/[escript]/trunk/finley/src/CPPAdapter/MeshAdapter.cpp
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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 3355 by caltinay, Tue Nov 16 06:35:06 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  extern "C" {  extern "C" {
22  #include "finley/finleyC/Finley.h"  #include "esysUtils/blocktimer.h"
23  #include "finley/finleyC/Assemble.h"  }
24  #include "finley/finleyC/Mesh.h"  
25  #include "finley/finleyC/Finley.h"  #include <boost/python/import.hpp>
 #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>  
26    
27  using namespace std;  using namespace std;
28  using namespace escript;  using namespace escript;
29    
30  namespace finley {  namespace finley {
31    
 struct null_deleter  
 {  
   void operator()(void const *ptr) const  
   {  
   }  
 };  
   
32  //  //
33  // define the statics  // define the static constants
34  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;  MeshAdapter::FunctionSpaceNamesMapType MeshAdapter::m_functionSpaceTypeNames;
35  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;  const int MeshAdapter::DegreesOfFreedom=FINLEY_DEGREES_OF_FREEDOM;
36  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;  const int MeshAdapter::ReducedDegreesOfFreedom=FINLEY_REDUCED_DEGREES_OF_FREEDOM;
37  const int MeshAdapter::Nodes=FINLEY_NODES;  const int MeshAdapter::Nodes=FINLEY_NODES;
38    const int MeshAdapter::ReducedNodes=FINLEY_REDUCED_NODES;
39  const int MeshAdapter::Elements=FINLEY_ELEMENTS;  const int MeshAdapter::Elements=FINLEY_ELEMENTS;
40    const int MeshAdapter::ReducedElements=FINLEY_REDUCED_ELEMENTS;
41  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;  const int MeshAdapter::FaceElements=FINLEY_FACE_ELEMENTS;
42    const int MeshAdapter::ReducedFaceElements=FINLEY_REDUCED_FACE_ELEMENTS;
43  const int MeshAdapter::Points=FINLEY_POINTS;  const int MeshAdapter::Points=FINLEY_POINTS;
44  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;  const int MeshAdapter::ContactElementsZero=FINLEY_CONTACT_ELEMENTS_1;
45    const int MeshAdapter::ReducedContactElementsZero=FINLEY_REDUCED_CONTACT_ELEMENTS_1;
46  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;  const int MeshAdapter::ContactElementsOne=FINLEY_CONTACT_ELEMENTS_2;
47    const int MeshAdapter::ReducedContactElementsOne=FINLEY_REDUCED_CONTACT_ELEMENTS_2;
48    
49  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)  MeshAdapter::MeshAdapter(Finley_Mesh* finleyMesh)
50  {  {
51    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
52    //     //
53    // 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
54    // for us.     // for us.
55    m_finleyMesh.reset(finleyMesh,null_deleter());     m_finleyMesh.reset(finleyMesh,null_deleter());
56  }  }
57    
58  //  //
59  // The copy constructor should just increment the use count  // The copy constructor should just increment the use count
60  MeshAdapter::MeshAdapter(const MeshAdapter& in):  MeshAdapter::MeshAdapter(const MeshAdapter& in):
61  m_finleyMesh(in.m_finleyMesh)  m_finleyMesh(in.m_finleyMesh)
62  {  {
63    setFunctionSpaceTypeNames();     setFunctionSpaceTypeNames();
64  }  }
65    
66  MeshAdapter::~MeshAdapter()  MeshAdapter::~MeshAdapter()
67  {  {
68    //     //
69    // 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.
70    //  cout << "In MeshAdapter destructor." << endl;     //  cout << "In MeshAdapter destructor." << endl;
71    if (m_finleyMesh.unique()) {     if (m_finleyMesh.unique()) {
72      //   cout << "Calling dealloc." << endl;        Finley_Mesh_free(m_finleyMesh.get());
73      Finley_Mesh_dealloc(m_finleyMesh.get());     }
     //   cout << "Finished dealloc." << endl;  
   }  
74  }  }
75    
76    int MeshAdapter::getMPISize() const
77    {
78       return m_finleyMesh.get()->MPIInfo->size;
79    }
80    int MeshAdapter::getMPIRank() const
81    {
82       return m_finleyMesh.get()->MPIInfo->rank;
83    }
84    void MeshAdapter::MPIBarrier() const
85    {
86    #ifdef ESYS_MPI
87       MPI_Barrier(m_finleyMesh.get()->MPIInfo->comm);
88    #endif
89       return;
90    }
91    bool MeshAdapter::onMasterProcessor() const
92    {
93       return m_finleyMesh.get()->MPIInfo->rank == 0;
94    }
95    
96    
97    #ifdef ESYS_MPI
98      MPI_Comm
99    #else
100      unsigned int
101    #endif
102    MeshAdapter::getMPIComm() const
103    {
104    #ifdef ESYS_MPI
105        return m_finleyMesh->MPIInfo->comm;
106    #else
107        return 0;
108    #endif
109    }
110    
111    
112  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {  Finley_Mesh* MeshAdapter::getFinley_Mesh() const {
113     return m_finleyMesh.get();     return m_finleyMesh.get();
114  }  }
115    
116  void MeshAdapter::write(const std::string& fileName) const  void MeshAdapter::write(const string& fileName) const
117    {
118       char *fName = (fileName.size()+1>0) ? TMPMEMALLOC(fileName.size()+1,char) : (char*)NULL;
119       strcpy(fName,fileName.c_str());
120       Finley_Mesh_write(m_finleyMesh.get(),fName);
121       checkFinleyError();
122       TMPMEMFREE(fName);
123    }
124    
125    void MeshAdapter::Print_Mesh_Info(const bool full) const
126  {  {
127    char fName[fileName.size()+1];     Finley_PrintMesh_Info(m_finleyMesh.get(), full);
   strcpy(fName,fileName.c_str());  
   Finley_Mesh_write(m_finleyMesh.get(),fName);  
   checkFinleyError();  
128  }  }
129    
130  // void MeshAdapter::getTagList(int functionSpaceType,  void MeshAdapter::dump(const string& fileName) const
131  //                  int* numTags) const  {
132  // {  #ifdef USE_NETCDF
133  //   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};
134  //   return;     NcVar *ids;
135  // }     int *int_ptr;
136       Finley_Mesh *mesh = m_finleyMesh.get();
137       Finley_TagMap* tag_map;
138       int num_Tags = 0;
139       int mpi_size             = mesh->MPIInfo->size;
140       int mpi_rank             = mesh->MPIInfo->rank;
141       int numDim               = mesh->Nodes->numDim;
142       int numNodes             = mesh->Nodes->numNodes;
143       int num_Elements         = mesh->Elements->numElements;
144       int num_FaceElements         = mesh->FaceElements->numElements;
145       int num_ContactElements      = mesh->ContactElements->numElements;
146       int num_Points           = mesh->Points->numElements;
147       int num_Elements_numNodes        = mesh->Elements->numNodes;
148       int num_FaceElements_numNodes    = mesh->FaceElements->numNodes;
149       int num_ContactElements_numNodes = mesh->ContactElements->numNodes;
150    #ifdef ESYS_MPI
151       MPI_Status status;
152    #endif
153    
154    /* Incoming token indicates it's my turn to write */
155    #ifdef ESYS_MPI
156       if (mpi_rank>0) MPI_Recv(&num_Tags, 0, MPI_INT, mpi_rank-1, 81800, mesh->MPIInfo->comm, &status);
157    #endif
158    
159       char *newFileName = Esys_MPI_appendRankToFileName(fileName.c_str(),
160                                                         mpi_size, mpi_rank);
161    
162       /* Figure out how much storage is required for tags */
163       tag_map = mesh->TagMap;
164       num_Tags = 0;
165       while (tag_map) {
166          num_Tags++;
167          tag_map=tag_map->next;
168       }
169    
170       // NetCDF error handler
171       NcError err(NcError::verbose_nonfatal);
172       // Create the file.
173       NcFile dataFile(newFileName, NcFile::Replace);
174       string msgPrefix("Error in MeshAdapter::dump: NetCDF operation failed - ");
175       // check if writing was successful
176       if (!dataFile.is_valid())
177          throw DataException(msgPrefix+"Open file for output");
178    
179       // Define dimensions (num_Elements and dim_Elements are identical,
180       // dim_Elements only appears if > 0)
181       if (! (ncdims[0] = dataFile.add_dim("numNodes", numNodes)) )
182          throw DataException(msgPrefix+"add_dim(numNodes)");
183       if (! (ncdims[1] = dataFile.add_dim("numDim", numDim)) )
184          throw DataException(msgPrefix+"add_dim(numDim)");
185       if (! (ncdims[2] = dataFile.add_dim("mpi_size_plus_1", mpi_size+1)) )
186          throw DataException(msgPrefix+"add_dim(mpi_size)");
187       if (num_Elements>0)
188          if (! (ncdims[3] = dataFile.add_dim("dim_Elements", num_Elements)) )
189             throw DataException(msgPrefix+"add_dim(dim_Elements)");
190       if (num_FaceElements>0)
191          if (! (ncdims[4] = dataFile.add_dim("dim_FaceElements", num_FaceElements)) )
192             throw DataException(msgPrefix+"add_dim(dim_FaceElements)");
193       if (num_ContactElements>0)
194          if (! (ncdims[5] = dataFile.add_dim("dim_ContactElements", num_ContactElements)) )
195             throw DataException(msgPrefix+"add_dim(dim_ContactElements)");
196       if (num_Points>0)
197          if (! (ncdims[6] = dataFile.add_dim("dim_Points", num_Points)) )
198             throw DataException(msgPrefix+"add_dim(dim_Points)");
199       if (num_Elements>0)
200          if (! (ncdims[7] = dataFile.add_dim("dim_Elements_Nodes", num_Elements_numNodes)) )
201             throw DataException(msgPrefix+"add_dim(dim_Elements_Nodes)");
202       if (num_FaceElements>0)
203          if (! (ncdims[8] = dataFile.add_dim("dim_FaceElements_numNodes", num_FaceElements_numNodes)) )
204             throw DataException(msgPrefix+"add_dim(dim_FaceElements_numNodes)");
205       if (num_ContactElements>0)
206          if (! (ncdims[9] = dataFile.add_dim("dim_ContactElements_numNodes", num_ContactElements_numNodes)) )
207             throw DataException(msgPrefix+"add_dim(dim_ContactElements_numNodes)");
208       if (num_Tags>0)
209          if (! (ncdims[10] = dataFile.add_dim("dim_Tags", num_Tags)) )
210             throw DataException(msgPrefix+"add_dim(dim_Tags)");
211    
212       // Attributes: MPI size, MPI rank, Name, order, reduced_order
213       if (!dataFile.add_att("mpi_size", mpi_size) )
214          throw DataException(msgPrefix+"add_att(mpi_size)");
215       if (!dataFile.add_att("mpi_rank", mpi_rank) )
216          throw DataException(msgPrefix+"add_att(mpi_rank)");
217       if (!dataFile.add_att("Name",mesh->Name) )
218          throw DataException(msgPrefix+"add_att(Name)");
219       if (!dataFile.add_att("numDim",numDim) )
220          throw DataException(msgPrefix+"add_att(order)");
221       if (!dataFile.add_att("order",mesh->integrationOrder) )
222          throw DataException(msgPrefix+"add_att(order)");
223       if (!dataFile.add_att("reduced_order",mesh->reducedIntegrationOrder) )
224          throw DataException(msgPrefix+"add_att(reduced_order)");
225       if (!dataFile.add_att("numNodes",numNodes) )
226          throw DataException(msgPrefix+"add_att(numNodes)");
227       if (!dataFile.add_att("num_Elements",num_Elements) )
228          throw DataException(msgPrefix+"add_att(num_Elements)");
229       if (!dataFile.add_att("num_FaceElements",num_FaceElements) )
230          throw DataException(msgPrefix+"add_att(num_FaceElements)");
231       if (!dataFile.add_att("num_ContactElements",num_ContactElements) )
232          throw DataException(msgPrefix+"add_att(num_ContactElements)");
233       if (!dataFile.add_att("num_Points",num_Points) )
234          throw DataException(msgPrefix+"add_att(num_Points)");
235       if (!dataFile.add_att("num_Elements_numNodes",num_Elements_numNodes) )
236          throw DataException(msgPrefix+"add_att(num_Elements_numNodes)");
237       if (!dataFile.add_att("num_FaceElements_numNodes",num_FaceElements_numNodes) )
238          throw DataException(msgPrefix+"add_att(num_FaceElements_numNodes)");
239       if (!dataFile.add_att("num_ContactElements_numNodes",num_ContactElements_numNodes) )
240          throw DataException(msgPrefix+"add_att(num_ContactElements_numNodes)");
241       if (!dataFile.add_att("Elements_TypeId", mesh->Elements->referenceElementSet->referenceElement->Type->TypeId) )
242          throw DataException(msgPrefix+"add_att(Elements_TypeId)");
243       if (!dataFile.add_att("FaceElements_TypeId", mesh->FaceElements->referenceElementSet->referenceElement->Type->TypeId) )
244          throw DataException(msgPrefix+"add_att(FaceElements_TypeId)");
245       if (!dataFile.add_att("ContactElements_TypeId", mesh->ContactElements->referenceElementSet->referenceElement->Type->TypeId) )
246          throw DataException(msgPrefix+"add_att(ContactElements_TypeId)");
