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

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revision 1059 by gross, Fri Mar 23 11:01:53 2007 UTC revision 2989 by gross, Thu Mar 18 01:45:55 2010 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  
  *                                                                            *  
  * This software is the property of ACcESS. No part of this code              *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that person has a software    *  
  * license agreement with ACcESS.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
1    
2  #ifdef PASO_MPI  /*******************************************************
3  #include <mpi.h>  *
4  #endif  * Copyright (c) 2003-2010 by University of Queensland
5  #include "MeshAdapter.h"  * Earth Systems Science Computational Center (ESSCC)
6    * http://www.uq.edu.au/esscc
7    *
8    * Primary Business: Queensland, Australia
9    * Licensed under the Open Software License version 3.0
10    * http://www.opensource.org/licenses/osl-3.0.php
11    *
12    *******************************************************/
13    
14    
15    #include "MeshAdapter.h"
16  #include "escript/Data.h"  #include "escript/Data.h"
17  #include "escript/DataFactory.h"  #include "escript/DataFactory.h"
18    #ifdef USE_NETCDF
19    #include <netcdfcpp.h>
20    #endif
21    #ifdef PASO_MPI
22    #include <mpi.h>
23    #include "paso/Paso_MPI.h"
24    #endif
25    extern "C" {
26    #include "esysUtils/blocktimer.h"
27    }
28    
29  using namespace std;  using namespace std;
30  using namespace escript;  using namespace escript;
# Line 32  MeshAdapter::FunctionSpaceNamesMapType M Line 37  MeshAdapter::FunctionSpaceNamesMapType M
37  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
38  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
39  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
40    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
41  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
42  const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;  const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
43  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
# Line 44  const int MeshAdapter::ReducedContactEle Line 50  const int MeshAdapter::ReducedContactEle
50    
51  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
52  {  {
53    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
54    //     //
55    // need to use a null_deleter as Finley_Mesh_dealloc deletes the pointer     // need to use a null_deleter as Finley_Mesh_free deletes the pointer
56    // for us.     // for us.
57    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
58  }  }
59    
60  //  //
# Line 56  MeshAdapter::MeshAdapter(Finley_Mesh* fi Line 62  MeshAdapter::MeshAdapter(Finley_Mesh* fi
62  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
63  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
64  {  {
65    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
66  }  }
67    
68  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
69  {  {
70    //     //
71    // I hope the case for the pointer being zero has been taken care of.     // I hope the case for the pointer being zero has been taken care of.
72    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
73    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
74      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
75      Finley_Mesh_dealloc(m_finleyMesh.get());     }
     //   cout << "Finished dealloc." << endl;  
   }  
76  }  }
77    
78    int MeshAdapter::getMPISize() const
79    {
80       return m_finleyMesh.get()->MPIInfo->size;
81    }
82    int MeshAdapter::getMPIRank() const
83    {
84       return m_finleyMesh.get()->MPIInfo->rank;
85    }
86    void MeshAdapter::MPIBarrier() const
87    {
88    #ifdef PASO_MPI
89       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
90    #endif
91       return;
92    }
93    bool MeshAdapter::onMasterProcessor() const
94    {
95       return m_finleyMesh.get()->MPIInfo->rank == 0;
96    }
97    
98    
99    #ifdef PASO_MPI
100      MPI_Comm
101    #else
102      unsigned int
103    #endif
104    MeshAdapter::getMPIComm() const
105    {
106    #ifdef PASO_MPI
107        return m_finleyMesh->MPIInfo->comm;
108    #else
109        return 0;
110    #endif
111    }
112    
113    
114  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
115     return m_finleyMesh.get();     return m_finleyMesh.get();
116  }  }
117    
118  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
119    {
120       char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
121       strcpy(fName,fileName.c_str());
122       Finley_Mesh_write(m_finleyMesh.get(),fName);
123       checkFinleyError();
124       TMPMEMFREE(fName);
125    }
126    
127    void MeshAdapter::Print_Mesh_Info(const bool full) const
128  {  {
129    char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
130    strcpy(fName,fileName.c_str());  }
131    Finley_Mesh_write(m_finleyMesh.get(),fName);  
132    checkFinleyError();  void MeshAdapter::dump(const string& fileName) const
133    TMPMEMFREE(fName);  {
134    #ifdef USE_NETCDF
135       const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
136       NcVar *ids;
137       int *int_ptr;
138       Finley_Mesh *mesh = m_finleyMesh.get();
139       Finley_TagMap* tag_map;
140       int num_Tags = 0;
141       int mpi_size             = mesh->MPIInfo->size;
142       int mpi_rank             = mesh->MPIInfo->rank;
143       int numDim               = mesh->Nodes->numDim;
144       int numNodes             = mesh->Nodes->numNodes;
145       int num_Elements         = mesh->Elements->numElements;
146       int num_FaceElements         = mesh->FaceElements->numElements;
147       int num_ContactElements      = mesh->ContactElements->numElements;
148       int num_Points           = mesh->Points->numElements;
149       int num_Elements_numNodes        = mesh->Elements->numNodes;
150       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
151       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
152    #ifdef PASO_MPI
153       MPI_Status status;
154    #endif
155    
156    /* Incoming token indicates it's my turn to write */
157    #ifdef PASO_MPI
158       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
159    #endif
160    
161       char *newFileName = Paso_MPI_appendRankToFileName(fileName.c_str(),
162                                                         mpi_size, mpi_rank);
163    
164       /* Figure out how much storage is required for tags */
165       tag_map = mesh->TagMap;
166       num_Tags = 0;
167       while (tag_map) {
168          num_Tags++;
169          tag_map=tag_map->next;
170       }
171    
172       // NetCDF error handler
173       NcError err(NcError::verbose_nonfatal);
174       // Create the file.
175       NcFile dataFile(newFileName, NcFile::Replace);
176       string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
177       // check if writing was successful
178       if (!dataFile.is_valid())
179          throw DataException(msgPrefix+"Open file for output");
180    
181       // Define dimensions (num_Elements and dim_Elements are identical,
182       // dim_Elements only appears if > 0)
183       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
184          throw DataException(msgPrefix+"add_dim(numNodes)");
185       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
186          throw DataException(msgPrefix+"add_dim(numDim)");
187       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
188          throw DataException(msgPrefix+"add_dim(mpi_size)");
189       if (num_Elements>0)
190          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
191             throw DataException(msgPrefix+"add_dim(dim_Elements)");
192       if (num_FaceElements>0)
193          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
194             throw DataException(msgPrefix+"add_dim(dim_FaceElements)");
195       if (num_ContactElements>0)
196          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
197             throw DataException(msgPrefix+"add_dim(dim_ContactElements)");
198       if (num_Points>0)
199          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
200             throw DataException(msgPrefix+"add_dim(dim_Points)");
201       if (num_Elements>0)
202          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
203             throw DataException(msgPrefix+"add_dim(dim_Elements_Nodes)");
204       if (num_FaceElements>0)
205          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
206             throw DataException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
207       if (num_ContactElements>0)
208          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
209             throw DataException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
210       if (num_Tags>0)
211          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
212             throw DataException(msgPrefix+"add_dim(dim_Tags)");
213    
214       // Attributes: MPI size, MPI rank, Name, order, reduced_order
215       if (!dataFile.add_att("mpi_size", mpi_size) )
216          throw DataException(msgPrefix+"add_att(mpi_size)");
217       if (!dataFile.add_att("mpi_rank", mpi_rank) )
218          throw DataException(msgPrefix+"add_att(mpi_rank)");
219       if (!dataFile.add_att("Name",mesh->Name) )
220          throw DataException(msgPrefix+"add_att(Name)");
221       if (!dataFile.add_att("numDim",numDim) )
222          throw DataException(msgPrefix+"add_att(order)");
223       if (!dataFile.add_att("order",mesh->integrationOrder) )
224          throw DataException(msgPrefix+"add_att(order)");
225       if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
226          throw DataException(msgPrefix+"add_att(reduced_order)");
227       if (!dataFile.add_att("numNodes",numNodes) )
228          throw DataException(msgPrefix+"add_att(numNodes)");
229       if (!dataFile.add_att("num_Elements",num_Elements) )
230          throw DataException(msgPrefix+"add_att(num_Elements)");
231       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
232          throw DataException(msgPrefix+"add_att(num_FaceElements)");
233       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
234          throw DataException(msgPrefix+"add_att(num_ContactElements)");
235       if (!dataFile.add_att("num_Points",num_Points) )
236          throw DataException(msgPrefix+"add_att(num_Points)");
237       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
238          throw DataException(msgPrefix+"add_att(num_Elements_numNodes)");
239       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
240          throw DataException(msgPrefix+"add_att(num_FaceElements_numNodes)");
241       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
242          throw DataException(msgPrefix+"add_att(num_ContactElements_numNodes)");
243       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
244          throw DataException(msgPrefix+"add_att(Elements_TypeId)");
245       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
246          throw DataException(msgPrefix+"add_att(FaceElements_TypeId)");
247       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
248          throw DataException(msgPrefix+"add_att(ContactElements_TypeId)");
249       if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
250          throw DataException(msgPrefix+"add_att(Points_TypeId)");
251       if (!dataFile.add_att("num_Tags", num_Tags) )
252          throw DataException(msgPrefix+"add_att(num_Tags)");
253    
254       // // // // // Nodes // // // // //
255    
256       // Nodes nodeDistribution
257       if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
258          throw DataException(msgPrefix+"add_var(Nodes_NodeDistribution)");
259       int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
260       if (! (ids->put(int_ptr, mpi_size+1)) )
261          throw DataException(msgPrefix+"put(Nodes_NodeDistribution)");
262    
263       // Nodes degreesOfFreedomDistribution
264       if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
265          throw DataException(msgPrefix+"add_var(Nodes_DofDistribution)");
266       int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
267       if (! (ids->put(int_ptr, mpi_size+1)) )
268          throw DataException(msgPrefix+"put(Nodes_DofDistribution)");
269    
270       // Only write nodes if non-empty because NetCDF doesn't like empty arrays
271       // (it treats them as NC_UNLIMITED)
272       if (numNodes>0) {
273    
274          // Nodes Id
275          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
276             throw DataException(msgPrefix+"add_var(Nodes_Id)");
277          int_ptr = &mesh->Nodes->Id[0];
278          if (! (ids->put(int_ptr, numNodes)) )
279             throw DataException(msgPrefix+"put(Nodes_Id)");
280    
281          // Nodes Tag
282          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
283             throw DataException(msgPrefix+"add_var(Nodes_Tag)");
284          int_ptr = &mesh->Nodes->Tag[0];
285          if (! (ids->put(int_ptr, numNodes)) )
286             throw DataException(msgPrefix+"put(Nodes_Tag)");
287    
288          // Nodes gDOF
289          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
290             throw DataException(msgPrefix+"add_var(Nodes_gDOF)");
291          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
292          if (! (ids->put(int_ptr, numNodes)) )
293             throw DataException(msgPrefix+"put(Nodes_gDOF)");
294    
295          // Nodes global node index
296          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
297             throw DataException(msgPrefix+"add_var(Nodes_gNI)");
298          int_ptr = &mesh->Nodes->globalNodesIndex[0];
299          if (! (ids->put(int_ptr, numNodes)) )
300             throw DataException(msgPrefix+"put(Nodes_gNI)");
301    
302          // Nodes grDof
303          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
304             throw DataException(msgPrefix+"add_var(Nodes_grDfI)");
305          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
306          if (! (ids->put(int_ptr, numNodes)) )
307             throw DataException(msgPrefix+"put(Nodes_grDfI)");
308    
309          // Nodes grNI
310          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
311             throw DataException(msgPrefix+"add_var(Nodes_grNI)");
312          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
313          if (! (ids->put(int_ptr, numNodes)) )
314             throw DataException(msgPrefix+"put(Nodes_grNI)");
315    
316          // Nodes Coordinates
317          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
318             throw DataException(msgPrefix+"add_var(Nodes_Coordinates)");
319          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
320             throw DataException(msgPrefix+"put(Nodes_Coordinates)");
321    
322       }
323    
324       // // // // // Elements // // // // //
325    
326       if (num_Elements>0) {
327    
328          // Elements_Id
329          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
330             throw DataException(msgPrefix+"add_var(Elements_Id)");
331          int_ptr = &mesh->Elements->Id[0];
332          if (! (ids->put(int_ptr, num_Elements)) )
333             throw DataException(msgPrefix+"put(Elements_Id)");
334    
335          // Elements_Tag
336          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
337             throw DataException(msgPrefix+"add_var(Elements_Tag)");
338          int_ptr = &mesh->Elements->Tag[0];
339          if (! (ids->put(int_ptr, num_Elements)) )
340             throw DataException(msgPrefix+"put(Elements_Tag)");
341    
342          // Elements_Owner
343          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
344             throw DataException(msgPrefix+"add_var(Elements_Owner)");
345          int_ptr = &mesh->Elements->Owner[0];
346          if (! (ids->put(int_ptr, num_Elements)) )
347             throw DataException(msgPrefix+"put(Elements_Owner)");
348    
349          // Elements_Color
350          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
351             throw DataException(msgPrefix+"add_var(Elements_Color)");
352          int_ptr = &mesh->Elements->Color[0];
