]);     /* win32 refactor */
1565           c_names[i]=&(names[i][0]);     TMPMEMFREE(data);
1566           if (n.length()>MAX_namelength-1) {     TMPMEMFREE(ptr_data);
1567              strncpy(c_names[i],n.c_str(),MAX_namelength-1);     for(int i=0; i<num_data; i++)
1568              c_names[i][MAX_namelength-1]='\0';     {
1569           } else {        TMPMEMFREE(names[i]);
1570              strcpy(c_names[i],n.c_str());     }
1571           }     TMPMEMFREE(names);
1572      }  
1573      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);     return;
1574      checkFinleyError();  }
1575      return;  
1576  }  //
1577                                                                                                                                                                            // saves mesh and optionally data arrays in VTK format
1578                                                                                                                                                                            //
1579  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1580  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  {
1581                        const int row_blocksize,      boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("_saveVTK");
1582                        const escript::FunctionSpace& row_functionspace,      pySaveVTK(filename, const_cast<MeshAdapter*>(this)->getPtr(),
1583                        const int column_blocksize,                metadata, metadata_schema, arg);
1584                        const escript::FunctionSpace& column_functionspace,  }
1585                        const int type) const  
1586  {  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1587      int reduceRowOrder=0;  {
1588      int reduceColOrder=0;  #ifdef ESYS_MPI
1589      // is the domain right?      index_t myFirstNode=0, myLastNode=0, k=0;
1590      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());      index_t* globalNodeIndex=0;
1591      if (row_domain!=*this)      Finley_Mesh* mesh_p=m_finleyMesh.get();
1592            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");      if (fs_code == FINLEY_REDUCED_NODES)
1593      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());      {
1594      if (col_domain!=*this)      myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1595            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");      myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1596      // is the function space type right      globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {  
         reduceRowOrder=0;  
     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {  
         reduceRowOrder=1;  
     } else {  
         throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");  
1597      }      }
1598      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      else
1599          reduceColOrder=0;      {
1600      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1601          reduceColOrder=1;      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1602      } else {      globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
         throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");  
1603      }      }
1604      // generate matrix:      k=globalNodeIndex[id];
1605            return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1606      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);  #endif
1607      checkFinleyError();      return true;
1608      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);  }
1609      checkPasoError();  
1610      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);  
1611      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  
1612    //
1613    // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1614    //
1615    ASM_ptr MeshAdapter::newSystemMatrix(
1616                                                     const int row_blocksize,
1617                                                     const escript::FunctionSpace& row_functionspace,
1618                                                     const int column_blocksize,
1619                                                     const escript::FunctionSpace& column_functionspace,
1620                                                     const int type) const
1621    {
1622       int reduceRowOrder=0;
1623       int reduceColOrder=0;
1624       // is the domain right?
1625       const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1626       if (row_domain!=*this)
1627          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1628       const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1629       if (col_domain!=*this)
1630          throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1631       // is the function space type right
1632       if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1633          reduceRowOrder=0;
1634       } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1635          reduceRowOrder=1;
1636       } else {
1637          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1638       }
1639       if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1640          reduceColOrder=0;
1641       } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1642          reduceColOrder=1;
1643       } else {
1644          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1645       }
1646       // generate matrix:
1647    
1648       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1649       checkFinleyError();
1650       Paso_SystemMatrix* fsystemMatrix;
1651       int trilinos = 0;
1652       if (trilinos) {
1653    #ifdef TRILINOS
1654          /* Allocation Epetra_VrbMatrix here */
1655    #endif
1656       }
1657       else {
1658          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1659       }
1660       checkPasoError();
1661       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1662       SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1663       return ASM_ptr(sma);
1664    //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1665    }
1666    
1667    //
1668    // creates a TransportProblemAdapter
1669    //
1670    ATP_ptr MeshAdapter::newTransportProblem(
1671                                                             const int blocksize,
1672                                                             const escript::FunctionSpace& functionspace,
1673                                                             const int type) const
1674    {
1675       int reduceOrder=0;
1676       // is the domain right?