247       if (!dataFile.add_att("Points_TypeId", mesh->Points->referenceElementSet->referenceElement->Type->TypeId) )
248          throw DataException(msgPrefix+"add_att(Points_TypeId)");
249       if (!dataFile.add_att("num_Tags", num_Tags) )
250          throw DataException(msgPrefix+"add_att(num_Tags)");
251    
252       // // // // // Nodes // // // // //
253    
254       // Nodes nodeDistribution
255       if (! ( ids = dataFile.add_var("Nodes_NodeDistribution", ncInt, ncdims[2])) )
256          throw DataException(msgPrefix+"add_var(Nodes_NodeDistribution)");
257       int_ptr = &mesh->Nodes->nodesDistribution->first_component[0];
258       if (! (ids->put(int_ptr, mpi_size+1)) )
259          throw DataException(msgPrefix+"put(Nodes_NodeDistribution)");
260    
261       // Nodes degreesOfFreedomDistribution
262       if (! ( ids = dataFile.add_var("Nodes_DofDistribution", ncInt, ncdims[2])) )
263          throw DataException(msgPrefix+"add_var(Nodes_DofDistribution)");
264       int_ptr = &mesh->Nodes->degreesOfFreedomDistribution->first_component[0];
265       if (! (ids->put(int_ptr, mpi_size+1)) )
266          throw DataException(msgPrefix+"put(Nodes_DofDistribution)");
267    
268       // Only write nodes if non-empty because NetCDF doesn't like empty arrays
269       // (it treats them as NC_UNLIMITED)
270       if (numNodes>0) {
271    
272          // Nodes Id
273          if (! ( ids = dataFile.add_var("Nodes_Id", ncInt, ncdims[0])) )
274             throw DataException(msgPrefix+"add_var(Nodes_Id)");
275          int_ptr = &mesh->Nodes->Id[0];
276          if (! (ids->put(int_ptr, numNodes)) )
277             throw DataException(msgPrefix+"put(Nodes_Id)");
278    
279          // Nodes Tag
280          if (! ( ids = dataFile.add_var("Nodes_Tag", ncInt, ncdims[0])) )
281             throw DataException(msgPrefix+"add_var(Nodes_Tag)");
282          int_ptr = &mesh->Nodes->Tag[0];
283          if (! (ids->put(int_ptr, numNodes)) )
284             throw DataException(msgPrefix+"put(Nodes_Tag)");
285    
286          // Nodes gDOF
287          if (! ( ids = dataFile.add_var("Nodes_gDOF", ncInt, ncdims[0])) )
288             throw DataException(msgPrefix+"add_var(Nodes_gDOF)");
289          int_ptr = &mesh->Nodes->globalDegreesOfFreedom[0];
290          if (! (ids->put(int_ptr, numNodes)) )
291             throw DataException(msgPrefix+"put(Nodes_gDOF)");
292    
293          // Nodes global node index
294          if (! ( ids = dataFile.add_var("Nodes_gNI", ncInt, ncdims[0])) )
295             throw DataException(msgPrefix+"add_var(Nodes_gNI)");
296          int_ptr = &mesh->Nodes->globalNodesIndex[0];
297          if (! (ids->put(int_ptr, numNodes)) )
298             throw DataException(msgPrefix+"put(Nodes_gNI)");
299    
300          // Nodes grDof
301          if (! ( ids = dataFile.add_var("Nodes_grDfI", ncInt, ncdims[0])) )
302             throw DataException(msgPrefix+"add_var(Nodes_grDfI)");
303          int_ptr = &mesh->Nodes->globalReducedDOFIndex[0];
304          if (! (ids->put(int_ptr, numNodes)) )
305             throw DataException(msgPrefix+"put(Nodes_grDfI)");
306    
307          // Nodes grNI
308          if (! ( ids = dataFile.add_var("Nodes_grNI", ncInt, ncdims[0])) )
309             throw DataException(msgPrefix+"add_var(Nodes_grNI)");
310          int_ptr = &mesh->Nodes->globalReducedNodesIndex[0];
311          if (! (ids->put(int_ptr, numNodes)) )
312             throw DataException(msgPrefix+"put(Nodes_grNI)");
313    
314          // Nodes Coordinates
315          if (! ( ids = dataFile.add_var("Nodes_Coordinates", ncDouble, ncdims[0], ncdims[1]) ) )
316             throw DataException(msgPrefix+"add_var(Nodes_Coordinates)");
317          if (! (ids->put(&(mesh->Nodes->Coordinates[INDEX2(0,0,numDim)]), numNodes, numDim)) )
318             throw DataException(msgPrefix+"put(Nodes_Coordinates)");
319    
320       }
321    
322       // // // // // Elements // // // // //
323    
324       if (num_Elements>0) {
325    
326          // Elements_Id
327          if (! ( ids = dataFile.add_var("Elements_Id", ncInt, ncdims[3])) )
328             throw DataException(msgPrefix+"add_var(Elements_Id)");
329          int_ptr = &mesh->Elements->Id[0];
330          if (! (ids->put(int_ptr, num_Elements)) )
331             throw DataException(msgPrefix+"put(Elements_Id)");
332    
333          // Elements_Tag
334          if (! ( ids = dataFile.add_var("Elements_Tag", ncInt, ncdims[3])) )
335             throw DataException(msgPrefix+"add_var(Elements_Tag)");
336          int_ptr = &mesh->Elements->Tag[0];
337          if (! (ids->put(int_ptr, num_Elements)) )
338             throw DataException(msgPrefix+"put(Elements_Tag)");
339    
340          // Elements_Owner
341          if (! ( ids = dataFile.add_var("Elements_Owner", ncInt, ncdims[3])) )
342             throw DataException(msgPrefix+"add_var(Elements_Owner)");
343          int_ptr = &mesh->Elements->Owner[0];
344          if (! (ids->put(int_ptr, num_Elements)) )
345             throw DataException(msgPrefix+"put(Elements_Owner)");
346    
347          // Elements_Color
348          if (! ( ids = dataFile.add_var("Elements_Color", ncInt, ncdims[3])) )
349             throw DataException(msgPrefix+"add_var(Elements_Color)");
350          int_ptr = &mesh->Elements->Color[0];
351          if (! (ids->put(int_ptr, num_Elements)) )
352             throw DataException(msgPrefix+"put(Elements_Color)");
353    
354          // Elements_Nodes
355          if (! ( ids = dataFile.add_var("Elements_Nodes", ncInt, ncdims[3], ncdims[7]) ) )
356             throw DataException(msgPrefix+"add_var(Elements_Nodes)");
357          if (! (ids->put(&(mesh->Elements->Nodes[0]), num_Elements, num_Elements_numNodes)) )
358             throw DataException(msgPrefix+"put(Elements_Nodes)");
359    
360       }
361    
362       // // // // // Face_Elements // // // // //
363    
364       if (num_FaceElements>0) {
365    
366          // FaceElements_Id
367          if (! ( ids = dataFile.add_var("FaceElements_Id", ncInt, ncdims[4])) )
368             throw DataException(msgPrefix+"add_var(FaceElements_Id)");
369          int_ptr = &mesh->FaceElements->Id[0];
370          if (! (ids->put(int_ptr, num_FaceElements)) )
371             throw DataException(msgPrefix+"put(FaceElements_Id)");
372    
373          // FaceElements_Tag
374          if (! ( ids = dataFile.add_var("FaceElements_Tag", ncInt, ncdims[4])) )
375             throw DataException(msgPrefix+"add_var(FaceElements_Tag)");
376          int_ptr = &mesh->FaceElements->Tag[0];
377          if (! (ids->put(int_ptr, num_FaceElements)) )
378             throw DataException(msgPrefix+"put(FaceElements_Tag)");
379    
380          // FaceElements_Owner
381          if (! ( ids = dataFile.add_var("FaceElements_Owner", ncInt, ncdims[4])) )
382             throw DataException(msgPrefix+"add_var(FaceElements_Owner)");
383          int_ptr = &mesh->FaceElements->Owner[0];
384          if (! (ids->put(int_ptr, num_FaceElements)) )
385             throw DataException(msgPrefix+"put(FaceElements_Owner)");
386    
387          // FaceElements_Color
388          if (! ( ids = dataFile.add_var("FaceElements_Color", ncInt, ncdims[4])) )
389             throw DataException(msgPrefix+"add_var(FaceElements_Color)");
390          int_ptr = &mesh->FaceElements->Color[0];
391          if (! (ids->put(int_ptr, num_FaceElements)) )
392             throw DataException(msgPrefix+"put(FaceElements_Color)");
393    
394          // FaceElements_Nodes
395          if (! ( ids = dataFile.add_var("FaceElements_Nodes", ncInt, ncdims[4], ncdims[8]) ) )
396             throw DataException(msgPrefix+"add_var(FaceElements_Nodes)");
397          if (! (ids->put(&(mesh->FaceElements->Nodes[0]), num_FaceElements, num_FaceElements_numNodes)) )
398             throw DataException(msgPrefix+"put(FaceElements_Nodes)");
399    
400       }
401    
402       // // // // // Contact_Elements // // // // //
403    
404       if (num_ContactElements>0) {
405    
406          // ContactElements_Id
407          if (! ( ids = dataFile.add_var("ContactElements_Id", ncInt, ncdims[5])) )
408             throw DataException(msgPrefix+"add_var(ContactElements_Id)");
409          int_ptr = &mesh->ContactElements->Id[0];
410          if (! (ids->put(int_ptr, num_ContactElements)) )
411             throw DataException(msgPrefix+"put(ContactElements_Id)");
412    
413          // ContactElements_Tag
414          if (! ( ids = dataFile.add_var("ContactElements_Tag", ncInt, ncdims[5])) )
415             throw DataException(msgPrefix+"add_var(ContactElements_Tag)");
416          int_ptr = &mesh->ContactElements->Tag[0];
417          if (! (ids->put(int_ptr, num_ContactElements)) )
418             throw DataException(msgPrefix+"put(ContactElements_Tag)");
419    
420          // ContactElements_Owner
421          if (! ( ids = dataFile.add_var("ContactElements_Owner", ncInt, ncdims[5])) )
422             throw DataException(msgPrefix+"add_var(ContactElements_Owner)");
423          int_ptr = &mesh->ContactElements->Owner[0];
424          if (! (ids->put(int_ptr, num_ContactElements)) )
425             throw DataException(msgPrefix+"put(ContactElements_Owner)");
426    
427          // ContactElements_Color
428          if (! ( ids = dataFile.add_var("ContactElements_Color", ncInt, ncdims[5])) )
429             throw DataException(msgPrefix+"add_var(ContactElements_Color)");
430          int_ptr = &mesh->ContactElements->Color[0];
431          if (! (ids->put(int_ptr, num_ContactElements)) )
432             throw DataException(msgPrefix+"put(ContactElements_Color)");
433    
434          // ContactElements_Nodes
435          if (! ( ids = dataFile.add_var("ContactElements_Nodes", ncInt, ncdims[5], ncdims[9]) ) )
436             throw DataException(msgPrefix+"add_var(ContactElements_Nodes)");
437          if (! (ids->put(&(mesh->ContactElements->Nodes[0]), num_ContactElements, num_ContactElements_numNodes)) )
438             throw DataException(msgPrefix+"put(ContactElements_Nodes)");
439    
440       }
441    
442       // // // // // Points // // // // //
443    
444       if (num_Points>0) {
445    
446          fprintf(stderr, "\n\n\nWARNING: MeshAdapter::dump has not been tested with Point elements\n\n\n");
447    
448          // Points_Id
449          if (! ( ids = dataFile.add_var("Points_Id", ncInt, ncdims[6])) )
450             throw DataException(msgPrefix+"add_var(Points_Id)");
451          int_ptr = &mesh->Points->Id[0];
452          if (! (ids->put(int_ptr, num_Points)) )
453             throw DataException(msgPrefix+"put(Points_Id)");
454    
455          // Points_Tag
456          if (! ( ids = dataFile.add_var("Points_Tag", ncInt, ncdims[6])) )
457             throw DataException(msgPrefix+"add_var(Points_Tag)");
458          int_ptr = &mesh->Points->Tag[0];
459          if (! (ids->put(int_ptr, num_Points)) )
460             throw DataException(msgPrefix+"put(Points_Tag)");
461    
462          // Points_Owner
463          if (! ( ids = dataFile.add_var("Points_Owner", ncInt, ncdims[6])) )
464             throw DataException(msgPrefix+"add_var(Points_Owner)");
465          int_ptr = &mesh->Points->Owner[0];
466          if (! (ids->put(int_ptr, num_Points)) )
467             throw DataException(msgPrefix+"put(Points_Owner)");
468    
469          // Points_Color
470          if (! ( ids = dataFile.add_var("Points_Color", ncInt, ncdims[6])) )
471             throw DataException(msgPrefix+"add_var(Points_Color)");
472          int_ptr = &mesh->Points->Color[0];
473          if (! (ids->put(int_ptr, num_Points)) )
474             throw DataException(msgPrefix+"put(Points_Color)");
475    
476          // Points_Nodes
477          // mesh->Nodes->Id[mesh->Points->Nodes[INDEX2(0,i,1)]]
478          if (! ( ids = dataFile.add_var("Points_Nodes", ncInt, ncdims[6]) ) )
479             throw DataException(msgPrefix+"add_var(Points_Nodes)");
480          if (! (ids->put(&(mesh->Points->Nodes[0]), num_Points)) )
481             throw DataException(msgPrefix+"put(Points_Nodes)");
482    
483       }
484    
485       // // // // // TagMap // // // // //
486    
487       if (num_Tags>0) {
488    
489          // Temp storage to gather node IDs
490          int *Tags_keys = TMPMEMALLOC(num_Tags, int);
491          char name_temp[4096];
492    
493          /* Copy tag data into temp arrays */
494          tag_map = mesh->TagMap;
495          if (tag_map) {