353          if (! (ids->put(int_ptr, num_Elements)) )
354             throw DataException(msgPrefix+"put(Elements_Color)");
355    
356          // Elements_Nodes
357          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
358             throw DataException(msgPrefix+"add_var(Elements_Nodes)");
359          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
360             throw DataException(msgPrefix+"put(Elements_Nodes)");
361    
362       }
363    
364       // // // // // Face_Elements // // // // //
365    
366       if (num_FaceElements>0) {
367    
368          // FaceElements_Id
369          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
370             throw DataException(msgPrefix+"add_var(FaceElements_Id)");
371          int_ptr = &mesh->FaceElements->Id[0];
372          if (! (ids->put(int_ptr, num_FaceElements)) )
373             throw DataException(msgPrefix+"put(FaceElements_Id)");
374    
375          // FaceElements_Tag
376          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
377             throw DataException(msgPrefix+"add_var(FaceElements_Tag)");
378          int_ptr = &mesh->FaceElements->Tag[0];
379          if (! (ids->put(int_ptr, num_FaceElements)) )
380             throw DataException(msgPrefix+"put(FaceElements_Tag)");
381    
382          // FaceElements_Owner
383          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
384             throw DataException(msgPrefix+"add_var(FaceElements_Owner)");
385          int_ptr = &mesh->FaceElements->Owner[0];
386          if (! (ids->put(int_ptr, num_FaceElements)) )
387             throw DataException(msgPrefix+"put(FaceElements_Owner)");
388    
389          // FaceElements_Color
390          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
391             throw DataException(msgPrefix+"add_var(FaceElements_Color)");
392          int_ptr = &mesh->FaceElements->Color[0];
393          if (! (ids->put(int_ptr, num_FaceElements)) )
394             throw DataException(msgPrefix+"put(FaceElements_Color)");
395    
396          // FaceElements_Nodes
397          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
398             throw DataException(msgPrefix+"add_var(FaceElements_Nodes)");
399          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
400             throw DataException(msgPrefix+"put(FaceElements_Nodes)");
401    
402       }
403    
404       // // // // // Contact_Elements // // // // //
405    
406       if (num_ContactElements>0) {
407    
408          // ContactElements_Id
409          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
410             throw DataException(msgPrefix+"add_var(ContactElements_Id)");
411          int_ptr = &mesh->ContactElements->Id[0];
412          if (! (ids->put(int_ptr, num_ContactElements)) )
413             throw DataException(msgPrefix+"put(ContactElements_Id)");
414    
415          // ContactElements_Tag
416          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
417             throw DataException(msgPrefix+"add_var(ContactElements_Tag)");
418          int_ptr = &mesh->ContactElements->Tag[0];
419          if (! (ids->put(int_ptr, num_ContactElements)) )
420             throw DataException(msgPrefix+"put(ContactElements_Tag)");
421    
422          // ContactElements_Owner
423          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
424             throw DataException(msgPrefix+"add_var(ContactElements_Owner)");
425          int_ptr = &mesh->ContactElements->Owner[0];
426          if (! (ids->put(int_ptr, num_ContactElements)) )
427             throw DataException(msgPrefix+"put(ContactElements_Owner)");
428    
429          // ContactElements_Color
430          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
431             throw DataException(msgPrefix+"add_var(ContactElements_Color)");
432          int_ptr = &mesh->ContactElements->Color[0];
433          if (! (ids->put(int_ptr, num_ContactElements)) )
434             throw DataException(msgPrefix+"put(ContactElements_Color)");
435    
436          // ContactElements_Nodes
437          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
438             throw DataException(msgPrefix+"add_var(ContactElements_Nodes)");
439          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
440             throw DataException(msgPrefix+"put(ContactElements_Nodes)");
441    
442       }
443    
444       // // // // // Points // // // // //
445    
446       if (num_Points>0) {
447    
448          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
449    
450          // Points_Id
451          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
452             throw DataException(msgPrefix+"add_var(Points_Id)");
453          int_ptr = &mesh->Points->Id[0];
454          if (! (ids->put(int_ptr, num_Points)) )
455             throw DataException(msgPrefix+"put(Points_Id)");
456    
457          // Points_Tag
458          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
459             throw DataException(msgPrefix+"add_var(Points_Tag)");
460          int_ptr = &mesh->Points->Tag[0];
461          if (! (ids->put(int_ptr, num_Points)) )
462             throw DataException(msgPrefix+"put(Points_Tag)");
463    
464          // Points_Owner
465          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
466             throw DataException(msgPrefix+"add_var(Points_Owner)");
467          int_ptr = &mesh->Points->Owner[0];
468          if (! (ids->put(int_ptr, num_Points)) )
469             throw DataException(msgPrefix+"put(Points_Owner)");
470    
471          // Points_Color
472          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
473             throw DataException(msgPrefix+"add_var(Points_Color)");
474          int_ptr = &mesh->Points->Color[0];
475          if (! (ids->put(int_ptr, num_Points)) )
476             throw DataException(msgPrefix+"put(Points_Color)");
477    
478          // Points_Nodes
479          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
480          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
481             throw DataException(msgPrefix+"add_var(Points_Nodes)");
482          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
483             throw DataException(msgPrefix+"put(Points_Nodes)");
484    
485       }
486    
487       // // // // // TagMap // // // // //
488    
489       if (num_Tags>0) {
490    
491          // Temp storage to gather node IDs
492          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
493          char name_temp[4096];
494    
495          /* Copy tag data into temp arrays */
496          tag_map = mesh->TagMap;
497          if (tag_map) {
498             int i = 0;
499             while (tag_map) {
500                Tags_keys[i++] = tag_map->tag_key;
501                tag_map=tag_map->next;
502             }
503          }
504    
505          // Tags_keys
506          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
507             throw DataException(msgPrefix+"add_var(Tags_keys)");
508          int_ptr = &Tags_keys[0];
509          if (! (ids->put(int_ptr, num_Tags)) )
510             throw DataException(msgPrefix+"put(Tags_keys)");
511    
512          // Tags_names_*
513          // This is an array of strings, it should be stored as an array but
514          // instead I have hacked in one attribute per string because the NetCDF
515          // manual doesn't tell how to do an array of strings
516          tag_map = mesh->TagMap;
517          if (tag_map) {
518             int i = 0;
519             while (tag_map) {
520                sprintf(name_temp, "Tags_name_%d", i);
521                if (!dataFile.add_att(name_temp, tag_map->name) )
522                   throw DataException(msgPrefix+"add_att(Tags_names_XX)");
523                tag_map=tag_map->next;
524                i++;
525             }
526          }
527    
528          TMPMEMFREE(Tags_keys);
529       }
530    
531    /* Send token to next MPI process so he can take his turn */
532    #ifdef PASO_MPI
533       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
534    #endif
535    
536       // NetCDF file is closed by destructor of NcFile object
537    
538    #else
539       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
540    #endif  /* USE_NETCDF */
541       checkFinleyError();
542  }  }
543    
544  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
545  {  {
546    return "FinleyMesh";     return "FinleyMesh";
547  }  }
548    
549  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
550  {  {
551    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
552    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
553    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
554      return "Invalid function space type code.";        return "Invalid function space type code.";
555    } else {     } else {
556      return loc->second;        return loc->second;
557    }     }
558  }  }
559    
560  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
561  {  {
562    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
563    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
564    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
565  }  }
566    
567  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
568  {  {
569    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
570      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
571    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
572      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
573    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
574      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
575    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
576      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
577    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
578      (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
579    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
580      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
581    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
582      (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
583    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
584      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
585    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
586      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
587    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
588      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
589    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
590      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
591    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
592      (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
593       m_functionSpaceTypeNames.insert
594       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
595  }  }
596    
597  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
598  {  {
599    return Nodes;     return Nodes;
600    }
601    int MeshAdapter::getReducedContinuousFunctionCode() const
602    {
603       return ReducedNodes;
604  }  }
605    
606  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
607  {  {
608    return Elements;     return Elements;
609  }  }
610  int MeshAdapter::getReducedFunctionCode() const  int MeshAdapter::getReducedFunctionCode() const
611  {  {
612    return ReducedElements;     return ReducedElements;
613  }  }
614    
615  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
616  {  {
617    return FaceElements;     return FaceElements;
618  }  }
619  int MeshAdapter::getReducedFunctionOnBoundaryCode() const  int MeshAdapter::getReducedFunctionOnBoundaryCode() const
620  {  {
621    return ReducedFaceElements;     return ReducedFaceElements;
622  }  }
623    
624  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
625  {  {
626    return ContactElementsZero;     return ContactElementsZero;
627  }  }
628  int MeshAdapter::getReducedFunctionOnContactZeroCode() const  int MeshAdapter::getReducedFunctionOnContactZeroCode() const
629  {  {
630    return ReducedContactElementsZero;     return ReducedContactElementsZero;
631  }  }
632    
633  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
634  {  {
635    return ContactElementsOne;     return ContactElementsOne;
636  }  }
637  int MeshAdapter::getReducedFunctionOnContactOneCode() const  int MeshAdapter::getReducedFunctionOnContactOneCode() const
638  {  {
639    return ReducedContactElementsOne;     return ReducedContactElementsOne;
640  }  }
641    
642  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
643  {  {
644    return DegreesOfFreedom;     return DegreesOfFreedom;
645  }  }
646    
647  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
648  {  {
649    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
650  }  }
651    
652  int MeshAdapter::getDiracDeltaFunctionCode() const  int MeshAdapter::getDiracDeltaFunctionCode() const
653  {  {
654    return Points;     return Points;
655  }  }
656    
657  //  //
# Line 196  int MeshAdapter::getDiracDeltaFunctionCo Line 659  int MeshAdapter::getDiracDeltaFunctionCo
659  //  //
660  int MeshAdapter::getDim() const  int MeshAdapter::getDim() const
661  {  {
662    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     Finley_Mesh* mesh=m_finleyMesh.get();
663    checkFinleyError();     int numDim=Finley_Mesh_getDim(mesh);
664    return numDim;     checkFinleyError();
665       return numDim;
666    }
667    
668    //
669    // Return the number of data points summed across all MPI processes
670    //
671    int MeshAdapter::getNumDataPointsGlobal() const
672    {
673       return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
674  }  }
675    
676  //  //
# Line 211  pair<int,int> MeshAdapter::getDataShape( Line 683  pair<int,int> MeshAdapter::getDataShape(
683     int numSamples=0;     int numSamples=0;
684     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
685     switch (functionSpaceCode) {     switch (functionSpaceCode) {
686        case(Nodes):     case(Nodes):
687             numDataPointsPerSample=1;     numDataPointsPerSample=1;
688             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
689             break;     break;
690        case(Elements):     case(ReducedNodes):
691             if (mesh->Elements!=NULL) {     numDataPointsPerSample=1;
692               numSamples=mesh->Elements->numElements;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
693               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
694             }     case(Elements):
695             break;     if (mesh->Elements!=NULL) {
696        case(FaceElements):        numSamples=mesh->Elements->numElements;
697             if (mesh->FaceElements!=NULL) {        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
698                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
699                  numSamples=mesh->FaceElements->numElements;     break;
700             }     case(ReducedElements):
701             break;     if (mesh->Elements!=NULL) {
702        case(Points):        numSamples=mesh->Elements->numElements;
703             if (mesh->Points!=NULL) {        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
704               numDataPointsPerSample=1;     }
705               numSamples=mesh->Points->numElements;     break;
706             }     case(FaceElements):
707             break;     if (mesh->FaceElements!=NULL) {
708        case(ContactElementsZero):        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
709             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
710               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
711               numSamples=mesh->ContactElements->numElements;     break;
712             }     case(ReducedFaceElements):
713             break;     if (mesh->FaceElements!=NULL) {
714        case(ContactElementsOne):        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
715             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
716               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
717               numSamples=mesh->ContactElements->numElements;     break;
718             }     case(Points):
719             break;     if (mesh->Points!=NULL) {
720        case(DegreesOfFreedom):        numDataPointsPerSample=1;