1677       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1678       if (domain!=*this)
1679          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1680       // is the function space type right
1681       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1682          reduceOrder=0;
1683       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1684          reduceOrder=1;
1685       } else {
1686          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1687       }
1688       // generate matrix:
1689    
1690       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1691       checkFinleyError();
1692       Paso_TransportProblem* transportProblem;
1693       transportProblem=Paso_TransportProblem_alloc(fsystemMatrixPattern,blocksize);
1694       checkPasoError();
1695       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1696       TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,blocksize,functionspace);
1697       return ATP_ptr(tpa);
1698    //   return TransportProblemAdapter(transportProblem, blocksize,functionspace);
1699  }  }
1700    
1701  //  //
# Line 904  SystemMatrixAdapter MeshAdapter::newSyst Line 1707  SystemMatrixAdapter MeshAdapter::newSyst
1707  // 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:
1708  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1709  {  {
1710    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1711         case(Nodes):     case(Nodes):
1712         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1713         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1714            return false;     return false;
1715            break;     break;
1716         case(Elements):     case(Elements):
1717         case(FaceElements):     case(FaceElements):
1718         case(Points):     case(Points):
1719         case(ContactElementsZero):     case(ContactElementsZero):
1720         case(ContactElementsOne):     case(ContactElementsOne):
1721            return true;     case(ReducedElements):
1722            break;     case(ReducedFaceElements):
1723         default:     case(ReducedContactElementsZero):
1724            stringstream temp;     case(ReducedContactElementsOne):
1725            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;     return true;
1726            throw FinleyAdapterException(temp.str());     break;
1727            break;     default:
1728    }        stringstream temp;
1729    checkFinleyError();        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1730    return false;        throw FinleyAdapterException(temp.str());
1731          break;
1732       }
1733       checkFinleyError();
1734       return false;
1735    }
1736    
1737    bool
1738    MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1739    {
1740       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1741        class 1: DOF <-> Nodes
1742        class 2: ReducedDOF <-> ReducedNodes
1743        class 3: Points
1744        class 4: Elements
1745        class 5: ReducedElements
1746        class 6: FaceElements
1747        class 7: ReducedFaceElements
1748        class 8: ContactElementZero <-> ContactElementOne
1749        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1750    
1751       There is also a set of lines. Interpolation is possible down a line but not between lines.
1752       class 1 and 2 belong to all lines so aren't considered.
1753        line 0: class 3
1754        line 1: class 4,5
1755        line 2: class 6,7
1756        line 3: class 8,9
1757    
1758       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1759       eg hasnodes is true if we have at least one instance of Nodes.
1760       */
1761        if (fs.empty())
1762        {
1763            return false;
1764        }
1765        vector<int> hasclass(10);
1766        vector<int> hasline(4);
1767        bool hasnodes=false;
1768        bool hasrednodes=false;
1769        bool hascez=false;
1770        bool hasrcez=false;
1771        for (int i=0;i<fs.size();++i)
1772        {
1773        switch(fs[i])
1774        {
1775        case(Nodes):   hasnodes=true;   // no break is deliberate
1776        case(DegreesOfFreedom):
1777            hasclass[1]=1;
1778            break;
1779        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1780        case(ReducedDegreesOfFreedom):
1781            hasclass[2]=1;
1782            break;
1783        case(Points):
1784            hasline[0]=1;
1785            hasclass[3]=1;
1786            break;
1787        case(Elements):
1788            hasclass[4]=1;
1789            hasline[1]=1;
1790            break;
1791        case(ReducedElements):
1792            hasclass[5]=1;
1793            hasline[1]=1;
1794            break;
1795        case(FaceElements):
1796            hasclass[6]=1;
1797            hasline[2]=1;
1798            break;
