/[escript]/branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp
ViewVC logotype

Diff of /branches/diaplayground/finley/src/CPPAdapter/MeshAdapter.cpp

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

trunk/esys2/finley/src/CPPAdapter/MeshAdapter.cpp revision 102 by jgs, Wed Dec 15 07:08:39 2004 UTC trunk/finley/src/CPPAdapter/MeshAdapter.cpp revision 2989 by gross, Thu Mar 18 01:45:55 2010 UTC
# Line 1  Line 1 
1  // $Id$  
2  /*  /*******************************************************
3   ******************************************************************************  *
4   *                                                                            *  * Copyright (c) 2003-2010 by University of Queensland
5   *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  * Earth Systems Science Computational Center (ESSCC)
6   *                                                                            *  * http://www.uq.edu.au/esscc
7   * This software is the property of ACcESS. No part of this code              *  *
8   * may be copied in any form or by any means without the expressed written    *  * Primary Business: Queensland, Australia
9   * consent of ACcESS.  Copying, use or modification of this software          *  * Licensed under the Open Software License version 3.0
10   * by any unauthorised person is illegal unless that person has a software    *  * http://www.opensource.org/licenses/osl-3.0.php
11   * license agreement with ACcESS.                                             *  *
12   *                                                                            *  *******************************************************/
13   ******************************************************************************  
14  */  
15    #include "MeshAdapter.h"
16    #include "escript/Data.h"
17    #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" {  extern "C" {
26  #include "finley/finleyC/Finley.h"  #include "esysUtils/blocktimer.h"
27  #include "finley/finleyC/Assemble.h"  }
 #include "finley/finleyC/Mesh.h"  
 #include "finley/finleyC/Finley.h"  
 #include "finley/finleyC/System.h"  
 }  
 #include "finley/CPPAdapter/SystemMatrixAdapter.h"  
 #include "finley/CPPAdapter/MeshAdapter.h"  
 #include "finley/CPPAdapter/FinleyError.h"  
 #include "finley/CPPAdapter/FinleyAdapterException.h"  
 #include "escript/Data/FunctionSpaceFactory.h"  
 #include "escript/Data/Data.h"  
 #include "escript/Data/DataArrayView.h"  
 #include "escript/Data/FunctionSpace.h"  
 #include "escript/Data/DataFactory.h"  
 #include <iostream>  
 #include <vector>  
 #include <sstream>  
28    
29  using namespace std;  using namespace std;
30  using namespace escript;  using namespace escript;
31    
32  namespace finley {  namespace finley {
33    
 struct null_deleter  
 {  
   void operator()(void const *ptr) const  
   {  
   }  
 };  
   
34  //  //
35  // define the statics  // define the static constants
36  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
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;
43  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
44    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
45  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
46  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
47    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
48  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
49    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
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  //  //
61  // The copy constructor should just increment the use count  // The copy constructor should just increment the use count
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];     char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
121    strcpy(fName,fileName.c_str());     strcpy(fName,fileName.c_str());
122    Finley_Mesh_write(m_finleyMesh.get(),fName);     Finley_Mesh_write(m_finleyMesh.get(),fName);
123    checkFinleyError();     checkFinleyError();
124       TMPMEMFREE(fName);
125    }
126    
127    void MeshAdapter::Print_Mesh_Info(const bool full) const
128    {
129       Finley_PrintMesh_Info(m_finleyMesh.get(), full);
130  }  }
131    
132  // void MeshAdapter::getTagList(int functionSpaceType,  void MeshAdapter::dump(const string& fileName) const
133  //                  int* numTags) const  {
134  // {  #ifdef USE_NETCDF
135  //   Finley_Mesh_tagList(m_finleyMesh.get(),functionSpaceType,tagList,numTags);     const NcDim* ncdims[12] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
136  //   return;     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(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
579    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
580      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
581    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
582      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
583    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
584      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
585       m_functionSpaceTypeNames.insert
586       (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
587       m_functionSpaceTypeNames.insert
588       (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
589       m_functionSpaceTypeNames.insert
590       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
591       m_functionSpaceTypeNames.insert
592       (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
611    {
612       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
620    {
621       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
629    {
630       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
638    {
639       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;
 }  
 int MeshAdapter::getDiracDeltaFunctionCode() const  
 {  
   return Points;  
650  }  }
651    
652  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getDiracDeltaFunctionCode() const
653  {  {
654    //     return Points;
   // It is assumed the sampleNo has been checked  
   // before calling this function.  