496             int i = 0;
497             while (tag_map) {
498                Tags_keys[i++] = tag_map->tag_key;
499                tag_map=tag_map->next;
500             }
501          }
502    
503          // Tags_keys
504          if (! ( ids = dataFile.add_var("Tags_keys", ncInt, ncdims[10])) )
505             throw DataException(msgPrefix+"add_var(Tags_keys)");
506          int_ptr = &Tags_keys[0];
507          if (! (ids->put(int_ptr, num_Tags)) )
508             throw DataException(msgPrefix+"put(Tags_keys)");
509    
510          // Tags_names_*
511          // This is an array of strings, it should be stored as an array but
512          // instead I have hacked in one attribute per string because the NetCDF
513          // manual doesn't tell how to do an array of strings
514          tag_map = mesh->TagMap;
515          if (tag_map) {
516             int i = 0;
517             while (tag_map) {
518                sprintf(name_temp, "Tags_name_%d", i);
519                if (!dataFile.add_att(name_temp, tag_map->name) )
520                   throw DataException(msgPrefix+"add_att(Tags_names_XX)");
521                tag_map=tag_map->next;
522                i++;
523             }
524          }
525    
526          TMPMEMFREE(Tags_keys);
527       }
528    
529    /* Send token to next MPI process so he can take his turn */
530    #ifdef ESYS_MPI
531       if (mpi_rank<mpi_size-1) MPI_Send(&num_Tags, 0, MPI_INT, mpi_rank+1, 81800, mesh->MPIInfo->comm);
532    #endif
533    
534       // NetCDF file is closed by destructor of NcFile object
535    
536    #else
537       Finley_setError(IO_ERROR, "MeshAdapter::dump: not configured with NetCDF. Please contact your installation manager.");
538    #endif  /* USE_NETCDF */
539       checkFinleyError();
540    }
541    
542  string MeshAdapter::getDescription() const  string MeshAdapter::getDescription() const
543  {  {
544    return "FinleyMesh";     return "FinleyMesh";
545  }  }
546    
547  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const  string MeshAdapter::functionSpaceTypeAsString(int functionSpaceType) const
548  {  {
549    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
550    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
551    if (loc==m_functionSpaceTypeNames.end()) {     if (loc==m_functionSpaceTypeNames.end()) {
552      return "Invalid function space type code.";        return "Invalid function space type code.";
553    } else {     } else {
554      return loc->second;        return loc->second;
555    }     }
556  }  }
557    
558  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const  bool MeshAdapter::isValidFunctionSpaceType(int functionSpaceType) const
559  {  {
560    FunctionSpaceNamesMapType::iterator loc;     FunctionSpaceNamesMapType::iterator loc;
561    loc=m_functionSpaceTypeNames.find(functionSpaceType);     loc=m_functionSpaceTypeNames.find(functionSpaceType);
562    return (loc!=m_functionSpaceTypeNames.end());     return (loc!=m_functionSpaceTypeNames.end());
563  }  }
564    
565  void MeshAdapter::setFunctionSpaceTypeNames()  void MeshAdapter::setFunctionSpaceTypeNames()
566  {  {
567    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
568      (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(DegreesOfFreedom,"Finley_DegreesOfFreedom"));
569    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
570      (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));     (FunctionSpaceNamesMapType::value_type(ReducedDegreesOfFreedom,"Finley_ReducedDegreesOfFreedom"));
571    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
572      (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));     (FunctionSpaceNamesMapType::value_type(Nodes,"Finley_Nodes"));
573    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
574      (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));     (FunctionSpaceNamesMapType::value_type(ReducedNodes,"Finley_Reduced_Nodes"));
575    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
576      (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));     (FunctionSpaceNamesMapType::value_type(Elements,"Finley_Elements"));
577    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
578      (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));     (FunctionSpaceNamesMapType::value_type(ReducedElements,"Finley_Reduced_Elements"));
579    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
580      (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));     (FunctionSpaceNamesMapType::value_type(FaceElements,"Finley_Face_Elements"));
581    m_functionSpaceTypeNames.insert     m_functionSpaceTypeNames.insert
582      (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));     (FunctionSpaceNamesMapType::value_type(ReducedFaceElements,"Finley_Reduced_Face_Elements"));
583       m_functionSpaceTypeNames.insert
584       (FunctionSpaceNamesMapType::value_type(Points,"Finley_Points"));
585       m_functionSpaceTypeNames.insert
586       (FunctionSpaceNamesMapType::value_type(ContactElementsZero,"Finley_Contact_Elements_0"));
587       m_functionSpaceTypeNames.insert
588       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsZero,"Finley_Reduced_Contact_Elements_0"));
589       m_functionSpaceTypeNames.insert
590       (FunctionSpaceNamesMapType::value_type(ContactElementsOne,"Finley_Contact_Elements_1"));
591       m_functionSpaceTypeNames.insert
592       (FunctionSpaceNamesMapType::value_type(ReducedContactElementsOne,"Finley_Reduced_Contact_Elements_1"));
593  }  }
594    
595  int MeshAdapter::getContinuousFunctionCode() const  int MeshAdapter::getContinuousFunctionCode() const
596  {  {
597    return Nodes;     return Nodes;
598  }  }
599    int MeshAdapter::getReducedContinuousFunctionCode() const
600    {
601       return ReducedNodes;
602    }
603    
604  int MeshAdapter::getFunctionCode() const  int MeshAdapter::getFunctionCode() const
605  {  {
606    return Elements;     return Elements;
607  }  }
608    int MeshAdapter::getReducedFunctionCode() const
609    {
610       return ReducedElements;
611    }
612    
613  int MeshAdapter::getFunctionOnBoundaryCode() const  int MeshAdapter::getFunctionOnBoundaryCode() const
614  {  {
615    return FaceElements;     return FaceElements;
616  }  }
617    int MeshAdapter::getReducedFunctionOnBoundaryCode() const
618    {
619       return ReducedFaceElements;
620    }
621    
622  int MeshAdapter::getFunctionOnContactZeroCode() const  int MeshAdapter::getFunctionOnContactZeroCode() const
623  {  {
624    return ContactElementsZero;     return ContactElementsZero;
625    }
626    int MeshAdapter::getReducedFunctionOnContactZeroCode() const
627    {
628       return ReducedContactElementsZero;
629  }  }
630    
631  int MeshAdapter::getFunctionOnContactOneCode() const  int MeshAdapter::getFunctionOnContactOneCode() const
632  {  {
633    return ContactElementsOne;     return ContactElementsOne;
634    }
635    int MeshAdapter::getReducedFunctionOnContactOneCode() const
636    {
637       return ReducedContactElementsOne;
638  }  }
639    
640  int MeshAdapter::getSolutionCode() const  int MeshAdapter::getSolutionCode() const
641  {  {
642    return DegreesOfFreedom;     return DegreesOfFreedom;
643  }  }
644    
645  int MeshAdapter::getReducedSolutionCode() const  int MeshAdapter::getReducedSolutionCode() const
646  {  {
647    return ReducedDegreesOfFreedom;     return ReducedDegreesOfFreedom;
 }  
 int MeshAdapter::getDiracDeltaFunctionCode() const  
 {  
   return Points;  
648  }  }
649    
650  int MeshAdapter::getTagFromSampleNo(int functionSpaceType, int sampleNo) const  int MeshAdapter::getDiracDeltaFunctionCode() const
651  {  {
652    //     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];  
653  }  }
654    
655  //  //
656  // returns a pointer to the tag list of samples of functionSpaceType  // return the spatial dimension of the Mesh:
657  //  //
658  void MeshAdapter::getTagList(int functionSpaceType, int** tagList,  int MeshAdapter::getDim() const
                  int* numTags) const  
659  {  {
660    *tagList=NULL;     Finley_Mesh* mesh=m_finleyMesh.get();
661    *numTags=0;     int numDim=Finley_Mesh_getDim(mesh);
662    Finley_Mesh* mesh=m_finleyMesh.get();     checkFinleyError();
663    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;  
664  }  }
665    
666  //  //
667  // return the spatial dimension of the Mesh:  // Return the number of data points summed across all MPI processes
668  //  //
669  int MeshAdapter::getDim() const  int MeshAdapter::getNumDataPointsGlobal() const
670  {  {
671    int numDim=Finley_Mesh_getDim(m_finleyMesh.get());     return Finley_NodeFile_getGlobalNumNodes(m_finleyMesh.get()->Nodes);
   checkFinleyError();  
   return numDim;  
672  }  }
673    
674  //  //
675  // 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
676  // 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 681  pair<int,int> MeshAdapter::getDataShape(
681     int numSamples=0;     int numSamples=0;
682     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
683     switch (functionSpaceCode) {     switch (functionSpaceCode) {
684        case(Nodes):     case(Nodes):
685             numDataPointsPerSample=1;     numDataPointsPerSample=1;
686             if (mesh->Nodes!=NULL) numSamples=mesh->Nodes->numNodes;     numSamples=Finley_NodeFile_getNumNodes(mesh->Nodes);
687             break;     break;
688        case(Elements):     case(ReducedNodes):
689             if (mesh->Elements!=NULL) {     numDataPointsPerSample=1;
690               numSamples=mesh->Elements->numElements;     numSamples=Finley_NodeFile_getNumReducedNodes(mesh->Nodes);
691               numDataPointsPerSample=mesh->Elements->ReferenceElement->numQuadNodes;     break;
692             }     case(Elements):
693             break;     if (mesh->Elements!=NULL) {
694        case(FaceElements):        numSamples=mesh->Elements->numElements;
695             if (mesh->FaceElements!=NULL) {        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
696                  numDataPointsPerSample=mesh->FaceElements->ReferenceElement->numQuadNodes;     }
697                  numSamples=mesh->FaceElements->numElements;     break;
698             }     case(ReducedElements):
699             break;     if (mesh->Elements!=NULL) {
700        case(Points):        numSamples=mesh->Elements->numElements;
701             if (mesh->Points!=NULL) {        numDataPointsPerSample=mesh->Elements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
702               numDataPointsPerSample=1;     }
703               numSamples=mesh->Points->numElements;     break;
704             }     case(FaceElements):
705             break;     if (mesh->FaceElements!=NULL) {
706        case(ContactElementsZero):        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
707             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
708               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
709               numSamples=mesh->ContactElements->numElements;     break;
710             }     case(ReducedFaceElements):
711             break;     if (mesh->FaceElements!=NULL) {
712        case(ContactElementsOne):        numDataPointsPerSample=mesh->FaceElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
713             if (mesh->ContactElements!=NULL) {        numSamples=mesh->FaceElements->numElements;
714               numDataPointsPerSample=mesh->ContactElements->ReferenceElement->numQuadNodes;     }
715               numSamples=mesh->ContactElements->numElements;     break;
716             }     case(Points):
717             break;     if (mesh->Points!=NULL) {
718        case(DegreesOfFreedom):        numDataPointsPerSample=1;
719             if (mesh->Nodes!=NULL) {        numSamples=mesh->Points->numElements;
720               numDataPointsPerSample=1;     }
721               numSamples=mesh->Nodes->numDegreesOfFreedom;     break;
722             }     case(ContactElementsZero):
723             break;     if (mesh->ContactElements!=NULL) {
724        case(ReducedDegreesOfFreedom):        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
725             if (mesh->Nodes!=NULL) {        numSamples=mesh->ContactElements->numElements;
726               numDataPointsPerSample=1;     }
727               numSamples=mesh->Nodes->reducedNumDegreesOfFreedom;     break;
728             }     case(ReducedContactElementsZero):