1799        case(ReducedFaceElements):
1800            hasclass[7]=1;
1801            hasline[2]=1;
1802            break;
1803        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1804        case(ContactElementsOne):
1805            hasclass[8]=1;
1806            hasline[3]=1;
1807            break;
1808        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1809        case(ReducedContactElementsOne):
1810            hasclass[9]=1;
1811            hasline[3]=1;
1812            break;
1813        default:
1814            return false;
1815        }
1816        }
1817        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1818        // fail if we have more than one leaf group
1819    
1820        if (totlines>1)
1821        {
1822        return false;   // there are at least two branches we can't interpolate between
1823        }
1824        else if (totlines==1)
1825        {
1826        if (hasline[0]==1)      // we have points
1827        {
1828            resultcode=Points;
1829        }
1830        else if (hasline[1]==1)
1831        {
1832            if (hasclass[5]==1)
1833            {
1834            resultcode=ReducedElements;
1835            }
1836            else
1837            {
1838            resultcode=Elements;
1839            }
1840        }
1841        else if (hasline[2]==1)
1842        {
1843            if (hasclass[7]==1)
1844            {
1845            resultcode=ReducedFaceElements;
1846            }
1847            else
1848            {
1849            resultcode=FaceElements;
1850            }
1851        }
1852        else    // so we must be in line3
1853        {
1854            if (hasclass[9]==1)
1855            {
1856            // need something from class 9
1857            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1858            }
1859            else
1860            {
1861            // something from class 8
1862            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1863            }
1864        }
1865        }
1866        else    // totlines==0
1867        {
1868        if (hasclass[2]==1)
1869        {
1870            // something from class 2
1871            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1872        }
1873        else
1874        {   // something from class 1
1875            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1876        }
1877        }
1878        return true;
1879  }  }
1880    
1881  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1882  {  {
1883    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1884       case(Nodes):     case(Nodes):
1885          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1886             case(Nodes):      case(Nodes):
1887             case(ReducedDegreesOfFreedom):      case(ReducedNodes):
1888             case(DegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1889             case(Elements):      case(DegreesOfFreedom):
1890             case(FaceElements):      case(Elements):
1891             case(Points):      case(ReducedElements):
1892             case(ContactElementsZero):      case(FaceElements):
1893             case(ContactElementsOne):      case(ReducedFaceElements):
1894                 return true;      case(Points):
1895             default:      case(ContactElementsZero):
1896                 stringstream temp;      case(ReducedContactElementsZero):
1897                 temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      case(ContactElementsOne):
1898                 throw FinleyAdapterException(temp.str());      case(ReducedContactElementsOne):
1899          }      return true;
1900          break;      default:
1901       case(Elements):            stringstream temp;
1902          if (functionSpaceType_target==Elements) {            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1903             return true;            throw FinleyAdapterException(temp.str());
1904       }
1905       break;
1906       case(ReducedNodes):
1907        switch(functionSpaceType_target) {
1908        case(ReducedNodes):
1909        case(ReducedDegreesOfFreedom):
1910        case(Elements):
1911        case(ReducedElements):
1912        case(FaceElements):
1913        case(ReducedFaceElements):
1914        case(Points):
1915        case(ContactElementsZero):
1916        case(ReducedContactElementsZero):
1917        case(ContactElementsOne):
1918        case(ReducedContactElementsOne):
1919        return true;
1920        case(Nodes):
1921        case(DegreesOfFreedom):
1922        return false;
1923        default:
1924            stringstream temp;
1925            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1926            throw FinleyAdapterException(temp.str());
1927       }
1928       break;
1929       case(Elements):
1930        if (functionSpaceType_target==Elements) {
1931          return true;