   int* tagList;  
   int numTags;  
   getTagList(functionSpaceType, &tagList, &numTags);  
   return tagList[sampleNo];  
655  }  }
656    
657  //  //
658  // returns a pointer to the tag list of samples of functionSpaceType  // return the spatial dimension of the Mesh:
659  //  //
660  void MeshAdapter::getTagList(int functionSpaceType, int** tagList,  int MeshAdapter::getDim() const
                  int* numTags) const  
661  {  {
662    *tagList=NULL;     Finley_Mesh* mesh=m_finleyMesh.get();
663    *numTags=0;     int numDim=Finley_Mesh_getDim(mesh);
664    Finley_Mesh* mesh=m_finleyMesh.get();     checkFinleyError();
665    switch (functionSpaceType) {     return numDim;
   case(Nodes):  
     if (mesh->Nodes!=NULL) {  
       *tagList=mesh->Nodes->Tag;  
       *numTags=mesh->Nodes->numNodes;  
     }  
     break;  
   case(Elements):  
     if (mesh->Elements!=NULL) {  
       *tagList=mesh->Elements->Tag;  
       *numTags=mesh->Elements->numElements;  
     }  
     break;  
   case(FaceElements):  
     if (mesh->FaceElements!=NULL) {  
       *tagList=mesh->FaceElements->Tag;  
       *numTags=mesh->FaceElements->numElements;  
     }  
     break;  
   case(Points):  
     if (mesh->Points!=NULL) {  
       *tagList=mesh->Points->Tag;  
       *numTags=mesh->Points->numElements;  
     }  
     break;  
   case(ContactElementsZero):  
     if (mesh->ContactElements!=NULL) {  
       *tagList=mesh->ContactElements->Tag;  
       *numTags=mesh->ContactElements->numElements;  
     }  
     break;  
   case(ContactElementsOne):  
     if (mesh->ContactElements!=NULL) {  
       *tagList=mesh->ContactElements->Tag;  
       *numTags=mesh->ContactElements->numElements;  
     }  
     break;  
   case(DegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *tagList=NULL;  
       *numTags=0;  
     }  
     break;  
   case(ReducedDegreesOfFreedom):  
     if (mesh->Nodes!=NULL) {  
       *tagList=NULL;  
       *numTags=0;  
     }  
     break;  
   default:  
     stringstream temp;  
     temp << "Error - Invalid function space type: "  
      << functionSpaceType << " for domain: " << getDescription();  
     throw FinleyAdapterException(temp.str());  
     break;  
   }  
   return;  
666  }  }
667    
668  //  //
669  // return the spatial dimension of the Mesh:  // Return the number of data points summed across all MPI processes
670  //  //
671  int MeshAdapter::getDim() const  int MeshAdapter::getNumDataPointsGlobal() const
672  {  {
673    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
   checkFinleyError();  
   return numDim;  
674  }  }
675    
676  //  //
677  // return the number of data points per sample and the number of samples  // return the number of data points per sample and the number of samples
678  // needed to represent data on a parts of the mesh.  // needed to represent data on a parts of the mesh.
# Line 278  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               numSamples=mesh->Nodes->numDegreesOfFreedom;     break;
724             }     case(ContactElementsZero):
725             break;     if (mesh->ContactElements!=NULL) {
726        case(ReducedDegreesOfFreedom):        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
727             if (mesh->Nodes!=NULL) {        numSamples=mesh->ContactElements->numElements;
728               numDataPointsPerSample=1;     }
729               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     break;
730             }     case(ReducedContactElementsZero):
731             break;     if (mesh->ContactElements!=NULL) {
732        default:        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
733          stringstream temp;        numSamples=mesh->ContactElements->numElements;
734          temp << "Error - Invalid function space type: "     }
735           << functionSpaceCode << " for domain: " << getDescription();     break;
736          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
737          break;     if (mesh->ContactElements!=NULL) {
738        }        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
739        return pair<int,int>(numDataPointsPerSample,numSamples);        numSamples=mesh->ContactElements->numElements;
740       }
741       break;
742       case(ReducedContactElementsOne):
743       if (mesh->ContactElements!=NULL) {
744          numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
745          numSamples=mesh->ContactElements->numElements;
746       }
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, Data& rhs,                                   SystemMatrixAdapter& mat, escript::Data& rhs,
774                       const Data& A, const Data& B, const Data& C,const  Data& D,const  Data& X,const  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 Data& d, const Data& y,                                   const escript::Data& d, const escript::Data& y,
776                       const Data& d_contact,const Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
777  {  {
778     Finley_Mesh* mesh=m_finleyMesh.get();     escriptDataC _rhs=rhs.getDataC();
779     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getFinley_SystemMatrix(),&(rhs.getDataC()),     escriptDataC _A  =A.getDataC();
780                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     escriptDataC _B=B.getDataC();
781     checkFinleyError();     escriptDataC _C=C.getDataC();
782     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,     escriptDataC _D=D.getDataC();
783                    mat.getFinley_SystemMatrix(),     escriptDataC _X=X.getDataC();
784                    &(rhs.getDataC()),     escriptDataC _Y=Y.getDataC();
785                                    &(d.getDataC()),&(y.getDataC()),     escriptDataC _d=d.getDataC();
786                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     escriptDataC _y=y.getDataC();
787     checkFinleyError();     escriptDataC _d_contact=d_contact.getDataC();
788     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,     escriptDataC _y_contact=y_contact.getDataC();
789                    mat.getFinley_SystemMatrix(),  
790                    &(rhs.getDataC()),     Finley_Mesh* mesh=m_finleyMesh.get();
791                                    &(d_contact.getDataC()),  
792                    &(y_contact.getDataC()),     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
793                                    Finley_Assemble_handelShapeMissMatch_Step_out);     checkFinleyError();
794    
795       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, mat.getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
796       checkFinleyError();
797    
798       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, mat.getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
799       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();     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  //  //
825  void MeshAdapter::addPDEToRHS( Data& rhs,  void MeshAdapter::addPDEToRHS( escript::Data& rhs, const  escript::Data& X,const  escript::Data& Y, const escript::Data& y, const escript::Data& y_contact) const
                      const  Data& X,const  Data& Y, const Data& y, const Data& y_contact) const  
826  {  {
827     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
828     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));  
829       escriptDataC _rhs=rhs.getDataC();
830       escriptDataC _X=X.getDataC();
831       escriptDataC _Y=Y.getDataC();
832       escriptDataC _y=y.getDataC();
833       escriptDataC _y_contact=y_contact.getDataC();
834    
835       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
836       checkFinleyError();
837    
838       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