721             if (mesh->Nodes!=NULL) {        numSamples=mesh->Points->numElements;
722               numDataPointsPerSample=1;     }
723  #ifndef PASO_MPI     break;
724               numSamples=mesh->Nodes->numDegreesOfFreedom;     case(ContactElementsZero):
725  #else     if (mesh->ContactElements!=NULL) {
726               numSamples=mesh->Nodes->degreeOfFreedomDistribution->numLocal;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
727  #endif        numSamples=mesh->ContactElements->numElements;
728             }     }
729             break;     break;
730        case(ReducedDegreesOfFreedom):     case(ReducedContactElementsZero):
731             if (mesh->Nodes!=NULL) {     if (mesh->ContactElements!=NULL) {
732               numDataPointsPerSample=1;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
733  #ifndef PASO_MPI        numSamples=mesh->ContactElements->numElements;
734               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     }
735  #else     break;
736               numSamples=mesh->Nodes->reducedDegreeOfFreedomDistribution->numLocal;     case(ContactElementsOne):
737  #endif     if (mesh->ContactElements!=NULL) {
738             }        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
739             break;        numSamples=mesh->ContactElements->numElements;
740        default:     }
741          stringstream temp;     break;
742          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();     case(ReducedContactElementsOne):
743          throw FinleyAdapterException(temp.str());     if (mesh->ContactElements!=NULL) {
744          break;        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
745        }        numSamples=mesh->ContactElements->numElements;
746        return pair<int,int>(numDataPointsPerSample,numSamples);     }
747       break;
748       case(DegreesOfFreedom):
749       if (mesh->Nodes!=NULL) {
750          numDataPointsPerSample=1;
751          numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
752       }
753       break;
754       case(ReducedDegreesOfFreedom):
755       if (mesh->Nodes!=NULL) {
756          numDataPointsPerSample=1;
757          numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
758       }
759       break;
760       default:
761          stringstream temp;
762          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
763          throw FinleyAdapterException(temp.str());
764          break;
765       }
766       return pair<int,int>(numDataPointsPerSample,numSamples);
767  }  }
768    
769  //  //
770  // adds linear PDE of second order into a given stiffness matrix and right hand side:  // adds linear PDE of second order into a given stiffness matrix and right hand side:
771  //  //
772  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
773                       SystemMatrixAdapter& mat, escript::Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
774                       const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,                                   const escript::Data& A, const escript::Data& B, const escript::Data& C,const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
775                       const escript::Data& d, const escript::Data& y,                                   const escript::Data& d, const escript::Data& y,
776                       const escript::Data& d_contact,const escript::Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
777  {  {
778     escriptDataC _rhs=rhs.getDataC();     escriptDataC _rhs=rhs.getDataC();
779     escriptDataC _A  =A.getDataC();     escriptDataC _A  =A.getDataC();
# Line 307  void MeshAdapter::addPDEToSystem( Line 799  void MeshAdapter::addPDEToSystem(
799     checkFinleyError();     checkFinleyError();
800  }  }
801    
802    void  MeshAdapter::addPDEToLumpedSystem(
803                                            escript::Data& mat,
804                                            const escript::Data& D,
805                                            const escript::Data& d) const
806    {
807       escriptDataC _mat=mat.getDataC();
808       escriptDataC _D=D.getDataC();
809       escriptDataC _d=d.getDataC();
810    
811       Finley_Mesh* mesh=m_finleyMesh.get();
812    
813       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
814       checkFinleyError();
815      
816       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
817       checkFinleyError();
818    
819    }
820    
821    
822  //  //
823  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
824  //  //
# Line 329  void MeshAdapter::addPDEToRHS( escript:: Line 841  void MeshAdapter::addPDEToRHS( escript::
841     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
842     checkFinleyError();     checkFinleyError();
843  }  }
844    //
845    // adds PDE of second order into a transport problem
846    //
847    void MeshAdapter::addPDEToTransportProblem(
848                                               TransportProblemAdapter& tp, escript::Data& source, const escript::Data& M,
849                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
850                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
851                                               const escript::Data& d, const escript::Data& y,
852                                               const escript::Data& d_contact,const escript::Data& y_contact) const
853    {
854       DataTypes::ShapeType shape;
855       source.expand();
856       escriptDataC _source=source.getDataC();
857       escriptDataC _M=M.getDataC();
858       escriptDataC _A=A.getDataC();
859       escriptDataC _B=B.getDataC();
860       escriptDataC _C=C.getDataC();
861       escriptDataC _D=D.getDataC();
862       escriptDataC _X=X.getDataC();
863       escriptDataC _Y=Y.getDataC();
864       escriptDataC _d=d.getDataC();
865       escriptDataC _y=y.getDataC();
866       escriptDataC _d_contact=d_contact.getDataC();
867       escriptDataC _y_contact=y_contact.getDataC();
868    
869       Finley_Mesh* mesh=m_finleyMesh.get();
870       Paso_TransportProblem* _tp = tp.getPaso_TransportProblem();
871    
872       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
873       checkFinleyError();
874    
875       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
876       checkFinleyError();
877    
878       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
879       checkFinleyError();
880    
881       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
882       checkFinleyError();
883    }
884    
885  //  //
886  // interpolates data between different function spaces:  // interpolates data between different function spaces:
887  //  //
888  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
889  {  {
890    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
891    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
892    if (inDomain!=*this)       if (inDomain!=*this)  
893      throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
894    if (targetDomain!=*this)     if (targetDomain!=*this)
895      throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
896    
897    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
898    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
899       case(Nodes):     escriptDataC _in=in.getDataC();
900          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
901             case(Nodes):     case(Nodes):
902             case(ReducedDegreesOfFreedom):        switch(target.getFunctionSpace().getTypeCode()) {
903             case(DegreesOfFreedom):        case(Nodes):
904                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        case(ReducedNodes):
905                 break;        case(DegreesOfFreedom):
906             case(Elements):        case(ReducedDegreesOfFreedom):
907                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
908                 break;        break;
909             case(FaceElements):        case(Elements):
910                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        case(ReducedElements):
911                 break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
912             case(Points):        break;
913                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        case(FaceElements):
914                 break;        case(ReducedFaceElements):
915             case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
916                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
917                 break;        case(Points):
918             case(ContactElementsOne):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
919                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
920                 break;        case(ContactElementsZero):
921             default:        case(ReducedContactElementsZero):
922                 stringstream temp;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
923                 temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        break;
924                 throw FinleyAdapterException(temp.str());        case(ContactElementsOne):
925                 break;        case(ReducedContactElementsOne):
926          }        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
927          break;        break;
928       case(Elements):        default:
929          if (target.getFunctionSpace().getTypeCode()==Elements) {           stringstream temp;
930             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();
931          } else {           throw FinleyAdapterException(temp.str());
932             throw FinleyAdapterException("Error - No interpolation with data on elements possible.");           break;
933          }        }
934          break;        break;
935       case(FaceElements):     case(ReducedNodes):
936          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        switch(target.getFunctionSpace().getTypeCode()) {
937             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));        case(Nodes):
938          } else {        case(ReducedNodes):
939             throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");        case(DegreesOfFreedom):
940             break;        case(ReducedDegreesOfFreedom):
941         }        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
942       case(Points):        break;
943          if (target.getFunctionSpace().getTypeCode()==Points) {        case(Elements):
944             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));        case(ReducedElements):
945          } else {        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
946             throw FinleyAdapterException("Error - No interpolation with data on points possible.");        break;
947             break;        case(FaceElements):
948          }        case(ReducedFaceElements):
949          break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
950       case(ContactElementsZero):        break;
951       case(ContactElementsOne):        case(Points):
952          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
953             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));        break;
954          } else {        case(ContactElementsZero):
955             throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");        case(ReducedContactElementsZero):
956             break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
957          }        break;
958          break;        case(ContactElementsOne):
959       case(DegreesOfFreedom):              case(ReducedContactElementsOne):
960          switch(target.getFunctionSpace().getTypeCode()) {        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
961             case(ReducedDegreesOfFreedom):        break;
962             case(DegreesOfFreedom):        default:
963             case(Nodes):           stringstream temp;
964                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();
965                break;           throw FinleyAdapterException(temp.str());
966  #ifndef PASO_MPI           break;
967             case(Elements):        }
968                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        break;
969                break;     case(Elements):
970             case(FaceElements):        if (target.getFunctionSpace().getTypeCode()==Elements) {
971                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
972                break;        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
973             case(Points):           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
974                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        } else {
975                break;           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
976             case(ContactElementsZero):        }
977             case(ContactElementsOne):        break;
978                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));     case(ReducedElements):
979               break;        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
980  #else           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
981             /* need to copy Degrees of freedom data to nodal data so that the external values are available */        } else {
982             case(Elements):           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
983             {        }
984                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );        break;
985                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(nodeTemp.getDataC()),&(target.getDataC()));     case(FaceElements):
986                break;        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
987             }           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
988             case(FaceElements):        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
989             {           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
990                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );        } else {
991                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(nodeTemp.getDataC()),&(target.getDataC()));           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
992                break;        }
993             }        break;
994             case(Points):     case(ReducedFaceElements):
995             {        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
996                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
997                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(nodeTemp.getDataC()),&(target.getDataC()));        } else {
998                break;           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
999             }        }
1000             case(ContactElementsZero):        break;
1001             case(ContactElementsOne):     case(Points):
1002             {        if (target.getFunctionSpace().getTypeCode()==Points) {
1003                escript::Data nodeTemp( in, continuousFunction(asAbstractContinuousDomain()) );           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1004                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(nodeTemp.getDataC()),&(target.getDataC()));        } else {
1005               break;           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1006             }        }
1007  #endif        break;
1008             default:     case(ContactElementsZero):
1009               stringstream temp;     case(ContactElementsOne):
1010               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1011               throw FinleyAdapterException(temp.str());           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1012               break;        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1013          }           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
1014          break;        } else {
1015       case(ReducedDegreesOfFreedom):           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1016         switch(target.getFunctionSpace().getTypeCode()) {        }
1017            case(ReducedDegreesOfFreedom):        break;
1018               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));     case(ReducedContactElementsZero):
1019               break;     case(ReducedContactElementsOne):