1932        } else if (functionSpaceType_target==ReducedElements) {
1933          return true;
1934          } else {          } else {
1935             return false;            return false;
         }  
      case(FaceElements):  
         if (functionSpaceType_target==FaceElements) {  
            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 {  
            return false;  
         }  
      case(DegreesOfFreedom):  
         switch(functionSpaceType_target) {  
            case(ReducedDegreesOfFreedom):  
            case(DegreesOfFreedom):  
            case(Nodes):  
            case(Elements):  
            case(FaceElements):  
            case(Points):  
            case(ContactElementsZero):  
            case(ContactElementsOne):  
               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());  
1936          }          }
1937          break;     case(ReducedElements):
1938       case(ReducedDegreesOfFreedom):      if (functionSpaceType_target==ReducedElements) {
1939         switch(functionSpaceType_target) {        return true;
1940            case(ReducedDegreesOfFreedom):      } else {
1941            case(Elements):            return false;
1942            case(FaceElements):      }
1943            case(Points):     case(FaceElements):
1944            case(ContactElementsZero):      if (functionSpaceType_target==FaceElements) {
1945            case(ContactElementsOne):              return true;
1946                return true;      } else if (functionSpaceType_target==ReducedFaceElements) {
1947            case(Nodes):              return true;
1948            case(DegreesOfFreedom):      } else {
1949               return false;              return false;
1950            default:      }
1951               stringstream temp;     case(ReducedFaceElements):
1952               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      if (functionSpaceType_target==ReducedFaceElements) {
1953               throw FinleyAdapterException(temp.str());              return true;
1954         }      } else {
1955         break;          return false;
1956       default:      }
1957          stringstream temp;     case(Points):
1958          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;      if (functionSpaceType_target==Points) {
1959          throw FinleyAdapterException(temp.str());              return true;
1960          break;      } else {
1961    }              return false;
1962    checkFinleyError();      }
1963    return false;     case(ContactElementsZero):
1964       case(ContactElementsOne):
1965        if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1966                return true;
1967        } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1968                return true;
1969        } else {
1970                return false;
1971        }
1972       case(ReducedContactElementsZero):
1973       case(ReducedContactElementsOne):
1974        if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1975                return true;
1976        } else {
1977                return false;
1978        }
1979       case(DegreesOfFreedom):
1980        switch(functionSpaceType_target) {
1981        case(ReducedDegreesOfFreedom):
1982        case(DegreesOfFreedom):
1983        case(Nodes):
1984        case(ReducedNodes):
1985        case(Elements):
1986        case(ReducedElements):
1987        case(Points):
1988        case(FaceElements):
1989        case(ReducedFaceElements):
1990        case(ContactElementsZero):
1991        case(ReducedContactElementsZero):
1992        case(ContactElementsOne):
1993        case(ReducedContactElementsOne):
1994        return true;
1995        default:
1996            stringstream temp;
1997            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1998            throw FinleyAdapterException(temp.str());
1999        }
2000        break;
2001       case(ReducedDegreesOfFreedom):
2002       switch(functionSpaceType_target) {
2003        case(ReducedDegreesOfFreedom):
2004        case(ReducedNodes):
2005        case(Elements):
2006        case(ReducedElements):
2007        case(FaceElements):
2008        case(ReducedFaceElements):
2009        case(Points):
2010        case(ContactElementsZero):
2011        case(ReducedContactElementsZero):
2012        case(ContactElementsOne):
2013        case(ReducedContactElementsOne):
2014        return true;
2015        case(Nodes):
2016        case(DegreesOfFreedom):
2017        return false;
2018        default:
2019            stringstream temp;
2020            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
2021            throw FinleyAdapterException(temp.str());
2022        }
2023        break;
2024       default:
2025          stringstream temp;
2026          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