729             break;     if (mesh->ContactElements!=NULL) {
730        default:        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
731          stringstream temp;        numSamples=mesh->ContactElements->numElements;
732          temp << "Error - Invalid function space type: "     }
733           << functionSpaceCode << " for domain: " << getDescription();     break;
734          throw FinleyAdapterException(temp.str());     case(ContactElementsOne):
735          break;     if (mesh->ContactElements!=NULL) {
736        }        numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElement->Parametrization->numQuadNodes;
737        return pair<int,int>(numDataPointsPerSample,numSamples);        numSamples=mesh->ContactElements->numElements;
738       }
739       break;
740       case(ReducedContactElementsOne):
741       if (mesh->ContactElements!=NULL) {
742          numDataPointsPerSample=mesh->ContactElements->referenceElementSet->referenceElementReducedQuadrature->Parametrization->numQuadNodes;
743          numSamples=mesh->ContactElements->numElements;
744       }
745       break;
746       case(DegreesOfFreedom):
747       if (mesh->Nodes!=NULL) {
748          numDataPointsPerSample=1;
749          numSamples=Finley_NodeFile_getNumDegreesOfFreedom(mesh->Nodes);
750       }
751       break;
752       case(ReducedDegreesOfFreedom):
753       if (mesh->Nodes!=NULL) {
754          numDataPointsPerSample=1;
755          numSamples=Finley_NodeFile_getNumReducedDegreesOfFreedom(mesh->Nodes);
756       }
757       break;
758       default:
759          stringstream temp;
760          temp << "Error - Invalid function space type: " << functionSpaceCode << " for domain: " << getDescription();
761          throw FinleyAdapterException(temp.str());
762          break;
763       }
764       return pair<int,int>(numDataPointsPerSample,numSamples);
765  }  }
766    
767  //  //
768  // 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:
769  //  //
770  void MeshAdapter::addPDEToSystem(  void MeshAdapter::addPDEToSystem(
771                       SystemMatrixAdapter& mat, Data& rhs,                                   AbstractSystemMatrix& mat, escript::Data& rhs,
772                       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,
773                       const Data& d, const Data& y,                                   const escript::Data& d, const escript::Data& y,
774                       const Data& d_contact,const Data& y_contact) const                                   const escript::Data& d_contact,const escript::Data& y_contact) const
775  {  {
776     Finley_Mesh* mesh=m_finleyMesh.get();     SystemMatrixAdapter* smat=dynamic_cast<SystemMatrixAdapter*>(&mat);
777     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,mat.getFinley_SystemMatrix(),&(rhs.getDataC()),     if (smat==0)
778                         &(A.getDataC()),&(B.getDataC()),&(C.getDataC()),&(D.getDataC()),&(X.getDataC()),&(Y.getDataC()));     {
779     checkFinleyError();      throw FinleyAdapterException("finley only supports its own system matrices.");
780     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,     }
781                    mat.getFinley_SystemMatrix(),     escriptDataC _rhs=rhs.getDataC();
782                    &(rhs.getDataC()),     escriptDataC _A  =A.getDataC();
783                                    &(d.getDataC()),&(y.getDataC()),     escriptDataC _B=B.getDataC();
784                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     escriptDataC _C=C.getDataC();
785     checkFinleyError();     escriptDataC _D=D.getDataC();
786     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,     escriptDataC _X=X.getDataC();
787                    mat.getFinley_SystemMatrix(),     escriptDataC _Y=Y.getDataC();
788                    &(rhs.getDataC()),     escriptDataC _d=d.getDataC();
789                                    &(d_contact.getDataC()),     escriptDataC _y=y.getDataC();
790                    &(y_contact.getDataC()),     escriptDataC _d_contact=d_contact.getDataC();
791                                    Finley_Assemble_handelShapeMissMatch_Step_out);     escriptDataC _y_contact=y_contact.getDataC();
792    
793       Finley_Mesh* mesh=m_finleyMesh.get();
794    
795       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,smat->getPaso_SystemMatrix(), &_rhs, &_A, &_B, &_C, &_D, &_X, &_Y );
796       checkFinleyError();
797    
798       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, smat->getPaso_SystemMatrix(), &_rhs, 0, 0, 0, &_d, 0, &_y );
799       checkFinleyError();
800    
801       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, smat->getPaso_SystemMatrix(), &_rhs , 0, 0, 0, &_d_contact, 0, &_y_contact );
802     checkFinleyError();     checkFinleyError();
803  }  }
804    
805    void  MeshAdapter::addPDEToLumpedSystem(
806                                            escript::Data& mat,
807                                            const escript::Data& D,
808                                            const escript::Data& d) const
809    {
810       escriptDataC _mat=mat.getDataC();
811       escriptDataC _D=D.getDataC();
812       escriptDataC _d=d.getDataC();
813    
814       Finley_Mesh* mesh=m_finleyMesh.get();
815    
816       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->Elements,&_mat, &_D);
817       checkFinleyError();
818      
819       Finley_Assemble_LumpedSystem(mesh->Nodes,mesh->FaceElements,&_mat, &_d);
820       checkFinleyError();
821    
822    }
823    
824    
825  //  //
826  // adds linear PDE of second order into the right hand side only  // adds linear PDE of second order into the right hand side only
827  //  //
828  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  
829  {  {
830     Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
831     Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,0,&(rhs.getDataC()),0,0,0,0,&(X.getDataC()),&(Y.getDataC()));  
832       escriptDataC _rhs=rhs.getDataC();
833       escriptDataC _X=X.getDataC();
834       escriptDataC _Y=Y.getDataC();
835       escriptDataC _y=y.getDataC();
836       escriptDataC _y_contact=y_contact.getDataC();
837    
838       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements, 0, &_rhs, 0, 0, 0, 0, &_X, &_Y );
839     checkFinleyError();     checkFinleyError();
840     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y.getDataC()),  
841                                    Finley_Assemble_handelShapeMissMatch_Mean_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, 0, &_rhs, 0, 0, 0, 0, 0, &_y );
 // cout << "Calling :addPDEToRHS." << endl;  
842     checkFinleyError();     checkFinleyError();
843     Finley_Assemble_RobinCondition(mesh->Nodes,mesh->FaceElements,0,&(rhs.getDataC()),0,&(y_contact.getDataC()),  
844                                    Finley_Assemble_handelShapeMissMatch_Step_out);     Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, 0, &_rhs , 0, 0, 0, 0, 0, &_y_contact );
 // cout << "Calling :addPDEToRHS." << endl;  
845     checkFinleyError();     checkFinleyError();
846  }  }
847  //  //
848    // adds PDE of second order into a transport problem
849    //
850    void MeshAdapter::addPDEToTransportProblem(
851                                               AbstractTransportProblem& tp, escript::Data& source, const escript::Data& M,
852                                               const escript::Data& A, const escript::Data& B, const escript::Data& C,
853                                               const  escript::Data& D,const  escript::Data& X,const  escript::Data& Y,
854                                               const escript::Data& d, const escript::Data& y,
855                                               const escript::Data& d_contact,const escript::Data& y_contact) const
856    {
857       TransportProblemAdapter* tpa=dynamic_cast<TransportProblemAdapter*>(&tp);
858       if (tpa==0)
859       {
860        throw FinleyAdapterException("finley only supports its own transport problems.");
861       }
862    
863    
864       DataTypes::ShapeType shape;
865       source.expand();
866       escriptDataC _source=source.getDataC();
867       escriptDataC _M=M.getDataC();
868       escriptDataC _A=A.getDataC();
869       escriptDataC _B=B.getDataC();
870       escriptDataC _C=C.getDataC();
871       escriptDataC _D=D.getDataC();
872       escriptDataC _X=X.getDataC();
873       escriptDataC _Y=Y.getDataC();
874       escriptDataC _d=d.getDataC();
875       escriptDataC _y=y.getDataC();
876       escriptDataC _d_contact=d_contact.getDataC();
877       escriptDataC _y_contact=y_contact.getDataC();
878    
879       Finley_Mesh* mesh=m_finleyMesh.get();
880       Paso_TransportProblem* _tp = tpa->getPaso_TransportProblem();
881    
882       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->mass_matrix, &_source, 0, 0, 0, &_M, 0, 0 );
883       checkFinleyError();
884    
885       Finley_Assemble_PDE(mesh->Nodes,mesh->Elements,_tp->transport_matrix, &_source, &_A, &_B, &_C, &_D, &_X, &_Y );
886       checkFinleyError();
887    
888       Finley_Assemble_PDE(mesh->Nodes,mesh->FaceElements, _tp->transport_matrix, &_source, 0, 0, 0, &_d, 0, &_y );
889       checkFinleyError();
890    
891       Finley_Assemble_PDE(mesh->Nodes,mesh->ContactElements, _tp->transport_matrix, &_source , 0, 0, 0, &_d_contact, 0, &_y_contact );
892       checkFinleyError();
893    }
894    
895    //
896  // interpolates data between different function spaces:  // interpolates data between different function spaces:
897  //  //
898  void MeshAdapter::interpolateOnDomain(Data& target,const Data& in) const  void MeshAdapter::interpolateOnDomain(escript::Data& target,const escript::Data& in) const
899  {  {
900    const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(in.getFunctionSpace().getDomain());     const MeshAdapter& inDomain=dynamic_cast<const MeshAdapter&>(*(in.getFunctionSpace().getDomain()));
901    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(*(target.getFunctionSpace().getDomain()));
902    if (inDomain!=*this)     if (inDomain!=*this)  
903       throw FinleyAdapterException("Error - Illegal domain of interpolant.");        throw FinleyAdapterException("Error - Illegal domain of interpolant.");
904    if (targetDomain!=*this)     if (targetDomain!=*this)
905       throw FinleyAdapterException("Error - Illegal domain of interpolation target.");        throw FinleyAdapterException("Error - Illegal domain of interpolation target.");
906    
907    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
908    switch(in.getFunctionSpace().getTypeCode()) {     escriptDataC _target=target.getDataC();
909       case(Nodes):     escriptDataC _in=in.getDataC();
910          switch(target.getFunctionSpace().getTypeCode()) {     switch(in.getFunctionSpace().getTypeCode()) {
911             case(Nodes):     case(Nodes):
912             case(ReducedDegreesOfFreedom):        switch(target.getFunctionSpace().getTypeCode()) {
913             case(DegreesOfFreedom):        case(Nodes):
914                 Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        case(ReducedNodes):
915                 break;        case(DegreesOfFreedom):
916             case(Elements):        case(ReducedDegreesOfFreedom):
917                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
918                 break;        break;
919             case(FaceElements):        case(Elements):
920                 Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));        case(ReducedElements):
921                 break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
922             case(Points):        break;
923                 Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        case(FaceElements):
924                 break;        case(ReducedFaceElements):
925             case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
926                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
927                 break;        case(Points):
928             case(ContactElementsOne):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
929                 Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));        break;
930                 break;        case(ContactElementsZero):
931             default:        case(ReducedContactElementsZero):
932                 Finley_ErrorCode=TYPE_ERROR;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