1020            case(Elements):        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1021               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1022               break;        } else {
1023            case(FaceElements):           throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1024               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        }
1025               break;        break;
1026            case(Points):     case(DegreesOfFreedom):      
1027               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        switch(target.getFunctionSpace().getTypeCode()) {
1028               break;        case(ReducedDegreesOfFreedom):
1029            case(ContactElementsZero):        case(DegreesOfFreedom):
1030            case(ContactElementsOne):        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1031               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
1032               break;    
1033            case(Nodes):        case(Nodes):
1034               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");        case(ReducedNodes):
1035               break;        if (getMPISize()>1) {
1036            case(DegreesOfFreedom):           escript::Data temp=escript::Data(in);
1037               throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");           temp.expand();
1038               break;           escriptDataC _in2 = temp.getDataC();
1039            default:           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1040               stringstream temp;        } else {
1041               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();           Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1042               throw FinleyAdapterException(temp.str());        }
1043               break;        break;
1044         }        case(Elements):
1045         break;        case(ReducedElements):
1046       default:        if (getMPISize()>1) {
1047          stringstream temp;           escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1048          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();           escriptDataC _in2 = temp.getDataC();
1049          throw FinleyAdapterException(temp.str());           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1050          break;        } else {
1051    }           Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1052    checkFinleyError();        }
1053          break;
1054          case(FaceElements):
1055          case(ReducedFaceElements):
1056          if (getMPISize()>1) {
1057             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1058             escriptDataC _in2 = temp.getDataC();
1059             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1060      
1061          } else {
1062             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1063          }
1064          break;
1065          case(Points):
1066          if (getMPISize()>1) {
1067             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1068             escriptDataC _in2 = temp.getDataC();
1069          } else {
1070             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1071          }
1072          break;
1073          case(ContactElementsZero):
1074          case(ContactElementsOne):
1075          case(ReducedContactElementsZero):
1076          case(ReducedContactElementsOne):
1077          if (getMPISize()>1) {
1078             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1079             escriptDataC _in2 = temp.getDataC();
1080             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1081          } else {
1082             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1083          }
1084          break;
1085          default:
1086             stringstream temp;
1087             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1088             throw FinleyAdapterException(temp.str());
1089             break;
1090          }
1091          break;
1092       case(ReducedDegreesOfFreedom):
1093          switch(target.getFunctionSpace().getTypeCode()) {
1094          case(Nodes):
1095          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1096          break;
1097          case(ReducedNodes):
1098          if (getMPISize()>1) {
1099             escript::Data temp=escript::Data(in);
1100             temp.expand();
1101             escriptDataC _in2 = temp.getDataC();
1102             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1103          } else {
1104             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1105          }
1106          break;
1107          case(DegreesOfFreedom):
1108          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1109          break;
1110          case(ReducedDegreesOfFreedom):
1111          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1112          break;
1113          case(Elements):
1114          case(ReducedElements):
1115          if (getMPISize()>1) {
1116             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1117             escriptDataC _in2 = temp.getDataC();
1118             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1119          } else {
1120             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1121          }
1122          break;
1123          case(FaceElements):
1124          case(ReducedFaceElements):
1125          if (getMPISize()>1) {
1126             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1127             escriptDataC _in2 = temp.getDataC();
1128             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1129          } else {
1130             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1131          }
1132          break;
1133          case(Points):
1134          if (getMPISize()>1) {
1135             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1136             escriptDataC _in2 = temp.getDataC();
1137             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1138          } else {
1139             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1140          }
1141          break;
1142          case(ContactElementsZero):
1143          case(ContactElementsOne):
1144          case(ReducedContactElementsZero):
1145          case(ReducedContactElementsOne):
1146          if (getMPISize()>1) {
1147             escript::Data temp=escript::Data( in,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1148             escriptDataC _in2 = temp.getDataC();
1149             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1150          } else {
1151             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1152          }
1153          break;
1154          default:
1155             stringstream temp;
1156             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1157             throw FinleyAdapterException(temp.str());
1158             break;
1159          }
1160          break;
1161       default:
1162          stringstream temp;
1163          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1164          throw FinleyAdapterException(temp.str());
1165          break;
1166       }
1167       checkFinleyError();
1168  }  }
1169    
1170  //  //
# Line 505  void MeshAdapter::interpolateOnDomain(es Line 1172  void MeshAdapter::interpolateOnDomain(es
1172  //  //
1173  void MeshAdapter::setToX(escript::Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1174  {  {
1175    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1176    if (argDomain!=*this)     if (argDomain!=*this)
1177       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1178    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1179    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1180    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1181       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1182    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1183       escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1184       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);
1185       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1186       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1187    }        // this is then interpolated onto arg:
1188    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1189       }
1190       checkFinleyError();
1191  }  }
1192    
1193  //  //
# Line 526  void MeshAdapter::setToX(escript::Data& Line 1195  void MeshAdapter::setToX(escript::Data&
1195  //  //
1196  void MeshAdapter::setToNormal(escript::Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1197  {  {
1198    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1199    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1200       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1201    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1202    switch(normal.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1203      case(Nodes):     escriptDataC _normal=normal.getDataC();
1204        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");     switch(normal.getFunctionSpace().getTypeCode()) {
1205        break;     case(Nodes):
1206      case(Elements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1207        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");     break;
1208        break;     case(ReducedNodes):
1209      case (FaceElements):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1210        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     break;
1211        break;     case(Elements):
1212      case(Points):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1213        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");     break;
1214        break;     case(ReducedElements):
1215      case (ContactElementsOne):     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1216      case (ContactElementsZero):     break;
1217        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (FaceElements):
1218        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1219      case(DegreesOfFreedom):     break;
1220        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");     case (ReducedFaceElements):
1221        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1222      case(ReducedDegreesOfFreedom):     break;
1223        throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");     case(Points):
1224        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1225      default:     break;
1226       case (ContactElementsOne):
1227       case (ContactElementsZero):
1228       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1229       break;
1230       case (ReducedContactElementsOne):
1231       case (ReducedContactElementsZero):
1232       Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1233       break;
1234       case(DegreesOfFreedom):
1235       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1236       break;
1237       case(ReducedDegreesOfFreedom):
1238       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1239       break;
1240       default:
1241        stringstream temp;        stringstream temp;
1242        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();
1243        throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
1244        break;        break;
1245    }     }
1246    checkFinleyError();     checkFinleyError();
1247  }  }
1248    
1249  //  //
# Line 567  void MeshAdapter::setToNormal(escript::D Line 1251  void MeshAdapter::setToNormal(escript::D
1251  //  //
1252  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1253  {  {
1254    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1255    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1256       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1257          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1258    
1259    throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
1260  }  }
1261    
1262  //  //
1263  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined of arg:
1264  //  //
1265  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const  void MeshAdapter::setToIntegrals(vector<double>& integrals,const escript::Data& arg) const
1266  {  {
1267    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1268    if (argDomain!=*this)     if (argDomain!=*this)
1269       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1270    
1271    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1272    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1273       case(Nodes):     escriptDataC _temp;
1274          throw FinleyAdapterException("Error - Integral of data on nodes is not supported.");     escript::Data temp;
1275          break;     escriptDataC _arg=arg.getDataC();
1276       case(Elements):     switch(arg.getFunctionSpace().getTypeCode()) {
1277          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     case(Nodes):
1278          break;     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1279       case(FaceElements):     _temp=temp.getDataC();
1280          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1281          break;     break;
1282       case(Points):     case(ReducedNodes):
1283          throw FinleyAdapterException("Error - Integral of data on points is not supported.");     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1284          break;     _temp=temp.getDataC();
1285       case(ContactElementsZero):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1286          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1287          break;     case(Elements):
1288       case(ContactElementsOne):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1289          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     break;
1290          break;     case(ReducedElements):
1291       case(DegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1292          throw FinleyAdapterException("Error - Integral of data on degrees of freedom is not supported.");     break;
1293          break;     case(FaceElements):
1294       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1295          throw FinleyAdapterException("Error - Integral of data on reduced degrees of freedom is not supported.");     break;
1296          break;     case(ReducedFaceElements):
1297       default:     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1298          stringstream temp;     break;
1299          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     case(Points):
1300          throw FinleyAdapterException(temp.str());     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1301          break;     break;
1302    }     case(ContactElementsZero):
1303    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1304       break;
1305       case(ReducedContactElementsZero):
1306       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1307       break;
1308       case(ContactElementsOne):
1309       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1310       break;
1311       case(ReducedContactElementsOne):
1312       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1313       break;
1314       case(DegreesOfFreedom):
1315       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1316       _temp=temp.getDataC();
1317       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1318       break;
1319       case(ReducedDegreesOfFreedom):
1320       temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1321       _temp=temp.getDataC();
1322       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1323       break;
1324       default:
1325          stringstream temp;
1326          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1327          throw FinleyAdapterException(temp.str());
1328          break;
1329       }
1330       checkFinleyError();
1331       blocktimer_increment("integrate()", blocktimer_start);
1332  }  }
1333    
1334  //  //
# Line 623  void MeshAdapter::setToIntegrals(std::ve Line 1336  void MeshAdapter::setToIntegrals(std::ve
1336  //  //
1337  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1338  {  {
1339    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1340    if (argDomain!=*this)     if (argDomain!=*this)
1341      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1342    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1343    if (gradDomain!=*this)     if (gradDomain!=*this)
1344       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1345    