2027          throw FinleyAdapterException(temp.str());
2028          break;
2029       }
2030       checkFinleyError();
2031       return false;
2032  }  }
2033    
2034  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
2035  {  {
2036      return false;     return false;
2037  }  }
2038    
2039  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
2040  {  {
2041    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
2042    if (temp!=0) {     if (temp!=0) {
2043      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
2044    } else {     } else {
2045      return false;        return false;
2046    }     }
2047  }  }
2048    
2049  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
2050  {  {
2051    return !(operator==(other));     return !(operator==(other));
2052  }  }
2053    
2054  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
2055  {  {
2056     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
2057     checkPasoError();     return SystemMatrixAdapter::getSystemMatrixTypeId(solver, preconditioner,
2058     return out;             package, symmetry, mesh->MPIInfo);
2059    }
2060    
2061    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2062    {
2063       Finley_Mesh* mesh=m_finleyMesh.get();
2064       return TransportProblemAdapter::getTransportTypeId(solver, preconditioner,
2065               package, symmetry, mesh->MPIInfo);
2066  }  }
2067    
2068  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2069  {  {
2070    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(*this).getX();
2071  }  }
2072    
2073  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2074  {  {
2075    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(*this).getNormal();
2076  }  }
2077    
2078  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2079  {  {
2080    return function(asAbstractContinuousDomain()).getSize();     return escript::function(*this).getSize();
2081  }  }
2082    
2083    const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2084    {
2085       int *out = NULL;
2086       Finley_Mesh* mesh=m_finleyMesh.get();
2087       switch (functionSpaceType) {
2088       case(Nodes):
2089       out=mesh->Nodes->Id;
2090       break;
2091       case(ReducedNodes):
2092       out=mesh->Nodes->reducedNodesId;
2093       break;
2094       case(Elements):
2095       out=mesh->Elements->Id;
2096       break;
2097       case(ReducedElements):
2098       out=mesh->Elements->Id;
2099       break;
2100       case(FaceElements):
2101       out=mesh->FaceElements->Id;
2102       break;
2103       case(ReducedFaceElements):
2104       out=mesh->FaceElements->Id;
2105       break;
2106       case(Points):
2107       out=mesh->Points->Id;
2108       break;
2109       case(ContactElementsZero):
2110       out=mesh->ContactElements->Id;
2111       break;
2112       case(ReducedContactElementsZero):
2113       out=mesh->ContactElements->Id;
2114       break;
2115       case(ContactElementsOne):
2116       out=mesh->ContactElements->Id;
2117       break;
2118       case(ReducedContactElementsOne):
2119       out=mesh->ContactElements->Id;
2120       break;
2121       case(DegreesOfFreedom):
2122       out=mesh->Nodes->degreesOfFreedomId;
2123       break;
2124       case(ReducedDegreesOfFreedom):
2125       out=mesh->Nodes->reducedDegreesOfFreedomId;
2126       break;
2127       default:
2128          stringstream temp;
2129          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2130          throw FinleyAdapterException(temp.str());
2131          break;
2132       }
2133       return out;
2134    }
2135  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2136  {  {
2137    int* tagList;     int out=0;
2138    int numTags;     Finley_Mesh* mesh=m_finleyMesh.get();
2139    getTagList(functionSpaceType, &tagList, &numTags);     switch (functionSpaceType) {
2140    return tagList[sampleNo];     case(Nodes):
2141       out=mesh->Nodes->Tag[sampleNo];
2142       break;
2143       case(ReducedNodes):
2144       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
2145       break;
2146       case(Elements):
2147       out=mesh->Elements->Tag[sampleNo];
2148       break;
2149       case(ReducedElements):
2150       out=mesh->Elements->Tag[sampleNo];
2151       break;
2152       case(FaceElements):
2153       out=mesh->FaceElements->Tag[sampleNo];
2154       break;
2155       case(ReducedFaceElements):
2156       out=mesh->FaceElements->Tag[sampleNo];
2157       break;
2158       case(Points):
2159       out=mesh->Points->Tag[sampleNo];
2160       break;
2161       case(ContactElementsZero):
2162       out=mesh->ContactElements->Tag[sampleNo];
2163       break;
2164       case(ReducedContactElementsZero):
2165       out=mesh->ContactElements->Tag[sampleNo];
2166       break;
2167       case(ContactElementsOne):
2168       out=mesh->ContactElements->Tag[sampleNo];