839       checkFinleyError();
840    
841       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
842       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();     checkFinleyError();
877     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),  
878                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
 // cout << "Calling :addPDEToRHS." << endl;  
879     checkFinleyError();     checkFinleyError();
880     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),  
881                                    Finley_Assemble_handelShapeMissMatch_Step_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
 // cout << "Calling :addPDEToRHS." << endl;  
882     checkFinleyError();     checkFinleyError();
883  }  }
884    
885  //  //
886  // interpolates data between different function spaces:  // interpolates data between different function spaces:
887  //  //
888  void MeshAdapter::interpolateOnDomain(Data& target,const 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                 Finley_ErrorCode=TYPE_ERROR;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
923                 sprintf(Finley_ErrorMsg,"Interpolation on Domain: Finley does not know anything about function space type %d",target.getFunctionSpace().getTypeCode());        break;
924                 break;        case(ContactElementsOne):
925          }        case(ReducedContactElementsOne):
926          break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
927       case(Elements):        break;
928          if (target.getFunctionSpace().getTypeCode()==Elements) {        default:
929             Finley_Assemble_CopyElementData(mesh->Elements,&(target.getDataC()),&(in.getDataC()));           stringstream temp;
930          } else {           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
931             Finley_ErrorCode=TYPE_ERROR;           throw FinleyAdapterException(temp.str());
932             sprintf(Finley_ErrorMsg,"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             Finley_ErrorCode=TYPE_ERROR;        case(DegreesOfFreedom):
940             sprintf(Finley_ErrorMsg,"No interpolation with data on face elements possible.");        case(ReducedDegreesOfFreedom):
941             break;        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
942         }        break;
943       case(Points):        case(Elements):
944          if (target.getFunctionSpace().getTypeCode()==Points) {        case(ReducedElements):
945             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
946          } else {        break;
947             Finley_ErrorCode=TYPE_ERROR;        case(FaceElements):
948             sprintf(Finley_ErrorMsg,"No interpolation with data on points possible.");        case(ReducedFaceElements):
949             break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
950          }        break;
951          break;        case(Points):
952       case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
953       case(ContactElementsOne):        break;
954          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        case(ContactElementsZero):
955             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));        case(ReducedContactElementsZero):
956          } else {        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
957             Finley_ErrorCode=TYPE_ERROR;        break;
958             sprintf(Finley_ErrorMsg,"No interpolation with data on contact elements possible.");        case(ContactElementsOne):
959             break;        case(ReducedContactElementsOne):
960          }        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
961          break;        break;
962       case(DegreesOfFreedom):        default:
963          switch(target.getFunctionSpace().getTypeCode()) {           stringstream temp;
964             case(ReducedDegreesOfFreedom):           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
965             case(DegreesOfFreedom):           throw FinleyAdapterException(temp.str());
966             case(Nodes):           break;
967                Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        }
968                break;        break;
969             case(Elements):     case(Elements):
970                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Elements) {
971                break;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
972             case(FaceElements):        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
973                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
974                break;        } else {
975             case(Points):           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
976                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        }
977                break;        break;
978             case(ContactElementsZero):     case(ReducedElements):
979             case(ContactElementsOne):        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
980                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
981               break;        } else {
982             default:           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
983               Finley_ErrorCode=TYPE_ERROR;        }
984               sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",target.getFunctionSpace().getTypeCode());        break;
985               break;     case(FaceElements):
986          }        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
987          break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
988       case(ReducedDegreesOfFreedom):        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
989         switch(target.getFunctionSpace().getTypeCode()) {           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
990            case(ReducedDegreesOfFreedom):        } else {
991            case(Nodes):           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
992               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        }
993               break;        break;
994            case(Elements):     case(ReducedFaceElements):
995               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
996               break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
997            case(FaceElements):        } else {
998               Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));           throw FinleyAdapterException("Error - No interpolation with data on face elements with reduced integration order possible.");
999               break;        }
1000            case(Points):        break;
1001               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     case(Points):
1002               break;        if (target.getFunctionSpace().getTypeCode()==Points) {
1003            case(ContactElementsZero):           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1004            case(ContactElementsOne):        } else {
1005               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1006               break;        }
1007            case(DegreesOfFreedom):        break;
1008               Finley_ErrorCode=TYPE_ERROR;     case(ContactElementsZero):
1009               sprintf(Finley_ErrorMsg,"Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ContactElementsOne):
1010               break;        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1011            default:           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1012               Finley_ErrorCode=TYPE_ERROR;        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1013               sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",target.getFunctionSpace().getTypeCode());           Finley_Assemble_AverageElementData(mesh->ContactElements,&_target,&_in);