933                 sprintf(Finley_ErrorMsg,"Interpolation on Domain: Finley does not know anything about function space type %d",target.getFunctionSpace().getTypeCode());        break;
934                 break;        case(ContactElementsOne):
935          }        case(ReducedContactElementsOne):
936          break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
937       case(Elements):        break;
938          if (target.getFunctionSpace().getTypeCode()==Elements) {        default:
939             Finley_Assemble_CopyElementData(mesh->Elements,&(target.getDataC()),&(in.getDataC()));           stringstream temp;
940          } else {           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
941             Finley_ErrorCode=TYPE_ERROR;           throw FinleyAdapterException(temp.str());
942             sprintf(Finley_ErrorMsg,"No interpolation with data on elements possible.");           break;
943          }        }
944          break;        break;
945       case(FaceElements):     case(ReducedNodes):
946          if (target.getFunctionSpace().getTypeCode()==FaceElements) {        switch(target.getFunctionSpace().getTypeCode()) {
947             Finley_Assemble_CopyElementData(mesh->FaceElements,&(target.getDataC()),&(in.getDataC()));        case(Nodes):
948          } else {        case(ReducedNodes):
949             Finley_ErrorCode=TYPE_ERROR;        case(DegreesOfFreedom):
950             sprintf(Finley_ErrorMsg,"No interpolation with data on face elements possible.");        case(ReducedDegreesOfFreedom):
951             break;        Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
952         }        break;
953       case(Points):        case(Elements):
954          if (target.getFunctionSpace().getTypeCode()==Points) {        case(ReducedElements):
955             Finley_Assemble_CopyElementData(mesh->Points,&(target.getDataC()),&(in.getDataC()));        Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
956          } else {        break;
957             Finley_ErrorCode=TYPE_ERROR;        case(FaceElements):
958             sprintf(Finley_ErrorMsg,"No interpolation with data on points possible.");        case(ReducedFaceElements):
959             break;        Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
960          }        break;
961          break;        case(Points):
962       case(ContactElementsZero):        Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
963       case(ContactElementsOne):        break;
964          if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {        case(ContactElementsZero):
965             Finley_Assemble_CopyElementData(mesh->ContactElements,&(target.getDataC()),&(in.getDataC()));        case(ReducedContactElementsZero):
966          } else {        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
967             Finley_ErrorCode=TYPE_ERROR;        break;
968             sprintf(Finley_ErrorMsg,"No interpolation with data on contact elements possible.");        case(ContactElementsOne):
969             break;        case(ReducedContactElementsOne):
970          }        Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
971          break;        break;
972       case(DegreesOfFreedom):        default:
973          switch(target.getFunctionSpace().getTypeCode()) {           stringstream temp;
974             case(ReducedDegreesOfFreedom):           temp << "Error - Interpolation on Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
975             case(DegreesOfFreedom):           throw FinleyAdapterException(temp.str());
976             case(Nodes):           break;
977                Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        }
978                break;        break;
979             case(Elements):     case(Elements):
980                Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==Elements) {
981                break;           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
982             case(FaceElements):        } else if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
983                Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_AverageElementData(mesh->Elements,&_target,&_in);
984                break;        } else {
985             case(Points):           throw FinleyAdapterException("Error - No interpolation with data on elements possible.");
986                Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));        }
987                break;        break;
988             case(ContactElementsZero):     case(ReducedElements):
989             case(ContactElementsOne):        if (target.getFunctionSpace().getTypeCode()==ReducedElements) {
990                Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));           Finley_Assemble_CopyElementData(mesh->Elements,&_target,&_in);
991               break;        } else {
992             default:           throw FinleyAdapterException("Error - No interpolation with data on elements with reduced integration order possible.");
993               Finley_ErrorCode=TYPE_ERROR;        }
994               sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",target.getFunctionSpace().getTypeCode());        break;
995               break;     case(FaceElements):
996          }        if (target.getFunctionSpace().getTypeCode()==FaceElements) {
997          break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
998       case(ReducedDegreesOfFreedom):        } else if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
999         switch(target.getFunctionSpace().getTypeCode()) {           Finley_Assemble_AverageElementData(mesh->FaceElements,&_target,&_in);
1000            case(ReducedDegreesOfFreedom):        } else {
1001            case(Nodes):           throw FinleyAdapterException("Error - No interpolation with data on face elements possible.");
1002               Finley_Assemble_CopyNodalData(mesh->Nodes,&(target.getDataC()),&(in.getDataC()));        }
1003               break;        break;
1004            case(Elements):     case(ReducedFaceElements):
1005               Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&(in.getDataC()),&(target.getDataC()));        if (target.getFunctionSpace().getTypeCode()==ReducedFaceElements) {
1006               break;           Finley_Assemble_CopyElementData(mesh->FaceElements,&_target,&_in);
1007            case(FaceElements):        } else {
1008               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.");
1009               break;        }
1010            case(Points):        break;
1011               Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&(in.getDataC()),&(target.getDataC()));     case(Points):
1012               break;        if (target.getFunctionSpace().getTypeCode()==Points) {
1013            case(ContactElementsZero):           Finley_Assemble_CopyElementData(mesh->Points,&_target,&_in);
1014            case(ContactElementsOne):        } else {
1015               Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&(in.getDataC()),&(target.getDataC()));           throw FinleyAdapterException("Error - No interpolation with data on points possible.");
1016               break;        }
1017            case(DegreesOfFreedom):        break;
1018               Finley_ErrorCode=TYPE_ERROR;     case(ContactElementsZero):
1019               sprintf(Finley_ErrorMsg,"Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");     case(ContactElementsOne):
1020               break;        if (target.getFunctionSpace().getTypeCode()==ContactElementsZero || target.getFunctionSpace().getTypeCode()==ContactElementsOne) {
1021            default:           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1022               Finley_ErrorCode=TYPE_ERROR;        } else if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1023               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);
1024               break;        } else {
1025         }           throw FinleyAdapterException("Error - No interpolation with data on contact elements possible.");
1026         break;        }
1027       default:        break;
1028          Finley_ErrorCode=TYPE_ERROR;     case(ReducedContactElementsZero):
1029          sprintf(Finley_ErrorMsg,"Interpolation On Domain: Finley does not know anything about function space type %d",in.getFunctionSpace().getTypeCode());     case(ReducedContactElementsOne):
1030          break;        if (target.getFunctionSpace().getTypeCode()==ReducedContactElementsZero || target.getFunctionSpace().getTypeCode()==ReducedContactElementsOne) {
1031    }           Finley_Assemble_CopyElementData(mesh->ContactElements,&_target,&_in);
1032    checkFinleyError();        } else {
1033             throw FinleyAdapterException("Error - No interpolation with data on contact elements with reduced integration order possible.");
1034          }
1035          break;
1036       case(DegreesOfFreedom):      
1037          switch(target.getFunctionSpace().getTypeCode()) {
1038          case(ReducedDegreesOfFreedom):
1039          case(DegreesOfFreedom):
1040          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1041          break;
1042      
1043          case(Nodes):
1044          case(ReducedNodes):
1045          if (getMPISize()>1) {
1046             escript::Data temp=escript::Data(in);
1047             temp.expand();
1048             escriptDataC _in2 = temp.getDataC();
1049             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1050          } else {
1051             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1052          }
1053          break;
1054          case(Elements):
1055          case(ReducedElements):
1056          if (getMPISize()>1) {
1057             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1058             escriptDataC _in2 = temp.getDataC();
1059             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1060          } else {
1061             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1062          }
1063          break;
1064          case(FaceElements):
1065          case(ReducedFaceElements):
1066          if (getMPISize()>1) {
1067             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1068             escriptDataC _in2 = temp.getDataC();
1069             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1070      
1071          } else {
1072             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1073          }
1074          break;
1075          case(Points):
1076          if (getMPISize()>1) {
1077             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1078             escriptDataC _in2 = temp.getDataC();
1079          } else {
1080             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1081          }
1082          break;
1083          case(ContactElementsZero):
1084          case(ContactElementsOne):
1085          case(ReducedContactElementsZero):
1086          case(ReducedContactElementsOne):
1087          if (getMPISize()>1) {
1088             escript::Data temp=escript::Data( in,  continuousFunction(*this) );
1089             escriptDataC _in2 = temp.getDataC();
1090             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1091          } else {
1092             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1093          }
1094          break;
1095          default:
1096             stringstream temp;
1097             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1098             throw FinleyAdapterException(temp.str());
1099             break;
1100          }
1101          break;
1102       case(ReducedDegreesOfFreedom):
1103          switch(target.getFunctionSpace().getTypeCode()) {
1104          case(Nodes):
1105          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to mesh nodes.");
1106          break;
1107          case(ReducedNodes):
1108          if (getMPISize()>1) {
1109             escript::Data temp=escript::Data(in);
1110             temp.expand();
1111             escriptDataC _in2 = temp.getDataC();
1112             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in2);
1113          } else {
1114             Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1115          }
1116          break;
1117          case(DegreesOfFreedom):
1118          throw FinleyAdapterException("Error - Finley does not support interpolation from reduced degrees of freedom to degrees of freedom");
1119          break;