2169       break;
2170       case(ReducedContactElementsOne):
2171       out=mesh->ContactElements->Tag[sampleNo];
2172       break;
2173       case(DegreesOfFreedom):
2174       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2175       break;
2176       case(ReducedDegreesOfFreedom):
2177       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2178       break;
2179       default:
2180          stringstream temp;
2181          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2182          throw FinleyAdapterException(temp.str());
2183          break;
2184       }
2185       return out;
2186    }
2187    
2188    
2189    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
2190    {
2191       Finley_Mesh* mesh=m_finleyMesh.get();
2192       escriptDataC tmp=mask.getDataC();
2193       switch(functionSpaceType) {
2194       case(Nodes):
2195       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
2196       break;
2197       case(ReducedNodes):
2198       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2199       break;
2200       case(DegreesOfFreedom):
2201       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2202       break;
2203       case(ReducedDegreesOfFreedom):
2204       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2205       break;
2206       case(Elements):
2207       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2208       break;
2209       case(ReducedElements):
2210       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2211       break;
2212       case(FaceElements):
2213       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2214       break;
2215       case(ReducedFaceElements):
2216       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2217       break;
2218       case(Points):
2219       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2220       break;
2221       case(ContactElementsZero):
2222       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2223       break;
2224       case(ReducedContactElementsZero):
2225       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2226       break;
2227       case(ContactElementsOne):
2228       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2229       break;
2230       case(ReducedContactElementsOne):
2231       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2232       break;
2233       default:
2234          stringstream temp;
2235          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2236          throw FinleyAdapterException(temp.str());
2237       }
2238       checkFinleyError();
2239       return;
2240    }
2241    
2242    void MeshAdapter::setTagMap(const string& name,  int tag)
2243    {
2244       Finley_Mesh* mesh=m_finleyMesh.get();
2245       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2246       checkFinleyError();
2247       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2248    }
2249    
2250    int MeshAdapter::getTag(const string& name) const
2251    {
2252       Finley_Mesh* mesh=m_finleyMesh.get();
2253       int tag=0;
2254       tag=Finley_Mesh_getTag(mesh, name.c_str());
2255       checkFinleyError();
2256       // throwStandardException("MeshAdapter::getTag is not implemented.");
2257       return tag;
2258    }
2259    
2260    bool MeshAdapter::isValidTagName(const string& name) const
2261    {
2262       Finley_Mesh* mesh=m_finleyMesh.get();
2263       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2264  }  }
2265    
2266  int MeshAdapter::getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const  string MeshAdapter::showTagNames() const
2267  {  {
2268    int* referenceNoList;     stringstream temp;
2269    int numReferenceNo;     Finley_Mesh* mesh=m_finleyMesh.get();
2270    getReferenceNoList(functionSpaceType, &referenceNoList, &numReferenceNo);     Finley_TagMap* tag_map=mesh->TagMap;
2271    return referenceNoList[sampleNo];     while (tag_map) {
2272          temp << tag_map->name;
2273          tag_map=tag_map->next;
2274          if (tag_map) temp << ", ";
2275       }
2276       return temp.str();
2277  }  }
2278    
2279    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2280    {
2281      Finley_Mesh* mesh=m_finleyMesh.get();
2282      dim_t numTags=0;
2283      switch(functionSpaceCode) {
2284       case(Nodes):
2285              numTags=mesh->Nodes->numTagsInUse;
2286              break;
2287       case(ReducedNodes):
2288              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2289              break;
2290       case(DegreesOfFreedom):
2291              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2292              break;
2293       case(ReducedDegreesOfFreedom):
2294              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2295              break;
2296       case(Elements):
2297       case(ReducedElements):