1014               break;        } else {
1015         }           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1016         break;        }
1017       default:        break;
1018          Finley_ErrorCode=TYPE_ERROR;     case(ReducedContactElementsZero):
1019          sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",in.getFunctionSpace().getTypeCode());     case(ReducedContactElementsOne):
1020          break;        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1021    }           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1022    checkFinleyError();        } else {
1023             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1024          }
1025          break;
1026       case(DegreesOfFreedom):      
1027          switch(target.getFunctionSpace().getTypeCode()) {
1028          case(ReducedDegreesOfFreedom):
1029          case(DegreesOfFreedom):
1030          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1031          break;
1032      
1033          case(Nodes):
1034          case(ReducedNodes):
1035          if (getMPISize()>1) {
1036             escript::Data temp=escript::Data(in);
1037             temp.expand();
1038             escriptDataC _in2 = temp.getDataC();
1039             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1040          } else {
1041             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1042          }
1043          break;
1044          case(Elements):
1045          case(ReducedElements):
1046          if (getMPISize()>1) {
1047             escript::Data temp=escript::Data( in,  continuousFunction(asAbstractContinuousDomain()) );
1048             escriptDataC _in2 = temp.getDataC();
1049             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1050          } else {
1051             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1052          }
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  //  //
1171  // copies the locations of sample points into x:  // copies the locations of sample points into x:
1172  //  //
1173  void MeshAdapter::setToX(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       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  //  //
1194  // return the normal vectors at the location of data points as a Data object:  // return the normal vectors at the location of data points as a Data object:
1195  //  //
1196  void MeshAdapter::setToNormal(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        Finley_ErrorCode=TYPE_ERROR;     switch(normal.getFunctionSpace().getTypeCode()) {
1205        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for nodes");     case(Nodes):
1206        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1207      case(Elements):     break;
1208        Finley_ErrorCode=TYPE_ERROR;     case(ReducedNodes):
1209        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for elements");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced nodes");
1210        break;     break;
1211      case (FaceElements):     case(Elements):
1212        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1213        break;     break;
1214      case(Points):     case(ReducedElements):
1215        Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1216        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for point elements");     break;
1217        break;     case (FaceElements):
1218      case (ContactElementsOne):     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1219      case (ContactElementsZero):     break;
1220        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (ReducedFaceElements):
1221        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1222      case(DegreesOfFreedom):     break;
1223        Finley_ErrorCode=TYPE_ERROR;     case(Points):
1224        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for degrees of freedom.");     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for point elements");
1225        break;     break;
1226      case(ReducedDegreesOfFreedom):     case (ContactElementsOne):
1227        Finley_ErrorCode=TYPE_ERROR;     case (ContactElementsZero):
1228        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for reduced degrees of freedom.");     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1229        break;     break;
1230      default:     case (ReducedContactElementsOne):
1231        Finley_ErrorCode=TYPE_ERROR;     case (ReducedContactElementsZero):
1232        sprintf(Finley_ErrorMsg,"Normal Vectors: Finley does not know anything about function space type %d",normal.getFunctionSpace().getTypeCode());     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;
1242          temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1243          throw FinleyAdapterException(temp.str());
1244        break;        break;
1245    }     }
1246    checkFinleyError();     checkFinleyError();
1247  }  }
1248    
1249  //  //
1250  // interpolates data to other domain:  // interpolates data to other domain:
1251  //  //
1252  void MeshAdapter::interpolateACross(Data& target,const 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    Finley_ErrorCode=SYSTEM_ERROR;  
1259    sprintf(Finley_ErrorMsg,"Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
   checkFinleyError();  
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 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          Finley_ErrorCode=TYPE_ERROR;     escript::Data temp;
1275          sprintf(Finley_ErrorMsg,"Integral of data on nodes is not supported.");     escriptDataC _arg=arg.getDataC();
1276          break;     switch(arg.getFunctionSpace().getTypeCode()) {
1277       case(Elements):     case(Nodes):
1278          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1279          break;     _temp=temp.getDataC();
1280       case(FaceElements):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1281          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     break;
1282          break;     case(ReducedNodes):
1283       case(Points):     temp=escript::Data( arg, escript::function(asAbstractContinuousDomain()) );
1284          Finley_ErrorCode=TYPE_ERROR;     _temp=temp.getDataC();
1285          sprintf(Finley_ErrorMsg,"Integral of data on points is not supported.");     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1286          break;     break;
1287       case(ContactElementsZero):     case(Elements):
1288          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1289          break;     break;
1290       case(ContactElementsOne):     case(ReducedElements):
1291          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1292          break;     break;
1293       case(DegreesOfFreedom):     case(FaceElements):
1294          Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1295          sprintf(Finley_ErrorMsg,"Integral of data on degrees of freedom is not supported.");     break;
1296          break;     case(ReducedFaceElements):
1297       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1298          Finley_ErrorCode=TYPE_ERROR;     break;
1299          sprintf(Finley_ErrorMsg,"Integral of data on reduced degrees of freedom is not supported.");     case(Points):
1300          break;     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1301       default:     break;
1302          Finley_ErrorCode=TYPE_ERROR;     case(ContactElementsZero):
1303          sprintf(Finley_ErrorMsg,"Integrals: Finley does not know anything about function space type %d",arg.getFunctionSpace().getTypeCode());     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1304          break;     break;
1305    }     case(ReducedContactElementsZero):