1346    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1347    escriptDataC nodeDataC;     escriptDataC _grad=grad.getDataC();
1348  #ifdef PASO_MPI     escriptDataC nodeDataC;
1349    escript::Data nodeTemp( arg, continuousFunction(asAbstractContinuousDomain()) );     escript::Data temp;
1350    if( arg.getFunctionSpace().getTypeCode() != Nodes )     if (getMPISize()>1) {
1351    {        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1352      Finley_Assemble_CopyNodalData(mesh->Nodes,&(nodeTemp.getDataC()),&(arg.getDataC()));           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1353      nodeDataC = nodeTemp.getDataC();           nodeDataC = temp.getDataC();
1354    }        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1355    else           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1356      nodeDataC = arg.getDataC();           nodeDataC = temp.getDataC();
1357  #else        } else {
1358    nodeDataC = arg.getDataC();           nodeDataC = arg.getDataC();
1359  #endif        }
1360    switch(grad.getFunctionSpace().getTypeCode()) {     } else {
1361         case(Nodes):        nodeDataC = arg.getDataC();
1362            throw FinleyAdapterException("Error - Gradient at nodes is not supported.");     }
1363            break;     switch(grad.getFunctionSpace().getTypeCode()) {
1364         case(Elements):     case(Nodes):
1365            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&nodeDataC);     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1366            break;     break;
1367         case(FaceElements):     case(ReducedNodes):
1368            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&nodeDataC);     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1369            break;     break;
1370         case(Points):     case(Elements):
1371            throw FinleyAdapterException("Error - Gradient at points is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1372            break;     break;
1373         case(ContactElementsZero):     case(ReducedElements):
1374            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1375            break;     break;
1376         case(ContactElementsOne):     case(FaceElements):
1377            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&nodeDataC);     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1378            break;     break;
1379         case(DegreesOfFreedom):     case(ReducedFaceElements):
1380            throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1381            break;     break;
1382         case(ReducedDegreesOfFreedom):     case(Points):
1383            throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");     throw FinleyAdapterException("Error - Gradient at points is not supported.");
1384            break;     break;
1385         default:     case(ContactElementsZero):
1386            stringstream temp;     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1387            temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();     break;
1388            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1389            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1390    }     break;
1391    checkFinleyError();     case(ContactElementsOne):
1392       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1393       break;
1394       case(ReducedContactElementsOne):
1395       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1396       break;
1397       case(DegreesOfFreedom):
1398       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1399       break;
1400       case(ReducedDegreesOfFreedom):
1401       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1402       break;
1403       default:
1404          stringstream temp;
1405          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1406          throw FinleyAdapterException(temp.str());
1407          break;
1408       }
1409       checkFinleyError();
1410  }  }
1411    
1412  //  //
# Line 683  void MeshAdapter::setToGradient(escript: Line 1414  void MeshAdapter::setToGradient(escript:
1414  //  //
1415  void MeshAdapter::setToSize(escript::Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1416  {  {
1417    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1418    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1419    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1420         case(Nodes):     case(Nodes):
1421            throw FinleyAdapterException("Error - Size of nodes is not supported.");     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1422            break;     break;
1423         case(Elements):     case(ReducedNodes):
1424            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1425            break;     break;
1426         case(FaceElements):     case(Elements):
1427            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1428            break;     break;
1429         case(Points):     case(ReducedElements):
1430            throw FinleyAdapterException("Error - Size of point elements is not supported.");     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1431            break;     break;
1432         case(ContactElementsZero):     case(FaceElements):
1433         case(ContactElementsOne):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1434            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     break;
1435            break;     case(ReducedFaceElements):
1436         case(DegreesOfFreedom):     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1437            throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");     break;
1438            break;     case(Points):
1439         case(ReducedDegreesOfFreedom):     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1440            throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");     break;
1441            break;     case(ContactElementsZero):
1442         default:     case(ContactElementsOne):
1443            stringstream temp;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1444            temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();     break;
1445            throw FinleyAdapterException(temp.str());     case(ReducedContactElementsZero):
1446            break;     case(ReducedContactElementsOne):
1447    }     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1448    checkFinleyError();     break;
1449       case(DegreesOfFreedom):
1450       throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1451       break;
1452       case(ReducedDegreesOfFreedom):
1453       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1454       break;
1455       default:
1456          stringstream temp;
1457          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1458          throw FinleyAdapterException(temp.str());
1459          break;
1460       }
1461       checkFinleyError();
1462  }  }
1463    
1464  // sets the location of nodes:  //
1465    // sets the location of nodes
1466    //
1467  void MeshAdapter::setNewX(const escript::Data& new_x)  void MeshAdapter::setNewX(const escript::Data& new_x)
1468  {  {
1469    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1470    escriptDataC tmp;     escriptDataC tmp;
1471    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1472    if (newDomain!=*this)     if (newDomain!=*this)
1473       throw FinleyAdapterException("Error - Illegal domain of new point locations");        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1474    tmp = new_x.getDataC();     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {
1475    Finley_Mesh_setCoordinates(mesh,&tmp);         tmp = new_x.getDataC();
1476    checkFinleyError();         Finley_Mesh_setCoordinates(mesh,&tmp);
1477  }     } else {
1478           escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );
1479  // saves a data array in openDX format:         tmp = new_x_inter.getDataC();
1480  void MeshAdapter::saveDX(const std::string& filename,const boost::python::dict& arg) const         Finley_Mesh_setCoordinates(mesh,&tmp);
1481  {     }
1482      int MAX_namelength=256;     checkFinleyError();
1483      const int num_data=boost::python::extract<int>(arg.attr("__len__")());  }
   /* win32 refactor */  
   char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
1484    
1485    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;  //
1486    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;  // Helper for the save* methods. Extracts optional data variable names and the
1487    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;  // corresponding pointers from python dictionary. Caller must free arrays.
1488    //
1489      boost::python::list keys=arg.keys();  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1490      for (int i=0;i<num_data;++i) {  {
1491           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     numData = boost::python::extract<int>(arg.attr("__len__")());
1492           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     /* win32 refactor */
1493               throw FinleyAdapterException("Error  in saveDX: Data must be defined on same Domain");     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1494           data[i]=d.getDataC();     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1495           ptr_data[i]=&(data[i]);     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1496           std::string n=boost::python::extract<std::string>(keys[i]);  
1497           c_names[i]=&(names[i][0]);     boost::python::list keys=arg.keys();
1498           if (n.length()>MAX_namelength-1) {     for (int i=0; i<numData; ++i) {
1499              strncpy(c_names[i],n.c_str(),MAX_namelength-1);        string n=boost::python::extract<string>(keys[i]);
1500              c_names[i][MAX_namelength-1]='\0';        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1501           } else {        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1502              strcpy(c_names[i],n.c_str());           throw FinleyAdapterException("Error: Data must be defined on same Domain");
1503           }        data[i] = d.getDataC();
1504      }        dataPtr[i] = &(data[i]);
1505      Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);        names[i] = TMPMEMALLOC(n.length()+1, char);
1506      checkFinleyError();        strcpy(names[i], n.c_str());
1507           }
1508        /* win32 refactor */  }
1509    TMPMEMFREE(c_names);  
1510    TMPMEMFREE(data);  //
1511    TMPMEMFREE(ptr_data);  // saves mesh and optionally data arrays in openDX format
1512    for(int i=0;i<num_data;i++)  //
1513    {  void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1514      TMPMEMFREE(names[i]);  {
1515    }     int num_data;
1516    TMPMEMFREE(names);     char **names;
1517       escriptDataC *data;
1518       escriptDataC **ptr_data;
1519    
1520      return;     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1521       Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1522       checkFinleyError();
1523    
1524       /* win32 refactor */
1525       TMPMEMFREE(data);
1526       TMPMEMFREE(ptr_data);
1527       for(int i=0; i<num_data; i++)
1528       {
1529          TMPMEMFREE(names[i]);
1530       }
1531       TMPMEMFREE(names);
1532    
1533       return;
1534  }  }
1535    
1536  // saves a data array in openVTK format:  //
1537  void MeshAdapter::saveVTK(const std::string& filename,const boost::python::dict& arg) const  // saves mesh and optionally data arrays in VTK format
1538    //
1539    void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1540  {  {
1541      int MAX_namelength=256;     int num_data;
1542      const int num_data=boost::python::extract<int>(arg.attr("__len__")());     char **names;
1543    /* win32 refactor */     escriptDataC *data;
1544    char* *names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     escriptDataC **ptr_data;
   for(int i=0;i<num_data;i++)  
   {  
     names[i] = (MAX_namelength>0) ? TMPMEMALLOC(MAX_namelength,char) : (char*)NULL;  
   }  
1545    
1546    char* *c_names = (num_data>0) ? TMPMEMALLOC(num_data,char*) : (char**)NULL;     extractArgsFromDict(arg, num_data, names, data, ptr_data);
1547    escriptDataC *data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC) : (escriptDataC*)NULL;     Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data, metadata.c_str(), metadata_schema.c_str());
1548    escriptDataC* *ptr_data = (num_data>0) ? TMPMEMALLOC(num_data,escriptDataC*) : (escriptDataC**)NULL;     checkFinleyError();
1549    
1550      boost::python::list keys=arg.keys();     /* win32 refactor */
1551      for (int i=0;i<num_data;++i) {     TMPMEMFREE(data);
1552           escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);     TMPMEMFREE(ptr_data);
1553           if (dynamic_cast<const MeshAdapter&>(d.getFunctionSpace().getDomain()) !=*this)     for(int i=0; i<num_data; i++)
1554               throw FinleyAdapterException("Error  in saveVTK: Data must be defined on same Domain");     {
1555           data[i]=d.getDataC();        TMPMEMFREE(names[i]);
1556           ptr_data[i]=&(data[i]);     }
1557           std::string n=boost::python::extract<std::string>(keys[i]);     TMPMEMFREE(names);
1558           c_names[i]=&(names[i][0]);  }
1559           if (n.length()>MAX_namelength-1) {  
1560              strncpy(c_names[i],n.c_str(),MAX_namelength-1);  bool MeshAdapter::ownSample(int fs_code, index_t id) const
1561              c_names[i][MAX_namelength-1]='\0';  {
1562           } else {  #ifdef PASO_MPI
1563              strcpy(c_names[i],n.c_str());      index_t myFirstNode=0, myLastNode=0, k=0;
1564           }      index_t* globalNodeIndex=0;
1565        Finley_Mesh* mesh_p=m_finleyMesh.get();
1566        if (fs_code == FINLEY_REDUCED_NODES)
1567        {
1568        myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1569        myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1570        globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1571      }      }
1572  #ifndef PASO_MPI          else
1573      Finley_Mesh_saveVTK(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);      {
1574  #else      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1575      Finley_Mesh_saveVTK_MPIO(filename.c_str(),m_finleyMesh.get(),num_data,c_names,ptr_data);      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1576        globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
1577        }
1578        k=globalNodeIndex[id];
1579        return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1580  #endif  #endif
1581        return true;
1582    }
1583    
 checkFinleyError();  
   /* win32 refactor */  
   TMPMEMFREE(c_names);  
   TMPMEMFREE(data);  
   TMPMEMFREE(ptr_data);  
   for(int i=0;i<num_data;i++)  
   {  
     TMPMEMFREE(names[i]);  
   }  
   TMPMEMFREE(names);  
1584    
1585      return;  
1586  }  //
1587                                                                                                                                                                            // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1588                                                                                                                                                                            //
 // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  
1589  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1590                        const int row_blocksize,                                                   const int row_blocksize,
1591                        const escript::FunctionSpace& row_functionspace,                                                   const escript::FunctionSpace& row_functionspace,
1592                        const int column_blocksize,                                                   const int column_blocksize,
1593                        const escript::FunctionSpace& column_functionspace,                                                   const escript::FunctionSpace& column_functionspace,
1594                        const int type) const                                                   const int type) const
1595  {  {
1596      int reduceRowOrder=0;     int reduceRowOrder=0;
1597      int reduceColOrder=0;     int reduceColOrder=0;
1598      // is the domain right?     // is the domain right?