2298              numTags=mesh->Elements->numTagsInUse;
2299              break;
2300       case(FaceElements):
2301       case(ReducedFaceElements):
2302              numTags=mesh->FaceElements->numTagsInUse;
2303              break;
2304       case(Points):
2305              numTags=mesh->Points->numTagsInUse;
2306              break;
2307       case(ContactElementsZero):
2308       case(ReducedContactElementsZero):
2309       case(ContactElementsOne):
2310       case(ReducedContactElementsOne):
2311              numTags=mesh->ContactElements->numTagsInUse;
2312              break;
2313       default:
2314          stringstream temp;
2315          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2316          throw FinleyAdapterException(temp.str());
2317      }
2318      return numTags;
2319    }
2320    
2321    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2322    {
2323      Finley_Mesh* mesh=m_finleyMesh.get();
2324      index_t* tags=NULL;
2325      switch(functionSpaceCode) {
2326       case(Nodes):
2327              tags=mesh->Nodes->tagsInUse;
2328              break;
2329       case(ReducedNodes):
2330              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2331              break;
2332       case(DegreesOfFreedom):
2333              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2334              break;
2335       case(ReducedDegreesOfFreedom):
2336              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2337              break;
2338       case(Elements):
2339       case(ReducedElements):
2340              tags=mesh->Elements->tagsInUse;
2341              break;
2342       case(FaceElements):
2343       case(ReducedFaceElements):
2344              tags=mesh->FaceElements->tagsInUse;
2345              break;
2346       case(Points):
2347              tags=mesh->Points->tagsInUse;
2348              break;
2349       case(ContactElementsZero):
2350       case(ReducedContactElementsZero):
2351       case(ContactElementsOne):
2352       case(ReducedContactElementsOne):
2353              tags=mesh->ContactElements->tagsInUse;
2354              break;
2355       default:
2356          stringstream temp;
2357          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2358          throw FinleyAdapterException(temp.str());
2359      }
2360      return tags;
2361    }
2362    
2363    
2364    bool MeshAdapter::canTag(int functionSpaceCode) const
2365    {
2366      switch(functionSpaceCode) {
2367       case(Nodes):
2368       case(Elements):
2369       case(ReducedElements):
2370       case(FaceElements):
2371       case(ReducedFaceElements):
2372       case(Points):
2373       case(ContactElementsZero):
2374       case(ReducedContactElementsZero):
2375       case(ContactElementsOne):
2376       case(ReducedContactElementsOne):
2377              return true;
2378       case(ReducedNodes):
2379       case(DegreesOfFreedom):
2380       case(ReducedDegreesOfFreedom):
2381          return false;
2382       default:
2383        return false;
2384      }
2385    }
2386    
2387    AbstractDomain::StatusType MeshAdapter::getStatus() const
2388    {
2389      Finley_Mesh* mesh=m_finleyMesh.get();
2390      return Finley_Mesh_getStatus(mesh);
2391    }
2392    
2393    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2394    {
2395      
2396      Finley_Mesh* mesh=m_finleyMesh.get();
2397      int order =-1;
2398      switch(functionSpaceCode) {
2399       case(Nodes):
2400       case(DegreesOfFreedom):
2401              order=mesh->approximationOrder;
2402              break;
2403       case(ReducedNodes):
2404       case(ReducedDegreesOfFreedom):
2405              order=mesh->reducedApproximationOrder;
2406              break;
2407       case(Elements):
2408       case(FaceElements):
2409       case(Points):
2410       case(ContactElementsZero):
2411       case(ContactElementsOne):
2412              order=mesh->integrationOrder;
2413              break;
2414       case(ReducedElements):
2415       case(ReducedFaceElements):
2416       case(ReducedContactElementsZero):
2417       case(ReducedContactElementsOne):
2418              order=mesh->reducedIntegrationOrder;
2419              break;
2420       default:
2421          stringstream temp;
2422          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2423          throw FinleyAdapterException(temp.str());
2424      }
2425      return order;
2426    }
2427    
2428    bool MeshAdapter::supportsContactElements() const
2429    {
2430      return true;
2431    }
2432    
2433    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2434    {
2435      m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2436    }
2437    
2438    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2439    {
2440      Finley_ReferenceElementSet_dealloc(m_refSet);
2441    }
2442    
2443    // points will be flattened