1306    checkFinleyError();     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  //  //
1335  // calculates the gradient of arg:  // calculates the gradient of arg:
1336  //  //
1337  void MeshAdapter::setToGradient(Data& grad,const 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    switch(grad.getFunctionSpace().getTypeCode()) {     escriptDataC _grad=grad.getDataC();
1348         case(Nodes):     escriptDataC nodeDataC;
1349            Finley_ErrorCode=TYPE_ERROR;     escript::Data temp;
1350            sprintf(Finley_ErrorMsg,"Gradient at nodes is not supported.");     if (getMPISize()>1) {
1351            break;        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1352         case(Elements):           temp=escript::Data( arg,  continuousFunction(asAbstractContinuousDomain()) );
1353            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));           nodeDataC = temp.getDataC();
1354            break;        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1355         case(FaceElements):           temp=escript::Data( arg,  reducedContinuousFunction(asAbstractContinuousDomain()) );
1356            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));           nodeDataC = temp.getDataC();
1357            break;        } else {
1358         case(Points):           nodeDataC = arg.getDataC();
1359            Finley_ErrorCode=TYPE_ERROR;        }
1360            sprintf(Finley_ErrorMsg,"Gradient at points is not supported.");     } else {
1361            break;        nodeDataC = arg.getDataC();
1362         case(ContactElementsZero):     }
1363            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     switch(grad.getFunctionSpace().getTypeCode()) {
1364            break;     case(Nodes):
1365         case(ContactElementsOne):     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1366            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     break;
1367            break;     case(ReducedNodes):
1368         case(DegreesOfFreedom):     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1369            Finley_ErrorCode=TYPE_ERROR;     break;
1370            sprintf(Finley_ErrorMsg,"Gradient at degrees of freedom is not supported.");     case(Elements):
1371            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1372         case(ReducedDegreesOfFreedom):     break;
1373            Finley_ErrorCode=TYPE_ERROR;     case(ReducedElements):
1374            sprintf(Finley_ErrorMsg,"Gradient at reduced degrees of freedom is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1375            break;     break;
1376         default:     case(FaceElements):
1377            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1378            sprintf(Finley_ErrorMsg,"Gradient: Finley does not know anything about function space type %d",arg.getFunctionSpace().getTypeCode());     break;
1379            break;     case(ReducedFaceElements):
1380    }     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1381    checkFinleyError();     break;
1382       case(Points):
1383       throw FinleyAdapterException("Error - Gradient at points is not supported.");
1384       break;
1385       case(ContactElementsZero):
1386       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1387       break;
1388       case(ReducedContactElementsZero):
1389       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1390       break;
1391       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  //  //
1413  // returns the size of elements:  // returns the size of elements:
1414  //  //
1415  void MeshAdapter::setToSize(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            Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1422            sprintf(Finley_ErrorMsg,"Size of nodes is not supported.");     break;
1423            break;     case(ReducedNodes):
1424         case(Elements):     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1425            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     break;
1426            break;     case(Elements):
1427         case(FaceElements):     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1428            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     break;
1429            break;     case(ReducedElements):
1430         case(Points):     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1431            Finley_ErrorCode=TYPE_ERROR;     break;
1432            sprintf(Finley_ErrorMsg,"Size of point elements is not supported.");     case(FaceElements):
1433            break;     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1434         case(ContactElementsZero):     break;
1435         case(ContactElementsOne):     case(ReducedFaceElements):
1436            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1437            break;     break;
1438         case(DegreesOfFreedom):     case(Points):
1439            Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1440            sprintf(Finley_ErrorMsg,"Size of degrees of freedom is not supported.");     break;
1441            break;     case(ContactElementsZero):
1442         case(ReducedDegreesOfFreedom):     case(ContactElementsOne):
1443            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1444            sprintf(Finley_ErrorMsg,"Size of reduced degrees of freedom is not supported.");     break;
1445            break;     case(ReducedContactElementsZero):
1446         default:     case(ReducedContactElementsOne):
1447            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1448            sprintf(Finley_ErrorMsg,"Element size: Finley does not know anything about function space type %d",size.getFunctionSpace().getTypeCode());     break;
1449            break;     case(DegreesOfFreedom):
1450    }     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1451    checkFinleyError();     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  // sets the location of nodes:  
1464  void MeshAdapter::setNewX(const Data& new_x)  //
1465    // sets the location of nodes
1466    //
1467    void MeshAdapter::setNewX(const escript::Data& new_x)
1468  {  {
1469    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1470    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     escriptDataC tmp;
1471    if (newDomain!=*this)     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1472       throw FinleyAdapterException("Error - Illegal domain of new point locations");     if (newDomain!=*this)
1473    Finley_NodeFile_setCoordinates(mesh->Nodes,&(new_x.getDataC()));        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1474    checkFinleyError();     if ( new_x.getFunctionSpace() == continuousFunction(asAbstractContinuousDomain()) ) {
1475  }         tmp = new_x.getDataC();
1476  // saves a data array in openDX format:         Finley_Mesh_setCoordinates(mesh,&tmp);
1477  void MeshAdapter::saveDX(const std::string& filename,const Data& arg) const     } else {
1478  {         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(asAbstractContinuousDomain()) );
1479    Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),&(arg.getDataC()));         tmp = new_x_inter.getDataC();
1480    checkFinleyError();         Finley_Mesh_setCoordinates(mesh,&tmp);
1481       }
1482       checkFinleyError();
1483  }  }
1484  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:  
1485  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  //
1486                        const int row_blocksize,  // Helper for the save* methods. Extracts optional data variable names and the
1487                        const escript::FunctionSpace& row_functionspace,  // corresponding pointers from python dictionary. Caller must free arrays.