1599      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1600      if (row_domain!=*this)     if (row_domain!=*this)
1601            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");        throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1602      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1603      if (col_domain!=*this)     if (col_domain!=*this)
1604            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");        throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1605      // is the function space type right     // is the function space type right
1606      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {     if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1607          reduceRowOrder=0;        reduceRowOrder=0;
1608      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1609          reduceRowOrder=1;        reduceRowOrder=1;
1610      } else {     } else {
1611          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1612      }     }
1613      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {     if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1614          reduceColOrder=0;        reduceColOrder=0;
1615      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {     } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1616          reduceColOrder=1;        reduceColOrder=1;
1617      } else {     } else {
1618          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");        throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1619      }     }
1620      // generate matrix:     // generate matrix:
1621        
1622      Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);     Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1623      checkFinleyError();     checkFinleyError();
1624      Paso_SystemMatrix* fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);     Paso_SystemMatrix* fsystemMatrix;
1625      checkPasoError();     int trilinos = 0;
1626      Paso_SystemMatrixPattern_dealloc(fsystemMatrixPattern);     if (trilinos) {
1627      return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  #ifdef TRILINOS
1628          /* Allocation Epetra_VrbMatrix here */
1629    #endif
1630       }
1631       else {
1632          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1633       }
1634       checkPasoError();
1635       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1636       return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1637    }
1638    
1639    //
1640    // creates a TransportProblemAdapter
1641    //
1642    TransportProblemAdapter MeshAdapter::newTransportProblem(
1643                                                             const bool useBackwardEuler,
1644                                                             const int blocksize,
1645                                                             const escript::FunctionSpace& functionspace,
1646                                                             const int type) const
1647    {
1648       int reduceOrder=0;
1649       // is the domain right?
1650       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1651       if (domain!=*this)
1652          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1653       // is the function space type right
1654       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1655          reduceOrder=0;
1656       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1657          reduceOrder=1;
1658       } else {
1659          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1660       }
1661       // generate matrix:
1662    
1663       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1664       checkFinleyError();
1665       Paso_TransportProblem* transportProblem;
1666       transportProblem=Paso_TransportProblem_alloc(useBackwardEuler,fsystemMatrixPattern,blocksize);
1667       checkPasoError();
1668       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1669       return TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1670  }  }
1671    
1672  //  //
# Line 882  SystemMatrixAdapter MeshAdapter::newSyst Line 1678  SystemMatrixAdapter MeshAdapter::newSyst
1678  // 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:
1679  bool MeshAdapter::isCellOriented(int functionSpaceCode) const  bool MeshAdapter::isCellOriented(int functionSpaceCode) const
1680  {  {
1681    switch(functionSpaceCode) {     switch(functionSpaceCode) {
1682         case(Nodes):     case(Nodes):
1683         case(DegreesOfFreedom):     case(DegreesOfFreedom):
1684         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
1685            return false;     return false;
1686            break;     break;
1687         case(Elements):     case(Elements):
1688         case(FaceElements):     case(FaceElements):
1689         case(Points):     case(Points):
1690         case(ContactElementsZero):     case(ContactElementsZero):
1691         case(ContactElementsOne):     case(ContactElementsOne):
1692            return true;     case(ReducedElements):
1693            break;     case(ReducedFaceElements):
1694         default:     case(ReducedContactElementsZero):
1695            stringstream temp;     case(ReducedContactElementsOne):
1696            temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;     return true;
1697            throw FinleyAdapterException(temp.str());     break;
1698            break;     default:
1699    }        stringstream temp;
1700    checkFinleyError();        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1701    return false;        throw FinleyAdapterException(temp.str());
1702          break;
1703       }
1704       checkFinleyError();
1705       return false;
1706    }
1707    
1708    bool
1709    MeshAdapter::commonFunctionSpace(const vector<int>& fs, int& resultcode) const
1710    {
1711       /* The idea is to use equivalence classes. [Types which can be interpolated back and forth]
1712        class 1: DOF <-> Nodes
1713        class 2: ReducedDOF <-> ReducedNodes
1714        class 3: Points
1715        class 4: Elements
1716        class 5: ReducedElements
1717        class 6: FaceElements
1718        class 7: ReducedFaceElements
1719        class 8: ContactElementZero <-> ContactElementOne
1720        class 9: ReducedContactElementZero <-> ReducedContactElementOne
1721    
1722       There is also a set of lines. Interpolation is possible down a line but not between lines.
1723       class 1 and 2 belong to all lines so aren't considered.
1724        line 0: class 3
1725        line 1: class 4,5
1726        line 2: class 6,7
1727        line 3: class 8,9
1728    
1729       For classes with multiple members (eg class 2) we have vars to record if there is at least one instance.
1730       eg hasnodes is true if we have at least one instance of Nodes.
1731       */
1732        if (fs.empty())
1733        {
1734            return false;
1735        }
1736        vector<int> hasclass(10);
1737        vector<int> hasline(4);
1738        bool hasnodes=false;
1739        bool hasrednodes=false;
1740        bool hascez=false;
1741        bool hasrcez=false;
1742        for (int i=0;i<fs.size();++i)
1743        {
1744        switch(fs[i])
1745        {
1746        case(Nodes):   hasnodes=true;   // no break is deliberate
1747        case(DegreesOfFreedom):
1748            hasclass[1]=1;
1749            break;
1750        case(ReducedNodes):    hasrednodes=true;    // no break is deliberate
1751        case(ReducedDegreesOfFreedom):
1752            hasclass[2]=1;
1753            break;
1754        case(Points):
1755            hasline[0]=1;
1756            hasclass[3]=1;
1757            break;
1758        case(Elements):
1759            hasclass[4]=1;
1760            hasline[1]=1;
1761            break;
1762        case(ReducedElements):
1763            hasclass[5]=1;
1764            hasline[1]=1;
1765            break;
1766        case(FaceElements):
1767            hasclass[6]=1;
1768            hasline[2]=1;
1769            break;
1770        case(ReducedFaceElements):
1771            hasclass[7]=1;
1772            hasline[2]=1;
1773            break;
1774        case(ContactElementsZero):  hascez=true;    // no break is deliberate
1775        case(ContactElementsOne):
1776            hasclass[8]=1;
1777            hasline[3]=1;
1778            break;
1779        case(ReducedContactElementsZero):   hasrcez=true;   // no break is deliberate
1780        case(ReducedContactElementsOne):
1781            hasclass[9]=1;
1782            hasline[3]=1;
1783            break;
1784        default:
1785            return false;
1786        }
1787        }
1788        int totlines=hasline[0]+hasline[1]+hasline[2]+hasline[3];
1789        // fail if we have more than one leaf group
1790    
1791        if (totlines>1)
1792        {
1793        return false;   // there are at least two branches we can't interpolate between
1794        }
1795        else if (totlines==1)
1796        {
1797        if (hasline[0]==1)      // we have points
1798        {
1799            resultcode=Points;
1800        }
1801        else if (hasline[1]==1)
1802        {
1803            if (hasclass[5]==1)
1804            {
1805            resultcode=ReducedElements;
1806            }
1807            else
1808            {
1809            resultcode=Elements;
1810            }
1811        }
1812        else if (hasline[2]==1)
1813        {
1814            if (hasclass[7]==1)
1815            {
1816            resultcode=ReducedFaceElements;
1817            }
1818            else
1819            {
1820            resultcode=FaceElements;
1821            }
1822        }
1823        else    // so we must be in line3
1824        {
1825            if (hasclass[9]==1)
1826            {
1827            // need something from class 9
1828            resultcode=(hasrcez?ReducedContactElementsZero:ReducedContactElementsOne);
1829            }
1830            else
1831            {
1832            // something from class 8
1833            resultcode=(hascez?ContactElementsZero:ContactElementsOne);
1834            }
1835        }
1836        }
1837        else    // totlines==0
1838        {
1839        if (hasclass[2]==1)
1840        {
1841            // something from class 2
1842            resultcode=(hasrednodes?ReducedNodes:ReducedDegreesOfFreedom);
1843        }
1844        else
1845        {   // something from class 1
1846            resultcode=(hasnodes?Nodes:DegreesOfFreedom);
1847        }
1848        }
1849        return true;
1850  }  }
1851    
1852  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const  bool MeshAdapter::probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const
1853  {  {
1854    switch(functionSpaceType_source) {     switch(functionSpaceType_source) {
1855       case(Nodes):     case(Nodes):
1856          switch(functionSpaceType_target) {      switch(functionSpaceType_target) {
1857             case(Nodes):      case(Nodes):
1858             case(ReducedDegreesOfFreedom):      case(ReducedNodes):
1859             case(DegreesOfFreedom):      case(ReducedDegreesOfFreedom):
1860             case(Elements):      case(DegreesOfFreedom):
1861             case(FaceElements):      case(Elements):
1862             case(Points):      case(ReducedElements):
1863             case(ContactElementsZero):      case(FaceElements):
1864             case(ContactElementsOne):      case(ReducedFaceElements):
1865                 return true;      case(Points):
1866             default:      case(ContactElementsZero):
1867                 stringstream temp;      case(ReducedContactElementsZero):
1868                 temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      case(ContactElementsOne):
1869                 throw FinleyAdapterException(temp.str());      case(ReducedContactElementsOne):
1870          }      return true;
1871          break;      default:
1872       case(Elements):            stringstream temp;