1120          case(ReducedDegreesOfFreedom):
1121          Finley_Assemble_CopyNodalData(mesh->Nodes,&_target,&_in);
1122          break;
1123          case(Elements):
1124          case(ReducedElements):
1125          if (getMPISize()>1) {
1126             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1127             escriptDataC _in2 = temp.getDataC();
1128             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in2,&_target);
1129          } else {
1130             Finley_Assemble_interpolate(mesh->Nodes,mesh->Elements,&_in,&_target);
1131          }
1132          break;
1133          case(FaceElements):
1134          case(ReducedFaceElements):
1135          if (getMPISize()>1) {
1136             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1137             escriptDataC _in2 = temp.getDataC();
1138             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in2,&_target);
1139          } else {
1140             Finley_Assemble_interpolate(mesh->Nodes,mesh->FaceElements,&_in,&_target);
1141          }
1142          break;
1143          case(Points):
1144          if (getMPISize()>1) {
1145             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1146             escriptDataC _in2 = temp.getDataC();
1147             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in2,&_target);
1148          } else {
1149             Finley_Assemble_interpolate(mesh->Nodes,mesh->Points,&_in,&_target);
1150          }
1151          break;
1152          case(ContactElementsZero):
1153          case(ContactElementsOne):
1154          case(ReducedContactElementsZero):
1155          case(ReducedContactElementsOne):
1156          if (getMPISize()>1) {
1157             escript::Data temp=escript::Data( in,  reducedContinuousFunction(*this) );
1158             escriptDataC _in2 = temp.getDataC();
1159             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in2,&_target);
1160          } else {
1161             Finley_Assemble_interpolate(mesh->Nodes,mesh->ContactElements,&_in,&_target);
1162          }
1163          break;
1164          default:
1165             stringstream temp;
1166             temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << target.getFunctionSpace().getTypeCode();
1167             throw FinleyAdapterException(temp.str());
1168             break;
1169          }
1170          break;
1171       default:
1172          stringstream temp;
1173          temp << "Error - Interpolation On Domain: Finley does not know anything about function space type %d" << in.getFunctionSpace().getTypeCode();
1174          throw FinleyAdapterException(temp.str());
1175          break;
1176       }
1177       checkFinleyError();
1178  }  }
1179    
1180  //  //
1181  // copies the locations of sample points into x:  // copies the locations of sample points into x:
1182  //  //
1183  void MeshAdapter::setToX(Data& arg) const  void MeshAdapter::setToX(escript::Data& arg) const
1184  {  {
1185    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1186    if (argDomain!=*this)     if (argDomain!=*this)
1187       throw FinleyAdapterException("Error - Illegal domain of data point locations");        throw FinleyAdapterException("Error - Illegal domain of data point locations");
1188    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1189    // in case of values node coordinates we can do the job directly:     // in case of values node coordinates we can do the job directly:
1190    if (arg.getFunctionSpace().getTypeCode()==Nodes) {     if (arg.getFunctionSpace().getTypeCode()==Nodes) {
1191       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(arg.getDataC()));        escriptDataC _arg=arg.getDataC();
1192    } else {        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_arg);
1193       Data tmp_data=Vector(0.0,continuousFunction(asAbstractContinuousDomain()),true);     } else {
1194       Finley_Assemble_NodeCoordinates(mesh->Nodes,&(tmp_data.getDataC()));        escript::Data tmp_data=Vector(0.0,continuousFunction(*this),true);
1195       // this is then interpolated onto arg:        escriptDataC _tmp_data=tmp_data.getDataC();
1196       interpolateOnDomain(arg,tmp_data);        Finley_Assemble_NodeCoordinates(mesh->Nodes,&_tmp_data);
1197    }        // this is then interpolated onto arg:
1198    checkFinleyError();        interpolateOnDomain(arg,tmp_data);
1199       }
1200       checkFinleyError();
1201  }  }
1202    
1203  //  //
1204  // 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:
1205  //  //
1206  void MeshAdapter::setToNormal(Data& normal) const  void MeshAdapter::setToNormal(escript::Data& normal) const
1207  {  {
1208    const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());  /*   const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(normal.getFunctionSpace().getDomain());*/
1209    if (normalDomain!=*this)     const MeshAdapter& normalDomain=dynamic_cast<const MeshAdapter&>(*(normal.getFunctionSpace().getDomain()));
1210       throw FinleyAdapterException("Error - Illegal domain of normal locations");     if (normalDomain!=*this)
1211    Finley_Mesh* mesh=m_finleyMesh.get();        throw FinleyAdapterException("Error - Illegal domain of normal locations");
1212    switch(normal.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1213      case(Nodes):     escriptDataC _normal=normal.getDataC();
1214        Finley_ErrorCode=TYPE_ERROR;     switch(normal.getFunctionSpace().getTypeCode()) {
1215        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for nodes");     case(Nodes):
1216        break;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for nodes");
1217      case(Elements):     break;
1218        Finley_ErrorCode=TYPE_ERROR;     case(ReducedNodes):
1219        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");
1220        break;     break;
1221      case (FaceElements):     case(Elements):
1222        Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&(normal.getDataC()));     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements");
1223        break;     break;
1224      case(Points):     case(ReducedElements):
1225        Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Finley does not support surface normal vectors for elements with reduced integration order");
1226        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for point elements");     break;
1227        break;     case (FaceElements):
1228      case (ContactElementsOne):     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1229      case (ContactElementsZero):     break;
1230        Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&(normal.getDataC()));     case (ReducedFaceElements):
1231        break;     Finley_Assemble_setNormal(mesh->Nodes,mesh->FaceElements,&_normal);
1232      case(DegreesOfFreedom):     break;
1233        Finley_ErrorCode=TYPE_ERROR;     case(Points):
1234        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");
1235        break;     break;
1236      case(ReducedDegreesOfFreedom):     case (ContactElementsOne):
1237        Finley_ErrorCode=TYPE_ERROR;     case (ContactElementsZero):
1238        sprintf(Finley_ErrorMsg,"Finley does not support surface normal vectors for reduced degrees of freedom.");     Finley_Assemble_setNormal(mesh->Nodes,mesh->ContactElements,&_normal);
1239        break;     break;
1240      default:     case (ReducedContactElementsOne):
1241        Finley_ErrorCode=TYPE_ERROR;     case (ReducedContactElementsZero):
1242        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);
1243       break;
1244       case(DegreesOfFreedom):
1245       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for degrees of freedom.");
1246       break;
1247       case(ReducedDegreesOfFreedom):
1248       throw FinleyAdapterException("Error - Finley does not support surface normal vectors for reduced degrees of freedom.");
1249       break;
1250       default:
1251          stringstream temp;
1252          temp << "Error - Normal Vectors: Finley does not know anything about function space type " << normal.getFunctionSpace().getTypeCode();
1253          throw FinleyAdapterException(temp.str());
1254        break;        break;
1255    }     }
1256    checkFinleyError();     checkFinleyError();
1257  }  }
1258    
1259  //  //
1260  // interpolates data to other domain:  // interpolates data to other domain:
1261  //  //
1262  void MeshAdapter::interpolateACross(Data& target,const Data& source) const  void MeshAdapter::interpolateACross(escript::Data& target,const escript::Data& source) const
1263  {  {
1264    const MeshAdapter& targetDomain=dynamic_cast<const MeshAdapter&>(target.getFunctionSpace().getDomain());     const_Domain_ptr targetDomain_p=target.getFunctionSpace().getDomain();
1265    if (targetDomain!=*this)     const MeshAdapter* targetDomain=dynamic_cast<const MeshAdapter*>(targetDomain_p.get());
1266       throw FinleyAdapterException("Error - Illegal domain of interpolation target");     if (targetDomain!=this)
1267          throw FinleyAdapterException("Error - Illegal domain of interpolation target");
1268    Finley_ErrorCode=SYSTEM_ERROR;  
1269    sprintf(Finley_ErrorMsg,"Finley does not allow interpolation across domains yet.");     throw FinleyAdapterException("Error - Finley does not allow interpolation across domains yet.");
   checkFinleyError();  
1270  }  }
1271    
1272  //  //
1273  // calculates the integral of a function defined of arg:  // calculates the integral of a function defined of arg:
1274  //  //
1275  void MeshAdapter::setToIntegrals(std::vector<double>& integrals,const Data& arg) const  void MeshAdapter::setToIntegrals(vector<double>& integrals,const escript::Data& arg) const
1276  {  {
1277    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1278    if (argDomain!=*this)     if (argDomain!=*this)
1279       throw FinleyAdapterException("Error - Illegal domain of integration kernel");        throw FinleyAdapterException("Error - Illegal domain of integration kernel");
1280    
1281    Finley_Mesh* mesh=m_finleyMesh.get();     double blocktimer_start = blocktimer_time();
1282    switch(arg.getFunctionSpace().getTypeCode()) {     Finley_Mesh* mesh=m_finleyMesh.get();
1283       case(Nodes):     escriptDataC _temp;
1284          Finley_ErrorCode=TYPE_ERROR;     escript::Data temp;
1285          sprintf(Finley_ErrorMsg,"Integral of data on nodes is not supported.");     escriptDataC _arg=arg.getDataC();
1286          break;     switch(arg.getFunctionSpace().getTypeCode()) {
1287       case(Elements):     case(Nodes):
1288          Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&(arg.getDataC()),&integrals[0]);     temp=escript::Data( arg, escript::function(*this) );
1289          break;     _temp=temp.getDataC();
1290       case(FaceElements):     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1291          Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&(arg.getDataC()),&integrals[0]);     break;
1292          break;     case(ReducedNodes):
1293       case(Points):     temp=escript::Data( arg, escript::function(*this) );
1294          Finley_ErrorCode=TYPE_ERROR;     _temp=temp.getDataC();
1295          sprintf(Finley_ErrorMsg,"Integral of data on points is not supported.");     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1296          break;     break;
1297       case(ContactElementsZero):     case(Elements):
1298          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1299          break;     break;
1300       case(ContactElementsOne):     case(ReducedElements):
1301          Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&(arg.getDataC()),&integrals[0]);     Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_arg,&integrals[0]);
1302          break;     break;
1303       case(DegreesOfFreedom):     case(FaceElements):
1304          Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1305          sprintf(Finley_ErrorMsg,"Integral of data on degrees of freedom is not supported.");     break;
1306          break;     case(ReducedFaceElements):
1307       case(ReducedDegreesOfFreedom):     Finley_Assemble_integrate(mesh->Nodes,mesh->FaceElements,&_arg,&integrals[0]);
1308          Finley_ErrorCode=TYPE_ERROR;     break;
1309          sprintf(Finley_ErrorMsg,"Integral of data on reduced degrees of freedom is not supported.");     case(Points):
1310          break;     throw FinleyAdapterException("Error - Integral of data on points is not supported.");