1488                        const int column_blocksize,  //
1489                        const escript::FunctionSpace& column_functionspace,  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1490                        const int type) const  {
1491  {     numData = boost::python::extract<int>(arg.attr("__len__")());
1492      int reduceRowOrder=0;     /* win32 refactor */
1493      int reduceColOrder=0;     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1494      // is the domain right?     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1495      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1496      if (row_domain!=*this)  
1497            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");     boost::python::list keys=arg.keys();
1498      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());     for (int i=0; i<numData; ++i) {
1499      if (col_domain!=*this)        string n=boost::python::extract<string>(keys[i]);
1500            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1501      // is the function space type right        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1502      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {           throw FinleyAdapterException("Error: Data must be defined on same Domain");
1503          reduceRowOrder=0;        data[i] = d.getDataC();
1504      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {        dataPtr[i] = &(data[i]);
1505          reduceRowOrder=1;        names[i] = TMPMEMALLOC(n.length()+1, char);
1506      } else {        strcpy(names[i], n.c_str());
1507          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");     }
1508    }
1509    
1510    //
1511    // saves mesh and optionally data arrays in openDX format
1512    //
1513    void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1514    {
1515       int num_data;
1516       char **names;
1517       escriptDataC *data;
1518       escriptDataC **ptr_data;
1519    
1520       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    //
1537    // 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 num_data;
1542       char **names;
1543       escriptDataC *data;
1544       escriptDataC **ptr_data;
1545    
1546       extractArgsFromDict(arg, num_data, names, data, ptr_data);
1547       Finley_Mesh_saveVTK(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data, metadata.c_str(), metadata_schema.c_str());
1548       checkFinleyError();
1549    
1550       /* win32 refactor */
1551       TMPMEMFREE(data);
1552       TMPMEMFREE(ptr_data);
1553       for(int i=0; i<num_data; i++)
1554       {
1555          TMPMEMFREE(names[i]);
1556       }
1557       TMPMEMFREE(names);
1558    }
1559    
1560    bool MeshAdapter::ownSample(int fs_code, index_t id) const
1561    {
1562    #ifdef PASO_MPI
1563        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      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      else
1573          reduceColOrder=0;      {
1574      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1575          reduceColOrder=1;      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1576      } else {      globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
         throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");  
1577      }      }
1578      // generate matrix:      k=globalNodeIndex[id];
1579            return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1580      Finley_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);  #endif
1581      checkFinleyError();      return true;
     Finley_SystemMatrix* fsystemMatrix=Finley_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize);  
     checkFinleyError();  
     return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);  
1582  }  }
1583    
1584    
1585    
1586    //
1587    // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1588    //
1589    SystemMatrixAdapter MeshAdapter::newSystemMatrix(
1590                                                     const int row_blocksize,
1591                                                     const escript::FunctionSpace& row_functionspace,
1592                                                     const int column_blocksize,
1593                                                     const escript::FunctionSpace& column_functionspace,
1594                                                     const int type) const
1595    {
1596       int reduceRowOrder=0;
1597       int reduceColOrder=0;
1598       // is the domain right?