1873          if (functionSpaceType_target==Elements) {            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1874             return true;            throw FinleyAdapterException(temp.str());
1875          } else {     }
1876             return false;     break;
1877          }     case(ReducedNodes):
1878       case(FaceElements):      switch(functionSpaceType_target) {
1879          if (functionSpaceType_target==FaceElements) {      case(ReducedNodes):
1880             return true;      case(ReducedDegreesOfFreedom):
1881        case(Elements):
1882        case(ReducedElements):
1883        case(FaceElements):
1884        case(ReducedFaceElements):
1885        case(Points):
1886        case(ContactElementsZero):
1887        case(ReducedContactElementsZero):
1888        case(ContactElementsOne):
1889        case(ReducedContactElementsOne):
1890        return true;
1891        case(Nodes):
1892        case(DegreesOfFreedom):
1893        return false;
1894        default:
1895            stringstream temp;
1896            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1897            throw FinleyAdapterException(temp.str());
1898       }
1899       break;
1900       case(Elements):
1901        if (functionSpaceType_target==Elements) {
1902          return true;
1903        } else if (functionSpaceType_target==ReducedElements) {
1904          return true;
1905          } else {          } else {
1906             return false;            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());  
1907          }          }
1908          break;     case(ReducedElements):
1909       case(ReducedDegreesOfFreedom):      if (functionSpaceType_target==ReducedElements) {
1910         switch(functionSpaceType_target) {        return true;
1911            case(ReducedDegreesOfFreedom):      } else {
1912            case(Elements):            return false;
1913            case(FaceElements):      }
1914            case(Points):     case(FaceElements):
1915            case(ContactElementsZero):      if (functionSpaceType_target==FaceElements) {
1916            case(ContactElementsOne):              return true;
1917                return true;      } else if (functionSpaceType_target==ReducedFaceElements) {
1918            case(Nodes):              return true;
1919            case(DegreesOfFreedom):      } else {
1920               return false;              return false;
1921            default:      }
1922               stringstream temp;     case(ReducedFaceElements):
1923               temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;      if (functionSpaceType_target==ReducedFaceElements) {
1924               throw FinleyAdapterException(temp.str());              return true;
1925         }      } else {
1926         break;          return false;
1927       default:      }
1928          stringstream temp;     case(Points):
1929          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;      if (functionSpaceType_target==Points) {
1930          throw FinleyAdapterException(temp.str());              return true;
1931          break;      } else {
1932    }              return false;
1933    checkFinleyError();      }
1934    return false;     case(ContactElementsZero):
1935       case(ContactElementsOne):
1936        if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {
1937                return true;
1938        } else if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1939                return true;
1940        } else {
1941                return false;
1942        }
1943       case(ReducedContactElementsZero):
1944       case(ReducedContactElementsOne):
1945        if (functionSpaceType_target==ReducedContactElementsZero || functionSpaceType_target==ReducedContactElementsOne) {
1946                return true;
1947        } else {
1948                return false;
1949        }
1950       case(DegreesOfFreedom):
1951        switch(functionSpaceType_target) {
1952        case(ReducedDegreesOfFreedom):
1953        case(DegreesOfFreedom):
1954        case(Nodes):
1955        case(ReducedNodes):
1956        case(Elements):
1957        case(ReducedElements):
1958        case(Points):
1959        case(FaceElements):
1960        case(ReducedFaceElements):
1961        case(ContactElementsZero):
1962        case(ReducedContactElementsZero):
1963        case(ContactElementsOne):
1964        case(ReducedContactElementsOne):
1965        return true;
1966        default:
1967            stringstream temp;
1968            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1969            throw FinleyAdapterException(temp.str());
1970        }
1971        break;
1972       case(ReducedDegreesOfFreedom):
1973       switch(functionSpaceType_target) {
1974        case(ReducedDegreesOfFreedom):
1975        case(ReducedNodes):
1976        case(Elements):
1977        case(ReducedElements):
1978        case(FaceElements):
1979        case(ReducedFaceElements):
1980        case(Points):
1981        case(ContactElementsZero):
1982        case(ReducedContactElementsZero):
1983        case(ContactElementsOne):
1984        case(ReducedContactElementsOne):
1985        return true;
1986        case(Nodes):
1987        case(DegreesOfFreedom):
1988        return false;
1989        default:
1990            stringstream temp;
1991            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1992            throw FinleyAdapterException(temp.str());
1993        }
1994        break;
1995       default:
1996          stringstream temp;
1997          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_source;
1998          throw FinleyAdapterException(temp.str());
1999          break;
2000       }
2001       checkFinleyError();
2002       return false;
2003  }  }
2004    
2005  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
2006  {  {
2007      return false;     return false;
2008  }  }
2009    
2010  bool MeshAdapter::operator==(const AbstractDomain& other) const  bool MeshAdapter::operator==(const AbstractDomain& other) const
2011  {  {
2012    const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
2013    if (temp!=0) {     if (temp!=0) {
2014      return (m_finleyMesh==temp->m_finleyMesh);        return (m_finleyMesh==temp->m_finleyMesh);
2015    } else {     } else {
2016      return false;        return false;
2017    }     }
2018  }  }
2019    
2020  bool MeshAdapter::operator!=(const AbstractDomain& other) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
2021  {  {
2022    return !(operator==(other));     return !(operator==(other));
2023  }  }
2024    
2025  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
2026    {
2027       Finley_Mesh* mesh=m_finleyMesh.get();
2028       int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2029       checkPasoError();
2030       return out;
2031    }
2032    int MeshAdapter::getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const
2033  {  {
2034     int out=Paso_SystemMatrix_getSystemMatrixTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0);     Finley_Mesh* mesh=m_finleyMesh.get();
2035       int out=Paso_TransportProblem_getTypeId(SystemMatrixAdapter::mapOptionToPaso(solver),SystemMatrixAdapter::mapOptionToPaso(preconditioner), SystemMatrixAdapter::mapOptionToPaso(package),symmetry?1:0, mesh->MPIInfo);
2036     checkPasoError();     checkPasoError();
2037     return out;     return out;
2038  }  }
2039    
2040  escript::Data MeshAdapter::getX() const  escript::Data MeshAdapter::getX() const
2041  {  {
2042    return continuousFunction(asAbstractContinuousDomain()).getX();     return continuousFunction(asAbstractContinuousDomain()).getX();
2043  }  }
2044    
2045  escript::Data MeshAdapter::getNormal() const  escript::Data MeshAdapter::getNormal() const
2046  {  {
2047    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
2048  }  }
2049    
2050  escript::Data MeshAdapter::getSize() const  escript::Data MeshAdapter::getSize() const
2051  {  {
2052    return function(asAbstractContinuousDomain()).getSize();     return escript::function(asAbstractContinuousDomain()).getSize();
2053  }  }
2054    
2055  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2056  {  {
2057    int out=0;     int *out = NULL;
2058    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2059    switch (functionSpaceType) {     switch (functionSpaceType) {
2060    case(Nodes):     case(Nodes):
2061      out=mesh->Nodes->Tag[sampleNo];     out=mesh->Nodes->Id;
2062      break;     break;
2063    case(Elements):     case(ReducedNodes):
2064      out=mesh->Elements->Tag[sampleNo];     out=mesh->Nodes->reducedNodesId;
2065      break;     break;
2066    case(FaceElements):     case(Elements):
2067      out=mesh->FaceElements->Tag[sampleNo];     out=mesh->Elements->Id;
2068      break;     break;
2069    case(Points):     case(ReducedElements):
2070      out=mesh->Points->Tag[sampleNo];     out=mesh->Elements->Id;
2071      break;     break;
2072    case(ContactElementsZero):     case(FaceElements):
2073      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->FaceElements->Id;
2074      break;     break;
2075    case(ContactElementsOne):     case(ReducedFaceElements):
2076      out=mesh->ContactElements->Tag[sampleNo];     out=mesh->FaceElements->Id;
2077      break;     break;
2078    case(DegreesOfFreedom):     case(Points):
2079      break;     out=mesh->Points->Id;
2080    case(ReducedDegreesOfFreedom):     break;
2081      break;     case(ContactElementsZero):
2082    default:     out=mesh->ContactElements->Id;
2083      stringstream temp;     break;
2084      temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();     case(ReducedContactElementsZero):
2085      throw FinleyAdapterException(temp.str());     out=mesh->ContactElements->Id;
2086      break;     break;
2087    }     case(ContactElementsOne):
2088    return out;     out=mesh->ContactElements->Id;
2089       break;
2090       case(ReducedContactElementsOne):
2091       out=mesh->ContactElements->Id;
2092       break;
2093       case(DegreesOfFreedom):
2094       out=mesh->Nodes->degreesOfFreedomId;
2095       break;
2096       case(ReducedDegreesOfFreedom):
2097       out=mesh->Nodes->reducedDegreesOfFreedomId;
2098       break;
2099       default:
2100          stringstream temp;
2101          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2102          throw FinleyAdapterException(temp.str());
2103          break;
2104       }
2105       return out;
2106  }  }
2107  int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2108  {  {
2109    int *out=0,i;     int out=0;
2110    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
2111    switch (functionSpaceType) {     switch (functionSpaceType) {
2112    case(Nodes):     case(Nodes):
2113      if (mesh->Nodes!=NULL) {     out=mesh->Nodes->Tag[sampleNo];
2114        out=mesh->Nodes->Id;     break;
2115       case(ReducedNodes):
2116       throw FinleyAdapterException(" Error - ReducedNodes does not support tags.");
2117       break;
2118       case(Elements):
2119       out=mesh->Elements->Tag[sampleNo];
2120       break;
2121       case(ReducedElements):
2122       out=mesh->Elements->Tag[sampleNo];
2123       break;
2124       case(FaceElements):
2125       out=mesh->FaceElements->Tag[sampleNo];
2126       break;
2127       case(ReducedFaceElements):
2128       out=mesh->FaceElements->Tag[sampleNo];
2129       break;
2130       case(Points):
2131       out=mesh->Points->Tag[sampleNo];
2132       break;
2133       case(ContactElementsZero):
2134       out=mesh->ContactElements->Tag[sampleNo];
2135       break;
2136       case(ReducedContactElementsZero):
2137       out=mesh->ContactElements->Tag[sampleNo];
2138       break;
2139       case(ContactElementsOne):
2140       out=mesh->ContactElements->Tag[sampleNo];
2141       break;
2142       case(ReducedContactElementsOne):
2143       out=mesh->ContactElements->Tag[sampleNo];
2144       break;
2145       case(DegreesOfFreedom):
2146       throw FinleyAdapterException(" Error - DegreesOfFreedom does not support tags.");
2147       break;
2148       case(ReducedDegreesOfFreedom):