1311       default:     break;
1312          Finley_ErrorCode=TYPE_ERROR;     case(ContactElementsZero):
1313          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]);
1314          break;     break;
1315    }     case(ReducedContactElementsZero):
1316    checkFinleyError();     Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1317       break;
1318       case(ContactElementsOne):
1319       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1320       break;
1321       case(ReducedContactElementsOne):
1322       Finley_Assemble_integrate(mesh->Nodes,mesh->ContactElements,&_arg,&integrals[0]);
1323       break;
1324       case(DegreesOfFreedom):
1325       temp=escript::Data( arg, escript::function(*this) );
1326       _temp=temp.getDataC();
1327       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1328       break;
1329       case(ReducedDegreesOfFreedom):
1330       temp=escript::Data( arg, escript::function(*this) );
1331       _temp=temp.getDataC();
1332       Finley_Assemble_integrate(mesh->Nodes,mesh->Elements,&_temp,&integrals[0]);
1333       break;
1334       default:
1335          stringstream temp;
1336          temp << "Error - Integrals: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1337          throw FinleyAdapterException(temp.str());
1338          break;
1339       }
1340       checkFinleyError();
1341       blocktimer_increment("integrate()", blocktimer_start);
1342  }  }
1343    
1344  //  //
1345  // calculates the gradient of arg:  // calculates the gradient of arg:
1346  //  //
1347  void MeshAdapter::setToGradient(Data& grad,const Data& arg) const  void MeshAdapter::setToGradient(escript::Data& grad,const escript::Data& arg) const
1348  {  {
1349    const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(arg.getFunctionSpace().getDomain());     const MeshAdapter& argDomain=dynamic_cast<const MeshAdapter&>(*(arg.getFunctionSpace().getDomain()));
1350    if (argDomain!=*this)     if (argDomain!=*this)
1351      throw FinleyAdapterException("Error - Illegal domain of gradient argument");        throw FinleyAdapterException("Error - Illegal domain of gradient argument");
1352    const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(grad.getFunctionSpace().getDomain());     const MeshAdapter& gradDomain=dynamic_cast<const MeshAdapter&>(*(grad.getFunctionSpace().getDomain()));
1353    if (gradDomain!=*this)     if (gradDomain!=*this)
1354       throw FinleyAdapterException("Error - Illegal domain of gradient");        throw FinleyAdapterException("Error - Illegal domain of gradient");
1355    
1356    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1357    switch(grad.getFunctionSpace().getTypeCode()) {     escriptDataC _grad=grad.getDataC();
1358         case(Nodes):     escriptDataC nodeDataC;
1359            Finley_ErrorCode=TYPE_ERROR;     escript::Data temp;
1360            sprintf(Finley_ErrorMsg,"Gradient at nodes is not supported.");     if (getMPISize()>1) {
1361            break;        if( arg.getFunctionSpace().getTypeCode() == DegreesOfFreedom ) {
1362         case(Elements):           temp=escript::Data( arg,  continuousFunction(*this) );
1363            Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&(grad.getDataC()),&(arg.getDataC()));           nodeDataC = temp.getDataC();
1364            break;        } else if( arg.getFunctionSpace().getTypeCode() == ReducedDegreesOfFreedom ) {
1365         case(FaceElements):           temp=escript::Data( arg,  reducedContinuousFunction(*this) );
1366            Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&(grad.getDataC()),&(arg.getDataC()));           nodeDataC = temp.getDataC();
1367            break;        } else {
1368         case(Points):           nodeDataC = arg.getDataC();
1369            Finley_ErrorCode=TYPE_ERROR;        }
1370            sprintf(Finley_ErrorMsg,"Gradient at points is not supported.");     } else {
1371            break;        nodeDataC = arg.getDataC();
1372         case(ContactElementsZero):     }
1373            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     switch(grad.getFunctionSpace().getTypeCode()) {
1374            break;     case(Nodes):
1375         case(ContactElementsOne):     throw FinleyAdapterException("Error - Gradient at nodes is not supported.");
1376            Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&(grad.getDataC()),&(arg.getDataC()));     break;
1377            break;     case(ReducedNodes):
1378         case(DegreesOfFreedom):     throw FinleyAdapterException("Error - Gradient at reduced nodes is not supported.");
1379            Finley_ErrorCode=TYPE_ERROR;     break;
1380            sprintf(Finley_ErrorMsg,"Gradient at degrees of freedom is not supported.");     case(Elements):
1381            break;     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1382         case(ReducedDegreesOfFreedom):     break;
1383            Finley_ErrorCode=TYPE_ERROR;     case(ReducedElements):
1384            sprintf(Finley_ErrorMsg,"Gradient at reduced degrees of freedom is not supported.");     Finley_Assemble_gradient(mesh->Nodes,mesh->Elements,&_grad,&nodeDataC);
1385            break;     break;
1386         default:     case(FaceElements):
1387            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1388            sprintf(Finley_ErrorMsg,"Gradient: Finley does not know anything about function space type %d",arg.getFunctionSpace().getTypeCode());     break;
1389            break;     case(ReducedFaceElements):
1390    }     Finley_Assemble_gradient(mesh->Nodes,mesh->FaceElements,&_grad,&nodeDataC);
1391    checkFinleyError();     break;
1392       case(Points):
1393       throw FinleyAdapterException("Error - Gradient at points is not supported.");
1394       break;
1395       case(ContactElementsZero):
1396       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1397       break;
1398       case(ReducedContactElementsZero):
1399       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1400       break;
1401       case(ContactElementsOne):
1402       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1403       break;
1404       case(ReducedContactElementsOne):
1405       Finley_Assemble_gradient(mesh->Nodes,mesh->ContactElements,&_grad,&nodeDataC);
1406       break;
1407       case(DegreesOfFreedom):
1408       throw FinleyAdapterException("Error - Gradient at degrees of freedom is not supported.");
1409       break;
1410       case(ReducedDegreesOfFreedom):
1411       throw FinleyAdapterException("Error - Gradient at reduced degrees of freedom is not supported.");
1412       break;
1413       default:
1414          stringstream temp;
1415          temp << "Error - Gradient: Finley does not know anything about function space type " << arg.getFunctionSpace().getTypeCode();
1416          throw FinleyAdapterException(temp.str());
1417          break;
1418       }
1419       checkFinleyError();
1420  }  }
1421    
1422  //  //
1423  // returns the size of elements:  // returns the size of elements:
1424  //  //
1425  void MeshAdapter::setToSize(Data& size) const  void MeshAdapter::setToSize(escript::Data& size) const
1426  {  {
1427    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1428    escriptDataC tmp=size.getDataC();     escriptDataC tmp=size.getDataC();
1429    switch(size.getFunctionSpace().getTypeCode()) {     switch(size.getFunctionSpace().getTypeCode()) {
1430         case(Nodes):     case(Nodes):
1431            Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Size of nodes is not supported.");
1432            sprintf(Finley_ErrorMsg,"Size of nodes is not supported.");     break;
1433            break;     case(ReducedNodes):
1434         case(Elements):     throw FinleyAdapterException("Error - Size of reduced nodes is not supported.");
1435            Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);     break;
1436            break;     case(Elements):
1437         case(FaceElements):     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1438            Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);     break;
1439            break;     case(ReducedElements):
1440         case(Points):     Finley_Assemble_getSize(mesh->Nodes,mesh->Elements,&tmp);
1441            Finley_ErrorCode=TYPE_ERROR;     break;
1442            sprintf(Finley_ErrorMsg,"Size of point elements is not supported.");     case(FaceElements):
1443            break;     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1444         case(ContactElementsZero):     break;
1445         case(ContactElementsOne):     case(ReducedFaceElements):
1446            Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);     Finley_Assemble_getSize(mesh->Nodes,mesh->FaceElements,&tmp);
1447            break;     break;
1448         case(DegreesOfFreedom):     case(Points):
1449            Finley_ErrorCode=TYPE_ERROR;     throw FinleyAdapterException("Error - Size of point elements is not supported.");
1450            sprintf(Finley_ErrorMsg,"Size of degrees of freedom is not supported.");     break;
1451            break;     case(ContactElementsZero):
1452         case(ReducedDegreesOfFreedom):     case(ContactElementsOne):
1453            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1454            sprintf(Finley_ErrorMsg,"Size of reduced degrees of freedom is not supported.");     break;
1455            break;     case(ReducedContactElementsZero):
1456         default:     case(ReducedContactElementsOne):
1457            Finley_ErrorCode=TYPE_ERROR;     Finley_Assemble_getSize(mesh->Nodes,mesh->ContactElements,&tmp);
1458            sprintf(Finley_ErrorMsg,"Element size: Finley does not know anything about function space type %d",size.getFunctionSpace().getTypeCode());     break;
1459            break;     case(DegreesOfFreedom):
1460    }     throw FinleyAdapterException("Error - Size of degrees of freedom is not supported.");
1461    checkFinleyError();     break;
1462       case(ReducedDegreesOfFreedom):
1463       throw FinleyAdapterException("Error - Size of reduced degrees of freedom is not supported.");
1464       break;
1465       default:
1466          stringstream temp;
1467          temp << "Error - Element size: Finley does not know anything about function space type " << size.getFunctionSpace().getTypeCode();
1468          throw FinleyAdapterException(temp.str());
1469          break;
1470       }
1471       checkFinleyError();
1472  }  }
1473  // sets the location of nodes:  
1474  void MeshAdapter::setNewX(const Data& new_x)  //
1475    // sets the location of nodes
1476    //
1477    void MeshAdapter::setNewX(const escript::Data& new_x)
1478  {  {
1479    Finley_Mesh* mesh=m_finleyMesh.get();     Finley_Mesh* mesh=m_finleyMesh.get();
1480    const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(new_x.getFunctionSpace().getDomain());     escriptDataC tmp;
1481    if (newDomain!=*this)     const MeshAdapter& newDomain=dynamic_cast<const MeshAdapter&>(*(new_x.getFunctionSpace().getDomain()));
1482       throw FinleyAdapterException("Error - Illegal domain of new point locations");     if (newDomain!=*this)
1483    Finley_NodeFile_setCoordinates(mesh->Nodes,&(new_x.getDataC()));        throw FinleyAdapterException("Error - Illegal domain of new point locations");
1484    checkFinleyError();     if ( new_x.getFunctionSpace() == continuousFunction(*this) ) {
1485  }         tmp = new_x.getDataC();
1486  // saves a data array in openDX format:         Finley_Mesh_setCoordinates(mesh,&tmp);
1487  void MeshAdapter::saveDX(const std::string& filename,const Data& arg) const     } else {
1488  {         escript::Data new_x_inter=escript::Data( new_x,  continuousFunction(*this) );
1489    Finley_Mesh_saveDX(filename.c_str(),m_finleyMesh.get(),&(arg.getDataC()));         tmp = new_x_inter.getDataC();
1490    checkFinleyError();         Finley_Mesh_setCoordinates(mesh,&tmp);
1491  }     }
1492  // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:     checkFinleyError();
1493  SystemMatrixAdapter MeshAdapter::newSystemMatrix(  }
1494                        const int row_blocksize,  
1495                        const escript::FunctionSpace& row_functionspace,  //
1496                        const int column_blocksize,  // Helper for the save* methods. Extracts optional data variable names and the
1497                        const escript::FunctionSpace& column_functionspace,  // corresponding pointers from python dictionary. Caller must free arrays.