1599       const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1600       if (row_domain!=*this)
1601          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()));
1603       if (col_domain!=*this)
1604          throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1605       // is the function space type right
1606       if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1607          reduceRowOrder=0;
1608       } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1609          reduceRowOrder=1;
1610       } else {
1611          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1612       }
1613       if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1614          reduceColOrder=0;
1615       } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1616          reduceColOrder=1;
1617       } else {
1618          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1619       }
1620       // generate matrix:
1621    
1622       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1623       checkFinleyError();
1624       Paso_SystemMatrix* fsystemMatrix;
1625       int trilinos = 0;
1626       if (trilinos) {
1627    #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  //  //
1673  // vtkObject MeshAdapter::createVtkObject() const  // vtkObject MeshAdapter::createVtkObject() const
1674  // TODO:  // TODO:
1675  //  //
1676    
1677  //  //
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            Finley_ErrorCode=TYPE_ERROR;     case(ReducedContactElementsOne):
1696            sprintf(Finley_ErrorMsg,"Cell: Finley does not know anything about function space type %d",functionSpaceCode);     return true;
1697            break;     break;
1698    }     default:
1699    checkFinleyError();        stringstream temp;
1700    return false;        temp << "Error - Cell: Finley does not know anything about function space type " << functionSpaceCode;
1701          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                 Finley_ErrorCode=TYPE_ERROR;      case(ReducedContactElementsZero):
1868                 sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",functionSpaceType_target);      case(ContactElementsOne):
1869          }      case(ReducedContactElementsOne):
1870          break;      return true;
1871       case(Elements):      default:
1872          if (functionSpaceType_target==Elements) {            stringstream temp;
1873             return true;            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1874          } else {            throw FinleyAdapterException(temp.str());
1875             return false;     }
1876          }     break;
1877       case(FaceElements):     case(ReducedNodes):
1878          if (functionSpaceType_target==FaceElements) {      switch(functionSpaceType_target) {
1879             return true;      case(ReducedNodes):
1880          } else {      case(ReducedDegreesOfFreedom):
1881             return false;      case(Elements):
1882          }      case(ReducedElements):
1883       case(Points):      case(FaceElements):
1884          if (functionSpaceType_target==Points) {      case(ReducedFaceElements):
1885             return true;      case(Points):
1886          } else {      case(ContactElementsZero):
1887             return false;      case(ReducedContactElementsZero):
1888          }      case(ContactElementsOne):
1889       case(ContactElementsZero):      case(ReducedContactElementsOne):
1890       case(ContactElementsOne):      return true;
1891          if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {      case(Nodes):
1892             return true;      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(DegreesOfFreedom):  
         switch(functionSpaceType_target) {  
            case(ReducedDegreesOfFreedom):  
            case(DegreesOfFreedom):  
            case(Nodes):  
            case(Elements):  
            case(FaceElements):  
            case(Points):  
            case(ContactElementsZero):  
            case(ContactElementsOne):  
               return true;  
            default:  
              Finley_ErrorCode=TYPE_ERROR;  
              sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",functionSpaceType_target);  
1907          }          }
1908          break;     case(ReducedElements):
1909       case(ReducedDegreesOfFreedom):      if (functionSpaceType_target==ReducedElements) {
1910         switch(functionSpaceType_target) {        return true;
1911            case(ReducedDegreesOfFreedom):      } else {
1912            case(Nodes):            return false;
1913            case(Elements):      }
1914            case(FaceElements):     case(FaceElements):
1915            case(Points):      if (functionSpaceType_target==FaceElements) {
1916            case(ContactElementsZero):              return true;
1917            case(ContactElementsOne):      } else if (functionSpaceType_target==ReducedFaceElements) {
1918                return true;              return true;
1919            case(DegreesOfFreedom):      } else {
1920               return false;              return false;
1921            default:      }
1922               Finley_ErrorCode=TYPE_ERROR;     case(ReducedFaceElements):
1923               sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",functionSpaceType_target);      if (functionSpaceType_target==ReducedFaceElements) {
1924         }              return true;
1925         break;      } else {
1926       default:          return false;
1927          Finley_ErrorCode=TYPE_ERROR;      }
1928          sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",functionSpaceType_source);     case(Points):
1929          break;      if (functionSpaceType_target==Points) {
1930    }              return true;
1931    checkFinleyError();      } else {
1932    return false;              return false;
1933        }
1934       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  bool MeshAdapter::operator==(const MeshAdapter& other) const  
2010    bool MeshAdapter::operator==(const AbstractDomain& other) const
2011  {  {
2012    return (m_finleyMesh==other.m_finleyMesh);     const MeshAdapter* temp=dynamic_cast<const MeshAdapter*>(&other);
2013       if (temp!=0) {
2014          return (m_finleyMesh==temp->m_finleyMesh);
2015       } else {
2016          return false;
2017       }
2018  }  }
2019    