2149       throw FinleyAdapterException(" Error - ReducedDegreesOfFreedom does not support tags.");
2150       break;
2151       default:
2152          stringstream temp;
2153          temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();
2154          throw FinleyAdapterException(temp.str());
2155        break;        break;
2156      }     }
2157    case(Elements):     return out;
     out=mesh->Elements->Id;  
     break;  
   case(FaceElements):  
     out=mesh->FaceElements->Id;  
     break;  
   case(Points):  
     out=mesh->Points->Id;  
     break;  
   case(ContactElementsZero):  
     out=mesh->ContactElements->Id;  
     break;  
   case(ContactElementsOne):  
     out=mesh->ContactElements->Id;  
     break;  
   case(DegreesOfFreedom):  
     out=mesh->Nodes->degreeOfFreedomId;  
     break;  
   case(ReducedDegreesOfFreedom):  
     out=mesh->Nodes->reducedDegreeOfFreedomId;  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: " << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
   }  
   return out;  
2158  }  }
2159    
2160    
2161  void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const  void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
2162  {  {
2163       Finley_Mesh* mesh=m_finleyMesh.get();
2164       escriptDataC tmp=mask.getDataC();
2165       switch(functionSpaceType) {
2166       case(Nodes):
2167       Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);
2168       break;
2169       case(ReducedNodes):
2170       throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2171       break;
2172       case(DegreesOfFreedom):
2173       throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2174       break;
2175       case(ReducedDegreesOfFreedom):
2176       throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2177       break;
2178       case(Elements):
2179       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2180       break;
2181       case(ReducedElements):
2182       Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);
2183       break;
2184       case(FaceElements):
2185       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2186       break;
2187       case(ReducedFaceElements):
2188       Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);
2189       break;
2190       case(Points):
2191       Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);
2192       break;
2193       case(ContactElementsZero):
2194       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2195       break;
2196       case(ReducedContactElementsZero):
2197       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2198       break;
2199       case(ContactElementsOne):
2200       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2201       break;
2202       case(ReducedContactElementsOne):
2203       Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);
2204       break;
2205       default:
2206          stringstream temp;
2207          temp << "Error - Finley does not know anything about function space type " << functionSpaceType;
2208          throw FinleyAdapterException(temp.str());
2209       }
2210       checkFinleyError();
2211       return;
2212    }
2213    
2214    void MeshAdapter::setTagMap(const string& name,  int tag)
2215    {
2216       Finley_Mesh* mesh=m_finleyMesh.get();
2217       Finley_Mesh_addTagMap(mesh, name.c_str(),tag);
2218       checkPasoError();
2219       // throwStandardException("MeshAdapter::set TagMap is not implemented.");
2220    }
2221    
2222    int MeshAdapter::getTag(const string& name) const
2223    {
2224       Finley_Mesh* mesh=m_finleyMesh.get();
2225       int tag=0;
2226       tag=Finley_Mesh_getTag(mesh, name.c_str());
2227       checkPasoError();
2228       // throwStandardException("MeshAdapter::getTag is not implemented.");
2229       return tag;
2230    }
2231    
2232    bool MeshAdapter::isValidTagName(const string& name) const
2233    {
2234       Finley_Mesh* mesh=m_finleyMesh.get();
2235       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2236    }
2237    
2238    string MeshAdapter::showTagNames() const
2239    {
2240       stringstream temp;
2241       Finley_Mesh* mesh=m_finleyMesh.get();
2242       Finley_TagMap* tag_map=mesh->TagMap;
2243       while (tag_map) {
2244          temp << tag_map->name;
2245          tag_map=tag_map->next;
2246          if (tag_map) temp << ", ";
2247       }
2248       return temp.str();
2249    }
2250    
2251    int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2252    {
2253    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2254    escriptDataC tmp=mask.getDataC();    dim_t numTags=0;
2255    switch(functionSpaceType) {    switch(functionSpaceCode) {
2256         case(Nodes):     case(Nodes):
2257            Finley_NodeFile_setTags(mesh->Nodes,newTag,&tmp);            numTags=mesh->Nodes->numTagsInUse;
2258              break;
2259       case(ReducedNodes):
2260              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2261            break;            break;
2262         case(DegreesOfFreedom):     case(DegreesOfFreedom):
2263            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2264            break;            break;
2265         case(ReducedDegreesOfFreedom):     case(ReducedDegreesOfFreedom):
2266            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2267            break;            break;
2268         case(Elements):     case(Elements):
2269            Finley_ElementFile_setTags(mesh->Elements,newTag,&tmp);     case(ReducedElements):
2270              numTags=mesh->Elements->numTagsInUse;
2271              break;
2272       case(FaceElements):
2273       case(ReducedFaceElements):
2274              numTags=mesh->FaceElements->numTagsInUse;
2275              break;
2276       case(Points):
2277              numTags=mesh->Points->numTagsInUse;
2278              break;
2279       case(ContactElementsZero):
2280       case(ReducedContactElementsZero):
2281       case(ContactElementsOne):
2282       case(ReducedContactElementsOne):
2283              numTags=mesh->ContactElements->numTagsInUse;
2284            break;            break;
2285         case(FaceElements):     default:
2286            Finley_ElementFile_setTags(mesh->FaceElements,newTag,&tmp);        stringstream temp;
2287          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2288          throw FinleyAdapterException(temp.str());
2289      }
2290      return numTags;
2291    }
2292    
2293    const int* MeshAdapter::borrowListOfTagsInUse(int functionSpaceCode) const
2294    {
2295      Finley_Mesh* mesh=m_finleyMesh.get();
2296      index_t* tags=NULL;
2297      switch(functionSpaceCode) {
2298       case(Nodes):
2299              tags=mesh->Nodes->tagsInUse;
2300              break;
2301       case(ReducedNodes):
2302              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2303            break;            break;
2304         case(Points):     case(DegreesOfFreedom):
2305            Finley_ElementFile_setTags(mesh->Points,newTag,&tmp);            throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2306            break;            break;
2307         case(ContactElementsZero):     case(ReducedDegreesOfFreedom):
2308            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);            throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2309            break;            break;
2310         case(ContactElementsOne):     case(Elements):
2311            Finley_ElementFile_setTags(mesh->ContactElements,newTag,&tmp);     case(ReducedElements):
2312              tags=mesh->Elements->tagsInUse;
2313              break;
2314       case(FaceElements):
2315       case(ReducedFaceElements):
2316              tags=mesh->FaceElements->tagsInUse;
2317              break;
2318       case(Points):
2319              tags=mesh->Points->tagsInUse;
2320              break;
2321       case(ContactElementsZero):
2322       case(ReducedContactElementsZero):
2323       case(ContactElementsOne):
2324       case(ReducedContactElementsOne):
2325              tags=mesh->ContactElements->tagsInUse;
2326            break;            break;
2327         default:     default:
2328            stringstream temp;        stringstream temp;
2329            temp << "Error - Finley does not know anything about function space type " << functionSpaceType;        temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2330            throw FinleyAdapterException(temp.str());        throw FinleyAdapterException(temp.str());
2331      }
2332      return tags;
2333    }
2334    
2335    
2336    bool MeshAdapter::canTag(int functionSpaceCode) const
2337    {
2338      switch(functionSpaceCode) {
2339       case(Nodes):
2340       case(Elements):
2341       case(ReducedElements):
2342       case(FaceElements):
2343       case(ReducedFaceElements):
2344       case(Points):
2345       case(ContactElementsZero):
2346       case(ReducedContactElementsZero):
2347       case(ContactElementsOne):
2348       case(ReducedContactElementsOne):
2349              return true;
2350       case(ReducedNodes):
2351       case(DegreesOfFreedom):
2352       case(ReducedDegreesOfFreedom):
2353          return false;
2354       default:
2355        return false;
2356    }    }
   checkFinleyError();  
   return;  
2357  }  }
2358    
2359  void MeshAdapter::setTagMap(const std::string& name,  int tag)  AbstractDomain::StatusType MeshAdapter::getStatus() const
2360  {  {
2361    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2362    Finley_Mesh_addTagMap(mesh, name.c_str(),tag);    return Finley_Mesh_getStatus(mesh);
   checkPasoError();  
   // throwStandardException("MeshAdapter::set TagMap is not implemented.");  
2363  }  }
2364    
2365  int MeshAdapter::getTag(const std::string& name) const  int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2366  {  {
2367      
2368    Finley_Mesh* mesh=m_finleyMesh.get();    Finley_Mesh* mesh=m_finleyMesh.get();
2369    int tag=0;    int order =-1;
2370    tag=Finley_Mesh_getTag(mesh, name.c_str());    switch(functionSpaceCode) {
2371    checkPasoError();     case(Nodes):
2372    // throwStandardException("MeshAdapter::getTag is not implemented.");     case(DegreesOfFreedom):
2373    return tag;            order=mesh->approximationOrder;
2374              break;
2375       case(ReducedNodes):
2376       case(ReducedDegreesOfFreedom):
2377              order=mesh->reducedApproximationOrder;
2378              break;
2379       case(Elements):
2380       case(FaceElements):
2381       case(Points):
2382       case(ContactElementsZero):
2383       case(ContactElementsOne):
2384              order=mesh->integrationOrder;
2385              break;
2386       case(ReducedElements):
2387       case(ReducedFaceElements):
2388       case(ReducedContactElementsZero):
2389       case(ReducedContactElementsOne):
2390              order=mesh->reducedIntegrationOrder;
2391              break;
2392       default:
2393          stringstream temp;
2394          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2395          throw FinleyAdapterException(temp.str());
2396      }
2397      return order;
2398  }  }
2399    
2400  bool MeshAdapter::isValidTagName(const std::string& name) const  ReferenceElementSetWrapper::ReferenceElementSetWrapper(ElementTypeId id, index_t order, index_t reducedOrder)
2401  {  {
2402    Finley_Mesh* mesh=m_finleyMesh.get();    m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
   return Finley_Mesh_isValidTagName(mesh,name.c_str());  
2403  }  }
2404    
2405  std::string MeshAdapter::showTagNames() const  ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2406  {  {
2407    stringstream temp;    Finley_ReferenceElementSet_dealloc(m_refSet);
   Finley_Mesh* mesh=m_finleyMesh.get();  
   Finley_TagMap* tag_map=mesh->TagMap;  
   while (tag_map) {  
      temp << tag_map->name;  
      tag_map=tag_map->next;  
      if (tag_map) temp << ", ";  
   }  
   return temp.str();  
2408  }  }
2409    
2410  }  // end of namespace  }  // end of namespace

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