2444    void MeshAdapter:: addDiracPoints(const std::vector<double>& points, const std::vector<int>& tags) const
2445    {
2446          const int dim = getDim();
2447          int numPoints=points.size()/dim;
2448          int numTags=tags.size();
2449          Finley_Mesh* mesh=m_finleyMesh.get();
2450          
2451          if ( points.size() % dim != 0 )
2452          {
2453        throw FinleyAdapterException("Error - number of coords does not appear to be a multiple of dimension.");
2454          }
2455          
2456          if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2457         throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2458          
2459          double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2460          int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2461          
2462          for (int i=0;i<numPoints;++i) {
2463           points_ptr[ i * dim     ] = points[i * dim ];
2464           if ( dim > 1 ) points_ptr[ i * dim + 1 ] = points[i * dim + 1];
2465           if ( dim > 2 ) points_ptr[ i * dim + 2 ] = points[i * dim + 2];    
2466               tags_ptr[i]=tags[i];
2467          }
2468          
2469          Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2470          checkFinleyError();
2471          
2472          TMPMEMFREE(points_ptr);
2473          TMPMEMFREE(tags_ptr);
2474    }
2475    
2476    
2477    // void MeshAdapter:: addDiracPoints(const boost::python::list& points, const boost::python::list& tags) const
2478    // {
2479    //       const int dim = getDim();
2480    //       int numPoints=boost::python::extract<int>(points.attr("__len__")());
2481    //       int numTags=boost::python::extract<int>(tags.attr("__len__")());
2482    //       Finley_Mesh* mesh=m_finleyMesh.get();
2483    //      
2484    //       if  ( (numTags > 0) && ( numPoints !=  numTags ) )
2485    //   throw FinleyAdapterException("Error - if tags are given number of tags and points must match.");
2486    //      
2487    //       double* points_ptr=TMPMEMALLOC(numPoints * dim, double);
2488    //       int*    tags_ptr= TMPMEMALLOC(numPoints, int);
2489    //      
2490    //       for (int i=0;i<numPoints;++i) {
2491    //     int tag_id=-1;
2492    //     int numComps=boost::python::extract<int>(points[i].attr("__len__")());
2493    //     if  ( numComps !=   dim ) {
2494    //                stringstream temp;            
2495    //                temp << "Error - illegal number of components " << numComps << " for point " << i;              
2496    //                throw FinleyAdapterException(temp.str());
2497    //     }
2498    //     points_ptr[ i * dim     ] = boost::python::extract<double>(points[i][0]);
2499    //     if ( dim > 1 ) points_ptr[ i * dim + 1 ] = boost::python::extract<double>(points[i][1]);
2500    //     if ( dim > 2 ) points_ptr[ i * dim + 2 ] = boost::python::extract<double>(points[i][2]);
2501    //    
2502    //     if ( numTags > 0) {
2503    //            boost::python::extract<string> ex_str(tags[i]);
2504    //        if  ( ex_str.check() ) {
2505    //            tag_id=getTag( ex_str());
2506    //        } else {
2507    //             boost::python::extract<int> ex_int(tags[i]);
2508    //             if ( ex_int.check() ) {
2509    //                 tag_id=ex_int();
2510    //             } else {
2511    //              stringstream temp;          
2512    //                  temp << "Error - unable to extract tag for point " << i;
2513    //              throw FinleyAdapterException(temp.str());
2514    //            }
2515    //        }
2516    //     }      
2517    //            tags_ptr[i]=tag_id;
2518    //       }
2519    //      
2520    //       Finley_Mesh_addPoints(mesh, numPoints, points_ptr, tags_ptr);
2521    //       checkPasoError();
2522    //      
2523    //       TMPMEMFREE(points_ptr);
2524    //       TMPMEMFREE(tags_ptr);
2525    // }
2526    
2527    /*
2528    void MeshAdapter:: addDiracPoint( const boost::python::list& point, const int tag) const
2529    {  
2530        boost::python::list points =  boost::python::list();
2531        boost::python::list tags =  boost::python::list();
2532        points.append(point);
2533        tags.append(tag);
2534        addDiracPoints(points, tags);
2535    }
2536    */
2537    
2538    /*
2539    void MeshAdapter:: addDiracPointWithTagName( const boost::python::list& point, const std::string& tag) const
2540    {
2541            boost::python::list points =   boost::python::list();
2542            boost::python::list tags =   boost::python::list();
2543            points.append(point);
2544            tags.append(tag);
2545            addDiracPoints(points, tags);
2546    }
2547    */
2548  }  // end of namespace  }  // end of namespace

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