2020  int MeshAdapter::getSystemMatrixTypeId(const int solver, const bool symmetry) const  bool MeshAdapter::operator!=(const AbstractDomain& other) const
2021  {  {
2022     int out=Finley_SystemMatrix_getSystemMatrixTypeId(solver,symmetry?1:0);     return !(operator==(other));
2023     checkFinleyError();  }
2024    
2025    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       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();
2037       return out;
2038    }
2039    
2040    escript::Data MeshAdapter::getX() const
2041    {
2042       return continuousFunction(asAbstractContinuousDomain()).getX();
2043    }
2044    
2045    escript::Data MeshAdapter::getNormal() const
2046    {
2047       return functionOnBoundary(asAbstractContinuousDomain()).getNormal();
2048    }
2049    
2050    escript::Data MeshAdapter::getSize() const
2051    {
2052       return escript::function(asAbstractContinuousDomain()).getSize();
2053    }
2054    
2055    const int* MeshAdapter::borrowSampleReferenceIDs(int functionSpaceType) const
2056    {
2057       int *out = NULL;
2058       Finley_Mesh* mesh=m_finleyMesh.get();
2059       switch (functionSpaceType) {
2060       case(Nodes):
2061       out=mesh->Nodes->Id;
2062       break;
2063       case(ReducedNodes):
2064       out=mesh->Nodes->reducedNodesId;
2065       break;
2066       case(Elements):
2067       out=mesh->Elements->Id;
2068       break;
2069       case(ReducedElements):
2070       out=mesh->Elements->Id;
2071       break;
2072       case(FaceElements):
2073       out=mesh->FaceElements->Id;
2074       break;
2075       case(ReducedFaceElements):
2076       out=mesh->FaceElements->Id;
2077       break;
2078       case(Points):
2079       out=mesh->Points->Id;
2080       break;
2081       case(ContactElementsZero):
2082       out=mesh->ContactElements->Id;
2083       break;
2084       case(ReducedContactElementsZero):
2085       out=mesh->ContactElements->Id;
2086       break;
2087       case(ContactElementsOne):
2088       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;     return out;
2106  }  }
2107  Data MeshAdapter::getX() const  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const
2108  {  {
2109    return continuousFunction(asAbstractContinuousDomain()).getX();     int out=0;
2110       Finley_Mesh* mesh=m_finleyMesh.get();
2111       switch (functionSpaceType) {
2112       case(Nodes):
2113       out=mesh->Nodes->Tag[sampleNo];
2114       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;
2156       }
2157       return out;
2158  }  }
2159  Data MeshAdapter::getNormal() const  
2160    
2161    void MeshAdapter::setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const
2162  {  {
2163    return functionOnBoundary(asAbstractContinuousDomain()).getNormal();     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  Data MeshAdapter::getSize() const  
2214    void MeshAdapter::setTagMap(const string& name,  int tag)
2215  {  {
2216    return function(asAbstractContinuousDomain()).getSize();     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::operator!=(const MeshAdapter& other) const  bool MeshAdapter::isValidTagName(const string& name) const
2233  {  {
2234    return !operator==(other);     Finley_Mesh* mesh=m_finleyMesh.get();
2235       return Finley_Mesh_isValidTagName(mesh,name.c_str());
2236  }  }
2237  // bool MeshAdapter::operator==(const AbstractDomain& other) const  
2238  // {  string MeshAdapter::showTagNames() const
2239    // try {  {
2240      // const MeshAdapter& ref = dynamic_cast<const MeshAdapter&>(other);     stringstream temp;
2241      // return (operator==(ref));     Finley_Mesh* mesh=m_finleyMesh.get();
2242    // }     Finley_TagMap* tag_map=mesh->TagMap;
2243    // catch (bad_cast) {     while (tag_map) {
2244      // return false;        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();
2254      dim_t numTags=0;
2255      switch(functionSpaceCode) {
2256       case(Nodes):
2257              numTags=mesh->Nodes->numTagsInUse;
2258              break;
2259       case(ReducedNodes):
2260              throw FinleyAdapterException("Error - ReducedNodes does not support tags");
2261              break;
2262       case(DegreesOfFreedom):
2263              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2264              break;
2265       case(ReducedDegreesOfFreedom):
2266              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2267              break;
2268       case(Elements):
2269       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;
2285       default:
2286          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;
2304       case(DegreesOfFreedom):
2305              throw FinleyAdapterException("Error - DegreesOfFreedom does not support tags");
2306              break;
2307       case(ReducedDegreesOfFreedom):
2308              throw FinleyAdapterException("Error - ReducedDegreesOfFreedom does not support tags");
2309              break;
2310       case(Elements):
2311       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;
2327       default:
2328          stringstream temp;
2329          temp << "Error - Finley does not know anything about function space type " << functionSpaceCode;
2330          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      }
2357    }
2358    
2359    AbstractDomain::StatusType MeshAdapter::getStatus() const
2360    {
2361      Finley_Mesh* mesh=m_finleyMesh.get();
2362      return Finley_Mesh_getStatus(mesh);
2363    }
2364    
2365    int MeshAdapter::getApproximationOrder(const int functionSpaceCode) const
2366    {
2367      
2368      Finley_Mesh* mesh=m_finleyMesh.get();
2369      int order =-1;
2370      switch(functionSpaceCode) {
2371       case(Nodes):
2372       case(DegreesOfFreedom):
2373              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    ReferenceElementSetWrapper::ReferenceElementSetWrapper(ElementTypeId id, index_t order, index_t reducedOrder)
2401    {
2402      m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2403    }
2404    
2405    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2406    {
2407      Finley_ReferenceElementSet_dealloc(m_refSet);
2408    }
2409    
2410  }  // end of namespace  }  // end of namespace

Legend:
Removed from v.102  
changed lines
  Added in v.2989

  ViewVC Help
Powered by ViewVC 1.1.26