1498                        const int type) const  //
1499  {  void MeshAdapter::extractArgsFromDict(const boost::python::dict& arg, int& numData, char**& names, escriptDataC*& data, escriptDataC**& dataPtr) const
1500      int reduceRowOrder=0;  {
1501      int reduceColOrder=0;     numData = boost::python::extract<int>(arg.attr("__len__")());
1502      // is the domain right?     /* win32 refactor */
1503      const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(row_functionspace.getDomain());     names = (numData>0) ? TMPMEMALLOC(numData, char*) : (char**)NULL;
1504      if (row_domain!=*this)     data = (numData>0) ? TMPMEMALLOC(numData,escriptDataC) : (escriptDataC*)NULL;
1505            throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");     dataPtr = (numData>0) ? TMPMEMALLOC(numData,escriptDataC*) : (escriptDataC**)NULL;
1506      const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(column_functionspace.getDomain());  
1507      if (col_domain!=*this)     boost::python::list keys=arg.keys();
1508            throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");     for (int i=0; i<numData; ++i) {
1509      // is the function space type right        string n=boost::python::extract<string>(keys[i]);
1510      if (row_functionspace.getTypeCode()==DegreesOfFreedom) {        escript::Data& d=boost::python::extract<escript::Data&>(arg[keys[i]]);
1511          reduceRowOrder=0;        if (dynamic_cast<const MeshAdapter&>(*(d.getFunctionSpace().getDomain())) !=*this)
1512      } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {           throw FinleyAdapterException("Error: Data must be defined on same Domain");
1513          reduceRowOrder=1;        data[i] = d.getDataC();
1514      } else {        dataPtr[i] = &(data[i]);
1515          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");        names[i] = TMPMEMALLOC(n.length()+1, char);
1516          strcpy(names[i], n.c_str());
1517       }
1518    }
1519    
1520    //
1521    // saves mesh and optionally data arrays in openDX format
1522    //
1523    void MeshAdapter::saveDX(const string& filename,const boost::python::dict& arg) const
1524    {
1525       int num_data;
1526       char **names;
1527       escriptDataC *data;
1528       escriptDataC **ptr_data;
1529    
1530       extractArgsFromDict(arg, num_data, names, data, ptr_data);
1531       Finley_Mesh_saveDX(filename.c_str(), m_finleyMesh.get(), num_data, names, ptr_data);
1532       checkFinleyError();
1533    
1534       /* win32 refactor */
1535       TMPMEMFREE(data);
1536       TMPMEMFREE(ptr_data);
1537       for(int i=0; i<num_data; i++)
1538       {
1539          TMPMEMFREE(names[i]);
1540       }
1541       TMPMEMFREE(names);
1542    
1543       return;
1544    }
1545    
1546    //
1547    // saves mesh and optionally data arrays in VTK format
1548    //
1549    void MeshAdapter::saveVTK(const string& filename,const boost::python::dict& arg,  const string& metadata, const string& metadata_schema) const
1550    {
1551        boost::python::object pySaveVTK = boost::python::import("esys.weipa").attr("_saveVTK");
1552        pySaveVTK(filename, const_cast<MeshAdapter*>(this)->getPtr(),
1553                  metadata, metadata_schema, arg);
1554    }
1555    
1556    bool MeshAdapter::ownSample(int fs_code, index_t id) const
1557    {
1558    #ifdef ESYS_MPI
1559        index_t myFirstNode=0, myLastNode=0, k=0;
1560        index_t* globalNodeIndex=0;
1561        Finley_Mesh* mesh_p=m_finleyMesh.get();
1562        if (fs_code == FINLEY_REDUCED_NODES)
1563        {
1564        myFirstNode = Finley_NodeFile_getFirstReducedNode(mesh_p->Nodes);
1565        myLastNode = Finley_NodeFile_getLastReducedNode(mesh_p->Nodes);
1566        globalNodeIndex = Finley_NodeFile_borrowGlobalReducedNodesIndex(mesh_p->Nodes);
1567      }      }
1568      if (column_functionspace.getTypeCode()==DegreesOfFreedom) {      else
1569          reduceColOrder=0;      {
1570      } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {      myFirstNode = Finley_NodeFile_getFirstNode(mesh_p->Nodes);
1571          reduceColOrder=1;      myLastNode = Finley_NodeFile_getLastNode(mesh_p->Nodes);
1572      } else {      globalNodeIndex = Finley_NodeFile_borrowGlobalNodesIndex(mesh_p->Nodes);
         throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");  
1573      }      }
1574      // generate matrix:      k=globalNodeIndex[id];
1575            return static_cast<bool>( (myFirstNode <= k) && (k < myLastNode) );
1576      Finley_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);  #endif
1577      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);  
1578  }  }
1579    
1580    
1581    
1582    //
1583    // creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros
1584    //
1585    ASM_ptr MeshAdapter::newSystemMatrix(
1586                                                     const int row_blocksize,
1587                                                     const escript::FunctionSpace& row_functionspace,
1588                                                     const int column_blocksize,
1589                                                     const escript::FunctionSpace& column_functionspace,
1590                                                     const int type) const
1591    {
1592       int reduceRowOrder=0;
1593       int reduceColOrder=0;
1594       // is the domain right?
1595       const MeshAdapter& row_domain=dynamic_cast<const MeshAdapter&>(*(row_functionspace.getDomain()));
1596       if (row_domain!=*this)
1597          throw FinleyAdapterException("Error - domain of row function space does not match the domain of matrix generator.");
1598       const MeshAdapter& col_domain=dynamic_cast<const MeshAdapter&>(*(column_functionspace.getDomain()));
1599       if (col_domain!=*this)
1600          throw FinleyAdapterException("Error - domain of columnn function space does not match the domain of matrix generator.");
1601       // is the function space type right
1602       if (row_functionspace.getTypeCode()==DegreesOfFreedom) {
1603          reduceRowOrder=0;
1604       } else if (row_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1605          reduceRowOrder=1;
1606       } else {
1607          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1608       }
1609       if (column_functionspace.getTypeCode()==DegreesOfFreedom) {
1610          reduceColOrder=0;
1611       } else if (column_functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1612          reduceColOrder=1;
1613       } else {
1614          throw FinleyAdapterException("Error - illegal function space type for system matrix columns.");
1615       }
1616       // generate matrix:
1617    
1618       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceRowOrder,reduceColOrder);
1619       checkFinleyError();
1620       Paso_SystemMatrix* fsystemMatrix;
1621       int trilinos = 0;
1622       if (trilinos) {
1623    #ifdef TRILINOS
1624          /* Allocation Epetra_VrbMatrix here */
1625    #endif
1626       }
1627       else {
1628          fsystemMatrix=Paso_SystemMatrix_alloc(type,fsystemMatrixPattern,row_blocksize,column_blocksize,FALSE);
1629       }
1630       checkPasoError();
1631       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1632       SystemMatrixAdapter* sma=new SystemMatrixAdapter(fsystemMatrix, row_blocksize, row_functionspace, column_blocksize, column_functionspace);
1633       return ASM_ptr(sma);
1634    //   return SystemMatrixAdapter(fsystemMatrix,row_blocksize,row_functionspace,column_blocksize,column_functionspace);
1635    }
1636    
1637    //
1638    // creates a TransportProblemAdapter
1639    //
1640    ATP_ptr MeshAdapter::newTransportProblem(
1641                                                             const bool useBackwardEuler,
1642                                                             const int blocksize,
1643                                                             const escript::FunctionSpace& functionspace,
1644                                                             const int type) const
1645    {
1646       int reduceOrder=0;
1647       // is the domain right?
1648       const MeshAdapter& domain=dynamic_cast<const MeshAdapter&>(*(functionspace.getDomain()));
1649       if (domain!=*this)
1650          throw FinleyAdapterException("Error - domain of function space does not match the domain of transport problem generator.");
1651       // is the function space type right
1652       if (functionspace.getTypeCode()==DegreesOfFreedom) {
1653          reduceOrder=0;
1654       } else if (functionspace.getTypeCode()==ReducedDegreesOfFreedom) {
1655          reduceOrder=1;
1656       } else {
1657          throw FinleyAdapterException("Error - illegal function space type for system matrix rows.");
1658       }
1659       // generate matrix:
1660    
1661       Paso_SystemMatrixPattern* fsystemMatrixPattern=Finley_getPattern(getFinley_Mesh(),reduceOrder,reduceOrder);
1662       checkFinleyError();
1663       Paso_TransportProblem* transportProblem;
1664       transportProblem=Paso_TransportProblem_alloc(useBackwardEuler,fsystemMatrixPattern,blocksize);
1665       checkPasoError();
1666       Paso_SystemMatrixPattern_free(fsystemMatrixPattern);
1667       TransportProblemAdapter* tpa=new TransportProblemAdapter(transportProblem,useBackwardEuler,blocksize,functionspace);
1668       return ATP_ptr(tpa);
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        case(ReducedDegreesOfFreedom):
1881        case(Elements):
1882        case(ReducedElements):
1883        case(FaceElements):
1884        case(ReducedFaceElements):
1885        case(Points):
1886        case(ContactElementsZero):
1887        case(ReducedContactElementsZero):
1888        case(ContactElementsOne):
1889        case(ReducedContactElementsOne):
1890        return true;
1891        case(Nodes):
1892        case(DegreesOfFreedom):
1893        return false;
1894        default:
1895            stringstream temp;
1896            temp << "Error - Interpolation On Domain: Finley does not know anything about function space type " << functionSpaceType_target;
1897            throw FinleyAdapterException(temp.str());
1898       }
1899       break;
1900       case(Elements):
1901        if (functionSpaceType_target==Elements) {
1902          return true;
1903        } else if (functionSpaceType_target==ReducedElements) {
1904          return true;
1905          } else {          } else {
1906             return false;            return false;
         }  
      case(Points):  
         if (functionSpaceType_target==Points) {  
            return true;  
         } else {  
            return false;  
         }  
      case(ContactElementsZero):  
      case(ContactElementsOne):  
         if (functionSpaceType_target==ContactElementsZero || functionSpaceType_target==ContactElementsOne) {  
            return true;  
         } else {  
            return false;  
         }  
      case(DegreesOfFreedom):  
         switch(functionSpaceType_target) {  
            case(ReducedDegreesOfFreedom):  
            case(DegreesOfFreedom):  
            case(Nodes):  
            case(Elements):  
            case(FaceElements):  
            case(Points):  
            case(ContactElementsZero):  
            case(ContactElementsOne):  
               return true;  
            default:  
              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(*this).getX();
2043    }
2044    
2045    escript::Data MeshAdapter::getNormal() const
2046    {
2047       return functionOnBoundary(*this).getNormal();
2048    }
2049    
2050    escript::Data MeshAdapter::getSize() const
2051    {
2052       return escript::function(*this).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    
2238    string MeshAdapter::showTagNames() const
2239    {
2240       stringstream temp;
2241       Finley_Mesh* mesh=m_finleyMesh.get();
2242       Finley_TagMap* tag_map=mesh->TagMap;
2243       while (tag_map) {
2244          temp << tag_map->name;
2245          tag_map=tag_map->next;
2246          if (tag_map) temp << ", ";
2247       }
2248       return temp.str();
2249  }  }
2250  // bool MeshAdapter::operator==(const AbstractDomain& other) const  
2251  // {  int MeshAdapter::getNumberOfTagsInUse(int functionSpaceCode) const
2252    // try {  {
2253      // const MeshAdapter& ref = dynamic_cast<const MeshAdapter&>(other);    Finley_Mesh* mesh=m_finleyMesh.get();
2254      // return (operator==(ref));    dim_t numTags=0;
2255    // }    switch(functionSpaceCode) {
2256    // catch (bad_cast) {     case(Nodes):
2257      // return false;            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    bool MeshAdapter::supportsContactElements() const
2401    {
2402      return true;
2403    }
2404    
2405    ReferenceElementSetWrapper::ReferenceElementSetWrapper(Finley_ElementTypeId id, index_t order, index_t reducedOrder)
2406    {
2407      m_refSet = Finley_ReferenceElementSet_alloc(id, order, reducedOrder);
2408    }
2409    
2410    ReferenceElementSetWrapper::~ReferenceElementSetWrapper()
2411    {
2412      Finley_ReferenceElementSet_dealloc(m_refSet);
2413    }
2414    
2415  }  // end of namespace  }  // end of namespace

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